RNA INTERFERENCE MEDIATED INHIBITION OF PLATELET DERIVED GROWTH FACTOR (PDGF) AND PLATELET DERIVED GROWTH FACTOR RECEPTOR (PDGFR) GENE EXPRESSION USING SHORT INTERFERING NUCLEIC ACID (siNA)

Abstract

This invention relates to compounds, compositions, and methods useful for modulating platelet derived growth factor (PDGF) and/or platelet derived growth factor receptor (PDGFr) gene expression using short interfering nucleic acid (siNA) molecules. This invention also relates to compounds, compositions, and methods useful for modulating the expression and activity of other genes involved in pathways of platelet derived growth factor (PDGF) and/or platelet derived growth factor receptor (PDGFr) gene expression and/or activity by RNA interference (RNAi) using small nucleic acid molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of platelet derived growth factor (PDGF) and/or platelet derived growth factor receptor (PDGFr) genes, such as PDGF and/or PDGFr.

Description

[0001] This application is a continuation of U.S. patent application Ser. No. 10/923,270, filed Aug. 20, 2004, which is a continuation-in-part of International Patent Application No. PCT/US03/03473, filed Feb. 5, 2003. The parent application Ser. No. 10/923,270 is also a continuation-in-part of International Patent Application No. PCT/US04/16390, filed May 24, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/826,966, filed Apr. 16, 2004 (now abandoned), which is continuation-in-part of U.S. patent application Ser. No. 10/757,803, filed Jan. 14, 2004, which is a continuation-in-part of U.S. patent application Ser. No. 10/720,448, filed Nov. 24, 2003 (now abandoned), which is a continuation-in-part of U.S. patent application Ser. No. 10/693,059, filed Oct. 23, 2003, which is a continuation-in-part of U.S. patent application Ser. No. 10/444,853, filed May 23, 2003, which is a continuation-in-part of International Patent Application No. PCT/US03/05346, filed Feb. 20, 2003, and a continuation-in-part of International Patent Application No. PCT/US03/05028, filed Feb. 20, 2003, both of which claim the benefit of U.S. Provisional Application No. 60/358,580 filed Feb. 20, 2002, U.S. Provisional Application No. 60/363,124 filed Mar. 11, 2002, U.S. Provisional Application No. 60/386,782 filed Jun. 6, 2002, U.S. Provisional Application No. 60/406,784 filed Aug. 29, 2002, U.S. Provisional Application No. 60/408,378 filed Sep. 5, 2002, U.S. Provisional Application No. 60/409,293 filed Sep. 9, 2002, and U.S. Provisional Application No. 60/440,129 filed Jan. 15, 2003. The parent application Ser. No. 10/923,270 also claims the benefit of U.S. Provisional Application No. 60/543,480, filed Feb. 10, 2004. The instant application claims the benefit of all the listed applications, which are hereby incorporated by reference herein in their entireties, including the drawings.

SEQUENCE LISTING

[0002] The sequence listing submitted via EFS, in compliance with 37 CFR .sctn.1.52(e)(5), is incorporated herein by reference. The sequence listing text file submitted via EFS contains the file "SequenceListing46USCNT", created on Dec. 12, 2008, which is 182,897 bytes in size.

FIELD OF THE INVENTION

[0003] The present invention relates to compounds, compositions, and methods for the study, diagnosis, and treatment of traits, diseases and conditions that respond to the modulation of platelet derived growth factor (PDGF) and platelet derived growth factor receptor (PDGFr) gene expression and/or activity. The present invention is also directed to compounds, compositions, and methods relating to traits, diseases and conditions that respond to the modulation of expression and/or activity of genes involved in platelet derived growth factor (PDGF) and platelet derived growth factor receptor (PDGFr) gene expression pathways or other cellular processes that mediate the maintenance or development of such traits, diseases and conditions. Specifically, the invention relates to small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules capable of mediating RNA interference (RNAi) against platelet derived growth factor (PDGF) and/or platelet derived growth factor receptor (PDGFr), such as PDGF and/or PDGFr gene expression. Such small nucleic acid molecules are useful, for example, in providing compositions for treatment of traits, diseases and conditions that can respond to modulation of PDGF and/or PDGFr expression in a subject, such as cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative traits, diseases, disorders, or conditions.

BACKGROUND OF THE INVENTION

[0004] The following is a discussion of relevant art pertaining to RNAi. The discussion is provided only for understanding of the invention that follows. The summary is not an admission that any of the work described below is prior art to the claimed invention.

[0005] RNA interference refers to the process of sequence-specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Fire et al., 1998, Nature, 391, 806; Hamilton et al., 1999, Science, 286, 950-951; Lin et al., 1999, Nature, 402, 128-129; Sharp, 1999, Genes & Dev., 13:139-141; and Strauss, 1999, Science, 286, 886). The corresponding process in plants (Heifetz et al., International PCT Publication No. WO 99/61631) is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes and is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or from the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response through a mechanism that has yet to be fully characterized. This mechanism appears to be different from other known mechanisms involving double stranded RNA-specific ribonucleases, such as the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2',5'-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L (see for example U.S. Pat. Nos. 6,107,094; 5,898,031; Clemens et al., 1997, J. Interferon & Cytokine Res., 17, 503-524; Adah et al., 2001, Curr. Med. Chem., 8, 1189).

[0006] The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as dicer (Bass, 2000, Cell, 101, 235; Zamore et al., 2000, Cell, 101, 25-33; Hammond et al., 2000, Nature, 404, 293). Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Zamore et al., 2000, Cell, 101, 25-33; Bass, 2000, Cell, 101, 235; Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes (Zamore et al., 2000, Cell, 101, 25-33; Elbashir et al., 2001, Genes Dev., 15, 188). Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence complementary to the antisense strand of the siRNA duplex. Cleavage of the target RNA takes place in the middle of the region complementary to the antisense strand of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188).

[0007] RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Bahramian and Zarbl, 1999, Molecular and Cellular Biology, 19, 274-283 and Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mammalian systems. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494 and Tuschl et al., International PCT Publication No. WO 01/75164, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates (Elbashir et al., 2001, EMBO J., 20, 6877 and Tuschl et al., International PCT Publication No. WO 01/75164) has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21-nucleotide siRNA duplexes are most active when containing 3'-terminal dinucleotide overhangs. Furthermore, complete substitution of one or both siRNA strands with 2'-deoxy (2'-H) or 2'-O-methyl nucleotides abolishes RNAi activity, whereas substitution of the 3'-terminal siRNA overhang nucleotides with 2'-deoxy nucleotides (2'-H) was shown to be tolerated. Single mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5'-end of the siRNA guide sequence rather than the 3'-end of the guide sequence (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5'-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5'-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309).

[0008] Studies have shown that replacing the 3'-terminal nucleotide overhanging segments of a 21-mer siRNA duplex having two-nucleotide 3'-overhangs with deoxyribonucleotides does not have an adverse effect on RNAi activity. Replacing up to four nucleotides on each end of the siRNA with deoxyribonucleotides has been reported to be well tolerated, whereas complete substitution with deoxyribonucleotides results in no RNAi activity (Elbashir et al., 2001, EMBO J., 20, 6877 and Tuschl et al., International PCT Publication No. WO 01/75164). In addition, Elbashir et al., supra, also report that substitution of siRNA with 2'-O-methyl nucleotides completely abolishes RNAi activity. Li et al., International PCT Publication No. WO 00/44914, and Beach et al., International PCT Publication No. WO 01/68836 preliminarily suggest that siRNA may include modifications to either the phosphate-sugar backbone or the nucleoside to include at least one of a nitrogen or sulfur heteroatom, however, neither application postulates to what extent such modifications would be tolerated in siRNA molecules, nor provides any further guidance or examples of such modified siRNA. Kreutzer et al., Canadian Patent Application No. 2,359,180, also describe certain chemical modifications for use in dsRNA constructs in order to counteract activation of double-stranded RNA-dependent protein kinase PKR, specifically 2'-amino or 2'-methyl nucleotides, and nucleotides containing a 2'-O or 4'-C methylene bridge. However, Kreutzer et al. similarly fails to provide examples or guidance as to what extent these modifications would be tolerated in dsRNA molecules.

[0009] Parrish et al., 2000, Molecular Cell, 6, 1077-1087, tested certain chemical modifications targeting the unc-22 gene in C. elegans using long (>25 nt) siRNA transcripts. The authors describe the introduction of thiophosphate residues into these siRNA transcripts by incorporating thiophosphate nucleotide analogs with T7 and T3 RNA polymerase and observed that RNAs with two phosphorothioate modified bases also had substantial decreases in effectiveness as RNAi. Further, Parrish et al. reported that phosphorothioate modification of more than two residues greatly destabilized the RNAs in vitro such that interference activities could not be assayed. Id. at 1081. The authors also tested certain modifications at the 2'-position of the nucleotide sugar in the long siRNA transcripts and found that substituting deoxynucleotides for ribonucleotides produced a substantial decrease in interference activity, especially in the case of Uridine to Thymidine and/or Cytidine to deoxy-Cytidine substitutions. Id. In addition, the authors tested certain base modifications, including substituting, in sense and antisense strands of the siRNA, 4-thiouracil, 5-bromouracil, 5-iodouracil, and 3-(aminoallyl)uracil for uracil, and inosine for guanosine. Whereas 4-thiouracil and 5-bromouracil substitution appeared to be tolerated, Parrish reported that inosine produced a substantial decrease in interference activity when incorporated in either strand. Parrish also reported that incorporation of 5-iodouracil and 3-(aminoallyl)uracil in the antisense strand resulted in a substantial decrease in RNAi activity as well.

[0010] The use of longer dsRNA has been described. For example, Beach et al., International PCT Publication No. WO 01/68836, describes specific methods for attenuating gene expression using endogenously-derived dsRNA. Tuschl et al., International PCT Publication No. WO 01/75164, describe a Drosophila in vitro RNAi system and the use of specific siRNA molecules for certain functional genomic and certain therapeutic applications; although Tuschl, 2001, Chem. Biochem., 2, 239-245, doubts that RNAi can be used to cure genetic diseases or viral infection due to the danger of activating interferon response. Li et al., International PCT Publication No. WO 00/44914, describe the use of specific long (141 bp-488 bp) enzymatically synthesized or vector expressed dsRNAs for attenuating the expression of certain target genes. Zernicka-Goetz et al., International PCT Publication No. WO 01/36646, describe certain methods for inhibiting the expression of particular genes in mammalian cells using certain long (550 bp-714 bp), enzymatically synthesized or vector expressed dsRNA molecules. Fire et al., International PCT Publication No. WO 99/32619, describe particular methods for introducing certain long dsRNA molecules into cells for use in inhibiting gene expression in nematodes. Plaetinck et al., International PCT Publication No. WO 00/01846, describe certain methods for identifying specific genes responsible for conferring a particular phenotype in a cell using specific long dsRNA molecules. Mello et al., International PCT Publication No. WO 01/29058, describe the identification of specific genes involved in dsRNA-mediated RNAi. Pachuck et al., International PCT Publication No. WO 00/63364, describe certain long (at least 200 nucleotide) dsRNA constructs. Deschamps Depaillette et al., International PCT Publication No. WO 99/07409, describe specific compositions consisting of particular dsRNA molecules combined with certain anti-viral agents. Waterhouse et al., International PCT Publication No. 99/53050 and 1998, PNAS, 95, 13959-13964, describe certain methods for decreasing the phenotypic expression of a nucleic acid in plant cells using certain dsRNAs. Driscoll et al., International PCT Publication No. WO 01/49844, describe specific DNA expression constructs for use in facilitating gene silencing in targeted organisms.

[0011] Others have reported on various RNAi and gene-silencing systems. For example, Parrish et al., 2000, Molecular Cell, 6, 1077-1087, describe specific chemically-modified dsRNA constructs targeting the unc-22 gene of C. elegans. Grossniklaus, International PCT Publication No. WO 01/38551, describes certain methods for regulating polycomb gene expression in plants using certain dsRNAs. Churikov et al., International PCT Publication No. WO 01/42443, describe certain methods for modifying genetic characteristics of an organism using certain dsRNAs. Cogoni et al, International PCT Publication No. WO 01/53475, describe certain methods for isolating a Neurospora silencing gene and uses thereof. Reed et al., International PCT Publication No. WO 01/68836, describe certain methods for gene silencing in plants. Honer et al., International PCT Publication No. WO 01/70944, describe certain methods of drug screening using transgenic nematodes as Parkinson's Disease models using certain dsRNAs. Deak et al., International PCT Publication No. WO 01/72774, describe certain Drosophila-derived gene products that may be related to RNAi in Drosophila. Arndt et al., International PCT Publication No. WO 01/92513 describe certain methods for mediating gene suppression by using factors that enhance RNAi. Tuschl et al., International PCT Publication No. WO 02/44321, describe certain synthetic siRNA constructs. Pachuk et al., International PCT Publication No. WO 00/63364, and Satishchandran et al., International PCT Publication No. WO 01/04313, describe certain methods and compositions for inhibiting the function of certain polynucleotide sequences using certain long (over 250 bp), vector expressed dsRNAs. Echeverri et al., International PCT Publication No. WO 02/38805, describe certain C. elegans genes identified via RNAi. Kreutzer et al., International PCT Publications Nos. WO 02/055692, WO 02/055693, and EP 1144623 B1 describes certain methods for inhibiting gene expression using dsRNA. Graham et al., International PCT Publications Nos. WO 99/49029 and WO 01/70949, and AU 4037501 describe certain vector expressed siRNA molecules. Fire et al., U.S. Pat. No. 6,506,559, describe certain methods for inhibiting gene expression in vitro using certain long dsRNA (299 bp-1033 bp) constructs that mediate RNAi. Martinez et al., 2002, Cell, 110, 563-574, describe certain single stranded siRNA constructs, including certain 5'-phosphorylated single stranded siRNAs that mediate RNA interference in Hela cells. Harborth et al., 2003, Antisense & Nucleic Acid Drug Development, 13, 83-105, describe certain chemically and structurally modified siRNA molecules. Chiu and Rana, 2003, RNA, 9, 1034-1048, describe certain chemically and structurally modified siRNA molecules. Woolf et al., International PCT Publication Nos. WO 03/064626 and WO 03/064625 describe certain chemically modified dsRNA constructs.

SUMMARY OF THE INVENTION

[0012] This invention relates to compounds, compositions, and methods useful for modulating platelet derived growth factor (PDGF) and platelet derived growth factor receptor (PDGFr) gene expression using short interfering nucleic acid (siNA) molecules. This invention also relates to compounds, compositions, and methods useful for modulating the expression and activity of other genes involved in pathways of platelet derived growth factor (PDGF) and platelet derived growth factor receptor (PDGFr) gene expression and/or activity by RNA interference (RNAi) using small nucleic acid molecules. In particular, the instant invention features small nucleic acid molecules, such as short interfering nucleic acid (siNA), short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), and short hairpin RNA (shRNA) molecules and methods used to modulate the expression of platelet derived growth factor (PDGF) and/or platelet derived growth factor receptor (PDGFr) genes.

[0013] A siNA of the invention can be unmodified or chemically-modified. A siNA of the instant invention can be chemically synthesized, expressed from a vector or enzymatically synthesized. The instant invention also features various chemically-modified synthetic short interfering nucleic acid (siNA) molecules capable of modulating PDGF and/or PDGFr gene expression or activity in cells by RNA interference (RNAi). The use of chemically-modified siNA improves various properties of native siNA molecules through increased resistance to nuclease degradation in vivo and/or through improved cellular uptake. Further, contrary to earlier published studies, siNA having multiple chemical modifications retains its RNAi activity. The siNA molecules of the instant invention provide useful reagents and methods for a variety of therapeutic, veterinary, diagnostic, target validation, genomic discovery, genetic engineering, and pharmacogenomic applications.

[0014] In one embodiment, the invention features one or more siNA molecules and methods that independently or in combination modulate the expression of PDGF and/or PDGFr genes encoding proteins, such as proteins comprising PDGF and/or PDGFr associated with the maintenance and/or development of cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders, such as genes encoding sequences comprising those sequences referred to by GenBank Accession Nos. shown in Table I, referred to herein generally as PDGF and/or PDGFr. The description below of the various aspects and embodiments of the invention is provided with reference to exemplary PDGF and PDGFr genes referred to herein as PDGF and PDGFr respectively. However, the various aspects and embodiments are also directed to other PDGF and PDGFr genes, such as homolog genes and transcript variants, and polymorphisms (e.g., single nucleotide polymorphism, (SNPs)) associated with certain PDGF and PDGFr genes. As such, the various aspects and embodiments are also directed to other genes that are involved in PDGF and PDGFr mediated pathways of signal transduction or gene expression that are involved, for example, in the maintenance or development of diseases, traits, or conditions described herein. These additional genes can be analyzed for target sites using the methods described for PDGF and PDGFr genes herein. Thus, the modulation of other genes and the effects of such modulation of the other genes can be performed, determined, and measured as described herein.

[0015] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGFr gene, wherein said siNA molecule comprises about 15 to about 28 base pairs.

[0016] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGFr gene, wherein said siNA molecule comprises about 15 to about 28 base pairs.

[0017] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of a PDGF and/or PDGFr RNA via RNA interference (RNAi), wherein the double stranded siNA molecule comprises a first and a second strand, each strand of the siNA molecule is about 15 to about 30 nucleotides in length, the first strand of the siNA molecule comprises nucleotide sequence having sufficient complementarity to the PDGF and/or PDGFr RNA for the siNA molecule to direct cleavage of the PDGF and/or PDGFr RNA via RNA interference, and the second strand of said siNA molecule comprises nucleotide sequence that is complementary to the first strand.

[0018] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of a PDGF and/or PDGFr RNA via RNA interference (RNAi), wherein the double stranded siNA molecule comprises a first and a second strand, each strand of the siNA molecule is about 18 to about 23 nucleotides in length, the first strand of the siNA molecule comprises nucleotide sequence having sufficient complementarity to the PDGF and/or PDGFr RNA for the siNA molecule to direct cleavage of the PDGF and/or PDGFr RNA via RNA interference, and the second strand of said siNA molecule comprises nucleotide sequence that is complementary to the first strand.

[0019] In one embodiment, the invention features a chemically synthesized double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of a PDGF and/or PDGFr RNA via RNA interference (RNAi), wherein each strand of the siNA molecule is about 18 to about 28 nucleotides in length; and one strand of the siNA molecule comprises nucleotide sequence having sufficient complementarity to the PDGF and/or PDGFr RNA for the siNA molecule to direct cleavage of the PDGF and/or PDGFr RNA via RNA interference.

[0020] In one embodiment, the invention features a chemically synthesized double stranded short interfering nucleic acid (siNA) molecule that directs cleavage of a PDGF and/or PDGFr RNA via RNA interference (RNAi), wherein each strand of the siNA molecule is about 18 to about 23 nucleotides in length; and one strand of the siNA molecule comprises nucleotide sequence having sufficient complementarity to the PDGF and/or PDGFr RNA for the siNA molecule to direct cleavage of the PDGF and/or PDGFr RNA via RNA interference.

[0021] In one embodiment, the invention features a siNA molecule that down-regulates expression of a PDGF gene, for example, wherein the PDGF gene comprises PDGF encoding sequence. In one embodiment, the invention features a siNA molecule that down-regulates expression of a PDGF gene, for example, wherein the PDGF gene comprises PDGF non-coding sequence or regulatory elements involved in PDGF gene expression.

[0022] In one embodiment, the invention features a siNA molecule that down-regulates expression of a PDGFr gene, for example, wherein the PDGFr gene comprises PDGFr encoding sequence. In one embodiment, the invention features a siNA molecule that down-regulates expression of a PDGFr gene, for example, wherein the PDGFr gene comprises PDGFr non-coding sequence or regulatory elements involved in PDGFr gene expression.

[0023] In one embodiment, a siNA of the invention is used to inhibit the expression of PDGF and/or PDGFr genes or a PDGF and/or PDGFr gene family wherein the genes or gene family sequences share sequence homology. Such homologous sequences can be identified as is known in the art, for example using sequence alignments. siNA molecules can be designed to target such homologous sequences, for example using perfectly complementary sequences or by incorporating non-canonical base pairs, for example mismatches and/or wobble base pairs, that can provide additional target sequences. In instances where mismatches are identified, non-canonical base pairs (for example, mismatches and/or wobble bases) can be used to generate siNA molecules that target more than one gene sequence. In a non-limiting example, non-canonical base pairs such as UU and CC base pairs are used to generate siNA molecules that are capable of targeting sequences for differing PDGF and/or PDGFr targets that share sequence homology. As such, one advantage of using siNAs of the invention is that a single siNA can be designed to include nucleic acid sequence that is complementary to the nucleotide sequence that is conserved between the homologous genes. In this approach, a single siNA can be used to inhibit expression of more than one gene instead of using more than one siNA molecule to target the different genes.

[0024] In one embodiment, the invention features a siNA molecule having RNAi activity against PDGF RNA, wherein the siNA molecule comprises a sequence complementary to any RNA having PDGF encoding sequence, such as those sequences having GenBank Accession Nos. shown in Table I. In another embodiment, the invention features a siNA molecule having RNAi activity against PDGF RNA, wherein the siNA molecule comprises a sequence complementary to an RNA having variant PDGF encoding sequence, for example other mutant PDGF genes not shown in Table I but known in the art to be associated with the maintenance and/or development of cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders. Chemical modifications as shown in Tables III and IV or otherwise described herein can be applied to any siNA construct of the invention. In another embodiment, a siNA molecule of the invention includes a nucleotide sequence that can interact with nucleotide sequence of a PDGF gene and thereby mediate silencing of PDGF gene expression, for example, wherein the siNA mediates regulation of PDGF gene expression by cellular processes that modulate the chromatin structure or methylation patterns of the PDGF gene and prevent transcription of the PDGF gene.

[0025] In one embodiment, the invention features a siNA molecule having RNAi activity against PDGFr RNA, wherein the siNA molecule comprises a sequence complementary to any RNA having PDGFr encoding sequence, such as those sequences having GenBank Accession Nos. shown in Table I. In another embodiment, the invention features a siNA molecule having RNAi activity against PDGFr RNA, wherein the siNA molecule comprises a sequence complementary to an RNA having variant PDGFr encoding sequence, for example other mutant PDGFr genes not shown in Table I but known in the art to be associated with the maintenance and/or development of cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders. Chemical modifications as shown in Tables III and IV or otherwise described herein can be applied to any siNA construct of the invention. In another embodiment, a siNA molecule of the invention includes a nucleotide sequence that can interact with nucleotide sequence of a PDGFr gene and thereby mediate silencing of PDGFr gene expression, for example, wherein the siNA mediates regulation of PDGFr gene expression by cellular processes that modulate the chromatin structure or methylation patterns of the PDGFr gene and prevent transcription of the PDGFr gene.

[0026] In one embodiment, siNA molecules of the invention are used to down regulate or inhibit the expression of PDGF and/or PDGFr proteins arising from PDGF and/or PDGFr haplotype polymorphisms that are associated with a disease or condition, (e.g., cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative traits, diseases, disorders, and/or conditions). Analysis of PDGF and/or PDGFr genes, or PDGF and/or PDGFr protein or RNA levels can be used to identify subjects with such polymorphisms or those subjects who are at risk of developing traits, conditions, or diseases described herein. These subjects are amenable to treatment, for example, treatment with siNA molecules of the invention and any other composition useful in treating diseases related to PDGF and/or PDGFr gene expression. As such, analysis of PDGF and/or PDGFr protein or RNA levels can be used to determine treatment type and the course of therapy in treating a subject. Monitoring of PDGF and/or PDGFr protein or RNA levels can be used to predict treatment outcome and to determine the efficacy of compounds and compositions that modulate the level and/or activity of certain PDGF and/or PDGFr proteins associated with a trait, condition, or disease.

[0027] In one embodiment of the invention a siNA molecule comprises an antisense strand comprising a nucleotide sequence that is complementary to a nucleotide sequence or a portion thereof encoding a PDGF and/or PDGFr protein. The siNA further comprises a sense strand, wherein said sense strand comprises a nucleotide sequence of a PDGF and/or PDGFr gene or a portion thereof.

[0028] In another embodiment, a siNA molecule comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence encoding a PDGF and/or PDGFr protein or a portion thereof. The siNA molecule further comprises a sense region, wherein said sense region comprises a nucleotide sequence of a PDGF and/or PDGFr gene or a portion thereof.

[0029] In another embodiment, the invention features a siNA molecule comprising a nucleotide sequence in the antisense region of the siNA molecule that is complementary to a nucleotide sequence or portion of sequence of a PDGF and/or PDGFr gene. In another embodiment, the invention features a siNA molecule comprising a region, for example, the antisense region of the siNA construct, complementary to a sequence comprising a PDGF and/or PDGFr gene sequence or a portion thereof.

[0030] In one embodiment, the antisense region of PDGF and/or PDGFr siNA constructs comprises a sequence complementary to sequence having any of SEQ ID NOs. 1-311 or 623-630. In one embodiment, the antisense region of PDGF and/or PDGFr constructs comprises sequence having any of SEQ ID NOs. 312-622, 639-646, 655-662, 671-678, 687-694, 703-726, 728, 730, 732, 735, 737, 739, 741, or 744. In another embodiment, the sense region of PDGF and/or PDGFr constructs comprises sequence having any of SEQ ID NOs. 1-311, 623-638, 647-654, 663-670, 679-686, 695-702, 727, 729, 731, 733, 734, 736, 738, 740, 742, or 743.

[0031] In one embodiment, a siNA molecule of the invention comprises any of SEQ ID NOs. 1-744. The sequences shown in SEQ ID NOs: 1-744 are not limiting. A siNA molecule of the invention can comprise any contiguous PDGF and/or PDGFr sequence (e.g., about 15 to about 25 or more, or about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25 or more contiguous PDGF and/or PDGFr nucleotides).

[0032] In yet another embodiment, the invention features a siNA molecule comprising a sequence, for example, the antisense sequence of the siNA construct, complementary to a sequence or portion of sequence comprising sequence represented by GenBank Accession Nos. shown in Table I. Chemical modifications in Tables III and IV and described herein can be applied to any siNA construct of the invention.

[0033] In one embodiment of the invention a siNA molecule comprises an antisense strand having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, wherein the antisense strand is complementary to a RNA sequence or a portion thereof encoding a PDGF and/or PDGFr protein, and wherein said siNA further comprises a sense strand having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, and wherein said sense strand and said antisense strand are distinct nucleotide sequences where at least about 15 nucleotides in each strand are complementary to the other strand.

[0034] In another embodiment of the invention a siNA molecule of the invention comprises an antisense region having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, wherein the antisense region is complementary to a RNA sequence encoding a PDGF and/or PDGFr protein, and wherein said siNA further comprises a sense region having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, wherein said sense region and said antisense region are comprised in a linear molecule where the sense region comprises at least about 15 nucleotides that are complementary to the antisense region.

[0035] In one embodiment, a siNA molecule of the invention has RNAi activity that modulates expression of RNA encoded by a PDGF and/or PDGFr gene. Because PDGF genes (e.g., PDGF superfamily) and PDGFr (e.g., PDGFr superfamily) genes can share some degree of sequence homology with each other, siNA molecules can be designed to target a class of PDGF or PDGFr genes or alternately specific PDGF or PDGFr genes (e.g., polymorphic variants) by selecting sequences that are either shared amongst different PDGF or PDGFr targets or alternatively that are unique for a specific PDGF or PDGFr target. Therefore, in one embodiment, the siNA molecule can be designed to target conserved regions of PDGF or PDGFr RNA sequences having homology among several PDGF or PDGFr gene variants so as to target a class of PDGF or PDGFr genes with one siNA molecule. Accordingly, in one embodiment, the siNA molecule of the invention modulates the expression of one or both PDGF or PDGFr alleles in a subject. In another embodiment, the siNA molecule can be designed to target a sequence that is unique to a specific PDGF or PDGFr RNA sequence (e.g., a single PDGF or PDGFr allele or PDGF or PDGFr single nucleotide polymorphism (SNP)) due to the high degree of specificity that the siNA molecule requires to mediate RNAi activity.

[0036] In one embodiment, nucleic acid molecules of the invention that act as mediators of the RNA interference gene silencing response are double-stranded nucleic acid molecules. In another embodiment, the siNA molecules of the invention consist of duplex nucleic acid molecules containing about 15 to about 30 base pairs between oligonucleotides comprising about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides. In yet another embodiment, siNA molecules of the invention comprise duplex nucleic acid molecules with overhanging ends of about 1 to about 3 (e.g., about 1, 2, or 3) nucleotides, for example, about 21-nucleotide duplexes with about 19 base pairs and 3'-terminal mononucleotide, dinucleotide, or trinucleotide overhangs. In yet another embodiment, siNA molecules of the invention comprise duplex nucleic acid molecules with blunt ends, where both ends are blunt, or alternatively, where one of the ends is blunt.

[0037] In one embodiment, the invention features one or more chemically-modified siNA constructs having specificity for PDGF and/or PDGFr expressing nucleic acid molecules, such as RNA encoding a PDGF and/or PDGFr protein. In one embodiment, the invention features a RNA based siNA molecule (e.g., a siNA comprising 2'-OH nucleotides) having specificity for PDGF and/or PDGFr expressing nucleic acid molecules that includes one or more chemical modifications described herein. Non-limiting examples of such chemical modifications include without limitation phosphorothioate internucleotide linkages, 2'-deoxyribonucleotides, 2'-O-methyl ribonucleotides, 2'-deoxy-2'-fluoro ribonucleotides, "universal base" nucleotides, "acyclic" nucleotides, 5-C-methyl nucleotides, and terminal glyceryl and/or inverted deoxy abasic residue incorporation. These chemical modifications, when used in various siNA constructs, (e.g., RNA based siNA constructs), are shown to preserve RNAi activity in cells while at the same time, dramatically increasing the serum stability of these compounds. Furthermore, contrary to the data published by Parrish et al., supra, applicant demonstrates that multiple (greater than one) phosphorothioate substitutions are well-tolerated and confer substantial increases in serum stability for modified siNA constructs.

[0038] In one embodiment, a siNA molecule of the invention comprises modified nucleotides while maintaining the ability to mediate RNAi. The modified nucleotides can be used to improve in vitro or in vivo characteristics such as stability, activity, and/or bioavailability. For example, a siNA molecule of the invention can comprise modified nucleotides as a percentage of the total number of nucleotides present in the siNA molecule. As such, a siNA molecule of the invention can generally comprise about 5% to about 100% modified nucleotides (e.g., about 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45%, 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95% or 100% modified nucleotides). The actual percentage of modified nucleotides present in a given siNA molecule will depend on the total number of nucleotides present in the siNA. If the siNA molecule is single stranded, the percent modification can be based upon the total number of nucleotides present in the single stranded siNA molecules. Likewise, if the siNA molecule is double stranded, the percent modification can be based upon the total number of nucleotides present in the sense strand, antisense strand, or both the sense and antisense strands.

[0039] One aspect of the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene. In one embodiment, the double stranded siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is about 21 nucleotides long. In one embodiment, the double-stranded siNA molecule does not contain any ribonucleotides. In another embodiment, the double-stranded siNA molecule comprises one or more ribonucleotides. In one embodiment, each strand of the double-stranded siNA molecule independently comprises about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, wherein each strand comprises about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides that are complementary to the nucleotides of the other strand. In one embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence or a portion thereof of the PDGF and/or PDGFr gene, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence of the PDGF and/or PDGFr gene or a portion thereof.

[0040] In another embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene comprising an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of the PDGF and/or PDGFr gene or a portion thereof, and a sense region, wherein the sense region comprises a nucleotide sequence substantially similar to the nucleotide sequence of the PDGF and/or PDGFr gene or a portion thereof. In one embodiment, the antisense region and the sense region independently comprise about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, wherein the antisense region comprises about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides that are complementary to nucleotides of the sense region.

[0041] In another embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the PDGF and/or PDGFr gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region.

[0042] In one embodiment, a siNA molecule of the invention comprises blunt ends, i.e., ends that do not include any overhanging nucleotides. For example, a siNA molecule comprising modifications described herein (e.g., comprising nucleotides having Formulae I-VII or siNA constructs comprising "Stab 00"-"Stab 32" (Table. IV) or any combination thereof (see Table IV)) and/or any length described herein can comprise blunt ends or ends with no overhanging nucleotides.

[0043] In one embodiment, any siNA molecule of the invention can comprise one or more blunt ends, i.e. where a blunt end does not have any overhanging nucleotides. In one embodiment, the blunt ended siNA molecule has a number of base pairs equal to the number of nucleotides present in each strand of the siNA molecule. In another embodiment, the siNA molecule comprises one blunt end, for example wherein the 5'-end of the antisense strand and the 3'-end of the sense strand do not have any overhanging nucleotides. In another example, the siNA molecule comprises one blunt end, for example wherein the 3'-end of the antisense strand and the 5'-end of the sense strand do not have any overhanging nucleotides. In another example, a siNA molecule comprises two blunt ends, for example wherein the 3'-end of the antisense strand and the 5'-end of the sense strand as well as the 5'-end of the antisense strand and 3'-end of the sense strand do not have any overhanging nucleotides. A blunt ended siNA molecule can comprise, for example, from about 15 to about 30 nucleotides (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides). Other nucleotides present in a blunt ended siNA molecule can comprise, for example, mismatches, bulges, loops, or wobble base pairs to modulate the activity of the siNA molecule to mediate RNA interference.

[0044] By "blunt ends" is meant symmetric termini or termini of a double stranded siNA molecule having no overhanging nucleotides. The two strands of a double stranded siNA molecule align with each other without over-hanging nucleotides at the termini. For example, a blunt ended siNA construct comprises terminal nucleotides that are complementary between the sense and antisense regions of the siNA molecule.

[0045] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. The sense region can be connected to the antisense region via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker.

[0046] In one embodiment, the invention features double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene, wherein the siNA molecule comprises about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) base pairs, and wherein each strand of the siNA molecule comprises one or more chemical modifications. In another embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of a PDGF and/or PDGFr gene or a portion thereof, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence or a portion thereof of the PDGF and/or PDGFr gene. In another embodiment, one of the strands of the double-stranded siNA molecule comprises a nucleotide sequence that is complementary to a nucleotide sequence of a PDGF and/or PDGFr gene or portion thereof, and the second strand of the double-stranded siNA molecule comprises a nucleotide sequence substantially similar to the nucleotide sequence or portion thereof of the PDGF and/or PDGFr gene. In another embodiment, each strand of the siNA molecule comprises about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides, and each strand comprises at least about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides that are complementary to the nucleotides of the other strand. The PDGF and/or PDGFr gene can comprise, for example, sequences referred to in Table I.

[0047] In one embodiment, a siNA molecule of the invention comprises no ribonucleotides. In another embodiment, a siNA molecule of the invention comprises ribonucleotides.

[0048] In one embodiment, a siNA molecule of the invention comprises an antisense region comprising a nucleotide sequence that is complementary to a nucleotide sequence of a PDGF and/or PDGFr gene or a portion thereof, and the siNA further comprises a sense region comprising a nucleotide sequence substantially similar to the nucleotide sequence of the PDGF and/or PDGFr gene or a portion thereof. In another embodiment, the antisense region and the sense region each comprise about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides and the antisense region comprises at least about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides that are complementary to nucleotides of the sense region. The PDGF and/or PDGFr gene can comprise, for example, sequences referred to in Table I. In another embodiment, the siNA is a double stranded nucleic acid molecule, where each of the two strands of the siNA molecule independently comprise about 15 to about 40 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 23, 33, 34, 35, 36, 37, 38, 39, or 40) nucleotides, and where one of the strands of the siNA molecule comprises at least about 15 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24 or 25 or more) nucleotides that are complementary to the nucleic acid sequence of the PDGF and/or PDGFr gene or a portion thereof.

[0049] In one embodiment, a siNA molecule of the invention comprises a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by a PDGF and/or PDGFr gene, or a portion thereof, and the sense region comprises a nucleotide sequence that is complementary to the antisense region. In one embodiment, the siNA molecule is assembled from two separate oligonucleotide fragments, wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. In another embodiment, the sense region is connected to the antisense region via a linker molecule. In another embodiment, the sense region is connected to the antisense region via a linker molecule, such as a nucleotide or non-nucleotide linker. The PDGF and/or PDGFr gene can comprise, for example, sequences referred in to Table I.

[0050] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the PDGF and/or PDGFr gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region, and wherein the siNA molecule has one or more modified pyrimidine and/or purine nucleotides. In one embodiment, the pyrimidine nucleotides in the sense region are 2'-O-methylpyrimidine nucleotides or 2'-deoxy-2'-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2'-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2'-O-methyl purine nucleotides. In another embodiment, the pyrimidine nucleotides in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2'-deoxy purine nucleotides. In one embodiment, the pyrimidine nucleotides in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides and the purine nucleotides present in the antisense region are 2'-O-methyl or 2'-deoxy purine nucleotides. In another embodiment of any of the above-described siNA molecules, any nucleotides present in a non-complementary region of the sense strand (e.g. overhang region) are 2'-deoxy nucleotides.

[0051] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule, and wherein the fragment comprising the sense region includes a terminal cap moiety at the 5'-end, the 3'-end, or both of the 5' and 3' ends of the fragment. In one embodiment, the terminal cap moiety is an inverted deoxy abasic moiety or glyceryl moiety. In one embodiment, each of the two fragments of the siNA molecule independently comprise about 15 to about 30 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides. In another embodiment, each of the two fragments of the siNA molecule independently comprise about 15 to about 40 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 23, 33, 34, 35, 36, 37, 38, 39, or 40) nucleotides. In a non-limiting example, each of the two fragments of the siNA molecule comprise about 21 nucleotides.

[0052] In one embodiment, the invention features a siNA molecule comprising at least one modified nucleotide, wherein the modified nucleotide is a 2'-deoxy-2'-fluoro nucleotide. The siNA can be, for example, about 15 to about 40 nucleotides in length. In one embodiment, all pyrimidine nucleotides present in the siNA are 2'-deoxy-2'-fluoro pyrimidine nucleotides. In one embodiment, the modified nucleotides in the siNA include at least one 2'-deoxy-2'-fluoro cytidine or 2'-deoxy-2'-fluoro uridine nucleotide. In another embodiment, the modified nucleotides in the siNA include at least one 2'-fluoro cytidine and at least one 2'-deoxy-2'-fluoro uridine nucleotides. In one embodiment, all uridine nucleotides present in the siNA are 2'-deoxy-2'-fluoro uridine nucleotides. In one embodiment, all cytidine nucleotides present in the siNA are 2'-deoxy-2'-fluoro cytidine nucleotides. In one embodiment, all adenosine nucleotides present in the siNA are 2'-deoxy-2'-fluoro adenosine nucleotides. In one embodiment, all guanosine nucleotides present in the siNA are 2'-deoxy-2'-fluoro guanosine nucleotides. The siNA can further comprise at least one modified internucleotidic linkage, such as phosphorothioate linkage. In one embodiment, the 2'-deoxy-2'-fluoronucleotides are present at specifically selected locations in the siNA that are sensitive to cleavage by ribonucleases, such as locations having pyrimidine nucleotides.

[0053] In one embodiment, the invention features a method of increasing the stability of a siNA molecule against cleavage by ribonucleases comprising introducing at least one modified nucleotide into the siNA molecule, wherein the modified nucleotide is a 2'-deoxy-2'-fluoro nucleotide. In one embodiment, all pyrimidine nucleotides present in the siNA are 2'-deoxy-2'-fluoro pyrimidine nucleotides. In one embodiment, the modified nucleotides in the siNA include at least one 2'-deoxy-2'-fluoro cytidine or 2'-deoxy-2'-fluoro uridine nucleotide. In another embodiment, the modified nucleotides in the siNA include at least one 2'-fluoro cytidine and at least one 2'-deoxy-2'-fluoro uridine nucleotides. In one embodiment, all uridine nucleotides present in the siNA are 2'-deoxy-2'-fluoro uridine nucleotides. In one embodiment, all cytidine nucleotides present in the siNA are 2'-deoxy-2'-fluoro cytidine nucleotides. In one embodiment, all adenosine nucleotides present in the siNA are 2'-deoxy-2'-fluoro adenosine nucleotides.

[0054] In one embodiment, all guanosine nucleotides present in the siNA are 2'-deoxy-2'-fluoro guanosine nucleotides. The siNA can further comprise at least one modified internucleotidic linkage, such as phosphorothioate linkage. In one embodiment, the 2'-deoxy-2'-fluoronucleotides are present at specifically selected locations in the siNA that are sensitive to cleavage by ribonucleases, such as locations having pyrimidine nucleotides.

[0055] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene comprising a sense region and an antisense region, wherein the antisense region comprises a nucleotide sequence that is complementary to a nucleotide sequence of RNA encoded by the PDGF and/or PDGFr gene or a portion thereof and the sense region comprises a nucleotide sequence that is complementary to the antisense region, and wherein the purine nucleotides present in the antisense region comprise 2'-deoxy-purine nucleotides. In an alternative embodiment, the purine nucleotides present in the antisense region comprise 2'-O-methyl purine nucleotides. In either of the above embodiments, the antisense region can comprise a phosphorothioate internucleotide linkage at the 3' end of the antisense region. Alternatively, in either of the above embodiments, the antisense region can comprise a glyceryl modification at the 3' end of the antisense region. In another embodiment of any of the above-described siNA molecules, any nucleotides present in a non-complementary region of the antisense strand (e.g. overhang region) are 2'-deoxy nucleotides.

[0056] In one embodiment, the antisense region of a siNA molecule of the invention comprises sequence complementary to a portion of a PDGF and/or PDGFr transcript having sequence unique to a particular PDGF and/or PDGFr disease related allele, such as sequence comprising a single nucleotide polymorphism (SNP) associated with the disease specific allele. As such, the antisense region of a siNA molecule of the invention can comprise sequence complementary to sequences that are unique to a particular allele to provide specificity in mediating selective RNAi against the disease, condition, or trait related allele.

[0057] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that down-regulates expression of a PDGF and/or PDGFr gene, wherein the siNA molecule is assembled from two separate oligonucleotide fragments wherein one fragment comprises the sense region and the second fragment comprises the antisense region of the siNA molecule. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule, where each strand is about 21 nucleotides long and where about 19 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule, wherein at least two 3' terminal nucleotides of each fragment of the siNA molecule are not base-paired to the nucleotides of the other fragment of the siNA molecule. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule, where each strand is about 19 nucleotide long and where the nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule to form at least about 15 (e.g., 15, 16, 17, 18, or 19) base pairs, wherein one or both ends of the siNA molecule are blunt ends. In one embodiment, each of the two 3' terminal nucleotides of each fragment of the siNA molecule is a 2'-deoxy-pyrimidine nucleotide, such as a 2'-deoxy-thymidine. In another embodiment, all nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule of about 19 to about 25 base pairs having a sense region and an antisense region, where about 19 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the PDGF and/or PDGFr gene. In another embodiment, about 21 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the PDGF and/or PDGFr gene. In any of the above embodiments, the 5'-end of the fragment comprising said antisense region can optionally include a phosphate group.

[0058] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits the expression of a PDGF and/or PDGFr RNA sequence (e.g., wherein said target RNA sequence is encoded by a PDGF and/or PDGFr gene involved in the PDGF and/or PDGFr pathway), wherein the siNA molecule does not contain any ribonucleotides and wherein each strand of the double-stranded siNA molecule is about 15 to about 30 nucleotides. In one embodiment, the siNA molecule is 21 nucleotides in length. Examples of non-ribonucleotide containing siNA constructs are combinations of stabilization chemistries shown in Table IV in any combination of Sense/Antisense chemistries, such as Stab 7/8, Stab 7/11, Stab 8/8, Stab 18/8, Stab 18/11, Stab 12/13, Stab 7/13, Stab 18/13, Stab 7/19, Stab 8/19, Stab 18/19, Stab 7/20, Stab 8/20, Stab 18/20, Stab 7/32, Stab 8/32, or Stab 18/32 (e.g., any siNA having Stab 7, 8, 11, 12, 13, 14, 15, 17, 18, 19, 20, or 32 sense or antisense strands or any combination thereof).

[0059] In one embodiment, the invention features a chemically synthesized double stranded RNA molecule that directs cleavage of a PDGF and/or PDGFr RNA via RNA interference, wherein each strand of said RNA molecule is about 15 to about 30 nucleotides in length; one strand of the RNA molecule comprises nucleotide sequence having sufficient complementarity to the PDGF and/or PDGFr RNA for the RNA molecule to direct cleavage of the PDGF and/or PDGFr RNA via RNA interference; and wherein at least one strand of the RNA molecule optionally comprises one or more chemically modified nucleotides described herein, such as without limitation deoxynucleotides, 2'-O-methyl nucleotides, 2'-deoxy-2'-fluoro nucleotides, 2'-O-methoxyethyl nucleotides etc.

[0060] In one embodiment, the invention features a medicament comprising a siNA molecule of the invention.

[0061] In one embodiment, the invention features an active ingredient comprising a siNA molecule of the invention.

[0062] In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule to inhibit, down-regulate, or reduce expression of a PDGF and/or PDGFr gene, wherein the siNA molecule comprises one or more chemical modifications and each strand of the double-stranded siNA is independently about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 or more) nucleotides long. In one embodiment, the siNA molecule of the invention is a double stranded nucleic acid molecule comprising one or more chemical modifications, where each of the two fragments of the siNA molecule independently comprise about 15 to about 40 (e.g. about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 23, 33, 34, 35, 36, 37, 38, 39, or 40) nucleotides and where one of the strands comprises at least 15 nucleotides that are complementary to nucleotide sequence of PDGF and/or PDGFr encoding RNA or a portion thereof. In a non-limiting example, each of the two fragments of the siNA molecule comprise about 21 nucleotides. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule comprising one or more chemical modifications, where each strand is about 21 nucleotide long and where about 19 nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule, wherein at least two 3' terminal nucleotides of each fragment of the siNA molecule are not base-paired to the nucleotides of the other fragment of the siNA molecule. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule comprising one or more chemical modifications, where each strand is about 19 nucleotide long and where the nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule to form at least about 15 (e.g., 15, 16, 17, 18, or 19) base pairs, wherein one or both ends of the siNA molecule are blunt ends. In one embodiment, each of the two 3' terminal nucleotides of each fragment of the siNA molecule is a 2'-deoxy-pyrimidine nucleotide, such as a 2'-deoxy-thymidine. In another embodiment, all nucleotides of each fragment of the siNA molecule are base-paired to the complementary nucleotides of the other fragment of the siNA molecule. In another embodiment, the siNA molecule is a double stranded nucleic acid molecule of about 19 to about 25 base pairs having a sense region and an antisense region and comprising one or more chemical modifications, where about 19 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the PDGF and/or PDGFr gene. In another embodiment, about 21 nucleotides of the antisense region are base-paired to the nucleotide sequence or a portion thereof of the RNA encoded by the PDGF and/or PDGFr gene. In any of the above embodiments, the 5'-end of the fragment comprising said antisense region can optionally include a phosphate group.

[0063] In one embodiment, the invention features the use of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits, down-regulates, or reduces expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification.

[0064] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits, down-regulates, or reduces expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA or a portion thereof, wherein the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification.

[0065] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits, down-regulates, or reduces expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA that encodes a protein or portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification. In one embodiment, each strand of the siNA molecule comprises about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more) nucleotides, wherein each strand comprises at least about 15 nucleotides that are complementary to the nucleotides of the other strand. In one embodiment, the siNA molecule is assembled from two oligonucleotide fragments, wherein one fragment comprises the nucleotide sequence of the antisense strand of the siNA molecule and a second fragment comprises nucleotide sequence of the sense region of the siNA molecule. In one embodiment, the sense strand is connected to the antisense strand via a linker molecule, such as a polynucleotide linker or a non-nucleotide linker. In a further embodiment, the pyrimidine nucleotides present in the sense strand are 2'-deoxy-2'fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2'-deoxy purine nucleotides. In another embodiment, the pyrimidine nucleotides present in the sense strand are 2'-deoxy-2'fluoro pyrimidine nucleotides and the purine nucleotides present in the sense region are 2'-O-methyl purine nucleotides. In still another embodiment, the pyrimidine nucleotides present in the antisense strand are 2'-deoxy-2'-fluoro pyrimidine nucleotides and any purine nucleotides present in the antisense strand are 2'-deoxy purine nucleotides. In another embodiment, the antisense strand comprises one or more 2'-deoxy-2'-fluoro pyrimidine nucleotides and one or more 2'-O-methyl purine nucleotides. In another embodiment, the pyrimidine nucleotides present in the antisense strand are 2'-deoxy-2'-fluoro pyrimidine nucleotides and any purine nucleotides present in the antisense strand are 2'-O-methyl purine nucleotides. In a further embodiment the sense strand comprises a 3'-end and a 5'-end, wherein a terminal cap moiety (e.g., an inverted deoxy abasic moiety or inverted deoxy nucleotide moiety such as inverted thymidine) is present at the 5'-end, the 3'-end, or both of the 5' and 3' ends of the sense strand. In another embodiment, the antisense strand comprises a phosphorothioate internucleotide linkage at the 3' end of the antisense strand. In another embodiment, the antisense strand comprises a glyceryl modification at the 3' end. In another embodiment, the 5'-end of the antisense strand optionally includes a phosphate group.

[0066] In any of the above-described embodiments of a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a PDGF and/or PDGFr gene, wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, each of the two strands of the siNA molecule can comprise about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more) nucleotides. In one embodiment, about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more) nucleotides of each strand of the siNA molecule are base-paired to the complementary nucleotides of the other strand of the siNA molecule. In another embodiment, about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more) nucleotides of each strand of the siNA molecule are base-paired to the complementary nucleotides of the other strand of the siNA molecule, wherein at least two 3' terminal nucleotides of each strand of the siNA molecule are not base-paired to the nucleotides of the other strand of the siNA molecule. In another embodiment, each of the two 3' terminal nucleotides of each fragment of the siNA molecule is a 2'-deoxy-pyrimidine, such as 2'-deoxy-thymidine. In one embodiment, each strand of the siNA molecule is base-paired to the complementary nucleotides of the other strand of the siNA molecule. In one embodiment, about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides of the antisense strand are base-paired to the nucleotide sequence of the PDGF and/or PDGFr RNA or a portion thereof. In one embodiment, about 18 to about 25 (e.g., about 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides of the antisense strand are base-paired to the nucleotide sequence of the PDGF and/or PDGFr RNA or a portion thereof.

[0067] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the 5'-end of the antisense strand optionally includes a phosphate group.

[0068] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA or a portion thereof, the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand and wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the nucleotide sequence or a portion thereof of the antisense strand is complementary to a nucleotide sequence of the untranslated region or a portion thereof of the PDGF and/or PDGFr RNA.

[0069] In one embodiment, the invention features a double-stranded short interfering nucleic acid (siNA) molecule that inhibits expression of a PDGF and/or PDGFr gene, wherein one of the strands of the double-stranded siNA molecule is an antisense strand which comprises nucleotide sequence that is complementary to nucleotide sequence of PDGF and/or PDGFr RNA or a portion thereof, wherein the other strand is a sense strand which comprises nucleotide sequence that is complementary to a nucleotide sequence of the antisense strand, wherein a majority of the pyrimidine nucleotides present in the double-stranded siNA molecule comprises a sugar modification, and wherein the nucleotide sequence of the antisense strand is complementary to a nucleotide sequence of the PDGF and/or PDGFr RNA or a portion thereof that is present in the PDGF and/or PDGFr RNA.

[0070] In one embodiment, the invention features a composition comprising a siNA molecule of the invention in a pharmaceutically acceptable carrier or diluent.

[0071] In a non-limiting example, the introduction of chemically-modified nucleotides into nucleic acid molecules provides a powerful tool in overcoming potential limitations of in vivo stability and bioavailability inherent to native RNA molecules that are delivered exogenously. For example, the use of chemically-modified nucleic acid molecules can enable a lower dose of a particular nucleic acid molecule for a given therapeutic effect since chemically-modified nucleic acid molecules tend to have a longer half-life in serum. Furthermore, certain chemical modifications can improve the bioavailability of nucleic acid molecules by targeting particular cells or tissues and/or improving cellular uptake of the nucleic acid molecule. Therefore, even if the activity of a chemically-modified nucleic acid molecule is reduced as compared to a native nucleic acid molecule, for example, when compared to an all-RNA nucleic acid molecule, the overall activity of the modified nucleic acid molecule can be greater than that of the native molecule due to improved stability and/or delivery of the molecule. Unlike native unmodified siNA, chemically-modified siNA can also minimize the possibility of activating interferon activity in humans.

[0072] In any of the embodiments of siNA molecules described herein, the antisense region of a siNA molecule of the invention can comprise a phosphorothioate internucleotide linkage at the 3'-end of said antisense region. In any of the embodiments of siNA molecules described herein, the antisense region can comprise about one to about five phosphorothioate internucleotide linkages at the 5'-end of said antisense region. In any of the embodiments of siNA molecules described herein, the 3'-terminal nucleotide overhangs of a siNA molecule of the invention can comprise ribonucleotides or deoxyribonucleotides that are chemically-modified at a nucleic acid sugar, base, or backbone. In any of the embodiments of siNA molecules described herein, the 3'-terminal nucleotide overhangs can comprise one or more universal base ribonucleotides. In any of the embodiments of siNA molecules described herein, the 3'-terminal nucleotide overhangs can comprise one or more acyclic nucleotides.

[0073] One embodiment of the invention provides an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention in a manner that allows expression of the nucleic acid molecule. Another embodiment of the invention provides a mammalian cell comprising such an expression vector. The mammalian cell can be a human cell. The siNA molecule of the expression vector can comprise a sense region and an antisense region. The antisense region can comprise sequence complementary to a RNA or DNA sequence encoding PDGF and/or PDGFr and the sense region can comprise sequence complementary to the antisense region. The siNA molecule can comprise two distinct strands having complementary sense and antisense regions. The siNA molecule can comprise a single strand having complementary sense and antisense regions.

[0074] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides comprising a backbone modified internucleotide linkage having Formula I:

##STR00001##

wherein each R1 and R2 is independently any nucleotide, non-nucleotide, or polynucleotide which can be naturally-occurring or chemically-modified, each X and Y is independently O, S, N, alkyl, or substituted alkyl, each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, aralkyl, or acetyl and wherein W, X, Y, and Z are optionally not all O. In another embodiment, a backbone modification of the invention comprises a phosphonoacetate and/or thiophosphonoacetate internucleotide linkage (see for example Sheehan et al., 2003, Nucleic Acids Research, 31, 4109-4118).

[0075] The chemically-modified internucleotide linkages having Formula I, for example, wherein any Z, W, X, and/or Y independently comprises a sulphur atom, can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) chemically-modified internucleotide linkages having Formula I at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified internucleotide linkages having Formula I at the 5'-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine nucleotides with chemically-modified internucleotide linkages having Formula I in the sense strand, the antisense strand, or both strands. In another embodiment, a siNA molecule of the invention having internucleotide linkage(s) of Formula I also comprises a chemically-modified nucleotide or non-nucleotide having any of Formulae I-VII.

[0076] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula II:

##STR00002##

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-SH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO.sub.2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S.dbd.O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

[0077] The chemically-modified nucleotide or non-nucleotide of Formula II can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotides or non-nucleotides of Formula II at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 5'-end of the sense strand, the antisense strand, or both strands. In anther non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotides or non-nucleotides of Formula II at the 3'-end of the sense strand, the antisense strand, or both strands.

[0078] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) nucleotides or non-nucleotides having Formula III:

##STR00003##

wherein each R3, R4, R5, R6, R7, R8, R10, R11 and R12 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-SH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S.dbd.O, CHF, or CF2, and B is a nucleosidic base such as adenine, guanine, uracil, cytosine, thymine, 2-aminoadenosine, 5-methylcytosine, 2,6-diaminopurine, or any other non-naturally occurring base that can be employed to be complementary or non-complementary to target RNA or a non-nucleosidic base such as phenyl, naphthyl, 3-nitropyrrole, 5-nitroindole, nebularine, pyridone, pyridinone, or any other non-naturally occurring universal base that can be complementary or non-complementary to target RNA.

[0079] The chemically-modified nucleotide or non-nucleotide of Formula III can be present in one or both oligonucleotide strands of the siNA duplex, for example, in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more chemically-modified nucleotides or non-nucleotides of Formula III at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide(s) or non-nucleotide(s) of Formula III at the 5'-end of the sense strand, the antisense strand, or both strands. In anther non-limiting example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) chemically-modified nucleotide or non-nucleotide of Formula III at the 3'-end of the sense strand, the antisense strand, or both strands.

[0080] In another embodiment, a siNA molecule of the invention comprises a nucleotide having Formula II or III, wherein the nucleotide having Formula II or III is in an inverted configuration. For example, the nucleotide having Formula II or III is connected to the siNA construct in a 3'-3',3'-2',2'-3', or 5'-5' configuration, such as at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of one or both siNA strands.

[0081] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a 5'-terminal phosphate group having Formula IV:

##STR00004##

wherein each X and Y is independently O, S, N, alkyl, substituted alkyl, or alkylhalo;

[0082] wherein each Z and W is independently O, S, N, alkyl, substituted alkyl, O-alkyl, S-alkyl, alkaryl, aralkyl, alkylhalo, or acetyl; and wherein W, X, Y and Z are not all O.

[0083] In one embodiment, the invention features a siNA molecule having a 5'-terminal phosphate group having Formula IV on the target-complementary strand, for example, a strand complementary to a target RNA, wherein the siNA molecule comprises an all RNA siNA, molecule. In another embodiment, the invention features a siNA molecule having a 5'-terminal phosphate group having Formula IV on the target-complementary strand wherein the siNA molecule also comprises about 1 to about 3 (e.g., about 1, 2, or 3) nucleotide 3'-terminal nucleotide overhangs having about 1 to about 4 (e.g., about 1, 2, 3, or 4) deoxyribonucleotides on the 3'-end of one or both strands. In another embodiment, a 5'-terminal phosphate group having Formula IV is present on the target-complementary strand of a siNA molecule of the invention, for example a siNA molecule having chemical modifications having any of Formulae I-VII.

[0084] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises one or more phosphorothioate internucleotide linkages. For example, in a non-limiting example, the invention features a chemically-modified short interfering nucleic acid (siNA) having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in one siNA strand. In yet another embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) individually having about 1, 2, 3, 4, 5, 6, 7, 8 or more phosphorothioate internucleotide linkages in both siNA strands. The phosphorothioate internucleotide linkages can be present in one or both oligonucleotide strands of the siNA duplex, for example in the sense strand, the antisense strand, or both strands. The siNA molecules of the invention can comprise one or more phosphorothioate internucleotide linkages at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the sense strand, the antisense strand, or both strands. For example, an exemplary siNA molecule of the invention can comprise about 1 to about 5 or more (e.g., about 1, 2, 3, 4, 5, or more) consecutive phosphorothioate internucleotide linkages at the 5'-end of the sense strand, the antisense strand, or both strands. In another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) pyrimidine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands. In yet another non-limiting example, an exemplary siNA molecule of the invention can comprise one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) purine phosphorothioate internucleotide linkages in the sense strand, the antisense strand, or both strands.

[0085] In one embodiment, the invention features a siNA molecule, wherein the sense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2'-deoxy, 2'-O-methyl and/or 2'-deoxy-2'-fluoro nucleotides, with or without one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends, being present in the same or different strand.

[0086] In another embodiment, the invention features a siNA molecule, wherein the sense strand comprises about 1 to about 5, specifically about 1, 2, 3, 4, or 5 phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3-end, the 5'-end, or both of the 3'- and 5'-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more, pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2'-deoxy, 2'-O-methyl and/or 2'-deoxy-2'-fluoro nucleotides, with or without about 1 to about 5 or more, for example about 1, 2, 3, 4, 5, or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends, being present in the same or different strand.

[0087] In one embodiment, the invention features a siNA molecule, wherein the sense strand comprises one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more phosphorothioate internucleotide linkages, and/or about one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 10 or more, specifically about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2'-deoxy, 2'-O-methyl and/or 2'-deoxy-2'-fluoro nucleotides, with or without one or more, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3' and 5'-ends, being present in the same or different strand.

[0088] In another embodiment, the invention features a siNA molecule, wherein the sense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the sense strand; and wherein the antisense strand comprises about 1 to about 5 or more, specifically about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) 2'-deoxy, 2'-O-methyl, 2'-deoxy-2'-fluoro, and/or one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more) universal base modified nucleotides, and optionally a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of the antisense strand. In another embodiment, one or more, for example about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 or more pyrimidine nucleotides of the sense and/or antisense siNA strand are chemically-modified with 2'-deoxy, 2'-O-methyl and/or 2'-deoxy-2'-fluoro nucleotides, with or without about 1 to about 5, for example about 1, 2, 3, 4, 5 or more phosphorothioate internucleotide linkages and/or a terminal cap molecule at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends, being present in the same or different strand.

[0089] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule having about 1 to about 5 or more (specifically about 1, 2, 3, 4, 5 or more) phosphorothioate internucleotide linkages in each strand of the siNA molecule.

[0090] In another embodiment, the invention features a siNA molecule comprising 2'-5' internucleotide linkages. The 2'-5' internucleotide linkage(s) can be at the 3'-end, the 5'-end, or both of the 3'- and 5'-ends of one or both siNA sequence strands. In addition, the 2'-5' internucleotide linkage(s) can be present at various other positions within one or both siNA sequence strands, for example, about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a pyrimidine nucleotide in one or both strands of the siNA molecule can comprise a 2'-5' internucleotide linkage, or about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more including every internucleotide linkage of a purine nucleotide in one or both strands of the siNA molecule can comprise a 2'-5' internucleotide linkage.

[0091] In another embodiment, a chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified, wherein each strand is independently about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length, wherein the duplex has about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) base pairs, and wherein the chemical modification comprises a structure having any of Formulae I-VII. For example, an exemplary chemically-modified siNA molecule of the invention comprises a duplex having two strands, one or both of which can be chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein each strand consists of about 21 nucleotides, each having a 2-nucleotide 3'-terminal nucleotide overhang, and wherein the duplex has about 19 base pairs. In another embodiment, a siNA molecule of the invention comprises a single stranded hairpin structure, wherein the siNA is about 36 to about 70 (e.g., about 36, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) base pairs, and wherein the siNA can include a chemical modification comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms a hairpin structure having about 19 to about 21 (e.g., 19, 20, or 21) base pairs and a 2-nucleotide 3'-terminal nucleotide overhang. In another embodiment, a linear hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. For example, a linear hairpin siNA molecule of the invention is designed such that degradation of the loop portion of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3'-terminal overhangs, such as 3'-terminal nucleotide overhangs comprising about 2 nucleotides.

[0092] In another embodiment, a siNA molecule of the invention comprises a hairpin structure, wherein the siNA is about 25 to about 50 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides in length having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 25 to about 35 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35) nucleotides that is chemically-modified with one or more chemical modifications having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms a hairpin structure having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs and a 5'-terminal phosphate group that can be chemically modified as described herein (for example a 5'-terminal phosphate group having Formula IV). In another embodiment, a linear hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. In one embodiment, a linear hairpin siNA molecule of the invention comprises a loop portion comprising a non-nucleotide linker.

[0093] In another embodiment, a siNA molecule of the invention comprises an asymmetric hairpin structure, wherein the siNA is about 25 to about 50 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides in length having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a linear oligonucleotide having about 25 to about 35 (e.g., about 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, or 35) nucleotides that is chemically-modified with one or more chemical modifications having any of Formulae I-VII or any combination thereof, wherein the linear oligonucleotide forms an asymmetric hairpin structure having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs and a 5'-terminal phosphate group that can be chemically modified as described herein (for example a 5'-terminal phosphate group having Formula IV). In one embodiment, an asymmetric hairpin siNA molecule of the invention contains a stem loop motif, wherein the loop portion of the siNA molecule is biodegradable. In another embodiment, an asymmetric hairpin siNA molecule of the invention comprises a loop portion comprising a non-nucleotide linker.

[0094] In another embodiment, a siNA molecule of the invention comprises an asymmetric double stranded structure having separate polynucleotide strands comprising sense and antisense regions, wherein the antisense region is about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length, wherein the sense region is about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides in length, wherein the sense region and the antisense region have at least 3 complementary nucleotides, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises an asymmetric double stranded structure having separate polynucleotide strands comprising sense and antisense regions, wherein the antisense region is about 18 to about 23 (e.g., about 18, 19, 20, 21, 22, or 23) nucleotides in length and wherein the sense region is about 3 to about 15 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, or 15) nucleotides in length, wherein the sense region the antisense region have at least 3 complementary nucleotides, and wherein the siNA can include one or more chemical modifications comprising a structure having any of Formulae I-VII or any combination thereof. In another embodiment, the asymmetric double stranded siNA molecule can also have a 5'-terminal phosphate group that can be chemically modified as described herein (for example a 5'-terminal phosphate group having Formula IV).

[0095] In another embodiment, a siNA molecule of the invention comprises a circular nucleic acid molecule, wherein the siNA is about 38 to about 70 (e.g., about 38, 40, 45, 50, 55, 60, 65, or 70) nucleotides in length having about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) base pairs, and wherein the siNA can include a chemical modification, which comprises a structure having any of Formulae I-VII or any combination thereof. For example, an exemplary chemically-modified siNA molecule of the invention comprises a circular oligonucleotide having about 42 to about 50 (e.g., about 42, 43, 44, 45, 46, 47, 48, 49, or 50) nucleotides that is chemically-modified with a chemical modification having any of Formulae I-VII or any combination thereof, wherein the circular oligonucleotide forms a dumbbell shaped structure having about 19 base pairs and 2 loops.

[0096] In another embodiment, a circular siNA molecule of the invention contains two loop motifs, wherein one or both loop portions of the siNA molecule is biodegradable. For example, a circular siNA molecule of the invention is designed such that degradation of the loop portions of the siNA molecule in vivo can generate a double-stranded siNA molecule with 3'-terminal overhangs, such as 3'-terminal nucleotide overhangs comprising about 2 nucleotides.

[0097] In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) abasic moiety, for example a compound having Formula V:

##STR00005##

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-SH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S.dbd.O, CHF, or CF2.

[0098] In one embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) inverted abasic moiety, for example a compound having Formula VI:

##STR00006##

wherein each R3, R4, R5, R6, R7, R8, R10, R11, R12, and R13 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-SH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or group having Formula I or II; R9 is O, S, CH2, S.dbd.O, CHF, or CF2, and either R2, R3, R8 or R13 serve as points of attachment to the siNA molecule of the invention.

[0099] In another embodiment, a siNA molecule of the invention comprises at least one (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) substituted polyalkyl moieties, for example a compound having Formula VII:

##STR00007##

wherein each n is independently an integer from 1 to 12, each R1, R2 and R3 is independently H, OH, alkyl, substituted alkyl, alkaryl or aralkyl, F, Cl, Br, CN, CF3, OCF3, OCN, O-alkyl, S-alkyl, N-alkyl, O-alkenyl, S-alkenyl, N-alkenyl, SO-alkyl, alkyl-SH, alkyl-OH, O-alkyl-OH, O-alkyl-SH, S-alkyl-OH, S-alkyl-SH, alkyl-5-alkyl, alkyl-O-alkyl, ONO2, NO2, N3, NH2, aminoalkyl, aminoacid, aminoacyl, ONH2, O-aminoalkyl, O-aminoacid, O-aminoacyl, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalklylamino, substituted silyl, or a group having Formula I, and R1, R2 or R3 serves as points of attachment to the siNA molecule of the invention.

[0100] In another embodiment, the invention features a compound having Formula VII, wherein R1 and R2 are hydroxyl (OH) groups, n=1, and R3 comprises 0 and is the point of attachment to the 3'-end, the 5'-end, or both of the 3' and 5'-ends of one or both strands of a double-stranded siNA molecule of the invention or to a single-stranded siNA molecule of the invention. This modification is referred to herein as "glyceryl" (for example modification 6 in FIG. 10).

[0101] In another embodiment, a chemically modified nucleoside or non-nucleoside (e.g. a moiety having any of Formula V, VI or VII) of the invention is at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of a siNA molecule of the invention. For example, chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) can be present at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the antisense strand, the sense strand, or both antisense and sense strands of the siNA molecule. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the 5'-end and 3'-end of the sense strand and the 3'-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the terminal position of the 5'-end and 3'-end of the sense strand and the 3'-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the two terminal positions of the 5'-end and 3'-end of the sense strand and the 3'-end of the antisense strand of a double stranded siNA molecule of the invention. In one embodiment, the chemically modified nucleoside or non-nucleoside (e.g., a moiety having Formula V, VI or VII) is present at the penultimate position of the 5'-end and 3'-end of the sense strand and the 3'-end of the antisense strand of a double stranded siNA molecule of the invention. In addition, a moiety having Formula VII can be present at the 3'-end or the 5'-end of a hairpin siNA molecule as described herein.

[0102] In another embodiment, a siNA molecule of the invention comprises an abasic residue having Formula V or VI, wherein the abasic residue having Formula VI or VI is connected to the siNA construct in a 3'-3',3'-2',2'-3', or 5'-5' configuration, such as at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of one or both siNA strands.

[0103] In one embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) locked nucleic acid (LNA) nucleotides, for example, at the 5'-end, the 3'-end, both of the 5' and 3'-ends, or any combination thereof, of the siNA molecule.

[0104] In another embodiment, a siNA molecule of the invention comprises one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) acyclic nucleotides, for example, at the 5'-end, the 3'-end, both of the 5' and 3'-ends, or any combination thereof, of the siNA molecule.

[0105] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2'-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides).

[0106] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2'-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides), wherein any nucleotides comprising a 3'-terminal nucleotide overhang that are present in said sense region are 2'-deoxy nucleotides.

[0107] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides).

[0108] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising a sense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), wherein any (e.g., one or more or all) purine nucleotides present in the sense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides), and wherein any nucleotides comprising a 3'-terminal nucleotide overhang that are present in said sense region are 2'-deoxy nucleotides.

[0109] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides).

[0110] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides), and wherein any nucleotides comprising a 3'-terminal nucleotide overhang that are present in said antisense region are 2'-deoxy nucleotides.

[0111] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2'-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides).

[0112] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention comprising an antisense region, wherein any (e.g., one or more or all) pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any (e.g., one or more or all) purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides).

[0113] In one embodiment, the invention features a chemically-modified short interfering nucleic acid (siNA) molecule of the invention capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system comprising a sense region, wherein one or more pyrimidine nucleotides present in the sense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the sense region are 2'-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides), and an antisense region, wherein one or more pyrimidine nucleotides present in the antisense region are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and one or more purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides). The sense region and/or the antisense region can have a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the sense and/or antisense sequence. The sense and/or antisense region can optionally further comprise a 3'-terminal nucleotide overhang having about 1 to about 4 (e.g., about 1, 2, 3, or 4) 2'-deoxynucleotides. The overhang nucleotides can further comprise one or more (e.g., about 1, 2, 3, 4 or more) phosphorothioate, phosphonoacetate, and/or thiophosphonoacetate internucleotide linkages. Non-limiting examples of these chemically-modified siNAs are shown in FIGS. 4 and 5 and Tables III and IV herein. In any of these described embodiments, the purine nucleotides present in the sense region are alternatively 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides) and one or more purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides). Also, in any of these embodiments, one or more purine nucleotides present in the sense region are alternatively purine ribonucleotides (e.g., wherein all purine nucleotides are purine ribonucleotides or alternately a plurality of purine nucleotides are purine ribonucleotides) and any purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides). Additionally, in any of these embodiments, one or more purine nucleotides present in the sense region and/or present in the antisense region are alternatively selected from the group consisting of 2'-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2'-methoxyethyl nucleotides, 4'-thionucleotides, and 2'-O-methyl nucleotides (e.g., wherein all purine nucleotides are selected from the group consisting of 2'-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2'-methoxyethyl nucleotides, 4'-thionucleotides, and 2'-O-methyl nucleotides or alternately a plurality of purine nucleotides are selected from the group consisting of 2'-deoxy nucleotides, locked nucleic acid (LNA) nucleotides, 2'-methoxyethyl nucleotides, 4'-thionucleotides, and 2'-O-methyl nucleotides).

[0114] In another embodiment, any modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the siNA molecules of the invention, preferably in the antisense strand of the siNA molecules of the invention, but also optionally in the sense and/or both antisense and sense strands, are resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi. Non-limiting examples of nucleotides having a northern configuration include locked nucleic acid (LNA) nucleotides (e.g., 2'-O, 4'-C-methylene-(D-ribofuranosyl) nucleotides); 2'-methoxyethoxy (MOE) nucleotides; 2'-methyl-thio-ethyl, 2'-deoxy-2'-fluoro nucleotides, 2'-deoxy-2'-chloro nucleotides, 2'-azido nucleotides, and 2'-O-methyl nucleotides.

[0115] In one embodiment, the sense strand of a double stranded siNA molecule of the invention comprises a terminal cap moiety, (see for example FIG. 10) such as an inverted deoxyabasic moiety, at the 3'-end, 5'-end, or both 3' and 5'-ends of the sense strand.

[0116] In one embodiment, the invention features a chemically-modified short interfering nucleic acid molecule (siNA) capable of mediating RNA interference (RNAi) against PDGF and/or PDGFr inside a cell or reconstituted in vitro system, wherein the chemical modification comprises a conjugate covalently attached to the chemically-modified siNA molecule. Non-limiting examples of conjugates contemplated by the invention include conjugates and ligands described in Vargeese et al., U.S. Ser. No. 10/427,160, filed Apr. 30, 2003, incorporated by reference herein in its entirety, including the drawings. In another embodiment, the conjugate is covalently attached to the chemically-modified siNA molecule via a biodegradable linker. In one embodiment, the conjugate molecule is attached at the 3'-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In another embodiment, the conjugate molecule is attached at the 5'-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule. In yet another embodiment, the conjugate molecule is attached both the 3'-end and 5'-end of either the sense strand, the antisense strand, or both strands of the chemically-modified siNA molecule, or any combination thereof. In one embodiment, a conjugate molecule of the invention comprises a molecule that facilitates delivery of a chemically-modified siNA molecule into a biological system, such as a cell. In another embodiment, the conjugate molecule attached to the chemically-modified siNA molecule is a polyethylene glycol, human serum albumin, or a ligand for a cellular receptor that can mediate cellular uptake. Examples of specific conjugate molecules contemplated by the instant invention that can be attached to chemically-modified siNA molecules are described in Vargeese et al., U.S. Ser. No. 10/201,394, filed Jul. 22, 2002 incorporated by reference herein. The type of conjugates used and the extent of conjugation of siNA molecules of the invention can be evaluated for improved pharmacokinetic profiles, bioavailability, and/or stability of siNA constructs while at the same time maintaining the ability of the siNA to mediate RNAi activity. As such, one skilled in the art can screen siNA constructs that are modified with various conjugates to determine whether the siNA conjugate complex possesses improved properties while maintaining the ability to mediate RNAi, for example in animal models as are generally known in the art.

[0117] In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule of the invention, wherein the siNA further comprises a nucleotide, non-nucleotide, or mixed nucleotide/non-nucleotide linker that joins the sense region of the siNA to the antisense region of the siNA. In one embodiment, a nucleotide linker of the invention can be a linker of .gtoreq.2 nucleotides in length, for example about 3, 4, 5, 6, 7, 8, 9, or 10 nucleotides in length. In another embodiment, the nucleotide linker can be a nucleic acid aptamer. By "aptamer" or "nucleic acid aptamer" as used herein is meant a nucleic acid molecule that binds specifically to a target molecule wherein the nucleic acid molecule has sequence that comprises a sequence recognized by the target molecule in its natural setting. Alternately, an aptamer can be a nucleic acid molecule that binds to a target molecule where the target molecule does not naturally bind to a nucleic acid. The target molecule can be any molecule of interest. For example, the aptamer can be used to bind to a ligand-binding domain of a protein, thereby preventing interaction of the naturally occurring ligand with the protein. This is a non-limiting example and those in the art will recognize that other embodiments can be readily generated using techniques generally known in the art. (See, for example, Gold et al.; 1995, Annu. Rev. Biochem., 64, 763; Brody and Gold, 2000, J. Biotechnol., 74, 5; Sun, 2000, Curr. Opin. Mol. Ther., 2, 100; Kusser, 2000, J. Biotechnol., 74, 27; Hermann and Patel, 2000, Science, 287, 820; and Jayasena, 1999, Clinical Chemistry, 45, 1628.)

[0118] In yet another embodiment, a non-nucleotide linker of the invention comprises abasic nucleotide, polyether, polyamine, polyamide, peptide, carbohydrate, lipid, polyhydrocarbon, or other polymeric compounds (e.g. polyethylene glycols such as those having between 2 and 100 ethylene glycol units). Specific examples include those described by Seela and Kaiser, Nucleic Acids Res. 1990, 18:6353 and Nucleic Acids Res. 1987, 15:3113; Cload and Schepartz, J. Am. Chem. Soc. 1991, 113:6324; Richardson and Schepartz, J. Am. Chem. Soc. 1991, 113:5109; Ma et al., Nucleic Acids Res. 1993, 21:2585 and Biochemistry 1993, 32:1751; Durand et al., Nucleic Acids Res. 1990, 18:6353; McCurdy et al., Nucleosides & Nucleotides 1991, 10:287; Jschke et al., Tetrahedron Lett. 1993, 34:301; Ono et al., Biochemistry 1991, 30:9914; Arnold et al., International Publication No. WO 89/02439; Usman et al., International Publication No. WO 95/06731; Dudycz et al., International Publication No. WO 95/11910 and Ferentz and Verdine, J. Am. Chem. Soc. 1991, 113:4000, all hereby incorporated by reference herein. A "non-nucleotide" further means any group or compound that can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound can be abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine, for example at the C1 position of the sugar.

[0119] In one embodiment, the invention features a short interfering nucleic acid (siNA) molecule capable of mediating RNA interference (RNAi) inside a cell or reconstituted in vitro system, wherein one or both strands of the siNA molecule that are assembled from two separate oligonucleotides do not comprise any ribonucleotides. For example, a siNA molecule can be assembled from a single oligonucleotide where the sense and antisense regions of the siNA comprise separate oligonucleotides that do not have any ribonucleotides (e.g., nucleotides having a 2'-OH group) present in the oligonucleotides. In another example, a siNA molecule can be assembled from a single oligonucleotide where the sense and antisense regions of the siNA are linked or circularized by a nucleotide or non-nucleotide linker as described herein, wherein the oligonucleotide does not have any ribonucleotides (e.g., nucleotides having a 2'-OH group) present in the oligonucleotide. Applicant has surprisingly found that the presence of ribonucleotides (e.g., nucleotides having a 2'-hydroxyl group) within the siNA molecule is not required or essential to support RNAi activity. As such, in one embodiment, all positions within the siNA can include chemically modified nucleotides and/or non-nucleotides such as nucleotides and or non-nucleotides having Formula I, II, III, IV, V, VI, or VII or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

[0120] In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system comprising a single stranded polynucleotide having complementarity to a target nucleic acid sequence. In another embodiment, the single stranded siNA molecule of the invention comprises a 5'-terminal phosphate group. In another embodiment, the single stranded siNA molecule of the invention comprises a 5'-terminal phosphate group and a 3'-terminal phosphate group (e.g., a 2',3'-cyclic phosphate). In another embodiment, the single stranded siNA molecule of the invention comprises about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides. In yet another embodiment, the single stranded siNA molecule of the invention comprises one or more chemically modified nucleotides or non-nucleotides described herein. For example, all the positions within the siNA molecule can include chemically-modified nucleotides such as nucleotides having any of Formulae I-VII, or any combination thereof to the extent that the ability of the siNA molecule to support RNAi activity in a cell is maintained.

[0121] In one embodiment, a siNA molecule of the invention is a single stranded siNA molecule that mediates RNAi activity in a cell or reconstituted in vitro system comprising a single stranded polynucleotide having complementarity to a target nucleic acid sequence, wherein one or more pyrimidine nucleotides present in the siNA are 2'-deoxy-2'-fluoro pyrimidine nucleotides (e.g., wherein all pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides or alternately a plurality of pyrimidine nucleotides are 2'-deoxy-2'-fluoro pyrimidine nucleotides), and wherein any purine nucleotides present in the antisense region are 2'-O-methyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-O-methyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-O-methyl purine nucleotides), and a terminal cap modification, such as any modification described herein or shown in FIG. 10, that is optionally present at the 3'-end, the 5'-end, or both of the 3' and 5'-ends of the antisense sequence. The siNA optionally further comprises about 1 to about 4 or more (e.g., about 1, 2, 3, 4 or more) terminal 2'-deoxynucleotides at the 3'-end of the siNA molecule, wherein the terminal nucleotides can further comprise one or more (e.g., 1, 2, 3, 4 or more) phosphorothioate, phosphonoacetate, and/or thiophosphonoacetate internucleotide linkages, and wherein the siNA optionally further comprises a terminal phosphate group, such as a 5'-terminal phosphate group. In any of these embodiments, any purine nucleotides present in the antisense region are alternatively 2'-deoxy purine nucleotides (e.g., wherein all purine nucleotides are 2'-deoxy purine nucleotides or alternately a plurality of purine nucleotides are 2'-deoxy purine nucleotides). Also, in any of these embodiments, any purine nucleotides present in the siNA (i.e., purine nucleotides present in the sense and/or antisense region) can alternatively be locked nucleic acid (LNA) nucleotides (e.g., wherein all purine nucleotides are LNA nucleotides or alternately a plurality of purine nucleotides are LNA nucleotides). Also, in any of these embodiments, any purine nucleotides present in the siNA are alternatively 2'-methoxyethyl purine nucleotides (e.g., wherein all purine nucleotides are 2'-methoxyethyl purine nucleotides or alternately a plurality of purine nucleotides are 2'-methoxyethyl purine nucleotides). In another embodiment, any modified nucleotides present in the single stranded siNA molecules of the invention comprise modified nucleotides having properties or characteristics similar to naturally occurring ribonucleotides. For example, the invention features siNA molecules including modified nucleotides having a Northern conformation (e.g., Northern pseudorotation cycle, see for example Saenger, Principles of Nucleic Acid Structure, Springer-Verlag ed., 1984). As such, chemically modified nucleotides present in the single stranded siNA molecules of the invention are preferably resistant to nuclease degradation while at the same time maintaining the capacity to mediate RNAi.

[0122] In one embodiment, a siNA molecule of the invention comprises chemically modified nucleotides or non-nucleotides (e.g., having any of Formulae I-VII, such as 2'-deoxy, 2'-deoxy-2'-fluoro, or 2'-O-methyl nucleotides) at alternating positions within one or more strands or regions of the siNA molecule. For example, such chemical modifications can be introduced at every other position of a RNA based siNA molecule, starting at either the first or second nucleotide from the 3'-end or 5'-end of the siNA. In a non-limiting example, a double stranded siNA molecule of the invention in which each strand of the siNA is 21 nucleotides in length is featured wherein positions 1, 3, 5, 7, 9, 11, 13, 15, 17, 19 and 21 of each strand are chemically modified (e.g., with compounds having any of Formulae I-VII, such as such as 2'-deoxy, 2'-deoxy-2'-fluoro, or 2'-O-methyl nucleotides). In another non-limiting example, a double stranded siNA molecule of the invention in which each strand of the siNA is 21 nucleotides in length is featured wherein positions 2, 4, 6, 8, 10, 12, 14, 16, 18, and 20 of each strand are chemically modified (e.g., with compounds having any of Formulae I-VII, such as such as 2'-deoxy, 2'-deoxy-2'-fluoro, or 2'-O-methyl nucleotides). Such siNA molecules can further comprise terminal cap moieties and/or backbone modifications as described herein.

[0123] In one embodiment, the invention features a method for modulating the expression of a PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the cell.

[0124] In one embodiment, the invention features a method for modulating the expression of a PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the cell.

[0125] In another embodiment, the invention features a method for modulating the expression of more than one PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr genes; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the cell.

[0126] In another embodiment, the invention features a method for modulating the expression of two or more PDGF and/or PDGFr genes within a cell comprising: (a) synthesizing one or more siNA molecules of the invention, which can be chemically-modified, wherein the siNA strands comprise sequences complementary to RNA of the PDGF and/or PDGFr genes and wherein the sense strand sequences of the siNAs comprise sequences identical or substantially similar to the sequences of the target RNAs; and (b) introducing the siNA molecules into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the cell.

[0127] In another embodiment, the invention features a method for modulating the expression of more than one PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequences of the target RNAs; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the cell.

[0128] In one embodiment, siNA molecules of the invention are used as reagents in ex vivo applications. For example, siNA reagents are introduced into tissue or cells that are transplanted into a subject for therapeutic effect. The cells and/or tissue can be derived from an organism or subject that later receives the explant, or can be derived from another organism or subject prior to transplantation. The siNA molecules can be used to modulate the expression of one or more genes in the cells or tissue, such that the cells or tissue obtain a desired phenotype or are able to perform a function when transplanted in vivo. In one embodiment, certain target cells from a patient are extracted. These extracted cells are contacted with siNAs targeting a specific nucleotide sequence within the cells under conditions suitable for uptake of the siNAs by these cells (e.g. using delivery reagents such as cationic lipids, liposomes and the like or using techniques such as electroporation to facilitate the delivery of siNAs into cells). The cells are then reintroduced back into the same patient or other patients. In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in that organism.

[0129] In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene and wherein the sense strand sequence of the siNA comprises a sequence identical or substantially similar to the sequence of the target RNA; and (b) introducing the siNA molecule into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in that organism.

[0130] In another embodiment, the invention features a method of modulating the expression of more than one PDGF and/or PDGFr gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr genes; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the organism the tissue was derived from or into another organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in that organism.

[0131] In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a subject or organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecule into the subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism. The level of PDGF and/or PDGFr protein or RNA can be determined using various methods well-known in the art.

[0132] In another embodiment, the invention features a method of modulating the expression of more than one PDGF and/or PDGFr gene in a subject or organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein one of the siNA strands comprises a sequence complementary to RNA of the PDGF and/or PDGFr genes; and (b) introducing the siNA molecules into the subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the subject or organism. The level of PDGF and/or PDGFr protein or RNA can be determined as is known in the art.

[0133] In one embodiment, the invention features a method for modulating the expression of a PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecule into a cell under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the cell.

[0134] In another embodiment, the invention features a method for modulating the expression of more than one PDGF and/or PDGFr gene within a cell comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) contacting the cell in vitro or in vivo with the siNA molecule under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the cell.

[0135] In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a tissue explant comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) contacting a cell of the tissue explant derived from a particular subject or organism with the siNA molecule under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the subject or organism the tissue was derived from or into another subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in that subject or organism.

[0136] In another embodiment, the invention features a method of modulating the expression of more than one PDGF and/or PDGFr gene in a tissue explant comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecules into a cell of the tissue explant derived from a particular subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the tissue explant. In another embodiment, the method further comprises introducing the tissue explant back into the subject or organism the tissue was derived from or into another subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in that subject or organism.

[0137] In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a subject or organism comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecule into the subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0138] In another embodiment, the invention features a method of modulating the expression of more than one PDGF and/or PDGFr gene in a subject or organism comprising: (a) synthesizing siNA molecules of the invention, which can be chemically-modified, wherein the siNA comprises a single stranded sequence having complementarity to RNA of the PDGF and/or PDGFr gene; and (b) introducing the siNA molecules into the subject or organism under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the subject or organism.

[0139] In one embodiment, the invention features a method of modulating the expression of a PDGF and/or PDGFr gene in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0140] In one embodiment, the invention features a method for treating or preventing cancer in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0141] In one embodiment, the invention features a method for treating or preventing leukemia in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0142] In one embodiment, the invention features a method for treating or preventing obliterative bronchiolitis in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0143] In one embodiment, the invention features a method for treating or preventing acute glomerulonephritis in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0144] In one embodiment, the invention features a method for treating or preventing a stroke (CVA) in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0145] In one embodiment, the invention features a method for treating or preventing an inflammatory disease, disorder, and/or condition in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0146] In one embodiment, the invention features a method for treating or preventing a proliferative disease, disorder, and/or condition in a subject or organism comprising contacting the subject or organism with a siNA molecule of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr gene in the subject or organism.

[0147] In another embodiment, the invention features a method of modulating the expression of more than one PDGF and/or PDGFr genes in a subject or organism comprising contacting the subject or organism with one or more siNA molecules of the invention under conditions suitable to modulate the expression of the PDGF and/or PDGFr genes in the subject or organism.

[0148] The siNA molecules of the invention can be designed to down regulate or inhibit target (e.g., PDGF and/or PDGFr) gene expression through RNAi targeting of a variety of RNA molecules. In one embodiment, the siNA molecules of the invention are used to target various RNAs corresponding to a target gene. Non-limiting examples of such RNAs include messenger RNA (mRNA), alternate RNA splice variants of target gene(s), post-transcriptionally modified RNA of target gene(s), pre-mRNA of target gene(s), and/or RNA templates. If alternate splicing produces a family of transcripts that are distinguished by usage of appropriate exons, the instant invention can be used to inhibit gene expression through the appropriate exons to specifically inhibit or to distinguish among the functions of gene family members. For example, a protein that contains an alternatively spliced transmembrane domain can be expressed in both membrane bound and secreted forms. Use of the invention to target the exon containing the transmembrane domain can be used to determine the functional consequences of pharmaceutical targeting of membrane bound as opposed to the secreted form of the protein. Non-limiting examples of applications of the invention relating to targeting these RNA molecules include therapeutic pharmaceutical applications, pharmaceutical discovery applications, molecular diagnostic and gene function applications, and gene mapping, for example using single nucleotide polymorphism mapping with siNA molecules of the invention. Such applications can be implemented using known gene sequences or from partial sequences available from an expressed sequence tag (EST).

[0149] In another embodiment, the siNA molecules of the invention are used to target conserved sequences corresponding to a gene family or gene families such as PDGF and/or PDGFr family genes. As such, siNA molecules targeting multiple PDGF and/or PDGFr targets can provide increased therapeutic effect. In addition, siNA can be used to characterize pathways of gene function in a variety of applications. For example, the present invention can be used to inhibit the activity of target gene(s) in a pathway to determine the function of uncharacterized gene(s) in gene function analysis, mRNA function analysis, or translational analysis. The invention can be used to determine potential target gene pathways involved in various diseases and conditions toward pharmaceutical development. The invention can be used to understand pathways of gene expression involved in, for example cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative traits, diseases, disorders, and/or conditions.

[0150] In one embodiment, siNA molecule(s) and/or methods of the invention are used to down regulate the expression of gene(s) that encode RNA referred to by Genbank Accession, for example, PDGF and/or PDGFr genes encoding RNA sequence(s) referred to herein by Genbank Accession number, for example, Genbank Accession Nos. shown in Table I.

[0151] In one embodiment, the invention features a method comprising: (a) generating a library of siNA constructs having a predetermined complexity; and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target RNA sequence. In one embodiment, the siNA molecules of (a) have strands of a fixed length, for example, about 23 nucleotides in length. In another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

[0152] In one embodiment, the invention features a method comprising: (a) generating a randomized library of siNA constructs having a predetermined complexity, such as of 4.sup.N, where N represents the number of base paired nucleotides in each of the siNA construct strands (eg. for a siNA construct having 21 nucleotide sense and antisense strands with 19 base pairs, the complexity would be 4.sup.19); and (b) assaying the siNA constructs of (a) above, under conditions suitable to determine RNAi target sites within the target PDGF and/or PDGFr RNA sequence. In another embodiment, the siNA molecules of (a) have strands of a fixed length, for example about 23 nucleotides in length. In yet another embodiment, the siNA molecules of (a) are of differing length, for example having strands of about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described in Example 6 herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. In another embodiment, fragments of PDGF and/or PDGFr RNA are analyzed for detectable levels of cleavage, for example, by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target PDGF and/or PDGFr RNA sequence. The target PDGF and/or PDGFr RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by cellular expression in in vivo systems.

[0153] In another embodiment, the invention features a method comprising: (a) analyzing the sequence of a RNA target encoded by a target gene; (b) synthesizing one or more sets of siNA molecules having sequence complementary to one or more regions of the RNA of (a); and (c) assaying the siNA molecules of (b) under conditions suitable to determine RNAi targets within the target RNA sequence. In one embodiment, the siNA molecules of (b) have strands of a fixed length, for example about 23 nucleotides in length. In another embodiment, the siNA molecules of (b) are of differing length, for example having strands of about 15 to about 30 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) nucleotides in length. In one embodiment, the assay can comprise a reconstituted in vitro siNA assay as described herein. In another embodiment, the assay can comprise a cell culture system in which target RNA is expressed. Fragments of target RNA are analyzed for detectable levels of cleavage, for example by gel electrophoresis, northern blot analysis, or RNAse protection assays, to determine the most suitable target site(s) within the target RNA sequence. The target RNA sequence can be obtained as is known in the art, for example, by cloning and/or transcription for in vitro systems, and by expression in in vivo systems.

[0154] By "target site" is meant a sequence within a target RNA that is "targeted" for cleavage mediated by a siNA construct which contains sequences within its antisense region that are complementary to the target sequence.

[0155] By "detectable level of cleavage" is meant cleavage of target RNA (and formation of cleaved product RNAs) to an extent sufficient to discern cleavage products above the background of RNAs produced by random degradation of the target RNA. Production of cleavage products from 1-5% of the target RNA is sufficient to detect above the background for most methods of detection.

[0156] In one embodiment, the invention features a composition comprising a siNA molecule of the invention, which can be chemically-modified, in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a pharmaceutical composition comprising siNA molecules of the invention, which can be chemically-modified, targeting one or more genes in a pharmaceutically acceptable carrier or diluent. In another embodiment, the invention features a method for diagnosing a disease or condition in a subject comprising administering to the subject a composition of the invention under conditions suitable for the diagnosis of the disease or condition in the subject. In another embodiment, the invention features a method for treating or preventing a disease or condition in a subject, comprising administering to the subject a composition of the invention under conditions suitable for the treatment or prevention of the disease or condition in the subject, alone or in conjunction with one or more other therapeutic compounds. In yet another embodiment, the invention features a method for treating or preventing cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism comprising administering to the subject a composition of the invention under conditions suitable for the treatment or prevention of cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in the subject or organism.

[0157] In another embodiment, the invention features a method for validating a PDGF and/or PDGFr gene target, comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a PDGF and/or PDGFr target gene; (b) introducing the siNA molecule into a cell, tissue, subject, or organism under conditions suitable for modulating expression of the PDGF and/or PDGFr target gene in the cell, tissue, subject, or organism; and (c) determining the function of the gene by assaying for any phenotypic change in the cell, tissue, subject, or organism.

[0158] In another embodiment, the invention features a method for validating a PDGF and/or PDGFr target comprising: (a) synthesizing a siNA molecule of the invention, which can be chemically-modified, wherein one of the siNA strands includes a sequence complementary to RNA of a PDGF and/or PDGFr target gene; (b) introducing the siNA molecule into a biological system under conditions suitable for modulating expression of the PDGF and/or PDGFr target gene in the biological system; and (c) determining the function of the gene by assaying for any phenotypic change in the biological system.

[0159] By "biological system" is meant, material, in a purified or unpurified form, from biological sources, including but not limited to human or animal, wherein the system comprises the components required for RNAi activity. The term "biological system" includes, for example, a cell, tissue, subject, or organism, or extract thereof. The term biological system also includes reconstituted RNAi systems that can be used in an in vitro setting.

[0160] By "phenotypic change" is meant any detectable change to a cell that occurs in response to contact or treatment with a nucleic acid molecule of the invention (e.g., siNA). Such detectable changes include, but are not limited to, changes in shape, size, proliferation, motility, protein expression or RNA expression or other physical or chemical changes as can be assayed by methods known in the art. The detectable change can also include expression of reporter genes/molecules such as Green Florescent Protein (GFP) or various tags that are used to identify an expressed protein or any other cellular component that can be assayed.

[0161] In one embodiment, the invention features a kit containing a siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of a PDGF and/or PDGFr target gene in a biological system, including, for example, in a cell, tissue, subject, or organism. In another embodiment, the invention features a kit containing more than one siNA molecule of the invention, which can be chemically-modified, that can be used to modulate the expression of more than one PDGF and/or PDGFr target gene in a biological system, including, for example, in a cell, tissue, subject, or organism.

[0162] In one embodiment, the invention features a cell containing one or more siNA molecules of the invention, which can be chemically-modified. In another embodiment, the cell containing a siNA molecule of the invention is a mammalian cell. In yet another embodiment, the cell containing a siNA molecule of the invention is a human cell.

[0163] In one embodiment, the synthesis of a siNA molecule of the invention, which can be chemically-modified, comprises: (a) synthesis of two complementary strands of the siNA molecule; (b) annealing the two complementary strands together under conditions suitable to obtain a double-stranded siNA molecule. In another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase oligonucleotide synthesis. In yet another embodiment, synthesis of the two complementary strands of the siNA molecule is by solid phase tandem oligonucleotide synthesis.

[0164] In one embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing a first oligonucleotide sequence strand of the siNA molecule, wherein the first oligonucleotide sequence strand comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of the second oligonucleotide sequence strand of the siNA; (b) synthesizing the second oligonucleotide sequence strand of siNA on the scaffold of the first oligonucleotide sequence strand, wherein the second oligonucleotide sequence strand further comprises a chemical moiety than can be used to purify the siNA duplex; (c) cleaving the linker molecule of (a) under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex; and (d) purifying the siNA duplex utilizing the chemical moiety of the second oligonucleotide sequence strand. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example, under hydrolysis conditions using an alkylamine base such as methylamine. In one embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place concomitantly. In another embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group, which can be employed in a trityl-on synthesis strategy as described herein. In yet another embodiment, the chemical moiety, such as a dimethoxytrityl group, is removed during purification, for example, using acidic conditions.

[0165] In a further embodiment, the method for siNA synthesis is a solution phase synthesis or hybrid phase synthesis wherein both strands of the siNA duplex are synthesized in tandem using a cleavable linker attached to the first sequence which acts a scaffold for synthesis of the second sequence. Cleavage of the linker under conditions suitable for hybridization of the separate siNA sequence strands results in formation of the double-stranded siNA molecule.

[0166] In another embodiment, the invention features a method for synthesizing a siNA duplex molecule comprising: (a) synthesizing one oligonucleotide sequence strand of the siNA molecule, wherein the sequence comprises a cleavable linker molecule that can be used as a scaffold for the synthesis of another oligonucleotide sequence; (b) synthesizing a second oligonucleotide sequence having complementarity to the first sequence strand on the scaffold of (a), wherein the second sequence comprises the other strand of the double-stranded siNA molecule and wherein the second sequence further comprises a chemical moiety than can be used to isolate the attached oligonucleotide sequence; (c) purifying the product of (b) utilizing the chemical moiety of the second oligonucleotide sequence strand under conditions suitable for isolating the full-length sequence comprising both siNA oligonucleotide strands connected by the cleavable linker and under conditions suitable for the two siNA oligonucleotide strands to hybridize and form a stable duplex. In one embodiment, cleavage of the linker molecule in (c) above takes place during deprotection of the oligonucleotide, for example, under hydrolysis conditions. In another embodiment, cleavage of the linker molecule in (c) above takes place after deprotection of the oligonucleotide. In another embodiment, the method of synthesis comprises solid phase synthesis on a solid support such as controlled pore glass (CPG) or polystyrene, wherein the first sequence of (a) is synthesized on a cleavable linker, such as a succinyl linker, using the solid support as a scaffold. The cleavable linker in (a) used as a scaffold for synthesizing the second strand can comprise similar reactivity or differing reactivity as the solid support derivatized linker, such that cleavage of the solid support derivatized linker and the cleavable linker of (a) takes place either concomitantly or sequentially. In one embodiment, the chemical moiety of (b) that can be used to isolate the attached oligonucleotide sequence comprises a trityl group, for example a dimethoxytrityl group.

[0167] In another embodiment, the invention features a method for making a double-stranded siNA molecule in a single synthetic process comprising: (a) synthesizing an oligonucleotide having a first and a second sequence, wherein the first sequence is complementary to the second sequence, and the first oligonucleotide sequence is linked to the second sequence via a cleavable linker, and wherein a terminal 5'-protecting group, for example, a 5'-O-dimethoxytrityl group (5'-O-DMT) remains on the oligonucleotide having the second sequence; (b) deprotecting the oligonucleotide whereby the deprotection results in the cleavage of the linker joining the two oligonucleotide sequences; and (c) purifying the product of (b) under conditions suitable for isolating the double-stranded siNA molecule, for example using a trityl-on synthesis strategy as described herein.

[0168] In another embodiment, the method of synthesis of siNA molecules of the invention comprises the teachings of Scaringe et al., U.S. Pat. Nos. 5,889,136; 6,008,400; and 6,111,086, incorporated by reference herein in their entirety.

[0169] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications, for example, one or more chemical modifications having any of Formulae I-VII or any combination thereof that increases the nuclease resistance of the siNA construct.

[0170] In another embodiment, the invention features a method for generating siNA molecules with increased nuclease resistance comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased nuclease resistance.

[0171] In another embodiment, the invention features a method for generating siNA molecules with improved toxicologic profiles (e.g., have attenuated or no immunostimulatory properties) comprising (a) introducing nucleotides having any of Formula I-VII (e.g., siNA motifs referred to in Table IV) or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved toxicologic profiles.

[0172] In another embodiment, the invention features a method for generating siNA molecules that do not stimulate an interferon response (e.g., no interferon response or attenuated interferon response) in a cell, subject, or organism, comprising (a) introducing nucleotides having any of Formula I-VII (e.g., siNA motifs referred to in Table IV) or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules that do not stimulate an interferon response.

[0173] By "improved toxicologic profile", is meant that the chemically modified siNA construct exhibits decreased toxicity in a cell, subject, or organism compared to an unmodified siNA or siNA molecule having fewer modifications or modifications that are less effective in imparting improved toxicology. In a non-limiting example, siNA molecules with improved toxicologic profiles are associated with a decreased or attenuated immunostimulatory response in a cell, subject, or organism compared to an unmodified siNA or siNA molecule having fewer modifications or modifications that are less effective in imparting improved toxicology. In one embodiment, a siNA molecule with an improved toxicological profile comprises no ribonucleotides. In one embodiment, a siNA molecule with an improved toxicological profile comprises less than 5 ribonucleotides (e.g., 1, 2, 3, or 4 ribonucleotides). In one embodiment, a siNA molecule with an improved toxicological profile comprises Stab 7, Stab 8, Stab 11, Stab 12, Stab 13, Stab 16, Stab 17, Stab 18, Stab 19, Stab 20, Stab 23, Stab 24, Stab 25, Stab 26, Stab 27, Stab 28, Stab 29, Stab 30, Stab 31, Stab 32 or any combination thereof (see Table IV). In one embodiment, the level of immunostimulatory response associated with a given siNA molecule can be measured as is known in the art, for example by determining the level of PKR/interferon response, proliferation, B-cell activation, and/or cytokine production in assays to quantitate the immunostimulatory response of particular siNA molecules (see, for example, Leifer et al., 2003, J. Immunother. 26, 313-9; and U.S. Pat. No. 5,968,909, incorporated in its entirety by reference).

[0174] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the sense and antisense strands of the siNA construct.

[0175] In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the sense and antisense strands of the siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the sense and antisense strands of the siNA molecule.

[0176] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target RNA sequence within a cell.

[0177] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the binding affinity between the antisense strand of the siNA construct and a complementary target DNA sequence within a cell.

[0178] In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target RNA sequence.

[0179] In another embodiment, the invention features a method for generating siNA molecules with increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having increased binding affinity between the antisense strand of the siNA molecule and a complementary target DNA sequence.

[0180] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that modulate the polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA construct.

[0181] In another embodiment, the invention features a method for generating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to a chemically-modified siNA molecule comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules capable of mediating increased polymerase activity of a cellular polymerase capable of generating additional endogenous siNA molecules having sequence homology to the chemically-modified siNA molecule.

[0182] In one embodiment, the invention features chemically-modified siNA constructs that mediate RNAi against PDGF and/or PDGFr in a cell, wherein the chemical modifications do not significantly effect the interaction of siNA with a target RNA molecule, DNA molecule and/or proteins or other factors that are essential for RNAi in a manner that would decrease the efficacy of RNAi mediated by such siNA constructs.

[0183] In another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against PDGF and/or PDGFr comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity.

[0184] In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against PDGF and/or PDGFr target RNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target RNA.

[0185] In yet another embodiment, the invention features a method for generating siNA molecules with improved RNAi activity against PDGF and/or PDGFr target DNA comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved RNAi activity against the target DNA.

[0186] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that modulates the cellular uptake of the siNA construct.

[0187] In another embodiment, the invention features a method for generating siNA molecules against PDGF and/or PDGFr with improved cellular uptake comprising (a) introducing nucleotides having any of Formula I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved cellular uptake.

[0188] In one embodiment, the invention features siNA constructs that mediate RNAi against PDGF and/or PDGFr, wherein the siNA construct comprises one or more chemical modifications described herein that increases the bioavailability of the siNA construct, for example, by attaching polymeric conjugates such as polyethyleneglycol or equivalent conjugates that improve the pharmacokinetics of the siNA construct, or by attaching conjugates that target specific tissue types or cell types in vivo. Non-limiting examples of such conjugates are described in Vargeese et al., U.S. Ser. No. 10/201,394 incorporated by reference herein.

[0189] In one embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing a conjugate into the structure of a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such conjugates can include ligands for cellular receptors, such as peptides derived from naturally occurring protein ligands; protein localization sequences, including cellular ZIP code sequences; antibodies; nucleic acid aptamers; vitamins and other co-factors, such as folate and N-acetylgalactosamine; polymers, such as polyethyleneglycol (PEG); phospholipids; cholesterol; polyamines, such as spermine or spermidine; and others.

[0190] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence is chemically modified in a manner that it can no longer act as a guide sequence for efficiently mediating RNA interference and/or be recognized by cellular proteins that facilitate RNAi.

[0191] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein the second sequence is designed or modified in a manner that prevents its entry into the RNAi pathway as a guide sequence or as a sequence that is complementary to a target nucleic acid (e.g., RNA) sequence. Such design or modifications are expected to enhance the activity of siNA and/or improve the specificity of siNA molecules of the invention. These modifications are also expected to minimize any off-target effects and/or associated toxicity.

[0192] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence is incapable of acting as a guide sequence for mediating RNA interference.

[0193] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence does not have a terminal 5'-hydroxyl (5'-OH) or 5'-phosphate group.

[0194] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence comprises a terminal cap moiety at the 5'-end of said second sequence. In one embodiment, the terminal cap moiety comprises an inverted abasic, inverted deoxy abasic, inverted nucleotide moiety, a group shown in FIG. 10, an alkyl or cycloalkyl group, a heterocycle, or any other group that prevents RNAi activity in which the second sequence serves as a guide sequence or template for RNAi.

[0195] In one embodiment, the invention features a double stranded short interfering nucleic acid (siNA) molecule that comprises a first nucleotide sequence complementary to a target RNA sequence or a portion thereof, and a second sequence having complementarity to said first sequence, wherein said second sequence comprises a terminal cap moiety at the 5'-end and 3'-end of said second sequence. In one embodiment, each terminal cap moiety individually comprises an inverted abasic, inverted deoxy abasic, inverted nucleotide moiety, a group shown in FIG. 10, an alkyl or cycloalkyl group, a heterocycle, or any other group that prevents RNAi activity in which the second sequence serves as a guide sequence or template for RNAi.

[0196] In one embodiment, the invention features a method for generating siNA molecules of the invention with improved specificity for down regulating or inhibiting the expression of a target nucleic acid (e.g., a DNA or RNA such as a gene or its corresponding RNA), comprising (a) introducing one or more chemical modifications into the structure of a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved specificity. In another embodiment, the chemical modification used to improve specificity comprises terminal cap modifications at the 5'-end, 3'-end, or both 5' and 3'-ends of the siNA molecule. The terminal cap modifications can comprise, for example, structures shown in FIG. 10 (e.g. inverted deoxyabasic moieties) or any other chemical modification that renders a portion of the siNA molecule (e.g. the sense strand) incapable of mediating RNA interference against an off target nucleic acid sequence. In a non-limiting example, a siNA molecule is designed such that only the antisense sequence of the siNA molecule can serve as a guide sequence for RISC mediated degradation of a corresponding target RNA sequence. This can be accomplished by rendering the sense sequence of the siNA inactive by introducing chemical modifications to the sense strand that preclude recognition of the sense strand as a guide sequence by RNAi machinery. In one embodiment, such chemical modifications comprise any chemical group at the 5'-end of the sense strand of the siNA, or any other group that serves to render the sense strand inactive as a guide sequence for mediating RNA interference. These modifications, for example, can result in a molecule where the 5'-end of the sense strand no longer has a free 5'-hydroxyl (5'-OH) or a free 5'-phosphate group (e.g., phosphate, diphosphate, triphosphate, cyclic phosphate etc.). Non-limiting examples of such siNA constructs are described herein, such as "Stab 9/10", "Stab 7/8", "Stab 7/19", "Stab 17/22", "Stab 23/24", "Stab 24/25", and "Stab 24/26" (e.g., any siNA having Stab 7, 9, 17, 23, or 24 sense strands) chemistries and variants thereof (see Table IV) wherein the 5'-end and 3'-end of the sense strand of the siNA do not comprise a hydroxyl group or phosphate group.

[0197] In one embodiment, the invention features a method for generating siNA molecules of the invention with improved specificity for down regulating or inhibiting the expression of a target nucleic acid (e.g., a DNA or RNA such as a gene or its corresponding RNA), comprising introducing one or more chemical modifications into the structure of a siNA molecule that prevent a strand or portion of the siNA molecule from acting as a template or guide sequence for RNAi activity. In one embodiment, the inactive strand or sense region of the siNA molecule is the sense strand or sense region of the siNA molecule, i.e. the strand or region of the siNA that does not have complementarity to the target nucleic acid sequence. In one embodiment, such chemical modifications comprise any chemical group at the 5'-end of the sense strand or region of the siNA that does not comprise a 5'-hydroxyl (5'-OH) or 5'-phosphate group, or any other group that serves to render the sense strand or sense region inactive as a guide sequence for mediating RNA interference. Non-limiting examples of such siNA constructs are described herein, such as "Stab 9/10", "Stab 7/8", "Stab 7/19", "Stab 17/22", "Stab 23/24", "Stab 24/25", and "Stab 24/26" (e.g., any siNA having Stab 7, 9, 17, 23, or 24 sense strands) chemistries and variants thereof (see Table IV) wherein the 5'-end and 3'-end of the sense strand of the siNA do not comprise a hydroxyl group or phosphate group.

[0198] In one embodiment, the invention features a method for screening siNA molecules that are active in mediating RNA interference against a target nucleic acid sequence comprising (a) generating a plurality of unmodified siNA molecules, (b) screening the siNA molecules of step (a) under conditions suitable for isolating siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence, and (c) introducing chemical modifications (e.g. chemical modifications as described herein or as otherwise known in the art) into the active siNA molecules of (b).

[0199] In one embodiment, the method further comprises re-screening the chemically modified siNA molecules of step (c) under conditions suitable for isolating chemically modified siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence.

[0200] In one embodiment, the invention features a method for screening chemically modified siNA molecules that are active in mediating RNA interference against a target nucleic acid sequence comprising (a) generating a plurality of chemically modified siNA molecules (e.g. siNA molecules as described herein or as otherwise known in the art), and (b) screening the siNA molecules of step (a) under conditions suitable for isolating chemically modified siNA molecules that are active in mediating RNA interference against the target nucleic acid sequence.

[0201] The term "ligand" refers to any compound or molecule, such as a drug, peptide, hormone, or neurotransmitter, that is capable of interacting with another compound, such as a receptor, either directly or indirectly. The receptor that interacts with a ligand can be present on the surface of a cell or can alternately be an intercellular receptor. Interaction of the ligand with the receptor can result in a biochemical reaction, or can simply be a physical interaction or association.

[0202] In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing an excipient formulation to a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability. Such excipients include polymers such as cyclodextrins, lipids, cationic lipids, polyamines, phospholipids, nanoparticles, receptors, ligands, and others.

[0203] In another embodiment, the invention features a method for generating siNA molecules of the invention with improved bioavailability comprising (a) introducing nucleotides having any of Formulae I-VII or any combination thereof into a siNA molecule, and (b) assaying the siNA molecule of step (a) under conditions suitable for isolating siNA molecules having improved bioavailability.

[0204] In another embodiment, polyethylene glycol (PEG) can be covalently attached to siNA compounds of the present invention. The attached PEG can be any molecular weight, preferably from about 2,000 to about 50,000 daltons (Da).

[0205] The present invention can be used alone or as a component of a kit having at least one of the reagents necessary to carry out the in vitro or in vivo introduction of RNA to test samples and/or subjects. For example, preferred components of the kit include a siNA molecule of the invention and a vehicle that promotes introduction of the siNA into cells of interest as described herein (e.g., using lipids and other methods of transfection known in the art, see for example Beigelman et al, U.S. Pat. No. 6,395,713). The kit can be used for target validation, such as in determining gene function and/or activity, or in drug optimization, and in drug discovery (see for example Usman et al., U.S. Ser. No. 60/402,996). Such a kit can also include instructions to allow a user of the kit to practice the invention.

[0206] The term "short interfering nucleic acid", "siNA", "short interfering RNA", "siRNA", "short interfering nucleic acid molecule", "short interfering oligonucleotide molecule", or "chemically-modified short interfering nucleic acid molecule" as used herein refers to any nucleic acid molecule capable of inhibiting or down regulating gene expression or viral replication, for example by mediating RNA interference "RNAi" or gene silencing in a sequence-specific manner; see for example Zamore et al., 2000, Cell, 101, 25-33; Bass, 2001, Nature, 411, 428-429; Elbashir et al., 2001, Nature, 411, 494-498; and Kreutzer et al., International PCT Publication No. WO 00/44895; Zernicka-Goetz et al., International PCT Publication No. WO 01/36646; Fire, International PCT Publication No. WO 99/32619; Plaetinck et al., International PCT Publication No. WO 00/01846; Mello and Fire, International PCT Publication No. WO 01/29058; Deschamps-Depaillette, International PCT Publication No. WO 99/07409; and Li et al., International PCT Publication No. WO 00/44914; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237; Hutvagner and Zamore, 2002, Science, 297, 2056-60; McManus et al., 2002, RNA, 8, 842-850; Reinhart et al., 2002, Gene & Dev., 16, 1616-1626; and Reinhart & Bartel, 2002, Science, 297, 1831). Non limiting examples of siNA molecules of the invention are shown in FIGS. 4-6, and Tables II and III herein. For example the siNA can be a double-stranded polynucleotide molecule comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be assembled from two separate oligonucleotides, where one strand is the sense strand and the other is the antisense strand, wherein the antisense and sense strands are self-complementary (i.e. each strand comprises nucleotide sequence that is complementary to nucleotide sequence in the other strand; such as where the antisense strand and sense strand form a duplex or double stranded structure, for example wherein the double stranded region is about 15 to about 30, e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29 or 30 base pairs; the antisense strand comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense strand comprises nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof (e.g., about 15 to about 25 or more nucleotides of the siNA molecule are complementary to the target nucleic acid or a portion thereof). Alternatively, the siNA is assembled from a single oligonucleotide, where the self-complementary sense and antisense regions of the siNA are linked by means of a nucleic acid based or non-nucleic acid-based linker(s). The siNA can be a polynucleotide with a duplex, asymmetric duplex, hairpin or asymmetric hairpin secondary structure, having self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a separate target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof. The siNA can be a circular single-stranded polynucleotide having two or more loop structures and a stem comprising self-complementary sense and antisense regions, wherein the antisense region comprises nucleotide sequence that is complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof and the sense region having nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof, and wherein the circular polynucleotide can be processed either in vivo or in vitro to generate an active siNA molecule capable of mediating RNAi. The siNA can also comprise a single stranded polynucleotide having nucleotide sequence complementary to nucleotide sequence in a target nucleic acid molecule or a portion thereof (for example, where such siNA molecule does not require the presence within the siNA molecule of nucleotide sequence corresponding to the target nucleic acid sequence or a portion thereof), wherein the single stranded polynucleotide can further comprise a terminal phosphate group, such as a 5'-phosphate (see for example Martinez et al., 2002, Cell., 110, 563-574 and Schwarz et al., 2002, Molecular Cell, 10, 537-568), or 5',3'-diphosphate. In certain embodiments, the siNA molecule of the invention comprises separate sense and antisense sequences or regions, wherein the sense and antisense regions are covalently linked by nucleotide or non-nucleotide linkers molecules as is known in the art, or are alternately non-covalently linked by ionic interactions, hydrogen bonding, van der waals interactions, hydrophobic interactions, and/or stacking interactions. In certain embodiments, the siNA molecules of the invention comprise nucleotide sequence that is complementary to nucleotide sequence of a target gene. In another embodiment, the siNA molecule of the invention interacts with nucleotide sequence of a target gene in a manner that causes inhibition of expression of the target gene. As used herein, siNA molecules need not be limited to those molecules containing only RNA, but further encompasses chemically-modified nucleotides and non-nucleotides. In certain embodiments, the short interfering nucleic acid molecules of the invention lack 2'-hydroxy (2'-OH) containing nucleotides. Applicant describes in certain embodiments short interfering nucleic acids that do not require the presence of nucleotides having a 2'-hydroxy group for mediating RNAi and as such, short interfering nucleic acid molecules of the invention optionally do not include any ribonucleotides (e.g., nucleotides having a 2'-OH group). Such siNA molecules that do not require the presence of ribonucleotides within the siNA molecule to support RNAi can however have an attached linker or linkers or other attached or associated groups, moieties, or chains containing one or more nucleotides with 2'-OH groups. Optionally, siNA molecules can comprise ribonucleotides at about 5, 10, 20, 30, 40, or 50% of the nucleotide positions. The modified short interfering nucleic acid molecules of the invention can also be referred to as short interfering modified oligonucleotides "siMON." As used herein, the term siNA is meant to be equivalent to other terms used to describe nucleic acid molecules that are capable of mediating sequence specific RNAi, for example short interfering RNA (siRNA), double-stranded RNA (dsRNA), micro-RNA (miRNA), short hairpin RNA (shRNA), short interfering oligonucleotide, short interfering nucleic acid, short interfering modified oligonucleotide, chemically-modified siRNA, post-transcriptional gene silencing RNA (ptgsRNA), and others. In addition, as used herein, the term RNAi is meant to be equivalent to other terms used to describe sequence specific RNA interference, such as post transcriptional gene silencing, translational inhibition, or epigenetics. For example, siNA molecules of the invention can be used to epigenetically silence genes at both the post-transcriptional level and the pre-transcriptional level. In a non-limiting example, epigenetic regulation of gene expression by siNA molecules of the invention can result from siNA mediated modification of chromatin structure or methylation pattern to alter gene expression (see, for example, Verdel et al., 2004, Science, 303, 672-676; Pal-Bhadra et al., 2004, Science, 303, 669-672; Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237).

[0207] In one embodiment, a siNA molecule of the invention is a duplex forming oligonucleotide "DFO", (see for example FIGS. 14-15 and Vaish et al., U.S. Ser. No. 10/727,780 filed Dec. 3, 2003 and International PCT Application No. US04/16390, filed May 24, 2004).

[0208] In one embodiment, a siNA molecule of the invention is a multifunctional siNA, (see for example FIGS. 16-21 and Jadhav et al., U.S. Ser. No. 60/543,480 filed Feb. 10, 2004 and International PCT Application No. US04/16390, filed May 24, 2004). The multifunctional siNA of the invention can comprise sequence targeting, for example, two regions of PDGF and/or PDGFr RNA (see for example target sequences in Tables II and III).

[0209] By "asymmetric hairpin" as used herein is meant a linear siNA molecule comprising an antisense region, a loop portion that can comprise nucleotides or non-nucleotides, and a sense region that comprises fewer nucleotides than the antisense region to the extent that the sense region has enough complementary nucleotides to base pair with the antisense region and form a duplex with loop. For example, an asymmetric hairpin siNA molecule of the invention can comprise an antisense region having length sufficient to mediate RNAi in a cell or in vitro system (e.g. about 15 to about 30, or about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides) and a loop region comprising about 4 to about 12 (e.g., about 4, 5, 6, 7, 8, 9, 10, 11, or 12) nucleotides, and a sense region having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides that are complementary to the antisense region. The asymmetric hairpin siNA molecule can also comprise a 5'-terminal phosphate group that can be chemically modified. The loop portion of the asymmetric hairpin siNA molecule can comprise nucleotides, non-nucleotides, linker molecules, or conjugate molecules as described herein.

[0210] By "asymmetric duplex" as used herein is meant a siNA molecule having two separate strands comprising a sense region and an antisense region, wherein the sense region comprises fewer nucleotides than the antisense region to the extent that the sense region has enough complementary nucleotides to base pair with the antisense region and form a duplex. For example, an asymmetric duplex siNA molecule of the invention can comprise an antisense region having length sufficient to mediate RNAi in a cell or in vitro system (e.g. about 15 to about 30, or about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides) and a sense region having about 3 to about 25 (e.g., about 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) nucleotides that are complementary to the antisense region.

[0211] By "modulate" is meant that the expression of the gene, or level of RNA molecule or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits is up regulated or down regulated, such that expression, level, or activity is greater than or less than that observed in the absence of the modulator. For example, the term "modulate" can mean "inhibit," but the use of the word "modulate" is not limited to this definition.

[0212] By "inhibit", "down-regulate", or "reduce", it is meant that the expression of the gene, or level of RNA molecules or equivalent RNA molecules encoding one or more proteins or protein subunits, or activity of one or more proteins or protein subunits, is reduced below that observed in the absence of the nucleic acid molecules (e.g., siNA) of the invention. In one embodiment, inhibition, down-regulation or reduction with an siNA molecule is below that level observed in the presence of an inactive or attenuated molecule. In another embodiment, inhibition, down-regulation, or reduction with siNA molecules is below that level observed in the presence of, for example, an siNA molecule with scrambled sequence or with mismatches. In another embodiment, inhibition, down-regulation, or reduction of gene expression with a nucleic acid molecule of the instant invention is greater in the presence of the nucleic acid molecule than in its absence. In one embodiment, inhibition, down regulation, or reduction of gene expression is associated with post transcriptional silencing, such as RNAi mediated cleavage of a target nucleic acid molecule (e.g. RNA) or inhibition of translation. In one embodiment, inhibition, down regulation, or reduction of gene expression is associated with pretranscriptional silencing.

[0213] By "gene", or "target gene", is meant a nucleic acid that encodes an RNA, for example, nucleic acid sequences including, but not limited to, structural genes encoding a polypeptide. A gene or target gene can also encode a functional RNA (fRNA) or non-coding RNA (ncRNA), such as small temporal RNA (stRNA), micro RNA (miRNA), small nuclear RNA (snRNA), short interfering RNA (siRNA), small nuclear RNA (snRNA), ribosomal RNA (rRNA), transfer RNA (tRNA) and precursor RNAs thereof. Such non-coding RNAs can serve as target nucleic acid molecules for siNA mediated RNA interference in modulating the activity of fRNA or ncRNA involved in functional or regulatory cellular processes. Aberrant fRNA or ncRNA activity leading to disease can therefore be modulated by siNA molecules of the invention. siNA molecules targeting fRNA and ncRNA can also be used to manipulate or alter the genotype or phenotype of a subject, organism or cell, by intervening in cellular processes such as genetic imprinting, transcription, translation, or nucleic acid processing (e.g., transamination, methylation etc.). The target gene can be a gene derived from a cell, an endogenous gene, a transgene, or exogenous genes such as genes of a pathogen, for example a virus, which is present in the cell after infection thereof. The cell containing the target gene can be derived from or contained in any organism, for example a plant, animal, protozoan, virus, bacterium, or fungus. Non-limiting examples of plants include monocots, dicots, or gymnosperms. Non-limiting examples of animals include vertebrates or invertebrates. Non-limiting examples of fungi include molds or yeasts. For a review, see for example Snyder and Gerstein, 2003, Science, 300, 258-260.

[0214] By "non-canonical base pair" is meant any non-Watson Crick base pair, such as mismatches and/or wobble base pairs, including flipped mismatches, single hydrogen bond mismatches, trans-type mismatches, triple base interactions, and quadruple base interactions. Non-limiting examples of such non-canonical base pairs include, but are not limited to, AC reverse Hoogsteen, AC wobble, AU reverse Hoogsteen, GU wobble, AA N7 amino, CC 2-carbonyl-amino(H1)-N-3-amino(H2), GA sheared, UC 4-carbonyl-amino, UU imino-carbonyl, AC reverse wobble, AU Hoogsteen, AU reverse Watson Crick, CG reverse Watson Crick, GC N3-amino-amino N3, AA N1-amino symmetric, AA N7-amino symmetric, GA N7-N1 amino-carbonyl, GA+ carbonyl-amino N7-N1, GG N1-carbonyl symmetric, GG N3-amino symmetric, CC carbonyl-amino symmetric, CC N3-amino symmetric, UU 2-carbonyl-imino symmetric, UU 4-carbonyl-imino symmetric, AA amino-N3, AA N1-amino, AC amino 2-carbonyl, AC N3-amino, AC N7-amino, AU amino-4-carbonyl, AU N1-imino, AU N3-imino, AU N7-imino, CC carbonyl-amino, GA amino-N1, GA amino-N7, GA carbonyl-amino, GA N3-amino, GC amino-N3, GC carbonyl-amino, GC N3-amino, GC N7-amino, GG amino-N7, GG carbonyl-imino, GG N7-amino, GU amino-2-carbonyl, GU carbonyl-imino, GU imino-2-carbonyl, GU N7-imino, psiU imino-2-carbonyl, UC 4-carbonyl-amino, UC imino-carbonyl, UU imino-4-carbonyl, AC C2-H--N3, GA carbonyl-C2-H, UU imino-4-carbonyl 2 carbonyl-C5-H, AC amino(A) N3(C)-carbonyl, GC imino amino-carbonyl, Gpsi imino-2-carbonyl amino-2-carbonyl, and GU imino amino-2-carbonyl base pairs.

[0215] By "PDGF" as used herein is meant any platelet derived growth factor protein, peptide, or polypeptide having any platelet derived growth factor activity, such as encoded by PDGF Genbank Accession Nos. shown in Table I. The term PDGF also refers to nucleic acid sequences encoding any platelet derived growth factor protein, peptide, or polypeptide having platelet derived growth factor activity. The term "PDGF" is also meant to include other platelet derived growth factor encoding sequence, such as other PDGF isoforms, mutant PDGF genes, splice variants of PDGF genes, and PDGF gene polymorphisms.

[0216] By "PDGFr" as used herein is meant any platelet derived growth factor receptor protein, peptide, or polypeptide having any platelet derived growth factor receptor activity, such as encoded by PDGFr Genbank Accession Nos. shown in Table I. The term PDGFr also refers to nucleic acid sequences encoding any platelet derived growth factor receptor protein, peptide, or polypeptide having PDGFr activity. The term "PDGFr" is also meant to include other platelet derived growth factor receptor encoding sequence, such as other PDGFr isoforms, mutant PDGFr genes, splice variants of PDGFr genes, and PDGFr gene polymorphisms.

[0217] By "homologous sequence" is meant, a nucleotide sequence that is shared by one or more polynucleotide sequences, such as genes, gene transcripts and/or non-coding polynucleotides. For example, a homologous sequence can be a nucleotide sequence that is shared by two or more genes encoding related but different proteins, such as different members of a gene family, different protein epitopes, different protein isoforms or completely divergent genes, such as a cytokine and its corresponding receptors. A homologous sequence can be a nucleotide sequence that is shared by two or more non-coding polynucleotides, such as noncoding DNA or RNA, regulatory sequences, introns, and sites of transcriptional control or regulation. Homologous sequences can also include conserved sequence regions shared by more than one polynucleotide sequence. Homology does not need to be perfect homology (e.g., 100%), as partially homologous sequences are also contemplated by the instant invention (e.g., 99%, 98%, 97%, 96%, 95%, 94%, 93%, 92%, 91%, 90%, 89%, 88%, 87%, 86%, 85%, 84%, 83%, 82%, 81%, 80% etc.).

[0218] By "conserved sequence region" is meant, a nucleotide sequence of one or more regions in a polynucleotide does not vary significantly between generations or from one biological system, subject, or organism to another biological system, subject, or organism. The polynucleotide can include both coding and non-coding DNA and RNA.

[0219] By "sense region" is meant a nucleotide sequence of a siNA molecule having complementarity to an antisense region of the siNA molecule. In addition, the sense region of a siNA molecule can comprise a nucleic acid sequence having homology with a target nucleic acid sequence.

[0220] By "antisense region" is meant a nucleotide sequence of a siNA molecule having complementarity to a target nucleic acid sequence. In addition, the antisense region of a siNA molecule can optionally comprise a nucleic acid sequence having complementarity to a sense region of the siNA molecule.

[0221] By "target nucleic acid" is meant any nucleic acid sequence whose expression or activity is to be modulated. The target nucleic acid can be DNA or RNA.

[0222] By "complementarity" is meant that a nucleic acid can form hydrogen bond(s) with another nucleic acid sequence by either traditional Watson-Crick or other non-traditional types. In reference to the nucleic molecules of the present invention, the binding free energy for a nucleic acid molecule with its complementary sequence is sufficient to allow the relevant function of the nucleic acid to proceed, e.g., RNAi activity. Determination of binding free energies for nucleic acid molecules is well known in the art (see, e.g., Turner et al., 1987, CSH Symp. Quant. Biol. LII pp. 123-133; Frier et al., 1986, Proc. Nat. Acad. Sci. USA 83:9373-9377; Turner et al., 1987, J. Am. Chem. Soc. 109:3783-3785). A percent complementarity indicates the percentage of contiguous residues in a nucleic acid molecule that can form hydrogen bonds (e.g., Watson-Crick base pairing) with a second nucleic acid sequence (e.g., 5, 6, 7, 8, 9, or 10 nucleotides out of a total of 10 nucleotides in the first oligonucleotide being based paired to a second nucleic acid sequence having 10 nucleotides represents 50%, 60%, 70%, 80%, 90%, and 100% complementary respectively). "Perfectly complementary" means that all the contiguous residues of a nucleic acid sequence will hydrogen bond with the same number of contiguous residues in a second nucleic acid sequence. In one embodiment, a siNA molecule of the invention comprises about 15 to about 30 or more (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 or more) nucleotides that are complementary to one or more target nucleic acid molecules or a portion thereof.

[0223] In one embodiment, siNA molecules of the invention that down regulate or reduce PDGF and/or PDGFr gene expression are used for preventing or treating cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism.

[0224] In one embodiment, the siNA molecules of the invention are used to treat cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism.

[0225] By "proliferative disease" or "cancer" as used herein is meant, any disease, condition, trait, genotype or phenotype characterized by unregulated cell growth or replication as is known in the art; including leukemias, for example, acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphocytic leukemia (ALL), and chronic lymphocytic leukemia, AIDS related cancers such as Kaposi's sarcoma; breast cancers; bone cancers such as Osteosarcoma, Chondrosarcomas, Ewing's sarcoma, Fibrosarcomas, Giant cell tumors, Adamantinomas, and Chordomas; Brain cancers such as Meningiomas, Glioblastomas, Lower-Grade Astrocytomas, Oligodendrocytomas, Pituitary Tumors, Schwannomas, and Metastatic brain cancers; cancers of the head and neck including various lymphomas such as mantle cell lymphoma, non-Hodgkins lymphoma, adenoma, squamous cell carcinoma, laryngeal carcinoma, gallbladder and bile duct cancers, cancers of the retina such as retinoblastoma, cancers of the esophagus, gastric cancers, multiple myeloma, ovarian cancer, uterine cancer, thyroid cancer, testicular cancer, endometrial cancer, melanoma, colorectal cancer, lung cancer, bladder cancer, prostate cancer, lung cancer (including non-small cell lung carcinoma), pancreatic cancer, sarcomas, Wilms' tumor, cervical cancer, head and neck cancer, skin cancers, nasopharyngeal carcinoma, liposarcoma, epithelial carcinoma, renal cell carcinoma, gallbladder adeno carcinoma, parotid adenocarcinoma, endometrial sarcoma, multidrug resistant cancers; and proliferative diseases and conditions, such as neovascularization associated with tumor angiogenesis, macular degeneration (e.g., wet/dry AMD), corneal neovascularization, diabetic retinopathy, neovascular glaucoma, myopic degeneration and other proliferative diseases and conditions such as restenosis and polycystic kidney disease, and any other cancer or proliferative disease, condition, trait, genotype or phenotype that can respond to the modulation of disease related gene expression in a cell or tissue, alone or in combination with other therapies.

[0226] By "leukemia" as used herein is meant any disease, disorder, condition, trait, genotype or phenotype characterized by, for example, the overproduction of immature atypical leukocytes, such as acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), acute lymphocytic leukemia (ALL), and chronic lympocytic leukemia, and any other leukemia that can respond to the modulation of disease related gene expression in a cell or tissue, alone or in combination with other therapies.

[0227] By "inflammatory disease" or "inflammatory condition" as used herein is meant any disease, condition, trait, genotype or phenotype characterized by an inflammatory or allergic process as is known in the art, such as inflammation, acute inflammation, chronic inflammation, respiratory disease, atherosclerosis, restenosis, asthma, allergic rhinitis, atopic dermatitis, septic shock, rheumatoid arthritis, inflammatory bowl disease, inflammatory pelvic disease, pain, ocular inflammatory disease, celiac disease, Leigh Syndrome, Glycerol Kinase Deficiency, Familial eosinophilia (FE), autosomal recessive spastic ataxia, laryngeal inflammatory disease; Tuberculosis, Chronic cholecystitis, Bronchiectasis, Silicosis and other pneumoconioses, and any other inflammatory disease, condition, trait, genotype or phenotype that can respond to the modulation of disease related gene expression in a cell or tissue, alone or in combination with other therapies.

[0228] In one embodiment of the present invention, each sequence of a siNA molecule of the invention is independently about 15 to about 30 nucleotides in length, in specific embodiments about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30 nucleotides in length. In another embodiment, the siNA duplexes of the invention independently comprise about 15 to about 30 base pairs (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30). In another embodiment, one or more strands of the siNA molecule of the invention independently comprises about 15 to about 30 nucleotides (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, or 30) that are complementary to a target nucleic acid molecule. In yet another embodiment, siNA molecules of the invention comprising hairpin or circular structures are about 35 to about 55 (e.g., about 35, 40, 45, 50 or 55) nucleotides in length, or about 38 to about 44 (e.g., about 38, 39, 40, 41, 42, 43, or 44) nucleotides in length and comprising about 15 to about 25 (e.g., about 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, or 25) base pairs. Exemplary siNA molecules of the invention are shown in Table II. Exemplary synthetic siNA molecules of the invention are shown in Table III and/or FIGS. 4-5.

[0229] As used herein "cell" is used in its usual biological sense, and does not refer to an entire multicellular organism, e.g., specifically does not refer to a human. The cell can be present in an organism, e.g., birds, plants and mammals such as humans, cows, sheep, apes, monkeys, swine, dogs, and cats. The cell can be prokaryotic (e.g., bacterial cell) or eukaryotic (e.g., mammalian or plant cell). The cell can be of somatic or germ line origin, totipotent or pluripotent, dividing or non-dividing. The cell can also be derived from or can comprise a gamete or embryo, a stem cell, or a fully differentiated cell.

[0230] The siNA molecules of the invention are added directly, or can be complexed with cationic lipids, packaged within liposomes, or otherwise delivered to target cells or tissues. The nucleic acid or nucleic acid complexes can be locally administered to relevant tissues ex vivo, or in vivo through direct dermal application, transdermal application, or injection, with or without their incorporation in biopolymers. In particular embodiments, the nucleic acid molecules of the invention comprise sequences shown in Tables II-III and/or FIGS. 4-5. Examples of such nucleic acid molecules consist essentially of sequences defined in these tables and figures. Furthermore, the chemically modified constructs described in Table IV can be applied to any siNA sequence of the invention.

[0231] In another aspect, the invention provides mammalian cells containing one or more siNA molecules of this invention. The one or more siNA molecules can independently be targeted to the same or different sites.

[0232] By "RNA" is meant a molecule comprising at least one ribonucleotide residue. By "ribonucleotide" is meant a nucleotide with a hydroxyl group at the 2' position of a D-ribofuranose moiety. The terms include double-stranded RNA, single-stranded RNA, isolated RNA such as partially purified RNA, essentially pure RNA, synthetic RNA, recombinantly produced RNA, as well as altered RNA that differs from naturally occurring RNA by the addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of the siNA or internally, for example at one or more nucleotides of the RNA. Nucleotides in the RNA molecules of the instant invention can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally-occurring RNA.

[0233] By "subject" is meant an organism, which is a donor or recipient of explanted cells or the cells themselves. "Subject" also refers to an organism to which the nucleic acid molecules of the invention can be administered. A subject can be a mammal or mammalian cells, including a human or human cells.

[0234] The term "phosphorothioate" as used herein refers to an internucleotide linkage having Formula I, wherein Z and/or W comprise a sulfur atom. Hence, the term phosphorothioate refers to both phosphorothioate and phosphorodithioate internucleotide linkages.

[0235] The term "phosphonoacetate" as used herein refers to an internucleotide linkage having Formula I, wherein Z and/or W comprise an acetyl or protected acetyl group.

[0236] The term "thiophosphonoacetate" as used herein refers to an internucleotide linkage having Formula I, wherein Z comprises an acetyl or protected acetyl group and W comprises a sulfur atom or alternately W comprises an acetyl or protected acetyl group and Z comprises a sulfur atom.

[0237] The term "universal base" as used herein refers to nucleotide base analogs that form base pairs with each of the natural DNA/RNA bases with little discrimination between them. Non-limiting examples of universal bases include C-phenyl, C-naphthyl and other aromatic derivatives, inosine, azole carboxamides, and nitroazole derivatives such as 3-nitropyrrole, 4-nitroindole, 5-nitroindole, and 6-nitroindole as known in the art (see for example Loakes, 2001, Nucleic Acids Research, 29, 2437-2447).

[0238] The term "acyclic nucleotide" as used herein refers to any nucleotide having an acyclic ribose sugar, for example where any of the ribose carbons (C1, C2, C3, C4, or C5), are independently or in combination absent from the nucleotide.

[0239] The nucleic acid molecules of the instant invention, individually, or in combination or in conjunction with other drugs, can be used to for preventing or treating cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism.

[0240] For example, the siNA molecules can be administered to a subject or can be administered to other appropriate cells evident to those skilled in the art, individually or in combination with one or more drugs under conditions suitable for the treatment.

[0241] In a further embodiment, the siNA molecules can be used in combination with other known treatments to prevent or cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism. For example, the described molecules could be used in combination with one or more known compounds, treatments, or procedures to prevent or treat cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders in a subject or organism as are known in the art.

[0242] In one embodiment, the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the invention, in a manner which allows expression of the siNA molecule. For example, the vector can contain sequence(s) encoding both strands of a siNA molecule comprising a duplex. The vector can also contain sequence(s) encoding a single nucleic acid molecule that is self-complementary and thus forms a siNA molecule. Non-limiting examples of such expression vectors are described in Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725.

[0243] In another embodiment, the invention features a mammalian cell, for example, a human cell, including an expression vector of the invention.

[0244] In yet another embodiment, the expression vector of the invention comprises a sequence for a siNA molecule having complementarity to a RNA molecule referred to by a Genbank Accession numbers, for example Genbank Accession Nos. shown in Table I.

[0245] In one embodiment, an expression vector of the invention comprises a nucleic acid sequence encoding two or more siNA molecules, which can be the same or different.

[0246] In another aspect of the invention, siNA molecules that interact with target RNA molecules and down-regulate gene encoding target RNA molecules (for example target RNA molecules referred to by Genbank Accession numbers herein) are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecules bind and down-regulate gene function or expression via RNA interference (RNAi). Delivery of siNA expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell.

[0247] By "vectors" is meant any nucleic acid- and/or viral-based technique used to deliver a desired nucleic acid.

[0248] Other features and advantages of the invention will be apparent from the following description of the preferred embodiments thereof, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

[0249] FIG. 1 shows a non-limiting example of a scheme for the synthesis of siNA molecules. The complementary siNA sequence strands, strand 1 and strand 2, are synthesized in tandem and are connected by a cleavable linkage, such as a nucleotide succinate or abasic succinate, which can be the same or different from the cleavable linker used for solid phase synthesis on a solid support. The synthesis can be either solid phase or solution phase, in the example shown, the synthesis is a solid phase synthesis. The synthesis is performed such that a protecting group, such as a dimethoxytrityl group, remains intact on the terminal nucleotide of the tandem oligonucleotide. Upon cleavage and deprotection of the oligonucleotide, the two siNA strands spontaneously hybridize to form a siNA duplex, which allows the purification of the duplex by utilizing the properties of the terminal protecting group, for example by applying a trityl on purification method wherein only duplexes/oligonucleotides with the terminal protecting group are isolated.

[0250] FIG. 2 shows a MALDI-TOF mass spectrum of a purified siNA duplex synthesized by a method of the invention. The two peaks shown correspond to the predicted mass of the separate siNA sequence strands. This result demonstrates that the siNA duplex generated from tandem synthesis can be purified as a single entity using a simple trityl-on purification methodology.

[0251] FIG. 3 shows a non-limiting proposed mechanistic representation of target RNA degradation involved in RNAi. Double-stranded RNA (dsRNA), which is generated by RNA-dependent RNA polymerase (RdRP) from foreign single-stranded RNA, for example viral, transposon, or other exogenous RNA, activates the DICER enzyme that in turn generates siNA duplexes. Alternately, synthetic or expressed siNA can be introduced directly into a cell by appropriate means. An active siNA complex forms which recognizes a target RNA, resulting in degradation of the target RNA by the RISC endonuclease complex or in the synthesis of additional RNA by RNA-dependent RNA polymerase (RdRP), which can activate DICER and result in additional siNA molecules, thereby amplifying the RNAi response.

[0252] FIG. 4A-F shows non-limiting examples of chemically-modified siNA constructs of the present invention. In the figure, N stands for any nucleotide (adenosine, guanosine, cytosine, uridine, or optionally thymidine, for example thymidine can be substituted in the overhanging regions designated by parenthesis (N N). Various modifications are shown for the sense and antisense strands of the siNA constructs.

[0253] FIG. 4A: The sense strand comprises 21 nucleotides wherein the two terminal 3'-nucleotides are optionally base paired and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, and wherein all nucleotides present are ribonucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the antisense strand.

[0254] FIG. 4B: The sense strand comprises 21 nucleotides wherein the two terminal 3'-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2'deoxy-2'-fluoro modified nucleotides and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety and wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the sense and antisense strand.

[0255] FIG. 4C: The sense strand comprises 21 nucleotides having 5'- and 3'-terminal cap moieties wherein the two terminal 3'-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2'-O-methyl or 2'-deoxy-2'-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety and wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the antisense strand.

[0256] FIG. 4D: The sense strand comprises 21 nucleotides having 5'- and 3'-terminal cap moieties wherein the two terminal 3'-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2'-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety and wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the antisense strand.

[0257] FIG. 4E: The sense strand comprises 21 nucleotides having 5'- and 3'-terminal cap moieties wherein the two terminal 3'-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety and wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides and all purine nucleotides that may be present are 2'-O-methyl modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the antisense strand.

[0258] FIG. 4F: The sense strand comprises 21 nucleotides having 5'- and 3'-terminal cap moieties wherein the two terminal 3'-nucleotides are optionally base paired and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein and wherein and all purine nucleotides that may be present are 2'-deoxy nucleotides. The antisense strand comprises 21 nucleotides, optionally having a 3'-terminal glyceryl moiety and wherein the two terminal 3'-nucleotides are optionally complementary to the target RNA sequence, and having one 3'-terminal phosphorothioate internucleotide linkage and wherein all pyrimidine nucleotides that may be present are 2'-deoxy-2'-fluoro modified nucleotides and all purine nucleotides that may be present are 2'-deoxy nucleotides except for (N N) nucleotides, which can comprise ribonucleotides, deoxynucleotides, universal bases, or other chemical modifications described herein. A modified internucleotide linkage, such as a phosphorothioate, phosphorodithioate or other modified internucleotide linkage as described herein, shown as "s", optionally connects the (N N) nucleotides in the antisense strand. The antisense strand of constructs A-F comprise sequence complementary to any target nucleic acid sequence of the invention. Furthermore, when a glyceryl moiety (L) is present at the 3'-end of the antisense strand for any construct shown in FIG. 4 A-F, the modified internucleotide linkage is optional.

[0259] FIG. 5A-F shows non-limiting examples of specific chemically-modified siNA sequences of the invention. A-F applies the chemical modifications described in FIG. 4A-F to a PDGFr siNA sequence. Such chemical modifications can be applied to any PDGF and/or PDGFr sequence and/or PDGF and/or PDGFr polymorphism sequence.

[0260] FIG. 6 shows non-limiting examples of different siNA constructs of the invention. The examples shown (constructs 1, 2, and 3) have 19 representative base pairs; however, different embodiments of the invention include any number of base pairs described herein. Bracketed regions represent nucleotide overhangs, for example, comprising about 1, 2, 3, or 4 nucleotides in length, preferably about 2 nucleotides. Constructs 1 and 2 can be used independently for RNAi activity. Construct 2 can comprise a polynucleotide or non-nucleotide linker, which can optionally be designed as a biodegradable linker. In one embodiment, the loop structure shown in construct 2 can comprise a biodegradable linker that results in the formation of construct 1 in vivo and/or in vitro. In another example, construct 3 can be used to generate construct 2 under the same principle wherein a linker is used to generate the active siNA construct 2 in vivo and/or in vitro, which can optionally utilize another biodegradable linker to generate the active siNA construct 1 in vivo and/or in vitro. As such, the stability and/or activity of the siNA constructs can be modulated based on the design of the siNA construct for use in vivo or in vitro and/or in vitro.

[0261] FIG. 7A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate siNA hairpin constructs.

[0262] FIG. 7A: A DNA oligomer is synthesized with a 5'-restriction site (R1) sequence followed by a region having sequence identical (sense region of siNA) to a predetermined PDGF and/or PDGFr target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, which is followed by a loop sequence of defined sequence (X), comprising, for example, about 3 to about 10 nucleotides.

[0263] FIG. 7B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence that will result in a siNA transcript having specificity for a PDGF and/or PDGFr target sequence and having self-complementary sense and antisense regions.

[0264] FIG. 7C: The construct is heated (for example to about 95.degree. C.) to linearize the sequence, thus allowing extension of a complementary second DNA strand using a primer to the 3'-restriction sequence of the first strand. The double-stranded DNA is then inserted into an appropriate vector for expression in cells. The construct can be designed such that a 3'-terminal nucleotide overhang results from the transcription, for example, by engineering restriction sites and/or utilizing a poly-U termination region as described in Paul et al., 2002, Nature Biotechnology, 29, 505-508.

[0265] FIG. 8A-C is a diagrammatic representation of a scheme utilized in generating an expression cassette to generate double-stranded siNA constructs.

[0266] FIG. 8A: A DNA oligomer is synthesized with a 5'-restriction (R1) site sequence followed by a region having sequence identical (sense region of siNA) to a predetermined PDGF and/or PDGFr target sequence, wherein the sense region comprises, for example, about 19, 20, 21, or 22 nucleotides (N) in length, and which is followed by a 3'-restriction site (R2) which is adjacent to a loop sequence of defined sequence (X).

[0267] FIG. 8B: The synthetic construct is then extended by DNA polymerase to generate a hairpin structure having self-complementary sequence.

[0268] FIG. 8C: The construct is processed by restriction enzymes specific to R1 and R2 to generate a double-stranded DNA which is then inserted into an appropriate vector for expression in cells. The transcription cassette is designed such that a U6 promoter region flanks each side of the dsDNA which generates the separate sense and antisense strands of the siNA. Poly T termination sequences can be added to the constructs to generate U overhangs in the resulting transcript.

[0269] FIG. 9A-E is a diagrammatic representation of a method used to determine target sites for siNA mediated RNAi within a particular target nucleic acid sequence, such as messenger RNA.

[0270] FIG. 9A: A pool of siNA oligonucleotides are synthesized wherein the antisense region of the siNA constructs has complementarity to target sites across the target nucleic acid sequence, and wherein the sense region comprises sequence complementary to the antisense region of the siNA.

[0271] FIGS. 9B&C: (FIG. 9B) The sequences are pooled and are inserted into vectors such that (FIG. 9C) transfection of a vector into cells results in the expression of the siNA.

[0272] FIG. 9D: Cells are sorted based on phenotypic change that is associated with modulation of the target nucleic acid sequence.

[0273] FIG. 9E: The siNA is isolated from the sorted cells and is sequenced to identify efficacious target sites within the target nucleic acid sequence.

[0274] FIG. 10 shows non-limiting examples of different stabilization chemistries (1-10) that can be used, for example, to stabilize the 3'-end of siNA sequences of the invention, including (1) [3-3']-inverted deoxyribose; (2) deoxyribonucleotide; (3) [5'-3']-3'-deoxyribonucleotide; (4) [5'-3']-ribonucleotide; (5) [5'-3']-3'-O-methyl ribonucleotide; (6) 3'-glyceryl; (7) [3'-5']-3'-deoxyribonucleotide; (8) [3'-3']-deoxyribonucleotide; (9) [5'-2']-deoxyribonucleotide; and (10) [5-3']-dideoxyribonucleotide. In addition to modified and unmodified backbone chemistries indicated in the figure, these chemistries can be combined with different backbone modifications as described herein, for example, backbone modifications having Formula I. In addition, the 2'-deoxy nucleotide shown 5' to the terminal modifications shown can be another modified or unmodified nucleotide or non-nucleotide described herein, for example modifications having any of Formulae I-VII or any combination thereof.

[0275] FIG. 11 shows a non-limiting example of a strategy used to identify chemically modified siNA constructs of the invention that are nuclease resistance while preserving the ability to mediate RNAi activity. Chemical modifications are introduced into the siNA construct based on educated design parameters (e.g. introducing 2'-mofications, base modifications, backbone modifications, terminal cap modifications etc). The modified construct in tested in an appropriate system (e.g. human serum for nuclease resistance, shown, or an animal model for PK/delivery parameters). In parallel, the siNA construct is tested for RNAi activity, for example in a cell culture system such as a luciferase reporter assay). Lead siNA constructs are then identified which possess a particular characteristic while maintaining RNAi activity, and can be further modified and assayed once again. This same approach can be used to identify siNA-conjugate molecules with improved pharmacokinetic profiles, delivery, and RNAi activity.

[0276] FIG. 12 shows non-limiting examples of phosphorylated siNA molecules of the invention, including linear and duplex constructs and asymmetric derivatives thereof.

[0277] FIG. 13 shows non-limiting examples of chemically modified terminal phosphate groups of the invention.

[0278] FIG. 14A shows a non-limiting example of methodology used to design self complementary DFO constructs utilizing palindrome and/or repeat nucleic acid sequences that are identified in a target nucleic acid sequence. (i) A palindrome or repeat sequence is identified in a nucleic acid target sequence. (ii) A sequence is designed that is complementary to the target nucleic acid sequence and the palindrome sequence. (iii) An inverse repeat sequence of the non-palindrome/repeat portion of the complementary sequence is appended to the 3'-end of the complementary sequence to generate a self complementary DFO molecule comprising sequence complementary to the nucleic acid target. (iv) The DFO molecule can self-assemble to form a double stranded oligonucleotide. FIG. 14B shows a non-limiting representative example of a duplex forming oligonucleotide sequence. FIG. 14C shows a non-limiting example of the self assembly schematic of a representative duplex forming oligonucleotide sequence. FIG. 14D shows a non-limiting example of the self assembly schematic of a representative duplex forming oligonucleotide sequence followed by interaction with a target nucleic acid sequence resulting in modulation of gene expression.

[0279] FIG. 15 shows a non-limiting example of the design of self complementary DFO constructs utilizing palindrome and/or repeat nucleic acid sequences that are incorporated into the DFO constructs that have sequence complementary to any target nucleic acid sequence of interest. Incorporation of these palindrome/repeat sequences allow the design of DFO constructs that form duplexes in which each strand is capable of mediating modulation of target gene expression, for example by RNAi. First, the target sequence is identified. A complementary sequence is then generated in which nucleotide or non-nucleotide modifications (shown as X or Y) are introduced into the complementary sequence that generate an artificial palindrome (shown as XYXYXY in the Figure). An inverse repeat of the non-palindrome/repeat complementary sequence is appended to the 3'-end of the complementary sequence to generate a self complementary DFO comprising sequence complementary to the nucleic acid target. The DFO can self-assemble to form a double stranded oligonucleotide.

[0280] FIG. 16 shows non-limiting examples of multifunctional siNA molecules of the invention comprising two separate polynucleotide sequences that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences. FIG. 16A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 3'-ends of each polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 16B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 5'-ends of each polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences.

[0281] FIG. 17 shows non-limiting examples of multifunctional siNA molecules of the invention comprising a single polynucleotide sequence comprising distinct regions that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences. FIG. 17A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the second complementary region is situated at the 3'-end of the polynucleotide sequence in the multifunctional siNA. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 17B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first complementary region is situated at the 5'-end of the polynucleotide sequence in the multifunctional siNA. The dashed portion's of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. In one embodiment, these multifunctional siNA constructs are processed in vivo or in vitro to generate multifunctional siNA constructs as shown in FIG. 16.

[0282] FIG. 18 shows non-limiting examples of multifunctional siNA molecules of the invention comprising two separate polynucleotide sequences that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences and wherein the multifunctional siNA construct further comprises a self complementary, palindrome, or repeat region, thus enabling shorter bifunctional siNA constructs that can mediate RNA interference against differing target nucleic acid sequences. FIG. 18A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 3'-ends of each polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 18B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first and second complementary regions are situated at the 5'-ends of each polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences.

[0283] FIG. 19 shows non-limiting examples of multifunctional siNA molecules of the invention comprising a single polynucleotide sequence comprising distinct regions that are each capable of mediating RNAi directed cleavage of differing target nucleic acid sequences and wherein the multifunctional siNA construct further comprises a self complementary, palindrome, or repeat region, thus enabling shorter bifunctional siNA constructs that can mediate RNA interference against differing target nucleic acid sequences. FIG. 19A shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the second complementary region is situated at the 3'-end of the polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. FIG. 19B shows a non-limiting example of a multifunctional siNA molecule having a first region that is complementary to a first target nucleic acid sequence (complementary region 1) and a second region that is complementary to a second target nucleic acid sequence (complementary region 2), wherein the first complementary region is situated at the 5'-end of the polynucleotide sequence in the multifunctional siNA, and wherein the first and second complementary regions further comprise a self complementary, palindrome, or repeat region. The dashed portions of each polynucleotide sequence of the multifunctional siNA construct have complementarity with regard to corresponding portions of the siNA duplex, but do not have complementarity to the target nucleic acid sequences. In one embodiment, these multifunctional siNA constructs are processed in vivo or in vitro to generate multifunctional siNA constructs as shown in FIG. 18.

[0284] FIG. 20 shows a non-limiting example of how multifunctional siNA molecules of the invention can target two separate target nucleic acid molecules, such as separate RNA molecules encoding differing proteins, for example, a cytokine and its corresponding receptor, differing viral strains, a virus and a cellular protein involved in viral infection or replication, or differing proteins involved in a common or divergent biologic pathway that is implicated in the maintenance of progression of disease. Each strand of the multifunctional siNA construct comprises a region having complementarity to separate target nucleic acid molecules. The multifunctional siNA molecule is designed such that each strand of the siNA can be utilized by the RISC to initiate RNA interference mediated cleavage of its corresponding target. These design parameters can include destabilization of each end of the siNA construct (see for example Schwarz et al., 2003, Cell, 115, 199-208). Such destabilization can be accomplished for example by using guanosine-cytidine base pairs, alternate base pairs (e.g., wobbles), or destabilizing chemically modified nucleotides at terminal nucleotide positions as is known in the art.

[0285] FIG. 21 shows a non-limiting example of how multifunctional siNA molecules of the invention can target two separate target nucleic acid sequences within the same target nucleic acid molecule, such as alternate coding regions of a RNA, coding and non-coding regions of a RNA, or alternate splice variant regions of a RNA. Each strand of the multifunctional siNA construct comprises a region having complementarity to the separate regions of the target nucleic acid molecule. The multifunctional siNA molecule is designed such that each strand of the siNA can be utilized by the RISC to initiate RNA interference mediated cleavage of its corresponding target region. These design parameters can include destabilization of each end of the siNA construct (see for example Schwarz et al., 2003, Cell, 115, 199-208). Such destabilization can be accomplished for example by using guanosine-cytidine base pairs, alternate base pairs (e.g., wobbles), or destabilizing chemically modified nucleotides at terminal nucleotide positions as is known in the art.

DETAILED DESCRIPTION OF THE INVENTION

Mechanism of Action of Nucleic Acid Molecules of the Invention

[0286] The discussion that follows discusses the proposed mechanism of RNA interference mediated by short interfering RNA as is presently known, and is not meant to be limiting and is not an admission of prior art. Applicant demonstrates herein that chemically-modified short interfering nucleic acids possess similar or improved capacity to mediate RNAi as do siRNA molecules and are expected to possess improved stability and activity in vivo; therefore, this discussion is not meant to be limiting only to siRNA and can be applied to siNA as a whole. By "improved capacity to mediate RNAi" or "improved RNAi activity" is meant to include RNAi activity measured in vitro and/or in vivo where the RNAi activity is a reflection of both the ability of the siNA to mediate RNAi and the stability of the siNAs of the invention. In this invention, the product of these activities can be increased in vitro and/or in vivo compared to an all RNA siRNA or a siNA containing a plurality of ribonucleotides. In some cases, the activity or stability of the siNA molecule can be decreased (i.e., less than ten-fold), but the overall activity of the siNA molecule is enhanced in vitro and/or in vivo.

[0287] RNA interference refers to the process of sequence specific post-transcriptional gene silencing in animals mediated by short interfering RNAs (siRNAs) (Fire et al., 1998, Nature, 391, 806). The corresponding process in plants is commonly referred to as post-transcriptional gene silencing or RNA silencing and is also referred to as quelling in fungi. The process of post-transcriptional gene silencing is thought to be an evolutionarily-conserved cellular defense mechanism used to prevent the expression of foreign genes which is commonly shared by diverse flora and phyla (Fire et al., 1999, Trends Genet., 15, 358). Such protection from foreign gene expression may have evolved in response to the production of double-stranded RNAs (dsRNAs) derived from viral infection or the random integration of transposon elements into a host genome via a cellular response that specifically destroys homologous single-stranded RNA or viral genomic RNA. The presence of dsRNA in cells triggers the RNAi response though a mechanism that has yet to be fully characterized. This mechanism appears to be different from the interferon response that results from dsRNA-mediated activation of protein kinase PKR and 2',5'-oligoadenylate synthetase resulting in non-specific cleavage of mRNA by ribonuclease L.

[0288] The presence of long dsRNAs in cells stimulates the activity of a ribonuclease III enzyme referred to as Dicer. Dicer is involved in the processing of the dsRNA into short pieces of dsRNA known as short interfering RNAs (siRNAs) (Berstein et al., 2001, Nature, 409, 363). Short interfering RNAs derived from Dicer activity are typically about 21 to about 23 nucleotides in length and comprise about 19 base pair duplexes. Dicer has also been implicated in the excision of 21- and 22-nucleotide small temporal RNAs (stRNAs) from precursor RNA of conserved structure that are implicated in translational control (Hutvagner et al., 2001, Science, 293, 834). The RNAi response also features an endonuclease complex containing a siRNA, commonly referred to as an RNA-induced silencing complex (RISC), which mediates cleavage of single-stranded RNA having sequence homologous to the siRNA. Cleavage of the target RNA takes place in the middle of the region complementary to the guide sequence of the siRNA duplex (Elbashir et al., 2001, Genes Dev., 15, 188). In addition, RNA interference can also involve small RNA (e.g., micro-RNA or miRNA) mediated gene silencing, presumably though cellular mechanisms that regulate chromatin structure and thereby prevent transcription of target gene sequences (see for example Allshire, 2002, Science, 297, 1818-1819; Volpe et al., 2002, Science, 297, 1833-1837; Jenuwein, 2002, Science, 297, 2215-2218; and Hall et al., 2002, Science, 297, 2232-2237). As such, siNA molecules of the invention can be used to mediate gene silencing via interaction with RNA transcripts or alternately by interaction with particular gene sequences, wherein such interaction results in gene silencing either at the transcriptional level or post-transcriptional level.

[0289] RNAi has been studied in a variety of systems. Fire et al., 1998, Nature, 391, 806, were the first to observe RNAi in C. elegans. Wianny and Goetz, 1999, Nature Cell Biol., 2, 70, describe RNAi mediated by dsRNA in mouse embryos. Hammond et al., 2000, Nature, 404, 293, describe RNAi in Drosophila cells transfected with dsRNA. Elbashir et al., 2001, Nature, 411, 494, describe RNAi induced by introduction of duplexes of synthetic 21-nucleotide RNAs in cultured mammalian cells including human embryonic kidney and HeLa cells. Recent work in Drosophila embryonic lysates has revealed certain requirements for siRNA length, structure, chemical composition, and sequence that are essential to mediate efficient RNAi activity. These studies have shown that 21 nucleotide siRNA duplexes are most active when containing two 2-nucleotide 3'-terminal nucleotide overhangs. Furthermore, substitution of one or both siRNA strands with 2'-deoxy or 2'-O-methyl nucleotides abolishes RNAi activity, whereas substitution of 3'-terminal siRNA nucleotides with deoxy nucleotides was shown to be tolerated. Mismatch sequences in the center of the siRNA duplex were also shown to abolish RNAi activity. In addition, these studies also indicate that the position of the cleavage site in the target RNA is defined by the 5'-end of the siRNA guide sequence rather than the 3'-end (Elbashir et al., 2001, EMBO J., 20, 6877). Other studies have indicated that a 5'-phosphate on the target-complementary strand of a siRNA duplex is required for siRNA activity and that ATP is utilized to maintain the 5'-phosphate moiety on the siRNA (Nykanen et al., 2001, Cell, 107, 309); however, siRNA molecules lacking a 5'-phosphate are active when introduced exogenously, suggesting that 5'-phosphorylation of siRNA constructs may occur in vivo.

Synthesis of Nucleic Acid Molecules

[0290] Synthesis of nucleic acids greater than 100 nucleotides in length is difficult using automated methods, and the therapeutic cost of such molecules is prohibitive. In this invention, small nucleic acid motifs ("small" refers to nucleic acid motifs no more than 100 nucleotides in length, preferably no more than 80 nucleotides in length, and most preferably no more than 50 nucleotides in length; e.g., individual siNA oligonucleotide sequences or siNA sequences synthesized in tandem) are preferably used for exogenous delivery. The simple structure of these molecules increases the ability of the nucleic acid to invade targeted regions of protein and/or RNA structure. Exemplary molecules of the instant invention are chemically synthesized, and others can similarly be synthesized.

[0291] Oligonucleotides (e.g., certain modified oligonucleotides or portions of oligonucleotides lacking ribonucleotides) are synthesized using protocols known in the art, for example as described in Caruthers et al., 1992, Methods in Enzymology 211, 3-19, Thompson et al., International PCT Publication No. WO 99/54459, Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684, Wincott et al., 1997, Methods Mol. Bio., 74, 59, Brennan et al., 1998, Biotechnol Bioeng., 61, 33-45, and Brennan, U.S. Pat. No. 6,001,311. All of these references are incorporated herein by reference. The synthesis of oligonucleotides makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 .mu.mol scale protocol with a 2.5 min coupling step for 2'-O-methylated nucleotides and a 45 second coupling step for 2'-deoxy nucleotides or 2'-deoxy-2'-fluoro nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 .mu.mol scale can be performed on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 .mu.L of 0.11 M=6.6 .mu.mol) of 2'-O-methyl phosphoramidite and a 105-fold excess of S-ethyl tetrazole (60 .mu.L of 0.25 M=15 .mu.mol) can be used in each coupling cycle of 2'-O-methyl residues relative to polymer-bound 5'-hydroxyl. A 22-fold excess (40 .mu.L of 0.11 M=4.4 .mu.mol) of deoxy phosphoramidite and a 70-fold excess of S-ethyl tetrazole (40 .mu.L of 0.25 M=10 .mu.mol) can be used in each coupling cycle of deoxy residues relative to polymer-bound 5'-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); and oxidation solution is 16.9 mM 12, 49 mM pyridine, 9% water in THF (PerSeptive Biosystems, Inc.). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide, 0.05 M in acetonitrile) is used.

[0292] Deprotection of the DNA-based oligonucleotides is performed as follows: the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aqueous methylamine (1 mL) at 65.degree. C. for 10 minutes. After cooling to -20.degree. C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H2O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder.

[0293] The method of synthesis used for RNA including certain siNA molecules of the invention follows the procedure as described in Usman et al., 1987, J. Am. Chem. Soc., 109, 7845; Scaringe et al., 1990, Nucleic Acids Res., 18, 5433; and Wincott et al., 1995, Nucleic Acids Res. 23, 2677-2684 Wincott et al., 1997, Methods Mol. Bio., 74, 59, and makes use of common nucleic acid protecting and coupling groups, such as dimethoxytrityl at the 5'-end, and phosphoramidites at the 3'-end. In a non-limiting example, small scale syntheses are conducted on a 394 Applied Biosystems, Inc. synthesizer using a 0.2 .mu.mol scale protocol with a 7.5 min coupling step for alkylsilyl protected nucleotides and a 2.5 min coupling step for 2'-O-methylated nucleotides. Table V outlines the amounts and the contact times of the reagents used in the synthesis cycle. Alternatively, syntheses at the 0.2 .mu.mol scale can be done on a 96-well plate synthesizer, such as the instrument produced by Protogene (Palo Alto, Calif.) with minimal modification to the cycle. A 33-fold excess (60 .mu.L of 0.11 M=6.6 .mu.mol) of 2'-O-methyl phosphoramidite and a 75-fold excess of S-ethyl tetrazole (60 .mu.L of 0.25 M=15 .mu.mol) can be used in each coupling cycle of 2'-O-methyl residues relative to polymer-bound 5'-hydroxyl. A 66-fold excess (120 .mu.L of 0.11 M=13.2 .mu.mol) of alkylsilyl (ribo) protected phosphoramidite and a 150-fold excess of S-ethyl tetrazole (120 .mu.L of 0.25 M=30 .mu.mol) can be used in each coupling cycle of ribo residues relative to polymer-bound 5'-hydroxyl. Average coupling yields on the 394 Applied Biosystems, Inc. synthesizer, determined by colorimetric quantitation of the trityl fractions, are typically 97.5-99%. Other oligonucleotide synthesis reagents for the 394 Applied Biosystems, Inc. synthesizer include the following: detritylation solution is 3% TCA in methylene chloride. (ABI); capping is performed with 16% N-methyl imidazole in THF (ABI) and 10% acetic anhydride/10% 2,6-lutidine in THF (ABI); oxidation solution is 16.9 mM I.sub.2, 49 mM pyridine, 9% water in THF (PerSeptive Biosystems, Inc.). Burdick & Jackson Synthesis Grade acetonitrile is used directly from the reagent bottle. S-Ethyltetrazole solution (0.25 M in acetonitrile) is made up from the solid obtained from American International Chemical, Inc. Alternately, for the introduction of phosphorothioate linkages, Beaucage reagent (3H-1,2-Benzodithiol-3-one 1,1-dioxide 0.05 M in acetonitrile) is used.

[0294] Deprotection of the RNA is performed using either a two-pot or one-pot protocol. For the two-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 40% aq. methylamine (1 mL) at 65.degree. C. for 10 min. After cooling to -20.degree. C., the supernatant is removed from the polymer support. The support is washed three times with 1.0 mL of EtOH:MeCN:H2O/3:1:1, vortexed and the supernatant is then added to the first supernatant. The combined supernatants, containing the oligoribonucleotide, are dried to a white powder. The base deprotected oligoribonucleotide is resuspended in anhydrous TEA/HF/NMP solution (300 .mu.L of a solution of 1.5 mL N-methylpyrrolidinone, 750 .mu.L TEA and 1 mL TEA.3HF to provide a 1.4 M HF concentration) and heated to 65.degree. C. After 1.5 h, the oligomer is quenched with 1.5 M NH.sub.4HCO.sub.3.

[0295] Alternatively, for the one-pot protocol, the polymer-bound trityl-on oligoribonucleotide is transferred to a 4 mL glass screw top vial and suspended in a solution of 33% ethanolic methylamine/DMSO:1/1 (0.8 mL) at 65.degree. C. for 15 minutes. The vial is brought to room temperature TEA.3HF (0.1 mL) is added and the vial is heated at 65.degree. C. for 15 minutes. The sample is cooled at -20.degree. C. and then quenched with 1.5 M NH.sub.4HCO.sub.3.

[0296] For purification of the trityl-on oligomers, the quenched NH.sub.4HCO.sub.3 solution is loaded onto a C-18 containing cartridge that had been prewashed with acetonitrile followed by 50 mM TEAA. After washing the loaded cartridge with water, the RNA is detritylated with 0.5% TFA for 13 minutes. The cartridge is then washed again with water, salt exchanged with 1 M NaCl and washed with water again. The oligonucleotide is then eluted with 30% acetonitrile.

[0297] The average stepwise coupling yields are typically >98% (Wincott et al., 1995 Nucleic Acids Res. 23, 2677-2684). Those of ordinary skill in the art will recognize that the scale of synthesis can be adapted to be larger or smaller than the example described above including but not limited to 96-well format.

[0298] Alternatively, the nucleic acid molecules of the present invention can be synthesized separately and joined together post-synthetically, for example, by ligation (Moore et al., 1992, Science 256, 9923; Draper et al., International PCT publication No. WO 93/23569; Shabarova et al., 1991, Nucleic Acids Research 19, 4247; Bellon et al., 1997, Nucleosides & Nucleotides, 16, 951; Bellon et al., 1997, Bioconjugate Chem. 8, 204), or by hybridization following synthesis and/or deprotection.

[0299] The siNA molecules of the invention can also be synthesized via a tandem synthesis methodology as described in Example 1 herein, wherein both siNA strands are synthesized as a single contiguous oligonucleotide fragment or strand separated by a cleavable linker which is subsequently cleaved to provide separate siNA fragments or strands that hybridize and permit purification of the siNA duplex. The linker can be a polynucleotide linker or a non-nucleotide linker. The tandem synthesis of siNA as described herein can be readily adapted to both multiwell/multiplate synthesis platforms such as 96 well or similarly larger multi-well platforms. The tandem synthesis of siNA as described herein can also be readily adapted to large scale synthesis platforms employing batch reactors, synthesis columns and the like.

[0300] A siNA molecule can also be assembled from two distinct nucleic acid strands or fragments wherein one fragment includes the sense region and the second fragment includes the antisense region of the RNA molecule.

[0301] The nucleic acid molecules of the present invention can be modified extensively to enhance stability by modification with nuclease resistant groups, for example, 2'-amino, 2'-C-allyl, 2'-fluoro, 2'-O-methyl, 2'-H (for a review see Usman and Cedergren, 1992, TIBS 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163). siNA constructs can be purified by gel electrophoresis using general methods or can be purified by high pressure liquid chromatography (HPLC; see Wincott et al., supra, the totality of which is hereby incorporated herein by reference) and re-suspended in water.

[0302] In another aspect of the invention, siNA molecules of the invention are expressed from transcription units inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. The recombinant vectors capable of expressing the siNA molecules can be delivered as described herein, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of siNA molecules.

Optimizing Activity of the Nucleic Acid Molecule of the Invention.

[0303] Chemically synthesizing nucleic acid molecules with modifications (base, sugar and/or phosphate) can prevent their degradation by serum ribonucleases, which can increase their potency (see e.g., Eckstein et al., International Publication No. WO 92/07065; Perrault et al., 1990 Nature 344, 565; Pieken et al., 1991, Science 253, 314; Usman and Cedergren, 1992, Trends in Biochem. Sci. 17, 334; Usman et al., International Publication No. WO 93/15187; and Rossi et al., International Publication No. WO 91/03162; Sproat, U.S. Pat. No. 5,334,711; Gold et al., U.S. Pat. No. 6,300,074; and Burgin et al., supra; all of which are incorporated by reference herein). All of the above references describe various chemical modifications that can be made to the base, phosphate and/or sugar moieties of the nucleic acid molecules described herein. Modifications that enhance their efficacy in cells, and removal of bases from nucleic acid molecules to shorten oligonucleotide synthesis times and reduce chemical requirements are desired.

[0304] There are several examples in the art describing sugar, base and phosphate modifications that can be introduced into nucleic acid molecules with significant enhancement in their nuclease stability and efficacy. For example, oligonucleotides are modified to enhance stability and/or enhance biological activity by modification with nuclease resistant groups, for example, 2'-amino, 2'-C-allyl, 2'-fluoro, 2'-O-methyl, 2'-O-allyl, 2'-H, nucleotide base modifications (for a review see Usman and Cedergren, 1992, TIBS. 17, 34; Usman et al., 1994, Nucleic Acids Symp. Ser. 31, 163; Burgin et al., 1996, Biochemistry, 35, 14090). Sugar modification of nucleic acid molecules have been extensively described in the art (see Eckstein et al., International Publication PCT No. WO 92/07065; Perrault et al. Nature, 1990, 344, 565-568; Pieken et al. Science, 1991, 253, 314-317; Usman and Cedergren, Trends in Biochem. Sci., 1992, 17, 334-339; Usman et al. International Publication PCT No. WO 93/15187; Sproat, U.S. Pat. No. 5,334,711 and Beigelman et al., 1995, J. Biol. Chem., 270, 25702; Beigelman et al., International PCT publication No. WO 97/26270; Beigelman et al., U.S. Pat. No. 5,716,824; Usman et al., U.S. Pat. No. 5,627,053; Woolf et al., International PCT Publication No. WO 98/13526; Thompson et al., U.S. Ser. No. 60/082,404 which was filed on Apr. 20, 1998; Karpeisky et al., 1998, Tetrahedron Lett., 39, 1131; Earnshaw and Gait, 1998, Biopolymers (Nucleic Acid Sciences), 48, 39-55; Verma and Eckstein, 1998, Annu. Rev. Biochem., 67, 99-134; and Burlina et al., 1997, Bioorg. Med. Chem., 5, 1999-2010; all of the references are hereby incorporated in their totality by reference herein). Such publications describe general methods and strategies to determine the location of incorporation of sugar, base and/or phosphate modifications and the like into nucleic acid molecules without modulating catalysis, and are incorporated by reference herein. In view of such teachings, similar modifications can be used as described herein to modify the siNA nucleic acid molecules of the instant invention so long as the ability of siNA to promote RNAi is cells is not significantly inhibited.

[0305] While chemical modification of oligonucleotide internucleotide linkages with phosphorothioate, phosphorodithioate, and/or 5'-methylphosphonate linkages improves stability, excessive modifications can cause some toxicity or decreased activity. Therefore, when designing nucleic acid molecules, the amount of these internucleotide linkages should be minimized. The reduction in the concentration of these linkages should lower toxicity, resulting in increased efficacy and higher specificity of these molecules.

[0306] Short interfering nucleic acid (siNA) molecules having chemical modifications that maintain or enhance activity are provided. Such a nucleic acid is also generally more resistant to nucleases than an unmodified nucleic acid. Accordingly, the in vitro and/or in vivo activity should not be significantly lowered. In cases in which modulation is the goal, therapeutic nucleic acid molecules delivered exogenously should optimally be stable within cells until translation of the target RNA has been modulated long enough to reduce the levels of the undesirable protein. This period of time varies between hours to days depending upon the disease state. Improvements in the chemical synthesis of RNA and DNA (Wincott et al., 1995, Nucleic Acids Res. 23, 2677; Caruthers et al., 1992, Methods in Enzymology 211, 3-19 (incorporated by reference herein)) have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability, as described above.

[0307] In one embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) G-clamp nucleotides. A G-clamp nucleotide is a modified cytosine analog wherein the modifications confer the ability to hydrogen bond both Watson-Crick and Hoogsteen faces of a complementary guanine within a duplex, see for example Lin and Matteucci, 1998, J. Am. Chem. Soc., 120, 8531-8532. A single G-clamp analog substitution within an oligonucleotide can result in substantially enhanced helical thermal stability and mismatch discrimination when hybridized to complementary oligonucleotides. The inclusion of such nucleotides in nucleic acid molecules of the invention results in both enhanced affinity and specificity to nucleic acid targets, complementary sequences, or template strands. In another embodiment, nucleic acid molecules of the invention include one or more (e.g., about 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, or more) LNA "locked nucleic acid" nucleotides such as a 2',4'-C methylene bicyclo nucleotide (see for example Wengel et al., International PCT Publication No. WO 00/66604 and WO 99/14226).

[0308] In another embodiment, the invention features conjugates and/or complexes of siNA molecules of the invention. Such conjugates and/or complexes can be used to facilitate delivery of siNA molecules into a biological system, such as a cell. The conjugates and complexes provided by the instant invention can impart therapeutic activity by transferring therapeutic compounds across cellular membranes, altering the pharmacokinetics, and/or modulating the localization of nucleic acid molecules of the invention. The present invention encompasses the design and synthesis of novel conjugates and complexes for the delivery of molecules, including, but not limited to, small molecules, lipids, cholesterol, phospholipids, nucleosides, nucleotides, nucleic acids, antibodies, toxins, negatively charged polymers and other polymers, for example proteins, peptides, hormones, carbohydrates, polyethylene glycols, or polyamines, across cellular membranes. In general, the transporters described are designed to be used either individually or as part of a multi-component system, with or without degradable linkers. These compounds are expected to improve delivery and/or localization of nucleic acid molecules of the invention into a number of cell types originating from different tissues, in the presence or absence of serum (see Sullenger and Cech, U.S. Pat. No. 5,854,038). Conjugates of the molecules described herein can be attached to biologically active molecules via linkers that are biodegradable, such as biodegradable nucleic acid linker molecules.

[0309] The term "biodegradable linker" as used herein, refers to a nucleic acid or non-nucleic acid linker molecule that is designed as a biodegradable linker to connect one molecule to another molecule, for example, a biologically active molecule to a siNA molecule of the invention or the sense and antisense strands of a siNA molecule of the invention. The biodegradable linker is designed such that its stability can be modulated for a particular purpose, such as delivery to a particular tissue or cell type. The stability of a nucleic acid-based biodegradable linker molecule can be modulated by using various chemistries, for example combinations of ribonucleotides, deoxyribonucleotides, and chemically-modified nucleotides, such as 2'-O-methyl, 2'-fluoro, 2'-amino, 2'-O-amino, 2'-C-allyl, 2'-O-allyl, and other 2'-modified or base modified nucleotides. The biodegradable nucleic acid linker molecule can be a dimer, trimer, tetramer or longer nucleic acid molecule, for example, an oligonucleotide of about 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides in length, or can comprise a single nucleotide with a phosphorus-based linkage, for example, a phosphoramidate or phosphodiester linkage. The biodegradable nucleic acid linker molecule can also comprise nucleic acid backbone, nucleic acid sugar, or nucleic acid base modifications.

[0310] The term "biodegradable" as used herein, refers to degradation in a biological system, for example, enzymatic degradation or chemical degradation.

[0311] The term "biologically active molecule" as used herein refers to compounds or molecules that are capable of eliciting or modifying a biological response in a system. Non-limiting examples of biologically active siNA molecules either alone or in combination with other molecules contemplated by the instant invention include therapeutically active molecules such as antibodies, cholesterol, hormones, antivirals, peptides, proteins, chemotherapeutics, small molecules, vitamins, co-factors, nucleosides, nucleotides, oligonucleotides, enzymatic nucleic acids, antisense nucleic acids, triplex forming oligonucleotides, 2,5-A chimeras, siNA, dsRNA, allozymes, aptamers, decoys and analogs thereof. Biologically active molecules of the invention also include molecules capable of modulating the pharmacokinetics and/or pharmacodynamics of other biologically active molecules, for example, lipids and polymers such as polyamines, polyamides, polyethylene glycol and other polyethers.

[0312] The term "phospholipid" as used herein, refers to a hydrophobic molecule comprising at least one phosphorus group. For example, a phospholipid can comprise a phosphorus-containing group and saturated or unsaturated alkyl group, optionally substituted with OH, COOH, oxo, amine, or substituted or unsubstituted aryl groups.

[0313] Therapeutic nucleic acid molecules (e.g., siNA molecules) delivered exogenously optimally are stable within cells until reverse transcription of the RNA has been modulated long enough to reduce the levels of the RNA transcript. The nucleic acid molecules are resistant to nucleases in order to function as effective intracellular therapeutic agents. Improvements in the chemical synthesis of nucleic acid molecules described in the instant invention and in the art have expanded the ability to modify nucleic acid molecules by introducing nucleotide modifications to enhance their nuclease stability as described above.

[0314] In yet another embodiment, siNA molecules having chemical modifications that maintain or enhance enzymatic activity of proteins involved in RNAi are provided. Such nucleic acids are also generally more resistant to nucleases than unmodified nucleic acids. Thus, in vitro and/or in vivo the activity should not be significantly lowered.

[0315] Use of the nucleic acid-based molecules of the invention will lead to better treatments by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes; nucleic acid molecules coupled with known small molecule modulators; or intermittent treatment with combinations of molecules, including different motifs and/or other chemical or biological molecules). The treatment of subjects with siNA molecules can also include combinations of different types of nucleic acid molecules, such as enzymatic nucleic acid molecules (ribozymes), allozymes, antisense, 2,5-A oligoadenylate, decoys, and aptamers.

[0316] In another aspect a siNA molecule of the invention comprises one or more 5' and/or a 3'-cap structure, for example, on only the sense siNA strand, the antisense siNA strand, or both siNA strands.

[0317] By "cap structure" is meant chemical modifications, which have been incorporated at either terminus of the oligonucleotide (see, for example, Adamic et al., U.S. Pat. No. 5,998,203, incorporated by reference herein). These terminal modifications protect the nucleic acid molecule from exonuclease degradation, and may help in delivery and/or localization within a cell. The cap may be present at the 5'-terminus (5'-cap) or at the 3'-terminal (3'-cap) or may be present on both termini. In non-limiting examples, the 5'-cap includes, but is not limited to, glyceryl, inverted deoxy abasic residue (moiety); 4',5'-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide, 4'-thio nucleotide; carbocyclic nucleotide; 1,5-anhydrohexitol nucleotide; L-nucleotides; alpha-nucleotides; modified base nucleotide; phosphorodithioate linkage; threo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; acyclic 3,4-dihydroxybutyl nucleotide; acyclic 3,5-dihydroxypentyl nucleotide, 3'-3'-inverted nucleotide moiety; 3'-3'-inverted abasic moiety; 3'-2'-inverted nucleotide moiety; 3'-2'-inverted abasic moiety; 1,4-butanediol phosphate; 3'-phosphoramidate; hexylphosphate; aminohexyl phosphate; 3'-phosphate; 3'-phosphorothioate; phosphorodithioate; or bridging or non-bridging methylphosphonate moiety. Non-limiting examples of cap moieties are shown in FIG. 10.

[0318] Non-limiting examples of the 3'-cap include, but are not limited to, glyceryl, inverted deoxy abasic residue (moiety), 4',5'-methylene nucleotide; 1-(beta-D-erythrofuranosyl) nucleotide; 4'-thio nucleotide, carbocyclic nucleotide; 5'-amino-alkyl phosphate; 1,3-diamino-2-propyl phosphate; 3-aminopropyl phosphate; 6-aminohexyl phosphate; 1,2-aminododecyl phosphate; hydroxypropyl phosphate; 1,5-anhydrohexitol nucleotide; L-nucleotide; alpha-nucleotide; modified base nucleotide; phosphorodithioate; threo-pentofuranosyl nucleotide; acyclic 3',4'-seco nucleotide; 3,4-dihydroxybutyl nucleotide; 3,5-dihydroxypentyl nucleotide, 5'-5'-inverted nucleotide moiety; 5'-5'-inverted abasic moiety; 5'-phosphoramidate; 5'-phosphorothioate; 1,4-butanediol phosphate; 5'-amino; bridging and/or non-bridging 5'-phosphoramidate, phosphorothioate and/or phosphorodithioate, bridging or non bridging methylphosphonate and 5'-mercapto moieties (for more details see Beaucage and Iyer, 1993, Tetrahedron 49, 1925; incorporated by reference herein).

[0319] By the term "non-nucleotide" is meant any group or compound which can be incorporated into a nucleic acid chain in the place of one or more nucleotide units, including either sugar and/or phosphate substitutions, and allows the remaining bases to exhibit their enzymatic activity. The group or compound is abasic in that it does not contain a commonly recognized nucleotide base, such as adenosine, guanine, cytosine, uracil or thymine and therefore lacks a base at the 1'-position.

[0320] An "alkyl" group refers to a saturated aliphatic hydrocarbon, including straight-chain, branched-chain, and cyclic alkyl groups. Preferably, the alkyl group has 1 to 12 carbons. More preferably, it is a lower alkyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkyl group can be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, .dbd.O, .dbd.S, NO.sub.2 or N(CH.sub.3).sub.2, amino, or SH. The term also includes alkenyl groups that are unsaturated hydrocarbon groups containing at least one carbon-carbon double bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkenyl group has 1 to 12 carbons. More preferably, it is a lower alkenyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkenyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, .dbd.O, .dbd.S, NO.sub.2, halogen, N(CH.sub.3).sub.2, amino, or SH. The term "alkyl" also includes alkynyl groups that have an unsaturated hydrocarbon group containing at least one carbon-carbon triple bond, including straight-chain, branched-chain, and cyclic groups. Preferably, the alkynyl group has 1 to 12 carbons. More preferably, it is a lower alkynyl of from 1 to 7 carbons, more preferably 1 to 4 carbons. The alkynyl group may be substituted or unsubstituted. When substituted the substituted group(s) is preferably, hydroxyl, cyano, alkoxy, .dbd.O, .dbd.S, NO.sub.2 or N(CH.sub.3).sub.2, amino or SH.

[0321] Such alkyl groups can also include aryl, alkylaryl, carbocyclic aryl, heterocyclic aryl, amide and ester groups. An "aryl" group refers to an aromatic group that has at least one ring having a conjugated pi electron system and includes carbocyclic aryl, heterocyclic aryl and biaryl groups, all of which may be optionally substituted. The preferred substituent(s) of aryl groups are halogen, trihalomethyl, hydroxyl, SH, OH, cyano, alkoxy, alkyl, alkenyl, alkynyl, and amino groups. An "alkylaryl" group refers to an alkyl group (as described above) covalently joined to an aryl group (as described above). Carbocyclic aryl groups are groups wherein the ring atoms on the aromatic ring are all carbon atoms. The carbon atoms are optionally substituted. Heterocyclic aryl groups are groups having from 1 to 3 heteroatoms as ring atoms in the aromatic ring and the remainder of the ring atoms are carbon atoms. Suitable heteroatoms include oxygen, sulfur, and nitrogen, and include furanyl, thienyl, pyridyl, pyrrolyl, N-lower alkyl pyrrolo, pyrimidyl, pyrazinyl, imidazolyl and the like, all optionally substituted. An "amide" refers to an --C(O)--NH--R, where R is either alkyl, aryl, alkylaryl or hydrogen. An "ester" refers to an --C(O)--OR', where R is either alkyl, aryl, alkylaryl or hydrogen.

[0322] By "nucleotide" as used herein is as recognized in the art to include natural bases (standard), and modified bases well known in the art. Such bases are generally located at the 1' position of a nucleotide sugar moiety. Nucleotides generally comprise a base, sugar and a phosphate group. The nucleotides can be unmodified or modified at the sugar, phosphate and/or base moiety, (also referred to interchangeably as nucleotide analogs, modified nucleotides, non-natural nucleotides, non-standard nucleotides and other; see, for example, Usman and McSwiggen, supra; Eckstein et al., International PCT Publication No. WO 92/07065; Usman et al., International PCT Publication No. WO 93/15187; Uhlman & Peyman, supra, all are hereby incorporated by reference herein). There are several examples of modified nucleic acid bases known in the art as summarized by Limbach et al., 1994, Nucleic Acids Res. 22, 2183. Some of the non-limiting examples of base modifications that can be introduced into nucleic acid molecules include, inosine, purine, pyridin-4-one, pyridin-2-one, phenyl, pseudouracil, 2, 4, 6-trimethoxy benzene, 3-methyl uracil, dihydrouridine, naphthyl, aminophenyl, 5-alkylcytidines (e.g., 5-methylcytidine), 5-alkyluridines (e.g., ribothymidine), 5-halouridine (e.g., 5-bromouridine) or 6-azapyrimidines or 6-alkylpyrimidines (e.g. 6-methyluridine), propyne, and others (Burgin et al., 1996, Biochemistry, 35, 14090; Uhlman & Peyman, supra). By "modified bases" in this aspect is meant nucleotide bases other than adenine, guanine, cytosine and uracil at 1' position or their equivalents.

[0323] In one embodiment, the invention features modified siNA molecules, with phosphate backbone modifications comprising one or more phosphorothioate, phosphorodithioate, methylphosphonate, phosphotriester, morpholino, amidate carbamate, carboxymethyl, acetamidate, polyamide, sulfonate, sulfonamide, sulfamate, formacetal, thioformacetal, and/or alkylsilyl, substitutions. For a review of oligonucleotide backbone modifications, see Hunziker and Leumann, 1995, Nucleic Acid Analogues: Synthesis and Properties, in Modern Synthetic Methods, VCH, 331-417, and Mesmaeker et al., 1994, Novel Backbone Replacements for Oligonucleotides, in Carbohydrate Modifications in Antisense Research, ACS, 24-39.

[0324] By "abasic" is meant sugar moieties lacking a base or having other chemical groups in place of a base at the 1' position, see for example Adamic et al., U.S. Pat. No. 5,998,203.

[0325] By "unmodified nucleoside" is meant one of the bases adenine, cytosine, guanine, thymine, or uracil joined to the 1' carbon of .beta.-D-ribo-furanose.

[0326] By "modified nucleoside" is meant any nucleotide base which contains a modification in the chemical structure of an unmodified nucleotide base, sugar and/or phosphate. Non-limiting examples of modified nucleotides are shown by Formulae I-VII and/or other modifications described herein.

[0327] In connection with 2'-modified nucleotides as described for the present invention, by "amino" is meant 2'-NH.sub.2 or 2'-O--NH.sub.2, which can be modified or unmodified. Such modified groups are described, for example, in Eckstein et al., U.S. Pat. No. 5,672,695 and Matulic-Adamic et al., U.S. Pat. No. 6,248,878, which are both incorporated by reference in their entireties.

[0328] Various modifications to nucleic acid siNA structure can be made to enhance the utility of these molecules. Such modifications will enhance shelf-life, half-life in vitro, stability, and ease of introduction of such oligonucleotides to the target site, e.g., to enhance penetration of cellular membranes, and confer the ability to recognize and bind to targeted cells.

Administration of Nucleic Acid Molecules

[0329] A siNA molecule of the invention can be adapted for use to prevent or treat cancer, leukemia, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and/or inflammatory and proliferative diseases, traits, conditions and/or disorders, and/or any other trait, disease, disorder or condition that is related to or will respond to the levels of PDGF and/or PDGFr in a cell or tissue, alone or in combination with other therapies. For example, a siNA molecule can comprise a delivery vehicle, including liposomes, for administration to a subject, carriers and diluents and their salts, and/or can be present in pharmaceutically acceptable formulations. Methods for the delivery of nucleic acid molecules are described in Akhtar et al., 1992, Trends Cell Bio., 2, 139; Delivery Strategies for Antisense Oligonucleotide Therapeutics, ed. Akhtar, 1995, Maurer et al., 1999, Mol. Membr. Biol., 16, 129-140; Hofland and Huang, 1999, Handb. Exp. Pharmacol., 137, 165-192; and Lee et al., 2000, ACS Symp. Ser., 752, 184-192, all of which are incorporated herein by reference. Beigelman et al., U.S. Pat. No. 6,395,713 and Sullivan et al., PCT WO 94/02595 further describe the general methods for delivery of nucleic acid molecules. These protocols can be utilized for the delivery of virtually any nucleic acid molecule. Nucleic acid molecules can be administered to cells by a variety of methods known to those of skill in the art, including, but not restricted to, encapsulation in liposomes, by iontophoresis, or by incorporation into other vehicles, such as biodegradable polymers, hydrogels, cyclodextrins (see for example Gonzalez et al., 1999, Bioconjugate Chem., 10, 1068-1074; Wang et al., International PCT publication Nos. WO 03/47518 and WO 03/46185), poly(lactic-co-glycolic)acid (PLGA) and PLCA microspheres (see for example U.S. Pat. No. 6,447,796 and US Patent Application Publication No. US 2002130430), biodegradable nanocapsules, and bioadhesive microspheres, or by proteinaceous vectors (O'Hare and Normand, International PCT Publication No. WO 00/53722). Alternatively, the nucleic acid/vehicle combination is locally delivered by direct injection or by use of an infusion pump. Direct injection of the nucleic acid molecules of the invention, whether subcutaneous, intramuscular, or intradermal, can take place using standard needle and syringe methodologies, or by needle-free technologies such as those described in Conry et al., 1999, Clin. Cancer Res., 5, 2330-2337 and Barry et al., International PCT Publication No. WO 99/31262. The molecules of the instant invention can be used as pharmaceutical agents. Pharmaceutical agents prevent, modulate the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state in a subject.

[0330] In another embodiment, the nucleic acid molecules of the invention can also be formulated or complexed with polyethyleneimine and derivatives thereof, such as polyethyleneimine-polyethyleneglycol-N-acetylgalactosamine (PEI-PEG-GAL) or polyethyleneimine-polyethyleneglycol-tri-N-acetylgalactosamine (PEI-PEG-triGAL) derivatives. In one embodiment, the nucleic acid molecules of the invention are formulated as described in United States Patent Application Publication No. 20030077829, incorporated by reference herein in its entirety.

[0331] In one embodiment, a siNA molecule of the invention is complexed with membrane disruptive agents such as those described in U.S. Patent Application Publication No. 20010007666, incorporated by reference herein in its entirety including the drawings. In another embodiment, the membrane disruptive agent or agents and the siNA molecule are also complexed with a cationic lipid or helper lipid molecule, such as those lipids described in U.S. Pat. No. 6,235,310, incorporated by reference herein in its entirety including the drawings.

[0332] In one embodiment, a siNA molecule of the invention is complexed with delivery systems as described in U.S. Patent Application Publication No. 2003077829 and International PCT Publication Nos. WO 00/03683 and WO 02/087541, all incorporated by reference herein in their entirety including the drawings.

[0333] In one embodiment, the nucleic acid molecules of the invention are administered via pulmonary delivery, such as by inhalation of an aerosol or spray dried formulation administered by an inhalation device or nebulizer, providing rapid local uptake of the nucleic acid molecules into relevant pulmonary tissues. Solid particulate compositions containing respirable dry particles of micronized nucleic acid compositions can be prepared by grinding dried or lyophilized nucleic acid compositions, and then passing the micronized composition through, for example, a 400 mesh screen to break up or separate out large agglomerates. A solid particulate composition comprising the nucleic acid compositions of the invention can optionally contain a dispersant which serves to facilitate the formation of an aerosol as well as other therapeutic compounds. A suitable dispersant is lactose, which can be blended with the nucleic acid compound in any suitable ratio, such as a 1 to 1 ratio by weight.

[0334] Aerosols of liquid particles comprising a nucleic acid composition of the invention can be produced by any suitable means, such as with a nebulizer (see for example U.S. Pat. No. 4,501,729). Nebulizers are commercially available devices which transform solutions or suspensions of an active ingredient into a therapeutic aerosol mist either by means of acceleration of a compressed gas, typically air or oxygen, through a narrow venturi orifice or by means of ultrasonic agitation. Suitable formulations for use in nebulizers comprise the active ingredient in a liquid carrier in an amount of up to 40% w/w preferably less than 20% w/w of the formulation. The carrier is typically water or a dilute aqueous alcoholic solution, preferably made isotonic with body fluids by the addition of, for example, sodium chloride or other suitable salts. Optional additives include preservatives if the formulation is not prepared sterile, for example, methyl hydroxybenzoate, anti-oxidants, flavorings, volatile oils, buffering agents and emulsifiers and other formulation surfactants. The aerosols of solid particles comprising the active composition and surfactant can likewise be produced with any solid particulate aerosol generator. Aerosol generators for administering solid particulate therapeutics to a subject produce particles which are respirable, as explained above, and generate a volume of aerosol containing a predetermined metered dose of a therapeutic composition at a rate suitable for human administration. One illustrative type of solid particulate aerosol generator is an insufflator. Suitable formulations for administration by insufflation include finely comminuted powders which can be delivered by means of an insufflator. In the insufflator, the powder, e.g., a metered dose thereof effective to carry out the treatments described herein, is contained in capsules or cartridges, typically made of gelatin or plastic, which are either pierced or opened in situ and the powder delivered by air drawn through the device upon inhalation or by means of a manually-operated pump. The powder employed in the insufflator consists either solely of the active ingredient or of a powder blend comprising the active ingredient, a suitable powder diluent, such as lactose, and an optional surfactant. The active ingredient typically comprises from 0.1 to 100 w/w of the formulation. A second type of illustrative aerosol generator comprises a metered dose inhaler. Metered dose inhalers are pressurized aerosol dispensers, typically containing a suspension or solution formulation of the active ingredient in a liquified propellant. During use these devices discharge the formulation through a valve adapted to deliver a metered volume to produce a fine particle spray containing the active ingredient. Suitable propellants include certain chlorofluorocarbon compounds, for example, dichlorodifluoromethane, trichlorofluoromethane, dichlorotetrafluoroethane and mixtures thereof. The formulation can additionally contain one or more co-solvents, for example, ethanol, emulsifiers and other formulation surfactants, such as oleic acid or sorbitan trioleate, anti-oxidants and suitable flavoring agents. Other methods for pulmonary delivery are described in, for example US Patent Application No. 20040037780, and U.S. Pat. Nos. 6,592,904; 6,582,728; 6,565,885.

[0335] In one embodiment, nucleic acid molecules of the invention are administered to the central nervous system (CNS) or peripheral nervous system (PNS). Experiments have demonstrated the efficient in vivo uptake of nucleic acids by neurons. As an example of local administration of nucleic acids to nerve cells, Sommer et al., 1998, Antisense Nuc. Acid Drug Dev., 8, 75, describe a study in which a 15 mer phosphorothioate antisense nucleic acid molecule to c-fos is administered to rats via microinjection into the brain. Antisense molecules labeled with tetramethylrhodamine-isothiocyanate (TRITC) or fluorescein isothiocyanate (FITC) were taken up by exclusively by neurons thirty minutes post-injection. A diffuse cytoplasmic staining and nuclear staining was observed in these cells. As an example of systemic administration of nucleic acid to nerve cells, Epa et al., 2000, Antisense Nuc. Acid Drug Dev., 10, 469, describe an in vivo mouse study in which beta-cyclodextrin-adamantane-oligonucleotide conjugates were used to target the p75 neurotrophin receptor in neuronally differentiated PC12 cells. Following a two week course of IP administration, pronounced uptake of p75 neurotrophin receptor antisense was observed in dorsal root ganglion (DRG) cells. In addition, a marked and consistent down-regulation of p75 was observed in DRG neurons. Additional approaches to the targeting of nucleic acid to neurons are described in Broaddus et al., 1998, J. Neurosurg., 88(4), 734; Karle et al., 1997, Eur. J. Pharmocol., 340(2/3), 153; Bannai et al., 1998, Brain Research, 784(1,2), 304; Rajakumar et al., 1997, Synapse, 26(3), 199; Wu-pong et al., 1999, BioPharm, 12(1), 32; Bannai et al., 1998, Brain Res. Protoc., 3(1), 83; Simantov et al., 1996, Neuroscience, 74(1), 39. Nucleic acid molecules of the invention are therefore amenable to delivery to and uptake by cells in the CNS and/or PNS.

[0336] The delivery of nucleic acid molecules of the invention to the CNS is provided by a variety of different strategies. Traditional approaches to CNS delivery that can be used include, but are not limited to, intrathecal and intracerebroventricular administration, implantation of catheters and pumps, direct injection or perfusion at the site of injury or lesion, injection into the brain arterial system, or by chemical or osmotic opening of the blood-brain barrier. Other approaches can include the use of various transport and carrier systems, for example though the use of conjugates and biodegradable polymers. Furthermore, gene therapy approaches, for example as described in Kaplitt et al., U.S. Pat. No. 6,180,613 and Davidson, WO 04/013280, can be used to express nucleic acid molecules in the CNS.

[0337] In one embodiment, delivery systems of the invention include, for example, aqueous and nonaqueous gels, creams, multiple emulsions, microemulsions, liposomes, ointments, aqueous and nonaqueous solutions, lotions, aerosols, hydrocarbon bases and powders, and can contain excipients such as solubilizers, permeation enhancers (e.g., fatty acids, fatty acid esters, fatty alcohols and amino acids), and hydrophilic polymers (e.g., polycarbophil and polyvinylpyrolidone). In one embodiment, the pharmaceutically acceptable carrier is a liposome or a transdermal enhancer. Examples of liposomes which can be used in this invention include the following: (1) CellFectin, 1:1.5 (M/M) liposome formulation of the cationic lipid N,NI,NII,NIII-tetramethyl-N,NI,NII,NIII-tetrapalmit-y-spermine and dioleoyl phosphatidylethanolamine (DOPE) (GIBCO BRL); (2) Cytofectin GSV, 2:1 (M/M) liposome formulation of a cationic lipid and DOPE (Glen Research); (3) DOTAP (N-[1-(2,3-dioleoyloxy)-N,N,N-tri-methyl-ammoniummethylsulfate) (Boehringer Manheim); and (4) Lipofectamine, 3:1 (M/M) liposome formulation of the polycationic lipid DOSPA and the neutral lipid DOPE (GIBCO BRL).

[0338] In one embodiment, delivery systems of the invention include patches, tablets, suppositories, pessaries, gels and creams, and can contain excipients such as solubilizers and enhancers (e.g., propylene glycol, bile salts and amino acids), and other vehicles (e.g., polyethylene glycol, fatty acid esters and derivatives, and hydrophilic polymers such as hydroxypropylmethylcellulose and hyaluronic acid).

[0339] In one embodiment, siNA molecules of the invention are formulated or complexed with polyethylenimine (e.g., linear or branched PEI) and/or polyethylenimine derivatives, including for example grafted PEIs such as galactose PEI, cholesterol PEI, antibody derivatized PEI, and polyethylene glycol PEI (PEG-PEI) derivatives thereof (see for example Ogris et al., 2001, AAPA PharmSci, 3, 1-11; Furgeson et al., 2003, Bioconjugate Chem., 14, 840-847; Kunath et al., 2002, Pharmaceutical Research, 19, 810-817; Choi et al., 2001, Bull. Korean Chem. Soc., 22, 46-52; Bettinger et al., 1999, Bioconjugate Chem., 10, 558-561; Peterson et al., 2002, Bioconjugate Chem., 13, 845-854; Erbacher et al., 1999, Journal of Gene Medicine Preprint, 1, 1-18; Godbey et al., 1999., PNAS USA, 96, 5177-5181; Godbey et al., 1999, Journal of Controlled Release, 60, 149-160; Diebold et al., 1999, Journal of Biological Chemistry, 274, 19087-19094; Thomas and Klibanov, 2002, PNAS USA, 99, 14640-14645; and Sagara, U.S. Pat. No. 6,586,524, incorporated by reference herein.

[0340] In one embodiment, a siNA molecule of the invention comprises a bioconjugate, for example a nucleic acid conjugate as described in Vargeese et al., U.S. Ser. No. 10/427,160, filed Apr. 30, 2003; U.S. Pat. No. 6,528,631; U.S. Pat. No. 6,335,434; U.S. Pat. No. 6,235,886; U.S. Pat. No. 6,153,737; U.S. Pat. No. 5,214,136; U.S. Pat. No. 5,138,045, all incorporated by reference herein.

[0341] Thus, the invention features a pharmaceutical composition comprising one or more nucleic acid(s) of the invention in an acceptable carrier, such as a stabilizer, buffer, and the like. The polynucleotides of the invention can be administered (e.g., RNA, DNA or protein) and introduced to a subject by any standard means, with or without stabilizers, buffers, and the like, to form a pharmaceutical composition. When it is desired to use a liposome delivery mechanism, standard protocols for formation of liposomes can be followed. The compositions of the present invention can also be formulated and used as creams, gels, sprays, oils and other suitable compositions for topical, dermal, or transdermal administration as is known in the art.

[0342] The present invention also includes pharmaceutically acceptable formulations of the compounds described. These formulations include salts of the above compounds, e.g., acid addition salts, for example, salts of hydrochloric, hydrobromic, acetic acid, and benzene sulfonic acid.

[0343] A pharmacological composition or formulation refers to a composition or formulation in a form suitable for administration, e.g., systemic or local administration, into a cell or subject, including for example a human. Suitable forms, in part, depend upon the use or the route of entry, for example oral, transdermal, or by injection. Such forms should not prevent the composition or formulation from reaching a target cell (i.e., a cell to which the negatively charged nucleic acid is desirable for delivery). For example, pharmacological compositions injected into the blood stream should be soluble. Other factors are known in the art, and include considerations such as toxicity and forms that prevent the composition or formulation from exerting its effect.

[0344] In one embodiment, siNA molecules of the invention are administered to a subject by systemic administration in a pharmaceutically acceptable composition or formulation. By "systemic administration" is meant in vivo systemic absorption or accumulation of drugs in the blood stream followed by distribution throughout the entire body. Administration routes that lead to systemic absorption include, without limitation: intravenous, subcutaneous, intraperitoneal, inhalation, oral, intrapulmonary and intramuscular. Each of these administration routes exposes the siNA molecules of the invention to an accessible diseased tissue. The rate of entry of a drug into the circulation has been shown to be a function of molecular weight or size. The use of a liposome or other drug carrier comprising the compounds of the instant invention can potentially localize the drug, for example, in certain tissue types, such as the tissues of the reticular endothelial system (RES). A liposome formulation that can facilitate the association of drug with the surface of cells, such as, lymphocytes and macrophages is also useful. This approach can provide enhanced delivery of the drug to target cells by taking advantage of the specificity of macrophage and lymphocyte immune recognition of abnormal cells.

[0345] By "pharmaceutically acceptable formulation" or "pharmaceutically acceptable composition" is meant, a composition or formulation that allows for the effective distribution of the nucleic acid molecules of the instant invention in the physical location most suitable for their desired activity. Non-limiting examples of agents suitable for formulation with the nucleic acid molecules of the instant invention include: P-glycoprotein inhibitors (such as Pluronic P85); biodegradable polymers, such as poly (DL-lactide-coglycolide) microspheres for sustained release delivery (Emerich, D F et al, 1999, Cell Transplant, 8, 47-58); and loaded nanoparticles, such as those made of polybutylcyanoacrylate. Other non-limiting examples of delivery strategies for the nucleic acid molecules of the instant invention include material described in Boado et al., 1998, J. Pharm. Sci., 87, 1308-1315; Tyler et al., 1999, FEBS Lett., 421, 280-284; Pardridge et al., 1995, PNAS USA., 92, 5592-5596; Boado, 1995, Adv. Drug Delivery Rev., 15, 73-107; Aldrian-Herrada et al., 1998, Nucleic Acids Res., 26, 4910-4916; and Tyler et al., 1999, PNAS USA., 96, 7053-7058.

[0346] The invention also features the use of the composition comprising surface-modified liposomes containing poly (ethylene glycol) lipids (PEG-modified, or long-circulating liposomes or stealth liposomes). These formulations offer a method for increasing the accumulation of drugs in target tissues. This class of drug carriers resists opsonization and elimination by the mononuclear phagocytic system (MPS or RES), thereby enabling longer blood circulation times and enhanced tissue exposure for the encapsulated drug (Lasic et al. Chem. Rev. 1995, 95, 2601-2627; Ishiwata et al., Chem. Pharm. Bull. 1995, 43, 1005-1011). Such liposomes have been shown to accumulate selectively in tumors, presumably by extravasation and capture in the neovascularized target tissues (Lasic et al., Science 1995, 267, 1275-1276; Oku et al., 1995, Biochim. Biophys. Acta, 1238, 86-90). The long-circulating liposomes enhance the pharmacokinetics and pharmacodynamics of DNA and RNA, particularly compared to conventional cationic liposomes which are known to accumulate in tissues of the MPS (Liu et al., J. Biol. Chem. 1995, 42, 24864-24870; Choi et al., International PCT Publication No. WO 96/10391; Ansell et al., International PCT Publication No. WO 96/10390; Holland et al., International PCT Publication No. WO 96/10392). Long-circulating liposomes are also likely to protect drugs from nuclease degradation to a greater extent compared to cationic liposomes, based on their ability to avoid accumulation in metabolically aggressive MPS tissues such as the liver and spleen.

[0347] The present invention also includes compositions prepared for storage or administration that include a pharmaceutically effective amount of the desired compounds in a pharmaceutically acceptable carrier or diluent. Acceptable carriers or diluents for therapeutic use are well known in the pharmaceutical art, and are described, for example, in Remington's Pharmaceutical Sciences, Mack Publishing Co. (A. R. Gennaro edit. 1985), hereby incorporated by reference herein. For example, preservatives, stabilizers, dyes and flavoring agents can be provided. These include sodium benzoate, sorbic acid and esters of p-hydroxybenzoic acid. In addition, antioxidants and suspending agents can be used.

[0348] A pharmaceutically effective dose is that dose required to prevent, inhibit the occurrence, or treat (alleviate a symptom to some extent, preferably all of the symptoms) of a disease state. The pharmaceutically effective dose depends on the type of disease, the composition used, the route of administration, the type of mammal being treated, the physical characteristics of the specific mammal under consideration, concurrent medication, and other factors that those skilled in the medical arts will recognize. Generally, an amount between 0.1 mg/kg and 100 mg/kg body weight/day of active ingredients is administered dependent upon potency of the negatively charged polymer.

[0349] The nucleic acid molecules of the invention and formulations thereof can be administered orally, topically, parenterally, by inhalation or spray, or rectally in dosage unit formulations containing conventional non-toxic pharmaceutically acceptable carriers, adjuvants and/or vehicles. The term parenteral as used herein includes percutaneous, subcutaneous, intravascular (e.g., intravenous), intramuscular, or intrathecal injection or infusion techniques and the like. In addition, there is provided a pharmaceutical formulation comprising a nucleic acid molecule of the invention and a pharmaceutically acceptable carrier. One or more nucleic acid molecules of the invention can be present in association with one or more non-toxic pharmaceutically acceptable carriers and/or diluents and/or adjuvants, and if desired other active ingredients. The pharmaceutical compositions containing nucleic acid molecules of the invention can be in a form suitable for oral use, for example, as tablets, troches, lozenges, aqueous or oily suspensions, dispersible powders or granules, emulsion, hard or soft capsules, or syrups or elixirs.

[0350] Compositions intended for oral use can be prepared according to any method known to the art for the manufacture of pharmaceutical compositions and such compositions can contain one or more such sweetening agents, flavoring agents, coloring agents or preservative agents in order to provide pharmaceutically elegant and palatable preparations. Tablets contain the active ingredient in admixture with non-toxic pharmaceutically acceptable excipients that are suitable for the manufacture of tablets. These excipients can be, for example, inert diluents; such as calcium carbonate, sodium carbonate, lactose, calcium phosphate or sodium phosphate; granulating and disintegrating agents, for example, corn starch, or alginic acid; binding agents, for example starch, gelatin or acacia; and lubricating agents, for example magnesium stearate, stearic acid or talc. The tablets can be uncoated or they can be coated by known techniques. In some cases such coatings can be prepared by known techniques to delay disintegration and absorption in the gastrointestinal tract and thereby provide a sustained action over a longer period. For example, a time delay material such as glyceryl monosterate or glyceryl distearate can be employed.

[0351] Formulations for oral use can also be presented as hard gelatin capsules wherein the active ingredient is mixed with an inert solid diluent, for example, calcium carbonate, calcium phosphate or kaolin, or as soft gelatin capsules wherein the active ingredient is mixed with water or an oil medium, for example peanut oil, liquid paraffin or olive oil.

[0352] Aqueous suspensions contain the active materials in a mixture with excipients suitable for the manufacture of aqueous suspensions. Such excipients are suspending agents, for example sodium carboxymethylcellulose, methylcellulose, hydropropyl-methylcellulose, sodium alginate, polyvinylpyrrolidone, gum tragacanth and gum acacia; dispersing or wetting agents can be a naturally-occurring phosphatide, for example, lecithin, or condensation products of an alkylene oxide with fatty acids, for example polyoxyethylene stearate, or condensation products of ethylene oxide with long chain aliphatic alcohols, for example heptadecaethyleneoxycetanol, or condensation products of ethylene oxide with partial esters derived from fatty acids and a hexitol such as polyoxyethylene sorbitol monooleate, or condensation products of ethylene oxide with partial esters derived from fatty acids and hexitol anhydrides, for example polyethylene sorbitan monooleate. The aqueous suspensions can also contain one or more preservatives, for example ethyl, or n-propyl p-hydroxybenzoate, one or more coloring agents, one or more flavoring agents, and one or more sweetening agents, such as sucrose or saccharin.

[0353] Oily suspensions can be formulated by suspending the active ingredients in a vegetable oil, for example arachis oil, olive oil, sesame oil or coconut oil, or in a mineral oil such as liquid paraffin. The oily suspensions can contain a thickening agent, for example beeswax, hard paraffin or cetyl alcohol. Sweetening agents and flavoring agents can be added to provide palatable oral preparations. These compositions can be preserved by the addition of an anti-oxidant such as ascorbic acid

[0354] Dispersible powders and granules suitable for preparation of an aqueous suspension by the addition of water provide the active ingredient in admixture with a dispersing or wetting agent, suspending agent and one or more preservatives. Suitable dispersing or wetting agents or suspending agents are exemplified by those already mentioned above. Additional excipients, for example sweetening, flavoring and coloring agents, can also be present.

[0355] Pharmaceutical compositions of the invention can also be in the form of oil-in-water emulsions. The oily phase can be a vegetable oil or a mineral oil or mixtures of these. Suitable emulsifying agents can be naturally-occurring gums, for example gum acacia or gum tragacanth, naturally-occurring phosphatides, for example soy bean, lecithin, and esters or partial esters derived from fatty acids and hexitol, anhydrides, for example sorbitan monooleate, and condensation products of the said partial esters with ethylene oxide, for example polyoxyethylene sorbitan monooleate. The emulsions can also contain sweetening and flavoring agents.

[0356] Syrups and elixirs can be formulated with sweetening agents, for example glycerol, propylene glycol, sorbitol, glucose or sucrose. Such formulations can also contain a demulcent, a preservative and flavoring and coloring agents. The pharmaceutical compositions can be in the form of a sterile injectable aqueous or oleaginous suspension. This suspension can be formulated according to the known art using those suitable dispersing or wetting agents and suspending agents that have been mentioned above. The sterile injectable preparation can also be a sterile injectable solution or suspension in a non-toxic parentally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that can be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose, any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid find use in the preparation of injectables.

[0357] The nucleic acid molecules of the invention can also be administered in the form of suppositories, e.g., for rectal administration of the drug. These compositions can be prepared by mixing the drug with a suitable non-irritating excipient that is solid at ordinary temperatures but liquid at the rectal temperature and will therefore melt in the rectum to release the drug. Such materials include cocoa butter and polyethylene glycols.

[0358] Nucleic acid molecules of the invention can be administered parenterally in a sterile medium. The drug, depending on the vehicle and concentration used, can either be suspended or dissolved in the vehicle. Advantageously, adjuvants such as local anesthetics, preservatives and buffering agents can be dissolved in the vehicle.

[0359] Dosage levels of the order of from about 0.1 mg to about 140 mg per kilogram of body weight per day are useful in the treatment of the above-indicated conditions (about 0.5 mg to about 7 g per subject per day). The amount of active ingredient that can be combined with the carrier materials to produce a single dosage form varies depending upon the host treated and the particular mode of administration. Dosage unit forms generally contain between from about 1 mg to about 500 mg of an active ingredient.

[0360] It is understood that the specific dose level for any particular subject depends upon a variety of factors including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, route of administration, and rate of excretion, drug combination and the severity of the particular disease undergoing therapy.

[0361] For administration to non-human animals, the composition can also be added to the animal feed or drinking water. It can be convenient to formulate the animal feed and drinking water compositions so that the animal takes in a therapeutically appropriate quantity of the composition along with its diet. It can also be convenient to present the composition as a premix for addition to the feed or drinking water.

[0362] The nucleic acid molecules of the present invention can also be administered to a subject in combination with other therapeutic compounds to increase the overall therapeutic effect. The use of multiple compounds to treat an indication can increase the beneficial effects while reducing the presence of side effects.

[0363] In one embodiment, the invention comprises compositions suitable for administering nucleic acid molecules of the invention to specific cell types. For example, the asialoglycoprotein receptor (ASGPr) (Wu and Wu, 1987, J. Biol. Chem. 262, 4429-4432) is unique to hepatocytes and binds branched galactose-terminal glycoproteins, such as asialoorosomucoid (ASOR). In another example, the folate receptor is overexpressed in many cancer cells. Binding of such glycoproteins, synthetic glycoconjugates, or folates to the receptor takes place with an affinity that strongly depends on the degree of branching of the oligosaccharide chain, for example, triatennary structures are bound with greater affinity than biatenarry or monoatennary chains (Baenziger and Fiete, 1980, Cell, 22, 611-620; Connolly et al., 1982, J. Biol. Chem., 257, 939-945). Lee and Lee, 1987, Glycoconjugate J., 4, 317-328, obtained this high specificity through the use of N-acetyl-D-galactosamine as the carbohydrate moiety, which has higher affinity for the receptor, compared to galactose. This "clustering effect" has also been described for the binding and uptake of mannosyl-terminating glycoproteins or glycoconjugates (Ponpipom et al., 1981, J. Med. Chem., 24, 1388-1395). The use of galactose, galactosamine, or folate based conjugates to transport exogenous compounds across cell membranes can provide a targeted delivery approach to, for example, the treatment of liver disease, cancers of the liver, or other cancers. The use of bioconjugates can also provide a reduction in the required dose of therapeutic compounds required for treatment. Furthermore, therapeutic bioavailability, pharmacodynamics, and pharmacokinetic parameters can be modulated through the use of nucleic acid bioconjugates of the invention. Non-limiting examples of such bioconjugates are described in Vargeese et al., U.S. Ser. No. 10/201,394, filed Aug. 13, 2001; and Matulic-Adamic et al., U.S. Ser. No. 60/362,016, filed Mar. 6, 2002.

[0364] Alternatively, certain siNA molecules of the instant invention can be expressed within cells from eukaryotic promoters (e.g., Izant and Weintraub, 1985, Science, 229, 345; McGarry and Lindquist, 1986, Proc. Natl. Acad. Sci., USA 83, 399; Scanlon et al., 1991, Proc. Natl. Acad. Sci. USA, 88, 10591-5; Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Dropulic et al., 1992, J. Virol., 66, 1432-41; Weerasinghe et al., 1991, J. Virol., 65, 5531-4; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Sarver et al., 1990 Science, 247, 1222-1225; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Good et al., 1997, Gene Therapy, 4, 45. Those skilled in the art realize that any nucleic acid can be expressed in eukaryotic cells from the appropriate DNA/RNA vector. The activity of such nucleic acids can be augmented by their release from the primary transcript by a enzymatic nucleic acid (Draper et al., PCT WO 93/23569, and Sullivan et al., PCT WO 94/02595; Ohkawa et al., 1992, Nucleic Acids Symp. Ser., 27, 15-6; Taira et al., 1991, Nucleic Acids Res., 19, 5125-30; Ventura et al., 1993, Nucleic Acids Res., 21, 3249-55; Chowrira et al., 1994, J. Biol. Chem., 269, 25856.

[0365] In another aspect of the invention, RNA molecules of the present invention can be expressed from transcription units (see for example Couture et al., 1996, TIG., 12, 510) inserted into DNA or RNA vectors. The recombinant vectors can be DNA plasmids or viral vectors. siNA expressing viral vectors can be constructed based on, but not limited to, adeno-associated virus, retrovirus, adenovirus, or alphavirus. In another embodiment, pol III based constructs are used to express nucleic acid molecules of the invention (see for example Thompson, U.S. Pats. Nos. 5,902,880 and 6,146,886). The recombinant vectors capable of expressing the siNA molecules can be delivered as described above, and persist in target cells. Alternatively, viral vectors can be used that provide for transient expression of nucleic acid molecules. Such vectors can be repeatedly administered as necessary. Once expressed, the siNA molecule interacts with the target mRNA and generates an RNAi response. Delivery of siNA molecule expressing vectors can be systemic, such as by intravenous or intramuscular administration, by administration to target cells ex-planted from a subject followed by reintroduction into the subject, or by any other means that would allow for introduction into the desired target cell (for a review see Couture et al., 1996, TIG., 12, 510).

[0366] In one aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one siNA molecule of the instant invention. The expression vector can encode one or both strands of a siNA duplex, or a single self-complementary strand that self hybridizes into a siNA duplex. The nucleic acid sequences encoding the siNA molecules of the instant invention can be operably linked in a manner that allows expression of the siNA molecule (see for example Paul et al., 2002, Nature Biotechnology, 19, 505; Miyagishi and Taira, 2002, Nature Biotechnology, 19, 497; Lee et al., 2002, Nature Biotechnology, 19, 500; and Novina et al., 2002, Nature Medicine, advance online publication doi:10.1038/nm725).

[0367] In another aspect, the invention features an expression vector comprising: a) a transcription initiation region (e.g., eukaryotic pol I, II or III initiation region); b) a transcription termination region (e.g., eukaryotic pol I, II or III termination region); and c) a nucleic acid sequence encoding at least one of the siNA molecules of the instant invention, wherein said sequence is operably linked to said initiation region and said termination region in a manner that allows expression and/or delivery of the siNA molecule. The vector can optionally include an open reading frame (ORF) for a protein operably linked on the 5' side or the 3'-side of the sequence encoding the siNA of the invention; and/or an intron (intervening sequences).

[0368] Transcription of the siNA molecule sequences can be driven from a promoter for eukaryotic RNA polymerase I (pol I), RNA polymerase II (pol II), or RNA polymerase III (pol III). Transcripts from pol II or pol III promoters are expressed at high levels in all cells; the levels of a given pol II promoter in a given cell type depends on the nature of the gene regulatory sequences (enhancers, silencers, etc.) present nearby. Prokaryotic RNA polymerase promoters are also used, providing that the prokaryotic RNA polymerase enzyme is expressed in the appropriate cells (Elroy-Stein and Moss, 1990, Proc. Natl. Acad. Sci. USA, 87, 6743-7; Gao and Huang 1993, Nucleic Acids Res., 21, 2867-72; Lieber et al., 1993, Methods Enzymol., 217, 47-66; Zhou et al., 1990, Mol. Cell. Biol., 10, 4529-37). Several investigators have demonstrated that nucleic acid molecules expressed from such promoters can function in mammalian cells (e.g. Kashani-Sabet et al., 1992, Antisense Res. Dev., 2, 3-15; Ojwang et al., 1992, Proc. Natl. Acad. Sci. USA, 89, 10802-6; Chen et al., 1992, Nucleic Acids Res., 20, 4581-9; Yu et al., 1993, Proc. Natl. Acad. Sci. USA, 90, 6340-4; L'Huillier et al., 1992, EMBO J., 11, 4411-8; Lisziewicz et al., 1993, Proc. Natl. Acad. Sci. U.S.A, 90, 8000-4; Thompson et al., 1995, Nucleic Acids Res., 23, 2259; Sullenger & Cech, 1993, Science, 262, 1566). More specifically, transcription units such as the ones derived from genes encoding U6 small nuclear (snRNA), transfer RNA (tRNA) and adenovirus VA RNA are useful in generating high concentrations of desired RNA molecules such as siNA in cells (Thompson et al., supra; Couture and Stinchcomb, 1996, supra; Noonberg et al., 1994, Nucleic Acid Res., 22, 2830; Noonberg et al., U.S. Pat. No. 5,624,803; Good et al., 1997, Gene Ther., 4, 45; Beigelman et al., International PCT Publication No. WO 96/18736. The above siNA transcription units can be incorporated into a variety of vectors for introduction into mammalian cells, including but not restricted to, plasmid DNA vectors, viral DNA vectors (such as adenovirus or adeno-associated virus vectors), or viral RNA vectors (such as retroviral or alphavirus vectors) (for a review see Couture and Stinchcomb, 1996, supra).

[0369] In another aspect the invention features an expression vector comprising a nucleic acid sequence encoding at least one of the siNA molecules of the invention in a manner that allows expression of that siNA molecule. The expression vector comprises in one embodiment; a) a transcription initiation region; b) a transcription termination region; and c) a nucleic acid sequence encoding at least one strand of the siNA molecule, wherein the sequence is operably linked to the initiation region and the termination region in a manner that allows expression and/or delivery of the siNA molecule.

[0370] In another embodiment the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an open reading frame; and d) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3'-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the open reading frame and the termination region in a manner that allows expression and/or delivery of the siNA molecule. In yet another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; and d) a nucleic acid sequence encoding at least one siNA molecule, wherein the sequence is operably linked to the initiation region, the intron and the termination region in a manner which allows expression and/or delivery of the nucleic acid molecule.

[0371] In another embodiment, the expression vector comprises: a) a transcription initiation region; b) a transcription termination region; c) an intron; d) an open reading frame; and e) a nucleic acid sequence encoding at least one strand of a siNA molecule, wherein the sequence is operably linked to the 3'-end of the open reading frame and wherein the sequence is operably linked to the initiation region, the intron, the open reading frame and the termination region in a manner which allows expression and/or delivery of the siNA molecule.

PDGF/PDGFr Biology and Biochemistry

[0372] The following discussion is adapted from R&D Systems Mini-Reviews and Tech Notes, Cytokine Mini-Reviews, Platelet Derived Growth Factor, Copyright .COPYRGT.2002 R&D Systems. Historically, it has been a goal of tissue culture researchers to identify substances that provide universal growth or maintenance factor characteristics for various cell lines and isolates. Early tissue culture work demonstrated the superiority of serum over plasma in stimulating the proliferation of fibroblasts in vitro. These observations suggested that a factor released from platelets during degranulation was probably responsible for the stimulatory activity. Subsequent investigations clearly demonstrated that a certain factor released from platelets upon clotting was capable of promoting the growth of various types of cells. This factor was subsequently purified from platelets and given the name platelet-derived growth factor (PDGF). PDGF is now known to be produced by a number of cell types besides platelets and it has been found to be a mitogen for almost all mesenchymally-derived cells, such as blood, muscle, bone/cartilage, and connective tissue cells.

[0373] Three forms of PDGF have been identified to date. Each form consists of a 30 kDa homo- or heterodimeric combination of two genetically distinct, but structurally related, polypeptide chains which are designated A and B chains, respectively. Although considerable work has been done on the primary structure of each of the chains of human PDGF, the process has been complicated by the fact that each is synthesized as a propeptide, that splice variants exist for the A chain, and that C-terminal proteolytic processing apparently occurs for the B chain and possibly the A chain as well.

[0374] The PDGF A chain is the product of a seven exon chromosomal 7 gene that gives rise to one of two distinct splice variants. The "long" variant, a prepropeptide of 211 amino acid residues, is synthesized with a signal peptide of 20 amino acid residues, a propeptide sequence of 66 amino acid residues, and a mature chain of 125 amino acid residues. In contrast, the "short" 196 amino acid residue variant shows a 20 amino acid residue signal sequence, a 66 amino acid residue propeptide, and a 16-18 kDa, 110 amino acid residue mature form. The difference between the long and short results from alternative exon usage, with the extended form utilizing exon 6 (18 amino acid residues), but not exon 7, and the short form utilizing exon 7 (3 amino acid residues), but not exon 6. The difference between exon 6 utilization and exon 7 utilization is not, however, limited to length. Within the 18 amino acid residues of exon 6 lies an approximately 10 amino acid residue sequence that signals cell retention. Failure to remove this carboxyterminal peptide results in a failure to release freely circulating PDGF. Retention under these circumstances implies binding to either cell-surface glycosaminoglycans or intercellular matrix. The short version contains no retention sequence and is secreted into the circulatory system. It is presently unclear whether any C-terminal processing of A chains occurs, but the short variant's 110 amino acid residue mature peptide terminates with an arginine residue. This suggests the possibility, as is the case for the B chain, of a carboxypeptidase-mediated C-terminal truncation to 109 amino acid residues with equilization of A and B chain lengths for dimerization. No definitive mechanism for C-terminus processing of the long form of the A chain has been elucidated and it is not presently clear if this form is secreted. One potential N-linked glycosylation site exists in the mature A chain, but not the B chain, and it is suggested to be utilized. Normal cells such as endothelial cell, macrophages, and fibroblasts are known to concurrently express both types of A chain, with the short version being the most abundant.

[0375] The PDGF B chain is the product of a six exon gene on chromosome 22. The B chain gene is known to be identical to the human c-sis gene, the normal human cell counterpart to the monkey v-sis (simian sarcoma) virus gene. The protein coded for by c-sis is a 27 kDa, 241 amino acid residue prepropeptide with a 20 amino acid residue signal sequence, 61 amino acid residue propeptide, and a 16 kDa, 160 amino acid residue "mature" polypeptide. C-terminal cleavage of the mature B chain is believed to occur, resulting in a final mature product of 12 kDa and 109 amino acid residues. This is proposed to occur in two stages with a trypsin-like cleavage of residues 111 to 160, followed by a carboxypeptidase cleavage of the remaining arginine at residue 110. As with the long form of chain A, a particular retention sequence approximately 10 amino acid residues in length has also been identified in the B chain C-terminus. Failure to remove this peptide also results in B chain glycosaminoglycan retention. Dimerization of the A and B chains involves two interchain disulfide bonds, and each chain overlaps the other with a 6 or 7 amino acid residue extension at either end. Within the 103 overlapping amino acid residues, the two chains exhibit about 50% sequence identity.

[0376] Cells known to express PDGF are diverse. Cells that are reported to express the A chain protein (both long and short variants) include fibroblasts, endothelial cells, osteoblasts, platelets, vascular smooth muscle cells, macrophages and Langerhans cells, and fetal fibroblasts. Cells producing B chain protein include fetal fibroblasts, endothelial cells, platelets, macrophages, neurons and breast ductal epithelium. A number of cell types have also been shown to express mRNA for the PDGF chains. In particular, A chain mRNA has been found in type I astrocytes, embryonic endodermal respiratory epithelium, renal mesangial cells, and osteoclasts and chrondrocytes, while B chain mRNA has been localized to embryonic endodermal respiratory epithelium, renal mesangial cells and osteoblasts.

[0377] As with many growth factors, PDGF is now considered to be a member of a larger family of factors. In addition to PDGF, this family includes the homodimeric factors VEGF (vascular endothelial growth factor) and PIGF (placental growth factor), VEGF/PIGF heterodimers, and CTGF (connective tissue growth factor), a PDGF-like factor secreted by human vascular endothelial cells and fibroblasts. Relative to the PDGF isoforms, VEGF shows distant analogy to PDGF-BB while PIGF corresponds to PDGF-AA. CTGF shows little amino acid identity with PDGF A or B, but reacts with anitsera produced against PDGF. Recently, the status of PDGF has been re-evaluated based on analysis of its 3-dimensional structure. Along with NGF, TGF-beta and glycoprotein hormones (human chorionic gonadotrophic), PDGF is now classified as a member of the cysteine-knot growth factor superfamily. Each member of this group occurs as a dimer and is characterized by six cysteines which link together to form a "molecular knot". The existence of this knot is only revealed by 3-D analysis, making the criteria for admission to this family unique among superfamilies.

[0378] An association is known to exist between alpha-2 macroglobulin (alpha-2M) and the B chain-containing PDGF forms, AB and BB. alpha-2M is a circulating 720 kDa homotetrameric glycoprotein produced by hepatocytes, macrophages and astrocytes whose most widely reported function is that of a scavenger of proteases. Although PDGF does not interact with the region associated with protease entrapment, it does bind to other alpha-2M sites not influenced by activation. PDGF-BB has been noted to bind to both fast and slow alpha-2M and does so principally in a noncovalent manner. Significantly, the binding is reversible, and PDGF dissociation is suggested to occur at either low pH or when equilibrium kinetics favor dissociation, such as might be the case when PDGF is removed from circulation by binding to its own receptors. Functionally, it is not clear what the role is for B chain binding to alpha-2M. PDGF binding to the slow form seems to result in its storage, as the alpha-2M receptor binding motif(s) are not exposed, and the PDGF-alpha-2M complex simply circulates. On the other hand, binding to fast or activated alpha-2M results in its rapid clearance via alpha-2M receptors, bringing the PDGF molecule close to its own receptors and perhaps facilitating a secondary PDGF-PDGFR interaction.

[0379] Two distinct human PDGF receptor transmembrane binding proteins have been identified, a 170 kDa, 1066 amino acid residue alpha-receptor (PDGFR alpha) and a 190 kDa, 1074 amino acid residue beta-receptor (PDGFR beta). The two receptor proteins are structurally related and consist of an extracellular portion containing five immunoglobulin-like domains, a single transmembrane region, and an intracellular portion with a protein-tyrosine kinase domain. A functional PDGF receptor is formed when the two chains of a dimeric PDGF molecule each bind one of the above receptor molecules, resulting in their approximation, dimerization and activation. Between the two proteins, there is 44% overall sequence identity. Within the extracellular domain, 30% of the amino acid residues are identical. In addition, a 90 kDa soluble form of PDGFR alpha, consisting of the extracellular segment of the alpha-receptor, has been found in cell culture medium and in human plasma. The above two transmembrane receptors share characteristics with other growth factor receptors, such as the M-CSF receptor, c-kit, and the FGF receptor family. High-affinity binding of PDGF involves dimerization of the receptors, forming either homodimers or heterodimers with the alpha and beta receptors/chains. Although it appears that each subunit of dimeric PDGF binds to one receptor monomer, it is unclear if these PDGF subunits need to be covalently linked. Recent evidence suggests noncovalently linked B chains are able to activate the PDGFR.

[0380] PDGFR alpha binds each of the three forms of PDGF dimers with high affinity. Although PDGFR beta binds both PDGF-BB and PDGF-AB with high affinity, it has no reported binding to PDGF-AA. The apparent high-affinity binding of the AB dimer to the beta-receptor must be interpreted with caution, however. Although PDGF-AB can bind to mutant 3T3 cells displaying only beta-receptors, it requires 100-fold more PDGF-AB to dimerize the beta-receptors and activate the cells than is required for cells also displaying alpha-receptors. Cells known to express only alpha-receptors include oligodendroglial progenitors, liver endothelial cells and mesothelium, and platelets. Cells expressing only beta-receptors include CNS capillary endothelium, neurons and Ito (fat storing) cells of the liver, plus monocytes/macrophages. Cells showing coincident expression of alpha and beta receptors include smooth muscle cells, fibroblasts, and Schwann cells.

[0381] Receptor binding by PDGF is known to activate intracellular tyrosine kinase, leading to autophosphorylation of the cytoplasmic domain of the receptor as well as phosphorylation of other intracellular substrates. This reaction is described as one in trans, i.e., the two receptor molecules of the receptor dimer phosphorylate each other. Specific substrates identified with the beta-receptor include Src, GTPase Activating Protein (GAP), phospholypase Cg (PLCg) and phosphotidylinositol 3-phosphate. Both PLCg and GAP seem to bind with different affinities to the a- and beta-receptors, suggesting that the particular response of a cell depends on the type of receptor it expresses and the type of PDGF dimer to which it is exposed. In addition to the above, a non-tyrosine phosphorylation-associated signal transduction pathway can also be activated that involves the zinc finger protein erg-1 (early growth response gene 1).

[0382] Because there are differences between cells relative to the amounts of alpha- and beta-receptors that they express, and because of the variability in PDGF isomer binding to receptors, there is a large range of possibilities for biological responses by PDGF. This is reflected in at least four experimental systems where different isoforms of PDGF elicit different results. Vascular smooth muscle cells (SMC) and fibroblasts are both known to express both the alpha- and beta-receptors. In SMC, PDGF-AA initiates cellular hypertrophy (increased protein synthesis), while BB induces hyperplasia (mitosis). In fibroblasts, the BB isoform initiates chemotaxis, while AA inhibits chemotaxis. In dopaminergic neurons, PDGF-AA promotes embryonic neuron fiber development, while BB serves only as a survival or maintenance factor. Finally, within the developing lung, the BB isoform regulates the growth and number of respiratory tubule epithelial cells, while the AA isoform directs the actual formation of branches arising from the respiratory tubules.

[0383] In general, PDGF isoforms are potent mitogens for connective tissue cells, including dermal fibroblasts, arterial smooth muscle cells, chondrocytes and some epithelial and endothelial cells. In addition to its activity as a mitogen, PDGF is chemotactic for fibroblasts and smooth muscle cells, cells which also respond mitogenically to PDGF, and for neutrophils and mononuclear cells, cells for which PDGF is not a mitogen. There is a considerable body of evidence to indicate that PDGF derived from macrophages, acting as a chemotactic and mitogenic agent for smooth muscle cells, contributes to the myointimal thickening of arterial walls characteristic of atherosclerosis. Other reported activities for PDGF include the stimulation of granule release by neutrophils and monocytes, the facilitation of steroid synthesis by Leydig cells, stimulation of neutrophil phagocytosis, modulation of thrombospondin expression and secretion, upregulation of ICAM-1 in vascular smooth muscle cells, and the transient induction of T cell IL-2 secretion, accompanied by a down-regulation of IL-4 and IFN-gamma production, which allow clonal expansion of antigen-activated B and T helper lymphocytes prior to differentiation. PDGF also appears to be ubiquitous in neurons throughout the CNS, where it is suggested to play an important role in neuron survival and regeneration, and in mediation of glial cell proliferation, differentiation and migration.

[0384] The use of small interfering nucleic acid molecules targeting PDGF and its receptors therefore provides a class of novel therapeutic agents that can be used in the treatment of cancers, proliferative diseases (e.g., restenosis), inflammatory disease, or any other disease or condition that responds to modulation of PDGF and PDGFr genes.

EXAMPLES

[0385] The following are non-limiting examples showing the selection, isolation, synthesis and activity of nucleic acids of the instant invention.

Example 1

Tandem Synthesis of siNA Constructs

[0386] Exemplary siNA molecules of the invention are synthesized in tandem using a cleavable linker, for example, a succinyl-based linker. Tandem synthesis as described herein is followed by a one-step purification process that provides RNAi molecules in high yield. This approach is highly amenable to siNA synthesis in support of high throughput RNAi screening, and can be readily adapted to multi-column or multi-well synthesis platforms.

[0387] After completing a tandem synthesis of a siNA oligo and its complement in which the 5'-terminal dimethoxytrityl (5'-O-DMT) group remains intact (trityl on synthesis), the oligonucleotides are deprotected as described above. Following deprotection, the siNA sequence strands are allowed to spontaneously hybridize. This hybridization yields a duplex in which one strand has retained the 5'-O-DMT group while the complementary strand comprises a terminal 5'-hydroxyl. The newly formed duplex behaves as a single molecule during routine solid-phase extraction purification (Trityl-On purification) even though only one molecule has a dimethoxytrityl group. Because the strands form a stable duplex, this dimethoxytrityl group (or an equivalent group, such as other trityl groups or other hydrophobic moieties) is all that is required to purify the pair of oligos, for example, by using a C18 cartridge.

[0388] Standard phosphoramidite synthesis chemistry is used up to the point of introducing a tandem linker, such as an inverted deoxy abasic succinate or glyceryl succinate linker (see FIG. 1) or an equivalent cleavable linker. A non-limiting example of linker coupling conditions that can be used includes a hindered base such as diisopropylethylamine (DIPA) and/or DMAP in the presence of an activator reagent such as Bromotripyrrolidinophosphoniumhexafluororophosphate (PyBrOP). After the linker is coupled, standard synthesis chemistry is utilized to complete synthesis of the second sequence leaving the terminal the 5'-O-DMT intact. Following synthesis, the resulting oligonucleotide is deprotected according to the procedures described herein and quenched with a suitable buffer, for example with 50 mM NaOAc or 1.5M NH.sub.4H.sub.2CO.sub.3.

[0389] Purification of the siNA duplex can be readily accomplished using solid phase extraction, for example, using a Waters C18 SepPak Ig cartridge conditioned with 1 column volume (CV) of acetonitrile, 2 CV H2O, and 2 CV 50 mM NaOAc. The sample is loaded and then washed with 1 CV H2O or 50 mM NaOAc. Failure sequences are eluted with 1 CV 14% ACN (Aqueous with 50 mM NaOAc and 50 mM NaCl). The column is then washed, for example with 1 CV H2O followed by on-column detritylation, for example by passing 1 CV of 1% aqueous trifluoroacetic acid (TFA) over the column, then adding a second CV of 1% aqueous TFA to the column and allowing to stand for approximately 10 minutes. The remaining TFA solution is removed and the column washed with H20 followed by 1 CV 1M NaCl and additional H2O. The siNA duplex product is then eluted, for example, using 1 CV 20% aqueous CAN.

[0390] FIG. 2 provides an example of MALDI-TOF mass spectrometry analysis of a purified siNA construct in which each peak corresponds to the calculated mass of an individual siNA strand of the siNA duplex. The same purified siNA provides three peaks when analyzed by capillary gel electrophoresis (CGE), one peak presumably corresponding to the duplex siNA, and two peaks presumably corresponding to the separate siNA sequence strands. Ion exchange HPLC analysis of the same siNA contract only shows a single peak. Testing of the purified siNA construct using a luciferase reporter assay described below demonstrated the same RNAi activity compared to siNA constructs generated from separately synthesized oligonucleotide sequence strands.

Example 2

Identification of Potential siNA Target Sites in any RNA Sequence

[0391] The sequence of an RNA target of interest, such as a viral or human mRNA transcript, is screened for target sites, for example by using a computer folding algorithm. In a non-limiting example, the sequence of a gene or RNA gene transcript derived from a database, such as Genbank, is used to generate siNA targets having complementarity to the target. Such sequences can be obtained from a database, or can be determined experimentally as known in the art. Target sites that are known, for example, those target sites determined to be effective target sites based on studies with other nucleic acid molecules, for example ribozymes or antisense, or those targets known to be associated with a disease or condition such as those sites containing mutations or deletions, can be used to design siNA molecules targeting those sites. Various parameters can be used to determine which sites are the most suitable target sites within the target RNA sequence. These parameters include but are not limited to secondary or tertiary RNA structure, the nucleotide base composition of the target sequence, the degree of homology between various regions of the target sequence, or the relative position of the target sequence within the RNA transcript. Based on these determinations, any number of target sites within the RNA transcript can be chosen to screen siNA molecules for efficacy, for example by using in vitro RNA cleavage assays, cell culture, or animal models. In a non-limiting example, anywhere from 1 to 1000 target sites are chosen within the transcript based on the size of the siNA construct to be used. High throughput screening assays can be developed for screening siNA molecules using methods known in the art, such as with multi-well or multi-plate assays to determine efficient reduction in target gene expression.

Example 3

Selection of siNA Molecule Target Sites in a RNA

[0392] The following non-limiting steps can be used to carry out the selection of siNAs targeting a given gene sequence or transcript. [0393] 1. The target sequence is parsed in silico into a list of all fragments or subsequences of a particular length, for example 23 nucleotide fragments, contained within the target sequence. This step is typically carried out using a custom Perl script, but commercial sequence analysis programs such as Oligo, MacVector, or the GCG Wisconsin Package can be employed as well. [0394] 2. In some instances the siNAs correspond to more than one target sequence; such would be the case for example in targeting different transcripts of the same gene, targeting different transcripts of more than one gene, or for targeting both the human gene and an animal homolog. In this case, a subsequence list of a particular length is generated for each of the targets, and then the lists are compared to find matching sequences in each list. The subsequences are then ranked according to the number of target sequences that contain the given subsequence; the goal is to find subsequences that are present in most or all of the target sequences. Alternately, the ranking can identify subsequences that are unique to a target sequence, such as a mutant target sequence. Such an approach would enable the use of siNA to target specifically the mutant sequence and not effect the expression of the normal sequence. [0395] 3. In some instances the siNA subsequences are absent in one or more sequences while present in the desired target sequence; such would be the case if the siNA targets a gene with a paralogous family member that is to remain untargeted. As in case 2 above, a subsequence list of a particular length is generated for each of the targets, and then the lists are compared to find sequences that are present in the target gene but are absent in the untargeted paralog. [0396] 4. The ranked siNA subsequences can be further analyzed and ranked according to GC content. A preference can be given to sites containing 30-70% GC, with a further preference to sites containing 40-60% GC. [0397] 5. The ranked siNA subsequences can be further analyzed and ranked according to self-folding and internal hairpins. Weaker internal folds are preferred; strong hairpin structures are to be avoided. [0398] 6. The ranked siNA subsequences can be further analyzed and ranked according to whether they have runs of GGG or CCC in the sequence. GGG (or even more Gs) in either strand can make oligonucleotide synthesis problematic and can potentially interfere with RNAi activity, so it is avoided whenever better sequences are available. CCC is searched in the target strand because that will place GGG in the antisense strand. [0399] 7. The ranked siNA subsequences can be further analyzed and ranked according to whether they have the dinucleotide UU (uridine dinucleotide) on the 3'-end of the sequence, and/or AA on the 5'-end of the sequence (to yield 3' UU on the antisense sequence). These sequences allow one to design siNA molecules with terminal TT thymidine dinucleotides. [0400] 8. Four or five target sites are chosen from the ranked list of subsequences as described above. For example, in subsequences having 23 nucleotides, the right 21 nucleotides of each chosen 23-mer subsequence are then designed and synthesized for the upper (sense) strand of the siNA duplex, while the reverse complement of the left 21 nucleotides of each chosen 23-mer subsequence are then designed and synthesized for the lower (antisense) strand of the siNA duplex (see Tables II and III). If terminal TT residues are desired for the sequence (as described in paragraph 7), then the two 3' terminal nucleotides of both the sense and antisense strands are replaced by TT prior to synthesizing the oligos. [0401] 9. The siNA molecules are screened in an in vitro, cell culture or animal model system to identify the most active siNA molecule or the most preferred target site within the target RNA sequence. [0402] 10. Other design considerations can be used when selecting target nucleic acid sequences, see, for example, Reynolds et al., 2004, Nature Biotechnology Advanced Online Publication, 1 Feb. 2004, doi:10.1038/nbt936 and Ui-Tei et al., 2004, Nucleic Acids Research, 32, doi:10.1093/nar/gkh247.

[0403] In an alternate approach, a pool of siNA constructs specific to a PDGF and/or PDGFr target sequence is used to screen for target sites in cells expressing PDGF and/or PDGFr RNA, such as such human aortic smooth muscle cells (e.g., HASMC), HeLa cells, or A549 cells. The general strategy used in this approach is shown in FIG. 9. A non-limiting example of such is a pool comprising sequences having any of SEQ ID NOS 1-744. Cells expressing PDGF and/or PDGFr (e.g., HASMC, HeLa cells, or A549 cells) are transfected with the pool of siNA constructs and cells that demonstrate a phenotype associated with PDGF and/or PDGFr inhibition are sorted. The pool of siNA constructs can be expressed from transcription cassettes inserted into appropriate vectors (see for example FIG. 7 and FIG. 8). The siNA from cells demonstrating a positive phenotypic change (e.g., decreased proliferation, decreased PDGF and/or PDGFr mRNA levels or decreased PDGF and/or PDGFr protein expression), are sequenced to determine the most suitable target site(s) within the target PDGF and/or PDGFr RNA sequence.

Example 4

PDGF and/or PDGFr Targeted siNA Design

[0404] siNA target sites were chosen by analyzing sequences of the PDGF and/or PDGFr RNA target and optionally prioritizing the target sites on the basis of folding (structure of any given sequence analyzed to determine siNA accessibility to the target), by using a library of siNA molecules as described in Example 3, or alternately by using an in vitro siNA system as described in Example 6 herein. siNA molecules were designed that could bind each target and are optionally individually analyzed by computer folding to assess whether the siNA molecule can interact with the target sequence. Varying the length of the siNA molecules can be chosen to optimize activity. Generally, a sufficient number of complementary nucleotide bases are chosen to bind to, or otherwise interact with, the target RNA, but the degree of complementarity can be modulated to accommodate siNA duplexes or varying length or base composition. By using such methodologies, siNA molecules can be designed to target sites within any known RNA sequence, for example those RNA sequences corresponding to the any gene transcript.

[0405] Chemically modified siNA constructs are designed to provide nuclease stability for systemic administration in vivo and/or improved pharmacokinetic, localization, and delivery properties while preserving the ability to mediate RNAi activity. Chemical modifications as described herein are introduced synthetically using synthetic methods described herein and those generally known in the art. The synthetic siNA constructs are then assayed for nuclease stability in serum and/or cellular/tissue extracts (e.g. liver extracts). The synthetic siNA constructs are also tested in parallel for RNAi activity using an appropriate assay, such as a luciferase reporter assay as described herein or another suitable assay that can quantity RNAi activity. Synthetic siNA constructs that possess both nuclease stability and RNAi activity can be further modified and re-evaluated in stability and activity assays. The chemical modifications of the stabilized active siNA constructs can then be applied to any siNA sequence targeting any chosen RNA and used, for example, in target screening assays to pick lead siNA compounds for therapeutic development (see for example FIG. 11).

Example 5

Chemical Synthesis and Purification of siNA

[0406] siNA molecules can be designed to interact with various sites in the RNA message, for example, target sequences within the RNA sequences described herein. The sequence of one strand of the siNA molecule(s) is complementary to the target site sequences described above. The siNA molecules can be chemically synthesized using methods described herein. Inactive siNA molecules that are used as control sequences can be synthesized by scrambling the sequence of the siNA molecules such that it is not complementary to the target sequence. Generally, siNA constructs can by synthesized using solid phase oligonucleotide synthesis methods as described herein (see for example Usman et al., U.S. Pat. Nos. 5,804,683; 5,831,071; 5,998,203; 6,117,657; 6,353,098; 6,362,323; 6,437,117; 6,469,158; Scaringe et al., U.S. Pat. Nos. 5,889,136; 6,008,400; 6,111,086 all incorporated by reference herein in their entirety).

[0407] In a non-limiting example, RNA oligonucleotides are synthesized in a stepwise fashion using the phosphoramidite chemistry as is known in the art. Standard phosphoramidite chemistry involves the use of nucleosides comprising any of 5'-O-dimethoxytrityl, 2'-O-tert-butyldimethylsilyl, 3'-O-2-Cyanoethyl N,N-diisopropylphosphoroamidite groups, and exocyclic amine protecting groups (e.g. N6-benzoyl adenosine, N4 acetyl cytidine, and N2-isobutyryl guanosine). Alternately, 2'-O-Silyl Ethers can be used in conjunction with acid-labile 2'-O-orthoester protecting groups in the synthesis of RNA as described by Scaringe supra. Differing 2' chemistries can require different protecting groups, for example 2'-deoxy-2'-amino nucleosides can utilize N-phthaloyl protection as described by Usman et al., U.S. Pat. No. 5,631,360, incorporated by reference herein in its entirety).

[0408] During solid phase synthesis, each nucleotide is added sequentially (3'- to 5'-direction) to the solid support-bound oligonucleotide. The first nucleoside at the 3'-end of the chain is covalently attached to a solid support (e.g., controlled pore glass or polystyrene) using various linkers. The nucleotide precursor, a ribonucleoside phosphoramidite, and activator are combined resulting in the coupling of the second nucleoside phosphoramidite onto the 5'-end of the first nucleoside. The support is then washed and any unreacted 5'-hydroxyl groups are capped with a capping reagent such as acetic anhydride to yield inactive 5'-acetyl moieties. The trivalent phosphorus linkage is then oxidized to a more stable phosphate linkage. At the end of the nucleotide addition cycle, the 5'-O-protecting group is cleaved under suitable conditions (e.g., acidic conditions for trityl-based groups and Fluoride for silyl-based groups). The cycle is repeated for each subsequent nucleotide.

[0409] Modification of synthesis conditions can be used to optimize coupling efficiency, for example by using differing coupling times, differing reagent/phosphoramidite concentrations, differing contact times, differing solid supports and solid support linker chemistries depending on the particular chemical composition of the siNA to be synthesized. Deprotection and purification of the siNA can be performed as is generally described in Usman et al., U.S. Pat. No. 5,831,071, U.S. Pat. No. 6,353,098, U.S. Pat. No. 6,437,117, and Bellon et al., U.S. Pat. No. 6,054,576, U.S. Pat. No. 6,162,909, U.S. Pat. No. 6,303,773, or Scaringe supra, incorporated by reference herein in their entireties. Additionally, deprotection conditions can be modified to provide the best possible yield and purity of siNA constructs. For example, applicant has observed that oligonucleotides comprising 2'-deoxy-2'-fluoro nucleotides can degrade under inappropriate deprotection conditions. Such oligonucleotides are deprotected using aqueous methylamine at about 35.degree. C. for 30 minutes. If the 2'-deoxy-2'-fluoro containing oligonucleotide also comprises ribonucleotides, after deprotection with aqueous methylamine at about 35.degree. C. for 30 minutes, TEA-HF is added and the reaction maintained at about 65.degree. C. for an additional 15 minutes.

Example 6

RNAi In Vitro Assay to Assess siNA Activity

[0410] An in vitro assay that recapitulates RNAi in a cell-free system is used to evaluate siNA constructs targeting PDGF and/or PDGFr RNA targets. The assay comprises the system described by Tuschl et al., 1999, Genes and Development, 13, 3191-3197 and Zamore et al., 2000, Cell, 101, 25-33 adapted for use with PDGF and/or PDGFr target RNA. A Drosophila extract derived from syncytial blastoderm is used to reconstitute RNAi activity in vitro. Target RNA is generated via in vitro transcription from an appropriate PDGF and/or PDGFr expressing plasmid using T7 RNA polymerase or via chemical synthesis as described herein. Sense and antisense siNA strands (for example 20 uM each) are annealed by incubation in buffer (such as 100 mM potassium acetate, 30 mM HEPES-KOH, pH 7.4, 2 mM magnesium acetate) for 1 minute at 90.degree. C. followed by 1 hour at 37.degree. C., then diluted in lysis buffer (for example 100 mM potassium acetate, 30 mM HEPES-KOH at pH 7.4, 2 mM magnesium acetate). Annealing can be monitored by gel electrophoresis on an agarose gel in TBE buffer and stained with ethidium bromide. The Drosophila lysate is prepared using zero to two-hour-old embryos from Oregon R flies collected on yeasted molasses agar that are dechorionated and lysed. The lysate is centrifuged and the supernatant isolated. The assay comprises a reaction mixture containing 50% lysate [vol/vol], RNA (10-50 .mu.M final concentration), and 10% [vol/vol] lysis buffer containing siNA (10 nM final concentration). The reaction mixture also contains 10 mM creatine phosphate, 10 ug/ml creatine phosphokinase, 100 um GTP, 100 uM UTP, 100 uM CTP, 500 uM ATP, 5 mM DTT, 0.1 U/uL RNasin (Promega), and 100 uM of each amino acid. The final concentration of potassium acetate is adjusted to 100 mM. The reactions are pre-assembled on ice and preincubated at 25.degree. C. for 10 minutes before adding RNA, then incubated at 25.degree. C. for an additional 60 minutes. Reactions are quenched with 4 volumes of 1.25.times. Passive Lysis Buffer. (Promega). Target RNA cleavage is assayed by RT-PCR analysis or other methods known in the art and are compared to control reactions in which siNA is omitted from the reaction.

[0411] Alternately, internally-labeled target RNA for the assay is prepared by in vitro transcription in the presence of [alpha-.sup.32P] CTP, passed over a G50 Sephadex column by spin chromatography and used as target RNA without further purification. Optionally, target RNA is 5'-.sup.32P-end labeled using T4 polynucleotide kinase enzyme. Assays are performed as described above and target RNA and the specific RNA cleavage products generated by RNAi are visualized on an autoradiograph of a gel. The percentage of cleavage is determined by PHOSPHOR IMAGER.RTM. (autoradiography) quantitation of bands representing intact control RNA or RNA from control reactions without siNA and the cleavage products generated by the assay.

[0412] In one embodiment, this assay is used to determine target sites in the PDGF and/or PDGFr RNA target for siNA mediated RNAi cleavage, wherein a plurality of siNA constructs are screened for RNAi mediated cleavage of the PDGF and/or PDGFr RNA target, for example, by analyzing the assay reaction by electrophoresis of labeled target RNA, or by northern blotting, as well as by other methodology well known in the art.

Example 7

Nucleic Acid Inhibition of PDGF and/or PDGFr Target RNA

[0413] siNA molecules targeted to the human PDGF and/or PDGFr RNA are designed and synthesized as described above. These nucleic acid molecules can be tested for cleavage activity in vivo, for example, using the following procedure. The target sequences and the nucleotide location within the PDGF and/or PDGFr RNA are given in Tables II and III.

[0414] Two formats are used to test the efficacy of siNAs targeting PDGF and/or PDGFr. First, the reagents are tested in cell culture using, for example, HASMC, HeLa cells, or A549 cells to determine the extent of RNA and protein inhibition. siNA reagents (e.g.; see Tables II and III) are selected against the PDGF and/or PDGFr target as described herein. RNA inhibition is measured after delivery of these reagents by a suitable transfection agent to, for example, HASMC, HeLa cells, or A549 cells. Relative amounts of target RNA are measured versus actin using real-time PCR monitoring of amplification (e.g., ABI 7700 TAQMAN.RTM.). A comparison is made to a mixture of oligonucleotide sequences made to unrelated targets or to a randomized siNA control with the same overall length and chemistry, but randomly substituted at each position. Primary and secondary lead reagents are chosen for the target and optimization performed. After an optimal transfection agent concentration is chosen, a RNA time-course of inhibition is performed with the lead siNA molecule. In addition, a cell-plating format can be used to determine RNA inhibition.

Delivery of siNA to Cells

[0415] Cells such as HASMC, HeLa cells, or A549 cells are seeded, for example, at 1.times.10.sup.5 cells per well of a six-well dish in EGM-2 (BioWhittaker) the day before transfection. siNA (final concentration, for example 20 nM) and cationic lipid (e.g., final concentration 2 .mu.g/ml) are complexed in EGM basal media (Bio Whittaker) at 37.degree. C. for 30 minutes in polystyrene tubes. Following vortexing, the complexed siNA is added to each well and incubated for the times indicated. For initial optimization experiments, cells are seeded, for example, at 1.times.10.sup.3 in 96 well plates and siNA complex added as described. Efficiency of delivery of siNA to cells is determined using a fluorescent siNA complexed with lipid. Cells in 6-well dishes are incubated with siNA for 24 hours, rinsed with PBS and fixed in 2% paraformaldehyde for 15 minutes at room temperature. Uptake of siNA is visualized using a fluorescent microscope.

TAQMAN.RTM. (Real-Time PCR Monitoring of Amplification) and Lightcycler Quantification of mRNA

[0416] Total RNA is prepared from cells following siNA delivery, for example, using Qiagen RNA purification kits for 6-well or Rneasy extraction kits for 96-well assays. For TAQMAN.RTM. analysis (real-time PCR monitoring of amplification), dual-labeled probes are synthesized with the reporter dye, FAM or JOE, covalently linked at the 5'-end and the quencher dye TAMRA conjugated to the 3'-end. One-step RT-PCR amplifications are performed on, for example, an ABI PRISM 7700 Sequence Detector using 50 .mu.l reactions consisting of 10 .mu.l total RNA, 100 nM forward primer, 900 nM reverse primer, 100 nM probe, 1.times. TaqMan PCR reaction buffer (PE-Applied Biosystems), 5.5 mM MgCl.sub.2, 300 .mu.M each dATP, dCTP, dGTP, and dTTP, IOU RNase Inhibitor (Promega), 1.25 U AMPLITAQ GOLD.RTM. (DNA polymerase) (PE-Applied Biosystems) and 10 U M-MLV Reverse Transcriptase (Promega). The thermal cycling conditions can consist of 30 minutes at 48.degree. C., 10 minutes at 95.degree. C., followed by 40 cycles of 15 seconds at 95.degree. C. and 1 minute at 60.degree. C. Quantitation of mRNA levels is determined relative to standards generated from serially diluted total cellular RNA (300, 100, 33, 11 ng/rxn) and normalizing to .beta.-actin or GAPDH mRNA in parallel TAQMAN.RTM. reactions (real-time PCR monitoring of amplification). For each gene of interest an upper and lower primer and a fluorescently labeled probe are designed. Real time incorporation of SYBR Green I dye into a specific PCR product can be measured in glass capillary tubes using a lightcycler. A standard curve is generated for each primer pair using control cRNA. Values are represented as relative expression to GAPDH in each sample.

Western Blotting

[0417] Nuclear extracts can be prepared using a standard micro preparation technique (see for example Andrews and Faller, 1991, Nucleic Acids Research, 19, 2499). Protein extracts from supernatants are prepared, for example using TCA precipitation. An equal volume of 20% TCA is added to the cell supernatant, incubated on ice for 1 hour and pelleted by centrifugation for 5 minutes. Pellets are washed in acetone, dried and resuspended in water. Cellular protein extracts are run on a 10% Bis-Tris NuPage (nuclear extracts) or 4-12% Tris-Glycine (supernatant extracts) polyacrylamide gel and transferred onto nitro-cellulose membranes. Non-specific binding can be blocked by incubation, for example, with 5% non-fat milk for 1 hour followed by primary antibody for 16 hour at 4.degree. C. Following washes, the secondary antibody is applied, for example (1:10,000 dilution) for 1 hour at room temperature and the signal detected with SuperSignal reagent (Pierce).

Example 8

Models Useful to Evaluate the Down-Regulation of PDGF and/or PDGFr Gene Expression

Cell Culture

[0418] There are numerous cell culture systems that can be used to analyze reduction of PDGF and/or PDGFr levels either directly or indirectly by measuring downstream effects. For example, HASMC, HeLa, or A549 cells can be used in cell culture experiments to assess the efficacy of nucleic acid molecules of the invention. As such, HASMC, HeLa, or A549 cells treated with nucleic acid molecules of the invention (e.g., siNA) targeting PDGF and/or PDGFr RNA would be expected to have decreased PDGF and/or PDGFr expression capacity following stimulation with pro-inflammatory cytokines compared to matched control nucleic acid molecules having a scrambled or inactive sequence. In a non-limiting example, HASMC, HeLa, or A549 cells are cultured and PDGF and/or PDGFr expression is quantified, for example by time-resolved immunofluorometric assay. PDGF and/or PDGFr messenger-RNA expression is quantitated with RT-PCR in cultured cells. Untreated cells are compared to cells treated with siNA molecules transfected with a suitable reagent, for example, a cationic lipid such as lipofectamine, and PDGF and/or PDGFr protein and RNA levels are quantitated. Dose response assays are then performed to establish dose dependent inhibition of PDGF and/or PDGFr expression.

[0419] In several cell culture systems, cationic lipids have been shown to enhance the bioavailability of oligonucleotides to cells in culture (Bennet, et al., 1992, Mol. Pharmacology, 41, 1023-1033). In one embodiment, siNA molecules of the invention are complexed with cationic lipids for cell culture experiments. siNA and cationic lipid mixtures are prepared in serum-free DMEM immediately prior to addition to the cells. DMEM plus additives are warmed to room temperature (about 20-25.degree. C.) and cationic lipid is added to the final desired concentration and the solution is vortexed briefly. siNA molecules are added to the final desired concentration and the solution is again vortexed briefly and incubated for 10 minutes at room temperature. In dose response experiments, the RNA/lipid complex is serially diluted into DMEM following the 10 minute incubation.

Animal Models

[0420] Evaluating the efficacy of anti-PDGF and/or PDGFr agents in animal models is an important prerequisite to human clinical trials. Barisoni et al., 1995, Am J. Pathol., 147, 1728-35 describe a transgenic mouse model of polycystic kidney disease. Adult polycystic kidney disease is believed to be the most frequent ( 1/500) inherited genetic disorder in humans. Barisoni et al., supra generated a genetic model of the disease in transgenic mice by introducing a deregulated proto-oncogene c-myc specifically expressed in the kidney. All transgenic lines produced develop adult polycystic kidney disease in a reproducible manner. The clinical phenotype observed in mice is present at birth and leads to renal insufficiency in adulthood. Barisoni et al., supra determined that abnormal proliferation and programmed cell death are responsible for cystogenesis in polycystic kidney disease. Furthermore, this phenomena is controlled by a specific c-myc mechanism independent of the p53 pathway. A similar mechanism also prevails in human autosomal dominant polycystic kidney disease. Therefore, this murine model provides a useful model to understand the polycystic kidney disease pathogenesis and can be used to evaluate potential therapeutic agents such as siNA molecules of the invention.

[0421] Other animal models known in the art can be used to evaluate siNA molecules of the invention targeting PDGF and PDGFr for other disease conditions, see for example Karas et al., 1992, Coronary intimal proliferation after balloon injury and stenting in swine: An animal model of restenosis. J Am Coll Cardiol. 20, 467-474; Hele, 2001, The heterotopic tracheal allograft as an animal model of obliterative bronchiolitis. Respir. Res., 2, 169-183; Floege et al. 1999, Am. J. Pathol., 154, 169 (animal model of acute glomerulonephritis). Similarly, using various animal models of oncology known in the art, animals treated with siNA molecules of the invention targeting PDGF and/or PDGFr RNA can be evaluated for clinical response (e.g., decreased tumor size/metastasis) and/or decreased levels of Myc RNA or protein.

Example 9

RNAi Mediated Inhibition of PDGF and/or PDGFr Expression

[0422] siNA constructs (Table III) are tested for efficacy in reducing PDGF and/or PDGFr RNA expression in, for example, HASMC, HeLa cells, or A549 cells. Cells are plated approximately 24 hours before transfection in 96-well plates at 5,000-7,500 cells/well, 100 .mu.l/well, such that at the time of transfection cells are 70-90% confluent. For transfection, annealed siNAs are mixed with the transfection reagent (Lipofectamine 2000, Invitrogen) in a volume of 50 .mu.l/well and incubated for 20 minutes at room temperature. The siNA transfection mixtures are added to cells to give a final siNA concentration of 25 nM in a volume of 150 .mu.l. Each siNA transfection mixture is added to 3 wells for triplicate siNA treatments. Cells are incubated at 37.degree. for 24 hours in the continued presence of the siNA transfection mixture. At 24 hours, RNA is prepared from each well of treated cells. The supernatants with the transfection mixtures are first removed and discarded, then the cells are lysed and RNA prepared from each well. Target gene expression following treatment is evaluated by RT-PCR for the target gene and for a control gene (36B4, an RNA polymerase subunit) for normalization. The triplicate data is averaged and the standard deviations determined for each treatment. Normalized data are graphed and the percent reduction of target mRNA by active siNAs in comparison to their respective inverted control siNAs is determined.

Example 10

Indications

[0423] The present body of knowledge in PDGF and PDGFr research indicates the need for methods and compounds that can regulate PDGF and PDGFr gene product expression for research, diagnostic, and therapeutic use. As described herein, the nucleic acid molecules of the present invention can be used to treat leukemias, including acute myelogenous leukemia (AML), chronic myelogenous leukemia (CML), Acute lymphocytic leukemia (ALL), and chronic lymphocytic leukemia; ovarian cancer, breast cancer, cancers of the head and neck, lymphomas, such as mantle cell lymphoma, non-Hodgkin's lymphoma, and Burkitt's lymphoma, adenoma, squamous cell carcinoma, laryngeal carcinoma, multiple myeloma, melanoma, colorectal cancer, prostate cancer, and inflammatory and proliferative diseases such as restenosis, polycystic kidney disease, obliterative bronchiolitis, acute glomerulonephritis, stroke (CVA), and any other diseases or conditions that are related to or will respond to the levels of PDGF and/or PDGFr in a cell or tissue, alone or in combination with other therapies.

[0424] The use of radiation treatments and chemotherapeutics such as Gemcytabine and cyclophosphamide are non-limiting examples of chemotherapeutic agents that can be combined with or used in conjunction with the nucleic acid molecules (e.g. siNA molecules) of the instant invention. Those skilled in the art will recognize that other anti-cancer and/or antiproliferative compounds and therapies can be similarly be readily combined with the nucleic acid molecules of the instant invention (e.g. siNA molecules) and are hence within the scope of the instant invention. Such compounds and therapies are well known in the art (see for example Cancer: Principles and Practice of Oncology, Volumes 1 and 2, eds Devita, V. T., Hellman, S., and Rosenberg, S. A., J.B. Lippincott Company, Philadelphia, USA; incorporated herein by reference) and include, without limitations, folates, antifolates, pyrimidine analogs, fluoropyrimidines, purine analogs, adenosine analogs, topoisomerase I inhibitors, anthrapyrazoles, retinoids, antibiotics, anthacyclins, platinum analogs, alkylating agents, nitrosoureas, plant derived compounds such as vinca alkaloids, epipodophyllotoxins, tyrosine kinase inhibitors, taxols, radiation therapy, surgery, nutritional supplements, gene therapy, radiotherapy, for example 3D-CRT, immunotoxin therapy, for example ricin, and monoclonal antibodies. Specific examples of chemotherapeutic compounds that can be combined with or used in conjunction with the nucleic acid molecules of the invention include, but are not limited to, Paclitaxel; Docetaxel; Methotrexate; Doxorubin; Edatrexate; Vinorelbine; Tamoxifen; Leucovorin; 5-fluoro uridine (5-FU); Ionotecan; Cisplatin; Carboplatin; Amsacrine; Cytarabine; Bleomycin; Mitomycin C; Dactinomycin; Mithramycin; Hexamethylmelamine; Dacarbazine; L-asperginase; Nitrogen mustard; Melphalan, Chlorambucil; Busulfan; Ifosfamide; 4-hydroperoxycyclophosphamide, Thiotepa; Irinotecan (CAMPTOSAR.RTM., CPT-11, Camptothecin-11, Campto) Tamoxifen, Herceptin; IMC C225; ABX-EGF: and combinations thereof are non-limiting examples of compounds and/or methods that can be combined with or used in conjunction with the nucleic acid molecules (e.g. siNA) of the instant invention. Those skilled in the art will recognize that other drug compounds and therapies can be similarly be readily combined with the nucleic acid molecules of the instant invention (e.g., siNA molecules) are hence within the scope of the instant invention.

Example 11

Diagnostic Uses

[0425] The siNA molecules of the invention can be used in a variety of diagnostic applications, such as in the identification of molecular targets (e.g., RNA) in a variety of applications, for example, in clinical, industrial, environmental, agricultural and/or research settings. Such diagnostic use of siNA molecules involves utilizing reconstituted RNAi systems, for example, using cellular lysates or partially purified cellular lysates. siNA molecules of this invention can be used as diagnostic tools to examine genetic drift and mutations within diseased cells or to detect the presence of endogenous or exogenous, for example viral, RNA in a cell. The close relationship between siNA activity and the structure of the target RNA allows the detection of mutations in any region of the molecule, which alters the base-pairing and three-dimensional structure of the target RNA. By using multiple siNA molecules described in this invention, one can map nucleotide changes, which are important to RNA structure and function in vitro, as well as in cells and tissues. Cleavage of target RNAs with siNA molecules can be used to inhibit gene expression and define the role of specified gene products in the progression of disease or infection. In this manner, other genetic targets can be defined as important mediators of the disease. These experiments will lead to better treatment of the disease progression by affording the possibility of combination therapies (e.g., multiple siNA molecules targeted to different genes, siNA molecules coupled with known small molecule inhibitors, or intermittent treatment with combinations siNA molecules and/or other chemical or biological molecules). Other in vitro uses of siNA molecules of this invention are well known in the art, and include detection of the presence of mRNAs associated with a disease, infection, or related condition. Such RNA is detected by determining the presence of a cleavage product after treatment with a siNA using standard methodologies, for example, fluorescence resonance emission transfer (FRET).

[0426] In a specific example, siNA molecules that cleave only wild-type or mutant forms of the target RNA are used for the assay. The first siNA molecules (i.e., those that cleave only wild-type forms of target RNA) are used to identify wild-type RNA present in the sample and the second siNA molecules (i.e., those that cleave only mutant forms of target RNA) are used to identify mutant RNA in the sample. As reaction controls, synthetic substrates of both wild-type and mutant RNAs are cleaved by both siNA molecules to demonstrate the relative siNA efficiencies in the reactions and the absence of cleavage of the "non-targeted" RNA species. The cleavage products from the synthetic substrates also serve to generate size markers for the analysis of wild-type and mutant RNAs in the sample population. Thus, each analysis requires two siNA molecules, two substrates and one unknown sample, which is combined into six reactions. The presence of cleavage products is determined using an RNase protection assay so that full-length and cleavage fragments of each RNA can be analyzed in one lane of a polyacrylamide gel. It is not absolutely required to quantify the results to gain insight into the expression of mutant RNAs and putative risk of the desired phenotypic changes in target cells. The expression of mRNA whose protein product is implicated in the development of the phenotype (i.e., disease related or infection related) is adequate to establish risk. If probes of comparable specific activity are used for both transcripts, then a qualitative comparison of RNA levels is adequate and decreases the cost of the initial diagnosis. Higher mutant form to wild-type ratios are correlated with higher risk whether RNA levels are compared qualitatively or quantitatively.

[0427] All patents and publications mentioned in the specification are indicative of the levels of skill of those skilled in the art to which the invention pertains. All references cited in this disclosure are incorporated by reference to the same extent as if each reference had been incorporated by reference in its entirety individually.

[0428] One skilled in the art would readily appreciate that the present invention is well adapted to carry out the objects and obtain the ends and advantages mentioned, as well as those inherent therein. The methods and compositions described herein as presently representative of preferred embodiments are exemplary and are not intended as limitations on the scope of the invention. Changes therein and other uses will occur to those skilled in the art, which are encompassed within the spirit of the invention, are defined by the scope of the claims.

[0429] It will be readily apparent to one skilled in the art that varying substitutions and modifications can be made to the invention disclosed herein without departing from the scope and spirit of the invention. Thus, such additional embodiments are within the scope of the present invention and the following claims. The present invention teaches one skilled in the art to test various combinations and/or substitutions of chemical modifications described herein toward generating nucleic acid constructs with improved activity for mediating RNAi activity. Such improved activity can comprise improved stability, improved bioavailability, and/or improved activation of cellular responses mediating RNAi. Therefore, the specific embodiments described herein are not limiting and one skilled in the art can readily appreciate that specific combinations of the modifications described herein can be tested without undue experimentation toward identifying siNA molecules with improved RNAi activity.

[0430] The invention illustratively described herein suitably can be practiced in the absence of any element or elements, limitation or limitations that are not specifically disclosed herein. The terms and expressions which have been employed are used as terms of description and not of limitation, and there is no intention that in the use of such terms and expressions of excluding any equivalents of the features shown and described or portions thereof, but it is recognized that various modifications are possible within the scope of the invention claimed. Thus, it should be understood that although the present invention has been specifically disclosed by preferred embodiments, optional features, modification and variation of the concepts herein disclosed may be resorted to by those skilled in the art, and that such modifications and variations are considered to be within the scope of this invention as defined by the description and the appended claims.

[0431] In addition, where features or aspects of the invention are described in terms of Markush groups or other grouping of alternatives, those skilled in the art will recognize that the invention is also thereby described in terms of any individual member or subgroup of members of the Markush group or other group.

TABLE-US-00001 TABLE I PDGFr and PDGF Accession Numbers NM_002609 Homo sapiens platelet-derived growth factor receptor, beta polypeptide (PDGFRB), mRNA gi|15451788|ref|NM_002609.2|[15451788] NM_006206 Homo sapiens platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), mRNA gi|15451787|ref|NM_006206.2|[15451787] 1: BD166138 Platelet-derived growth factor receptors gi|27871950|dbj|BD166138.1||pat|JP|2002186490|3[27871950] BD166137 Platelet-derived growth factor receptors gi|27871949|dbj|BD166137.1||pat|JP|2002186490|2[27871949] BD166136 Platelet-derived growth factor receptors gi|27871948|dbj|BD166136.1||pat|JP|2002186490|1[27871948] NM_033016 Homo sapiens platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) (PDGFB), transcript variant 2, mRNA gi|15451785|ref|NM_033016.1|[15451785] NM_002608 Homo sapiens platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) (PDGFB), transcript variant 1, mRNA gi|4505680|ref|NM_002608.1|[4505680] M59423 Human platelet-derived growth factor A-chain (PDGF) gene, 5' end and promoter region gi|189877|gb|M59423.1|HUMPGDF[189877] Y14326 Homo sapiens platelet derived growth factor, B-chain 5'UTR gi|2832416|emb|Y14326.1|HSPDGFBC[2832416] X83705 H. sapiens mRNA for c-sis proto-oncogene gi|951023|emb|X83705.1|HSRNASIS[951023] X00562 Human proto-oncogene c-sis fragment for PDGF B chain precursor (platelet-derived growth factor) gi|36477|emb|X00562.1|HSSISB5[36477] X00561 Human proto-oncogene c-sis fragment for PDGF B chain precursor (platelet-derived growth factor) gi|36474|emb|X00561.1|HSSISB4[36474] X00560 Human proto-oncogene c-sis fragment for PDGF B chain precursor (platelet-derived growth factor) gi|36472|emb|X00560.1|HSSISB3[36472] X00559 Human proto-oncogene c-sis fragment for PDGF B chain precursor (platelet-derived growth factor) gi|36470|emb|X00559.1|HSSISB2[36470] X00556 Human proto-oncogene c-sis fragment for PDGF B chain precursor (platelet-derived growth factor) gi|36468|emb|X00556.1|HSSISB1[36468] X02811 Human mRNA for platelet-derived growth factor B chain (PDGF-B) gi|35371|emb|X02811.1|HSPDGFB[35371] X03795 Human mRNA for platelet derived growth factor A-chain (PDGF-A) gi|35365|emb|X03795.1|HSPDGFAR[35365] X06374 Human mRNA for platelet-derived growth factor PDGF-A gi|35363|emb|X06374.1|HSPDGFA[35363] AF417590 Homo sapiens platelet-derived growth factor A chain (PDGFA) gene, exon 1 and partial sequence gi|16033732|gb|AF417590.1|AF417590[16033732] NM_006206 Homo sapiens platelet-derived growth factor receptor, alpha polypeptide (PDGFRA), mRNA gi|15451787|ref|NM_006206.2|[15451787] AF244813 Homo sapiens platelet-derived growth factor C mRNA, complete cds gi|8886883|gb|AF244813.1|AF244813[8886883] NM_002607 Homo sapiens platelet-derived growth factor alpha polypeptide (PDGFA), transcript variant 1, mRNA gi|15208657|ref|NM_002607.2|[15208657]

TABLE-US-00002 TABLE II PDGFRB siNA AND TARGET SEQUENCES PDGFRB NM_002609.2 Seq Seq Seq Pos Seq ID UPos Upper seq ID LPos Lower seq ID 3 CCCCUCAGCCCUGCUGCCC 1 3 CCCCUCAGCCCUGCUGCCC 1 21 GGGCAGCAGGGCUGAGGGG 312 21 CAGCACGAGCCUGUGCUCG 2 21 CAGCACGAGCCUGUGCUCG 2 39 CGAGCACAGGCUCGUGCUG 313 39 GCCCUGCCCAACGCAGACA 3 39 GCCCUGCCCAACGCAGACA 3 57 UGUCUGCGUUGGGCAGGGC 314 57 AGCCAGACCCAGGGCGGCC 4 57 AGCCAGACCCAGGGCGGCC 4 75 GGCCGCCCUGGGUCUGGCU 315 75 CCCUCUGGCGGCUCUGCUC 5 75 CCCUCUGGCGGCUCUGCUC 5 93 GAGCAGAGCCGCCAGAGGG 316 93 CCUCCCGAAGGAUGCUUGG 6 93 CCUCCCGAAGGAUGCUUGG 6 111 CCAAGCAUCCUUCGGGAGG 317 111 GGGAGUGAGGCGAAGCUGG 7 111 GGGAGUGAGGCGAAGCUGG 7 129 CCAGCUUCGCCUCACUCCC 318 129 GGCGCUCCUCUCCCCUACA 8 129 GGCGCUCCUCUCCCCUACA 8 147 UGUAGGGGAGAGGAGCGCC 319 147 AGCAGCCCCCUUCCUCCAU 9 147 AGCAGCCCCCUUCCUCCAU 9 165 AUGGAGGAAGGGGGCUGCU 320 165 UCCCUCUGUUCUCCUGAGC 10 165 UCCCUCUGUUCUCCUGAGC 10 183 GCUCAGGAGAACAGAGGGA 321 183 CCUUCAGGAGCCUGCACCA 11 183 CCUUCAGGAGCCUGCACCA 11 201 UGGUGCAGGCUCCUGAAGG 322 201 AGUCCUGCCUGUCCUUCUA 12 201 AGUCCUGCCUGUCCUUCUA 12 219 UAGAAGGACAGGCAGGACU 323 219 ACUCAGCUGUUACCCACUC 13 219 ACUCAGCUGUUACCCACUC 13 237 GAGUGGGUAACAGCUGAGU 324 237 CUGGGACCAGCAGUCUUUC 14 237 CUGGGACCAGCAGUCUUUC 14 255 GAAAGACUGCUGGUCCCAG 325 255 CUGAUAACUGGGAGAGGGC 15 255 CUGAUAACUGGGAGAGGGC 15 273 GCCCUCUCCCAGUUAUCAG 326 273 CAGUAAGGAGGACUUCCUG 16 273 CAGUAAGGAGGACUUCCUG 16 291 CAGGAAGUCCUCCUUACUG 327 291 GGAGGGGGUGACUGUCCAG 17 291 GGAGGGGGUGACUGUCCAG 17 309 CUGGACAGUCACCCCCUCC 328 309 GAGCCUGGAACUGUGCCCA 18 309 GAGCCUGGAACUGUGCCCA 18 327 UGGGCACAGUUCCAGGCUC 329 327 ACACCAGAAGCCAUCAGCA 19 327 ACACCAGAAGCCAUCAGCA 19 345 UGCUGAUGGCUUCUGGUGU 330 345 AGCAAGGACACCAUGCGGC 20 345 AGCAAGGACACCAUGCGGC 20 363 GCCGCAUGGUGUCCUUGCU 331 363 CUUCCGGGUGCGAUGCCAG 21 363 CUUCCGGGUGCGAUGCCAG 21 381 CUGGCAUCGCACCCGGAAG 332 381 GCUCUGGCCCUCAAAGGCG 22 381 GCUCUGGCCCUCAAAGGCG 22 399 CGCCUUUGAGGGCCAGAGC 333 399 GAGCUGCUGUUGCUGUCUC 23 399 GAGCUGCUGUUGCUGUCUC 23 417 GAGACAGCAACAGCAGCUC 334 417 CUCCUGUUACUUCUGGAAC 24 417 CUCCUGUUACUUCUGGAAC 24 435 GUUCCAGAAGUAACAGGAG 335 435 CCACAGAUCUCUCAGGGCC 25 435 CCACAGAUCUCUCAGGGCC 25 453 GGCCCUGAGAGAUCUGUGG 336 453 CUGGUCGUCACACCCCCGG 26 453 CUGGUCGUCACACCCCCGG 26 471 CCGGGGGUGUGACGACCAG 337 471 GGGCCAGAGCUUGUCCUCA 27 471 GGGCCAGAGCUUGUCCUCA 27 489 UGAGGACAAGCUCUGGCCC 338 489 AAUGUCUCCAGCACCUUCG 28 489 AAUGUCUCCAGCACCUUCG 28 507 CGAAGGUGCUGGAGACAUU 339 507 GUUCUGACCUGCUCGGGUU 29 507 GUUCUGACCUGCUCGGGUU 29 525 AACCCGAGCAGGUCAGAAC 340 525 UCAGCUCCGGUGGUGUGGG 30 525 UCAGCUCCGGUGGUGUGGG 30 543 CCCACACCACCGGAGCUGA 341 543 GAACGGAUGUCCCAGGAGC 31 543 GAACGGAUGUCCCAGGAGC 31 561 GCUCCUGGGACAUCCGUUC 342 561 CCCCCACAGGAAAUGGCCA 32 561 CCCCCACAGGAAAUGGCCA 32 579 UGGCCAUUUCCUGUGGGGG 343 579 AAGGCCCAGGAUGGCACCU 33 579 AAGGCCCAGGAUGGCACCU 33 597 AGGUGCCAUCCUGGGCCUU 344 597 UUCUCCAGCGUGCUCACAC 34 597 UUCUCCAGCGUGCUCACAC 34 615 GUGUGAGCACGCUGGAGAA 345 615 CUGACCAACCUCACUGGGC 35 615 CUGACCAACCUCACUGGGC 35 633 GCCCAGUGAGGUUGGUCAG 346 633 CUAGACACGGGAGAAUACU 36 633 CUAGACACGGGAGAAUACU 36 651 AGUAUUCUCCCGUGUCUAG 347 651 UUUUGCACCCACAAUGACU 37 651 UUUUGCACCCACAAUGACU 37 669 AGUCAUUGUGGGUGCAAAA 348 669 UCCCGUGGACUGGAGACCG 38 669 UCCCGUGGACUGGAGACCG 38 687 CGGUCUCCAGUCCACGGGA 349 687 GAUGAGCGGAAACGGCUCU 39 687 GAUGAGCGGAAACGGCUCU 39 705 AGAGCCGUUUCCGCUCAUC 350 705 UACAUCUUUGUGCCAGAUC 40 705 UACAUCUUUGUGCCAGAUC 40 723 GAUCUGGCACAAAGAUGUA 351 723 CCCACCGUGGGCUUCCUCC 41 723 CCCACCGUGGGCUUCCUCC 41 741 GGAGGAAGCCCACGGUGGG 352 741 CCUAAUGAUGCCGAGGAAC 42 741 CCUAAUGAUGCCGAGGAAC 42 759 GUUCCUCGGCAUCAUUAGG 353 759 CUAUUCAUCUUUCUCACGG 43 759 CUAUUCAUCUUUCUCACGG 43 777 CCGUGAGAAAGAUGAAUAG 354 777 GAAAUAACUGAGAUCACCA 44 777 GAAAUAACUGAGAUCACCA 44 795 UGGUGAUCUCAGUUAUUUC 355 795 AUUCCAUGCCGAGUAACAG 45 795 AUUCCAUGCCGAGUAACAG 45 813 CUGUUACUCGGCAUGGAAU 356 813 GACCCACAGCUGGUGGUGA 46 813 GACCCACAGCUGGUGGUGA 46 831 UCACCACCAGCUGUGGGUC 357 831 ACACUGCACGAGAAGAAAG 47 831 ACACUGCACGAGAAGAAAG 47 849 CUUUCUUCUCGUGCAGUGU 358 849 GGGGACGUUGCACUGCCUG 48 849 GGGGACGUUGCACUGCCUG 48 867 CAGGCAGUGCAACGUCCCC 359 867 GUCCCCUAUGAUCACCAAC 49 867 GUCCCCUAUGAUCACCAAC 49 885 GUUGGUGAUCAUAGGGGAC 360 885 CGUGGCUUUUCUGGUAUCU 50 885 CGUGGCUUUUCUGGUAUCU 50 903 AGAUACCAGAAAAGCCACG 361 903 UUUGAGGACAGAAGCUACA 51 903 UUUGAGGACAGAAGCUACA 51 921 UGUAGCUUCUGUCCUCAAA 362 921 AUCUGCAAAACCACCAUUG 52 921 AUCUGCAAAACCACCAUUG 52 939 CAAUGGUGGUUUUGCAGAU 363 939 GGGGACAGGGAGGUGGAUU 53 939 GGGGACAGGGAGGUGGAUU 53 957 AAUCCACCUCCCUGUCCCC 364 957 UCUGAUGCCUACUAUGUCU 54 957 UCUGAUGCCUACUAUGUCU 54 975 AGACAUAGUAGGCAUCAGA 365 975 UACAGACUCCAGGUGUCAU 55 975 UACAGACUCCAGGUGUCAU 55 993 AUGACACCUGGAGUCUGUA 366 993 UCCAUCAACGUCUCUGUGA 56 993 UCCAUCAACGUCUCUGUGA 56 1011 UCACAGAGACGUUGAUGGA 367 1011 AACGCAGUGCAGACUGUGG 57 1011 AACGCAGUGCAGACUGUGG 57 1029 CCACAGUCUGCACUGCGUU 368 1029 GUCCGCCAGGGUGAGAACA 58 1029 GUCCGCCAGGGUGAGAACA 58 1047 UGUUCUCACCCUGGCGGAC 369 1047 AUCACCCUCAUGUGCAUUG 59 1047 AUCACCCUCAUGUGCAUUG 59 1065 CAAUGCACAUGAGGGUGAU 370 1065 GUGAUCGGGAAUGAGGUGG 60 1065 GUGAUCGGGAAUGAGGUGG 60 1083 CCACCUCAUUCCCGAUCAC 371 1083 GUCAACUUCGAGUGGACAU 61 1083 GUCAACUUCGAGUGGACAU 61 1101 AUGUCCACUCGAAGUUGAC 372 1101 UACCCCCGCAAAGAAAGUG 62 1101 UACCCCCGCAAAGAAAGUG 62 1119 CACUUUCUUUGCGGGGGUA 373 1119 GGGCGGCUGGUGGAGCCGG 63 1119 GGGCGGCUGGUGGAGCCGG 63 1137 CCGGCUCCACCAGCCGCCC 374 1137 GUGACUGACUUCCUCUUGG 64 1137 GUGACUGACUUCCUCUUGG 64 1155 CCAAGAGGAAGUCAGUCAC 375 1155 GAUAUGCCUUACCACAUCC 65 1155 GAUAUGCCUUACCACAUCC 65 1173 GGAUGUGGUAAGGCAUAUC 376 1173 CGCUCCAUCCUGCACAUCC 66 1173 CGCUCCAUCCUGCACAUCC 66 1191 GGAUGUGCAGGAUGGAGCG 377 1191 CCCAGUGCCGAGUUAGAAG 67 1191 CCCAGUGCCGAGUUAGAAG 67 1209 CUUCUAACUCGGCACUGGG 378 1209 GACUCGGGGACCUACACCU 68 1209 GACUCGGGGACCUACACCU 68 1227 AGGUGUAGGUCCCCCAGUC 379 1227 UGCAAUGUGACGGAGAGUG 69 1227 UGCAAUGUGACGGAGAGUG 69 1245 CACUCUCCGUCACAUUGCA 380 1245 GUGAAUGACCAUCAGGAUG 70 1245 GUGAAUGACCAUCAGGAUG 70 1263 CAUCCUGAUGGUCAUUCAC 381 1263 GAAAAGGCCAUCAACAUCA 71 1263 GAAAAGGCCAUCAACAUCA 71 1281 UGAUGUUGAUGGCCUUUUC 382 1281 ACCGUGGUUGAGAGCGGCU 72 1281 ACCGUGGUUGAGAGCGGCU 72 1299 AGCCGCUCUCAACCACGGU 383 1299 UACGUGCGGCUCCUGGGAG 73 1299 UACGUGCGGCUCCUGGGAG 73 1317 CUCCCAGGAGCCGCACGUA 384 1317 GAGGUGGGCACACUACAAU 74 1317 GAGGUGGGCACACUACAAU 74 1335 AUUGUAGUGUGCCCACCUC 385 1335 UUUGCUGAGCUGCAUCGGA 75 1335 UUUGCUGAGCUGCAUCGGA 75 1353 UCCGAUGCAGCUCAGCAAA 386 1353 AGCCGGACACUGCAGGUAG 76 1353 AGCCGGACACUGCAGGUAG 76 1371 CUACCUGCAGUGUCCGGCU 387 1371 GUGUUCGAGGCCUACCCAC 77 1371 GUGUUCGAGGCCUACCCAC 77 1389 GUGGGUAGGCCUCGAACAC 388 1389 CCGCCCACUGUCCUGUGGU 78 1389 CCGCCCACUGUCCUGUGGU 78 1407 ACCACAGGACAGUGGGCGG 389 1407 UUCAAAGACAACCGCACCC 79 1407 UUCAAAGACAACCGCACCC 79 1425 GGGUGCGGUUGUCUUUGAA 390 1425 CUGGGCGACUCCAGCGCUG 80 1425 CUGGGCGACUCCAGCGCUG 80 1443 CAGCGCUGGAGUCGCCCAG 391 1443 GGCGAAAUCGCCCUGUCCA 81 1443 GGCGAAAUCGCCCUGUCCA 81 1461 UGGACAGGGCGAUUUCGCC 392

1461 ACGCGCAACGUGUCGGAGA 82 1461 ACGCGCAACGUGUCGGAGA 82 1479 UCUCCGACACGUUGCGCGU 393 1479 ACCCGGUAUGUGUCAGAGC 83 1479 ACCCGGUAUGUGUCAGAGC 83 1497 GCUCUGACACAUACCGGGU 394 1497 CUGACACUGGUUCGCGUGA 84 1497 CUGACACUGGUUCGCGUGA 84 1515 UCACGCGAACCAGUGUCAG 395 1515 AAGGUGGCAGAGGCUGGCC 85 1515 AAGGUGGCAGAGGCUGGCC 85 1533 GGCCAGCCUCUGCCACCUU 396 1533 CACUACACCAUGCGGGCCU 86 1533 CACUACACCAUGCGGGCCU 86 1551 AGGCCCGCAUGGUGUAGUG 397 1551 UUCCAUGAGGAUGCUGAGG 87 1551 UUCCAUGAGGAUGCUGAGG 87 1569 CCUCAGCAUCCUCAUGGAA 398 1569 GUCCAGCUCUCCUUCCAGC 88 1569 GUCCAGCUCUCCUUCCAGC 88 1587 GCUGGAAGGAGAGCUGGAC 399 1587 CUACAGAUCAAUGUCCCUG 89 1587 CUACAGAUCAAUGUCCCUG 89 1605 CAGGGACAUUGAUCUGUAG 400 1605 GUCCGAGUGCUGGAGCUAA 90 1605 GUCCGAGUGCUGGAGCUAA 90 1623 UUAGCUCCAGCACUCGGAC 401 1623 AGUGAGAGCCACCCUGACA 91 1623 AGUGAGAGCCACCCUGACA 91 1641 UGUCAGGGUGGCUCUCACU 402 1641 AGUGGGGAACAGACAGUCC 92 1641 AGUGGGGAACAGACAGUCC 92 1659 GGACUGUCUGUUCCCCACU 403 1659 CGCUGUCGUGGCCGGGGCA 93 1659 CGCUGUCGUGGCCGGGGCA 93 1677 UGCCCCGGCCACGACAGCG 404 1677 AUGCCCCAGCCGAACAUCA 94 1677 AUGCCCCAGCCGAACAUCA 94 1695 UGAUGUUCGGCUGGGGCAU 405 1695 AUCUGGUCUGCCUGCAGAG 95 1695 AUCUGGUCUGCCUGCAGAG 95 1713 CUCUGCAGGCAGACCAGAU 406 1713 GACCUCAAAAGGUGUCCAC 96 1713 GACCUCAAAAGGUGUCCAC 96 1731 GUGGACACCUUUUGAGGUC 407 1731 CGUGAGCUGCCGCCCACGC 97 1731 CGUGAGCUGCCGCCCACGC 97 1749 GCGUGGGCGGCAGCUCACG 408 1749 CUGCUGGGGAACAGUUCCG 98 1749 CUGCUGGGGAACAGUUCCG 98 1767 CGGAACUGUUCCCCAGCAG 409 1767 GAAGAGGAGAGCCAGCUGG 99 1767 GAAGAGGAGAGCCAGCUGG 99 1785 CCAGCUGGCUCUCCUCUUC 410 1785 GAGACUAACGUGACGUACU 100 1785 GAGACUAACGUGACGUACU 100 1803 AGUACGUCACGUUAGUCUC 411 1803 UGGGAGGAGGAGCAGGAGU 101 1803 UGGGAGGAGGAGCAGGAGU 101 1821 ACUCCUGGUCCUCCUCCCA 412 1821 UUUGAGGUGGUGAGCACAC 102 1821 UUUGAGGUGGUGAGCACAC 102 1839 GUGUGCUCACCACCUCAAA 413 1839 CUGCGUCUGCAGCACGUGG 103 1839 CUGCGUCUGCAGCACGUGG 103 1857 CCACGUGCUGCAGACGCAG 414 1857 GAUCGGCCACUGUCGGUGC 104 1857 GAUCGGCCACUGUCGGUGC 104 1875 GCACCGACAGUGGCCGAUC 415 1875 CGCUGCACGCUGCGCAACG 105 1875 CGCUGCACGCUGCGCAACG 105 1893 CGUUGCGCAGCGUGCAGCG 416 1893 GCUGUGGGCCAGGACACGC 106 1893 GCUGUGGGCCAGGACACGC 106 1911 GCGUGUCCUGGCCCACAGC 417 1911 CAGGAGGUCAUCGUGGUGC 107 1911 CAGGAGGUCAUCGUGGUGC 107 1929 GCACCACGAUGACCUCCUG 418 1929 CCACACUCCUUGCCCUUUA 108 1929 CCACACUCCUUGCCCUUUA 108 1947 UAAAGGGCAAGGAGUGUGG 419 1947 AAGGUGGUGGUGAUCUCAG 109 1947 AAGGUGGUGGUGAUCUCAG 109 1965 CUGAGAUCACCACCACCUU 420 1965 GCCAUCCUGGCCCUGGUGG 110 1965 GCCAUCCUGGCCCUGGUGG 110 1983 CCACCAGGGCCAGGAUGGC 421 1983 GUGCUCACCAUCAUCUCCC 111 1983 GUGCUCACCAUCAUCUCCC 111 2001 GGGAGAUGAUGGUGAGCAC 422 2001 CUUAUCAUCCUCAUCAUGC 112 2001 CUUAUCAUCCUCAUCAUGC 112 2019 GCAUGAUGAGGAUGAUAAG 423 2019 CUUUGGCAGAAGAAGCCAC 113 2019 CUUUGGCAGAAGAAGCCAC 113 2037 GUGGCUUCUUCUGCCAAAG 424 2037 CGUUACGAGAUCCGAUGGA 114 2037 CGUUACGAGAUCCGAUGGA 114 2055 UCCAUCGGAUCUCGUAACG 425 2055 AAGGUGAUUGAGUCUGUGA 115 2055 AAGGUGAUUGAGUCUGUGA 115 2073 UCACAGACUCAAUCACCUU 426 2073 AGCUCUGACGGCCAUGAGU 116 2073 AGCUCUGACGGCCAUGAGU 116 2091 ACUCAUGGCCGUCAGAGCU 427 2091 UACAUCUACGUGGACCCCA 117 2091 UACAUCUACGUGGACCCCA 117 2109 UGGGGUCCACGUAGAUGUA 428 2109 AUGCAGCUGCCCUAUGACU 118 2109 AUGCAGCUGCCCUAUGACU 118 2127 AGUCAUAGGGCAGCUGCAU 429 2127 UCCACGUGGGAGCUGCCGC 119 2127 UCCACGUGGGAGCUGCCGC 119 2145 GCGGCAGCUCCCACGUGGA 430 2145 CGGGACCAGCUUGUGCUGG 120 2145 CGGGACCAGCUUGUGCUGG 120 2163 CCAGCACAAGCUGGUCCCG 431 2163 GGACGCACCCUCGGCUCUG 121 2163 GGACGCACCCUCGGCUCUG 121 2181 CAGAGCCGAGGGUGCGUCC 432 2181 GGGGCCUUUGGGCAGGUGG 122 2181 GGGGCCUUUGGGCAGGUGG 122 2199 CCACCUGCCCAAAGGCCCC 433 2199 GUGGAGGCCACGGCUCAUG 123 2199 GUGGAGGCCACGGCUCAUG 123 2217 CAUGAGCCGUGGCCUCCAC 434 2217 GGCCUGAGCCAUUCUCAGG 124 2217 GGCCUGAGCCAUUCUCAGG 124 2235 CCUGAGAAUGGCUCAGGCC 435 2235 GCCACGAUGAAAGUGGCCG 125 2235 GCCACGAUGAAAGUGGCCG 125 2253 CGGCCACUUUCAUCGUGGC 436 2253 GUCAAGAUGCUUAAAUCCA 126 2253 GUCAAGAUGCUUAAAUCCA 126 2271 UGGAUUUAAGCAUCUUGAC 437 2271 ACAGCCCGCAGCAGUGAGA 127 2271 ACAGCCCGCAGCAGUGAGA 127 2289 UCUCACUGCUGCGGGCUGU 438 2289 AAGCAAGCCCUUAUGUCGG 128 2289 AAGCAAGCCCUUAUGUCGG 128 2307 CCGACAUAAGGGCUUGCUU 439 2307 GAGCUGAAGAUCAUGAGUC 129 2307 GAGCUGAAGAUCAUGAGUC 129 2325 GACUCAUGAUCUUCAGCUC 440 2325 CACCUUGGGCCCCACCUGA 130 2325 CACCUUGGGCCCCACCUGA 130 2343 UCAGGUGGGGCCCAAGGUG 441 2343 AACGUGGUCAACCUGUUGG 131 2343 AACGUGGUCAACCUGUUGG 131 2361 CCAACAGGUUGACCACGUU 442 2361 GGGGCCUGCACCAAAGGAG 132 2361 GGGGCCUGCACCAAAGGAG 132 2379 CUCCUUUGGUGCAGGCCCC 443 2379 GGACCCAUCUAUAUCAUCA 133 2379 GGACCCAUCUAUAUCAUCA 133 2397 UGAUGAUAUAGAUGGGUCC 444 2397 ACUGAGUACUGCCGCUACG 134 2397 ACUGAGUACUGCCGCUACG 134 2415 CGUAGCGGCAGUACUCAGU 445 2415 GGAGACCUGGUGGACUACC 135 2415 GGAGACCUGGUGGACUACC 135 2433 GGUAGUCCACCAGGUCUCC 446 2433 CUGCACCGCAACAAACACA 136 2433 CUGCACCGCAACAAACACA 136 2451 UGUGUUUGUUGCGGUGCAG 447 2451 ACCUUCCUGCAGCACCACU 137 2451 ACCUUCCUGCAGCACCACU 137 2469 AGUGGUGCUGCAGGAAGGU 448 2469 UCCGACAAGCGCCGCCCGC 138 2469 UCCGACAAGCGCCGCCCGC 138 2487 GCGGGCGGCGCUUGUCGGA 449 2487 CCCAGCGCGGAGCUCUACA 139 2487 CCCAGCGCGGAGCUCUACA 139 2505 UGUAGAGCUCCGCGCUGGG 450 2505 AGCAAUGCUCUGCCCGUUG 140 2505 AGCAAUGCUCUGCCCGUUG 140 2523 CAACGGGCAGAGCAUUGCU 451 2523 GGGCUCCCCCUGCCCAGCC 141 2523 GGGCUCCCCCUGCCCAGCC 141 2541 GGCUGGGCAGGGGGAGCCC 452 2541 CAUGUGUCCUUGACCGGGG 142 2541 CAUGUGUCCUUGACCGGGG 142 2559 CCCCGGUCAAGGACACAUG 453 2559 GAGAGCGACGGUGGCUACA 143 2559 GAGAGCGACGGUGGCUACA 143 2577 UGUAGCCACCGUCGCUCUC 454 2577 AUGGACAUGAGCAAGGACG 144 2577 AUGGACAUGAGCAAGGACG 144 2595 CGUCCUUGCUCAUGUCCAU 455 2595 GAGUCGGUGGACUAUGUGC 145 2595 GAGUCGGUGGACUAUGUGC 145 2613 GCACAUAGUCCACCGACUC 456 2613 CCCAUGCUGGACAUGAAAG 146 2613 CCCAUGCUGGACAUGAAAG 146 2631 CUUUCAUGUCCAGCAUGGG 457 2631 GGAGACGUCAAAUAUGCAG 147 2631 GGAGACGUCAAAUAUGCAG 147 2649 CUGCAUAUUUGACGUCUCC 458 2649 GACAUCGAGUCCUCCAACU 148 2649 GACAUCGAGUCCUCCAACU 148 2667 AGUUGGAGGACUCGAUGUC 459 2667 UACAUGGCCCCUUACGAUA 149 2667 UACAUGGCCCCUUACGAUA 149 2685 UAUCGUAAGGGGCCAUGUA 460 2685 AACUACGUUCCCUCUGCCC 150 2685 AACUACGUUCCCUCUGCCC 150 2703 GGGCAGAGGGAACGUAGUU 461 2703 CCUGAGAGGACCUGCCGAG 151 2703 CCUGAGAGGACCUGCCGAG 151 2721 CUCGGCAGGUCCUCUCAGG 462 2721 GCAACUUUGAUCAACGAGU 152 2721 GCAACUUUGAUCAACGAGU 152 2739 ACUCGUUGAUCAAAGUUGC 463 2739 UCUCCAGUGCUAAGCUACA 153 2739 UCUCCAGUGCUAAGCUACA 153 2757 UGUAGCUUAGCACUGGAGA 464 2757 AUGGACCUCGUGGGCUUCA 154 2757 AUGGACCUCGUGGGCUUCA 154 2775 UGAAGCCCACGAGGUCCAU 465 2775 AGCUACCAGGUGGCCAAUG 155 2775 AGCUACCAGGUGGCCAAUG 155 2793 CAUUGGCCACCUGGUAGCU 466 2793 GGCAUGGAGUUUCUGGCCU 156 2793 GGCAUGGAGUUUCUGGCCU 156 2811 AGGCCAGAAACUCCAUGCC 467 2811 UCCAAGAACUGCGUCCACA 157 2811 UCCAAGAACUGCGUCCACA 157 2829 UGUGGACGCAGUUCUUGGA 468 2829 AGAGACCUGGCGGCUAGGA 158 2829 AGAGACCUGGCGGCUAGGA 158 2847 UCCUAGCCGCCAGGUCUCU 469 2847 AACGUGCUCAUCUGUGAAG 159 2847 AACGUGCUCAUCUGUGAAG 159 2865 CUUCACAGAUGAGCACGUU 470 2865 GGCAAGCUGGUCAAGAUCU 160 2865 GGCAAGCUGGUCAAGAUCU 160 2883 AGAUCUUGACCAGCUUGCC 471 2883 UGUGACUUUGGCCUGGCUC 161 2883 UGUGACUUUGGCCUGGCUC 161 2901 GAGCCAGGCCAAAGUCACA 472 2901 CGAGACAUCAUGCGGGACU 162 2901 CGAGACAUCAUGCGGGACU 162 2919 AGUCCCGGAUGAUGUCUCG 473 2919 UCGAAUUACAUCUCCAAAG 163 2919 UCGAAUUACAUCUCCAAAG 163 2937 CUUUGGAGAUGUAAUUCGA 474 2937 GGCAGCACCUUUUUGCCUU 164 2937 GGCAGCACCUUUUUGCCUU 164 2955 AAGGCAAAAAGGUGCUGCC 475 2955 UUAAAGUGGAUGGCUCCGG 165 2955 UUAAAGUGGAUGGCUCCGG 165 2973 CCGGAGCCAUCCACUUUAA 476

2973 GAGAGCAUCUUCAACAGCC 166 2973 GAGAGCAUCUUCAACAGCC 166 2991 GGCUGUUGAAGAUGCUCUC 477 2991 CUCUACACCACCCUGAGCG 167 2991 CUCUACACCACCCUGAGCG 167 3009 CGCUCAGGGUGGUGUAGAG 478 3009 GACGUGUGGUCCUUCGGGA 166 3009 GACGUGUGGUCCUUCGGGA 168 3027 UCCCGAAGGACCACACGUC 479 3027 AUCCUGCUCUGGGAGAUCU 169 3027 AUCCUGCUCUGGGAGAUCU 169 3045 AGAUCUCCCAGAGCAGGAU 480 3045 UUCACCUUGGGUGGCACCC 170 3045 UUCACCUUGGGUGGCACCC 170 3063 GGGUGCCACCCAAGGUGAA 481 3063 CCUUACCCAGAGCUGCCCA 171 3063 CCUUACCCAGAGCUGCCCA 171 3081 UGGGCAGCUCUGGGUAAGG 482 3081 AUGAACGAGCAGUUCUACA 172 3081 AUGAACGAGCAGUUCUACA 172 3099 UGUAGAACUGCUCGUUCAU 483 3099 AAUGCCAUCAAACGGGGUU 173 3099 AAUGCCAUCAAACGGGGUU 173 3117 AACCCCGUUUGAUGGCAUU 484 3117 UACCGCAUGGCCCAGCCUG 174 3117 UACCGCAUGGCCCAGCCUG 174 3135 CAGGCUGGGCCAUGCGGUA 485 3135 GCCCAUGCCUCCGACGAGA 175 3135 GCCCAUGCCUCCGACGAGA 175 3153 UCUCGUCGGAGGCAUGGGC 486 3153 AUCUAUGAGAUCAUGCAGA 176 3153 AUCUAUGAGAUCAUGCAGA 176 3171 UCUGCAUGAUCUCAUAGAU 487 3171 AAGUGCUGGGAAGAGAAGU 177 3171 AAGUGCUGGGAAGAGAAGU 177 3189 ACUUCUCUUCCCAGCACUU 488 3189 UUUGAGAUUCGGCCCCCCU 178 3189 UUUGAGAUUCGGCCCCCCU 178 3207 AGGGGGGCCGAAUCUCAAA 489 3207 UUCUCCCAGCUGGUGCUGC 179 3207 UUCUCCCAGCUGGUGCUGC 179 3225 GCAGCACCAGCUGGGAGAA 490 3225 CUUCUCGAGAGACUGUUGG 180 3225 CUUCUCGAGAGACUGUUGG 180 3243 CCAACAGUCUCUCGAGAAG 491 3243 GGCGAAGGUUACAAAAAGA 181 3243 GGCGAAGGUUACAAAAAGA 181 3261 UCUUUUUGUAACCUUCGCC 492 3261 AAGUACCAGCAGGUGGAUG 182 3261 AAGUACCAGCAGGUGGAUG 182 3279 CAUCCACCUGCUGGUACUU 493 3279 GAGGAGUUUCUGAGGAGUG 183 3279 GAGGAGUUUCUGAGGAGUG 183 3297 CACUCCUCAGAAACUCCUC 494 3297 GACCACCCAGCCAUCCUUC 184 3297 GACCACCCAGCCAUCCUUC 184 3315 GAAGGAUGGCUGGGUGGUC 495 3315 CGGUCCCAGGCCCGCUUGC 185 3315 CGGUCCCAGGCCCGCUUGC 185 3333 GCAAGCGGGCCUGGGACCG 496 3333 CCUGGGUUCCAUGGCCUCC 186 3333 CCUGGGUUCCAUGGCCUCC 186 3351 GGAGGCCAUGGAACCCAGG 497 3351 CGAUCUCCCCUGGACACCA 187 3351 CGAUCUCCCCUGGACACCA 187 3369 UGGUGUCCAGGGGAGAUCG 498 3369 AGCUCCGUCCUCUAUACUG 188 3369 AGCUCCGUCCUCUAUACUG 188 3387 CAGUAUAGAGGACGGAGCU 499 3387 GCCGUGCAGCCCAAUGAGG 189 3387 GCCGUGCAGCCCAAUGAGG 189 3405 CCUCAUUGGGCUGCACGGC 500 3405 GGUGACAACGACUAUAUCA 190 3405 GGUGACAACGACUAUAUCA 190 3423 UGAUAUAGUCGUUGUCACC 501 3423 AUCCCCCUGCCUGACCCCA 191 3423 AUCCCCCUGCCUGACCCCA 191 3441 UGGGGUCAGGCAGGGGGAU 502 3441 AAACCCGAGGUUGCUGACG 192 3441 AAACCCGAGGUUGCUGACG 192 3459 CGUCAGCAACCUCGGGUUU 503 3459 GAGGGCCCACUGGAGGGUU 193 3459 GAGGGCCCACUGGAGGGUU 193 3477 AACCCUCCAGUGGGCCCUC 504 3477 UCCCCCAGCCUAGCCAGCU 194 3477 UCCCCCAGCCUAGCCAGCU 194 3495 AGCUGGCUAGGCUGGGGGA 505 3495 UCCACCCUGAAUGAAGUCA 195 3495 UCCACCCUGAAUGAAGUCA 195 3513 UGACUUCAUUCAGGGUGGA 506 3513 AACACCUCCUCAACCAUCU 196 3513 AACACCUCCUCAACCAUCU 196 3531 AGAUGGUUGAGGAGGUGUU 507 3531 UCCUGUGACAGCCCCCUGG 197 3531 UCCUGUGACAGCCCCCUGG 197 3549 CCAGGGGGCUGUCACAGGA 508 3549 GAGCCCCAGGACGAACCAG 198 3549 GAGCCCCAGGACGAACCAG 198 3567 CUGGUUCGUCCUGGGGCUC 509 3567 GAGCCAGAGCCCCAGCUUG 199 3567 GAGCCAGAGCCCCAGCUUG 199 3585 CAAGCUGGGGCUCUGGCUC 510 3585 GAGCUCCAGGUGGAGCCGG 200 3585 GAGCUCCAGGUGGAGCCGG 200 3663 CCGGCUCCACCUGGAGCUC 511 3603 GAGCCAGAGCUGGAACAGU 201 3603 GAGCCAGAGCUGGAACAGU 201 3621 ACUGUUCCAGCUCUGGCUC 512 3621 UUGCCGGAUUCGGGGUGCC 202 3621 UUGCCGGAUUCGGGGUGCC 202 3639 GGCACCCCGAAUCCGGCAA 513 3639 CCUGCGCCUCGGGCGGAAG 203 3639 CCUGCGCCUCGGGCGGAAG 203 3657 CUUCCGCCCGAGGCGCAGG 514 3657 GCAGAGGAUAGCUUCCUGU 204 3657 GCAGAGGAUAGCUUCCUGU 204 3675 ACAGGAAGCUAUCCUCUGC 515 3675 UAGGGGGCUGGCCCCUACC 205 3675 UAGGGGGCUGGCCCCUACC 205 3693 GGUAGGGGCCAGCCCCCUA 516 3693 CCUGCCCUGCCUGAAGCUC 206 3693 CCUGCCCUGCCUGAAGCUC 206 3711 GAGCUUCAGGCAGGGCAGG 517 3711 CCCCCCCUGCCAGCACCCA 207 3711 CCCCCCCUGCCAGCACCCA 207 3729 UGGGUGCUGGCAGGGGGGG 518 3729 AGCAUCUCCUGGCCUGGCC 208 3729 AGCAUCUCCUGGCCUGGCC 208 3747 GGCCAGGCCAGGAGAUGCU 519 3747 CUGACCGGGCUUCCUGUCA 209 3747 CUGACCGGGCUUCCUGUCA 209 3765 UGACAGGAAGCCCGGUCAG 520 3765 AGCCAGGCUGCCCUUAUCA 210 3765 AGCCAGGCUGCCCUUAUCA 210 3783 UGAUAAGGGCAGCCUGGCU 521 3783 AGCUGUCCCCUUCUGGAAG 211 3783 AGCUGUCCCCUUCUGGAAG 211 3801 CUUCCAGAAGGGGACAGCU 522 3801 GCUUUCUGCUCCUGACGUG 212 3801 GCUUUCUGCUCCUGACGUG 212 3819 CACGUCAGGAGCAGAAAGC 523 3819 GUUGUGCCCCAAACCCUGG 213 3819 GUUGUGCCCCAAACCCUGG 213 3837 CCAGGGUUUGGGGCACAAC 524 3837 GGGCUGGCUUAGGAGGCAA 214 3837 GGGCUGGCUUAGGAGGCAA 214 3855 UUGCCUCCUAAGCCAGCCC 525 3855 AGAAAACUGCAGGGGCCGU 215 3855 AGAAAACUGCAGGGGCCGU 215 3873 ACGGCCCCUGCAGUUUUCU 526 3873 UGACCAGCCCUCUGCCUCC 216 3873 UGACCAGCCCUCUGCCUCC 216 3891 GGAGGCAGAGGGCUGGUCA 527 3891 CAGGGAGGCCAACUGACUC 217 3891 CAGGGAGGCCAACUGACUC 217 3909 GAGUCAGUUGGCCUCCCUG 528 3909 CUGAGCCAGGGUUCCCCCA 218 3909 CUGAGCCAGGGUUCCCCCA 218 3927 UGGGGGAACCCUGGCUCAG 529 3927 AGGGAACUCAGUUUUCCCA 219 3927 AGGGAACUCAGUUUUCCCA 219 3945 UGGGAAAACUGAGUUCCCU 530 3945 AUAUGUAAGAUGGGAAAGU 220 3945 AUAUGUAAGAUGGGAAAGU 220 3963 ACUUUCCCAUCUUACAUAU 531 3963 UUAGGCUUGAUGACCCAGA 221 3963 UUAGGCUUGAUGACCCAGA 221 3981 UCUGGGUCAUCAAGCCUAA 532 3981 AAUCUAGGAUUCUCUCCCU 222 3981 AAUCUAGGAUUCUCUCCCU 222 3999 AGGGAGAGAAUCCUAGAUU 533 3999 UGGCUGACAGGUGGGGAGA 223 3999 UGGCUGACAGGUGGGGAGA 223 4017 UCUCCCCACCUGUCAGCCA 534 4017 ACCGAAUCCCUCCCUGGGA 224 4017 ACCGAAUCCCUCCCUGGGA 224 4035 UCCCAGGGAGGGAUUCGGU 535 4035 AAGAUUCUUGGAGUUACUG 225 4035 AAGAUUCUUGGAGUUACUG 225 4053 CAGUAACUCCAAGAAUCUU 536 4053 GAGGUGGUAAAUUAACUUU 226 4053 GAGGUGGUAAAUUAACUUU 226 4071 AAAGUUAAUUUACCACCUC 537 4071 UUUUCUGUUCAGCCAGCUA 227 4071 UUUUCUGUUCAGCCAGCUA 227 4089 UAGCUGGCUGAACAGAAAA 538 4089 ACCCCUCAAGGAAUCAUAG 228 4089 ACCCCUCAAGGAAUCAUAG 228 4107 CUAUGAUUCCUUGAGGGGU 539 4107 GCUCUCUCCUCGCACUUUU 229 4107 GCUCUCUCCUCGCACUUUU 229 4125 AAAAGUGCGAGGAGAGAGC 540 4125 UUAUCCACCCAGGAGCUAG 230 4125 UUAUCCACCCAGGAGCUAG 230 4143 CUAGCUCCUGGGUGGAUAA 541 4143 GGGAAGAGACCCUAGCCUC 231 4143 GGGAAGAGACCCUAGCCUC 231 4161 GAGGCUAGGGUCUCUUCCC 542 4161 CCCUGGCUGCUGGCUGAGC 232 4161 CCCUGGCUGCUGGCUGAGC 232 4179 GCUCAGCCAGCAGCCAGGG 543 4179 CUAGGGCCUAGCCUUGAGC 233 4179 CUAGGGCCUAGCCUUGAGC 233 4197 GCUCAAGGCUAGGCCCUAG 544 4197 CAGUGUUGCCUCAUCCAGA 234 4197 CAGUGUUGCCUCAUCCAGA 234 4215 UCUGGAUGAGGCAACACUG 545 4215 AAGAAAGCCAGUCUCCUCC 235 4215 AAGAAAGCCAGUCUCCUCC 235 4233 GGAGGAGACUGGCUUUCUU 546 4233 CCUAUGAUGCCAGUCCCUG 236 4233 CCUAUGAUGCCAGUCCCUG 236 4251 CAGGGACUGGCAUCAUAGG 547 4251 GCGUUCCCUGGCCCGAGCU 237 4251 GCGUUCCCUGGCCCGAGCU 237 4269 AGCUCGGGCCAGGGAACGC 548 4269 UGGUCUGGGGCCAUUAGGC 238 4269 UGGUCUGGGGCCAUUAGGC 238 4287 GCCUAAUGGCCCCAGACCA 549 4287 CAGCCUAAUUAAUGCUGGA 239 4287 CAGCCUAAUUAAUGCUGGA 239 4305 UCCAGCAUUAAUUAGGCUG 550 4305 AGGCUGAGCCAAGUACAGG 240 4305 AGGCUGAGCCAAGUACAGG 240 4323 CCUGUACUUGGCUCAGCCU 551 4323 GACACCCCCAGCCUGCAGC 241 4323 GACACCCCCAGCCUGCAGC 241 4341 GCUGCAGGCUGGGGGUGUC 552 4341 CCCUUGCCCAGGGCACUUG 242 4341 CCCUUGCCCAGGGCACUUG 242 4359 CAAGUGCCCUGGGCAAGGG 553 4359 GGAGCACACGCAGCCAUAG 243 4359 GGAGCACACGCAGCCAUAG 243 4377 CUAUGGCUGCGUGUGCUCC 554 4377 GCAAGUGCCUGUGUCCCUG 244 4377 GCAAGUGCCUGUGUCCCUG 244 4395 CAGGGACACAGGCACUUGC 555 4395 GUCCUUCAGGCCCAUCAGU 245 4395 GUCCUUCAGGCCCAUCAGU 245 4413 ACUGAUGGGCCUGAAGGAC 556 4413 UCCUGGGGCUUUUUCUUUA 246 4413 UCCUGGGGCUUUUUCUUUA 246 4431 UAAAGAAAAAGCCCCAGGA 557 4431 AUCACCCUCAGUCUUAAUC 247 4431 AUCACCCUCAGUCUUAAUC 247 4449 GAUUAAGACUGAGGGUGAU 558 4449 CCAUCCACCAGAGUCUAGA 248 4449 CCAUCCACCAGAGUCUAGA 248 4467 UCUAGACUCUGGUGGAUGG 559 4467 AAGGCCAGACGGGCCCCGC 249 4467 AAGGCCAGACGGGCCCCGC 249 4485

GCGGGGCCCGUCUGGCCUU 560 4485 CAUCUGUGAUGAGAAUGUA 250 4485 CAUCUGUGAUGAGAAUGUA 250 4503 UACAUUCUCAUCACAGAUG 561 4503 AAAUGUGCCAGUGUGGAGU 251 4503 AAAUGUGCCAGUGUGGAGU 251 4521 ACUCCACACUGGCACAUUU 562 4521 UGGCCACGUGUGUGUGCCA 252 4521 UGGCCACGUGUGUGUGCCA 252 4539 UGGCACACACACGUGGCCA 563 4539 AGUAUAUGGCCCUGGCUCU 253 4539 AGUAUAUGGCCCUGGCUCU 253 4557 AGAGCCAGGGCCAUAUACU 564 4557 UGCAUUGGACCUGCUAUGA 254 4557 UGCAUUGGACCUGCUAUGA 254 4575 UCAUAGCAGGUCCAAUGCA 565 4575 AGGCUUUGGAGGAAUCCCU 255 4575 AGGCUUUGGAGGAAUCCCU 255 4593 AGGGAUUCCUCCAAAGCCU 566 4593 UCACCCUCUCUGGGCCUCA 256 4593 UCACCCUCUCUGGGCCUCA 256 4611 UGAGGCCCAGAGAGGGUGA 567 4611 AGUUUCCCCUUCAAAAAAU 257 4611 AGUUUCCCCUUCAAAAAAU 257 4629 AUUUUUUGAAGGGGAAACU 568 4629 UGAAUAAGUCGGACUUAUU 258 4629 UGAAUAAGUCGGACUUAUU 258 4647 AAUAAGUCCGACUUAUUCA 569 4647 UAACUCUGAGUGCCUUGCC 259 4647 UAACUCUGAGUGCCUUGCC 259 4665 GGCAAGGCACUCAGAGUUA 570 4665 CAGCACUAACAUUCUAGAG 260 4665 CAGCACUAACAUUCUAGAG 260 4683 CUCUAGAAUGUUAGUGCUG 571 4683 GUAUUCCAGGUGGUUGCAC 261 4683 GUAUUCCAGGUGGUUGCAC 261 4701 GUGCAACCACCUGGAAUAC 572 4701 CAUUUGUCCAGAUGAAGCA 262 4701 CAUUUGUCCAGAUGAAGCA 262 4719 UGCUUCAUCUGGACAAAUG 573 4719 AAGGCCAUAUACCCUAAAC 263 4719 AAGGCCAUAUACCCUAAAC 263 4737 GUUUAGGGUAUAUGGCCUU 574 4737 CUUCCAUCCUGGGGGUCAG 264 4737 CUUCCAUCCUGGGGGUCAG 264 4755 CUGACCCCCAGGAUGGAAG 575 4755 GCUGGGCUCCUGGGAGAUU 265 4755 GCUGGGCUCCUGGGAGAUU 265 4773 AAUCUCCCAGGAGCCCAGC 576 4773 UCCAGAUCACACAUCACAC 266 4773 UCCAGAUCACACAUCACAC 266 4791 GUGUGAUGUGUGAUCUGGA 577 4791 CUCUGGGGACUCAGGAACC 267 4791 CUCUGGGGACUCAGGAACC 267 4809 GGUUCCUGAGUCCCCAGAG 578 4809 CAUGCCCCUUCCCCAGGCC 268 4809 CAUGCCCCUUCCCCAGGCC 268 4827 GGCCUGGGGAAGGGGCAUG 579 4827 CCCCAGCAAGUCUCAAGAA 269 4827 CCCCAGCAAGUCUCAAGAA 269 4845 UUCUUGAGACUUGCUGGGG 580 4845 ACACAGCUGCACAGGCCUU 270 4845 ACACAGCUGCACAGGCCUU 270 4863 AAGGCCUGUGCAGCUGUGU 581 4863 UGACUUAGAGUGACAGCCG 271 4863 UGACUUAGAGUGACAGCCG 271 4881 CGGCUGUCACUCUAAGUCA 582 4881 GGUGUCCUGGAAAGCCCCA 272 4881 GGUGUCCUGGAAAGCCCCA 272 4899 UGGGGCUUUCCAGGACACC 583 4899 AAGCAGCUGCCCCAGGGAC 273 4899 AAGCAGCUGCCCCAGGGAC 273 4917 GUCCCUGGGGCAGCUGCUU 584 4917 CAUGGGAAGACCACGGGAC 274 4917 CAUGGGAAGACCACGGGAC 274 4935 GUCCCGUGGUCUUCCCAUG 585 4935 CCUCUUUCACUACCCACGA 275 4935 CCUCUUUCACUACCCACGA 275 4953 UCGUGGGUAGUGAAAGAGG 586 4953 AUGACCUCCGGGGGUAUCC 276 4953 AUGACCUCCGGGGGUAUCC 276 4971 GGAUACCCCCGGAGGUCAU 587 4971 CUGGGCAAAAGGGACAAAG 277 4971 CUGGGCAAAAGGGACAAAG 277 4989 CUUUGUCCCUUUUGCCCAG 588 4989 GAGGGCAAAUGAGAUCACC 278 4989 GAGGGCAAAUGAGAUCACC 278 5007 GGUGAUCUCAUUUGCCCUC 589 5007 CUCCUGCAGCCCACCACUC 279 5007 CUCCUGCAGCCCACCACUC 279 5025 GAGUGGUGGGCUGCAGGAG 590 5025 CCAGCACCUGUGCCGAGGU 280 5025 CCAGCACCUGUGCCGAGGU 280 5043 ACCUCGGCACAGGUGCUGG 591 5043 UCUGCGUCGAAGACAGAAU 281 5043 UCUGCGUCGAAGACAGAAU 281 5061 AUUCUGUCUUCGACGCAGA 592 5061 UGGACAGUGAGGACAGUUA 282 5061 UGGACAGUGAGGACAGUUA 282 5079 UAACUGUCCUCACUGUCCA 593 5079 AUGUCUUGUAAAAGACAAG 283 5079 AUGUCUUGUAAAAGACAAG 283 5097 CUUGUCUUUUACAAGACAU 594 5097 GAAGCUUCAGAUGGUACCC 284 5097 GAAGCUUCAGAUGGUACCC 284 5115 GGGUACCAUCUGAAGCUUC 595 5115 CCAAGAAGGAUGUGAGAGG 285 5115 CCAAGAAGGAUGUGAGAGG 285 5133 CCUCUCACAUCCUUCUUGG 596 5133 GUGGCCGCUUGGAGUUUGC 286 5133 GUGGCCGCUUGGAGUUUGC 286 5151 GCAAACUCCAAGCGGCCAC 597 5151 CCCCUCACCCACCAGCUGC 287 5151 CCCCUCACCCACCAGCUGC 287 5169 GCAGCUGGUGGGUGAGGGG 598 5169 CCCCAUCCCUGAGGCAGCG 288 5169 CCCCAUCCCUGAGGCAGCG 288 5187 CGCUGCCUCAGGGAUGGGG 599 5187 GCUCCAUGGGGGUAUGGUU 289 5187 GCUCCAUGGGGGUAUGGUU 289 5205 AACCAUACCCCCAUGGAGC 600 5205 UUUGUCACUGCCCAGACCU 290 5205 UUUGUCACUGCCCAGACCU 290 5223 AGGUCUGGGCAGUGACAAA 601 5223 UAGCAGUGACAUCUCAUUG 291 5223 UAGCAGUGACAUCUCAUUG 291 5241 CAAUGAGAUGUCACUGCUA 602 5241 GUCCCCAGCCCAGUGGGCA 292 5241 GUCCCCAGCCCAGUGGGCA 292 5259 UGCCCACUGGGCUGGGGAC 603 5259 AUUGGAGGUGCCAGGGGAG 293 5259 AUUGGAGGUGCCAGGGGAG 293 5277 CUCCCCUGGCACCUCCAAU 604 5277 GUCAGGGUUGUAGCCAAGA 294 5277 GUCAGGGUUGUAGCCAAGA 294 5295 UCUUGGCUACAACCCUGAC 605 5295 ACGCCCCCGCACGGGGAGG 295 5295 ACGCCCCCGCACGGGGAGG 295 5313 CCUCCCCGUGCGGGGGCGU 606 5313 GGUUGGGAAGGGGGUGCAG 296 5313 GGUUGGGAAGGGGGUGCAG 296 5331 CUGCACCCCCUUCCCAACC 607 5331 GGAAGCUCAACCCCUCUGG 297 5331 GGAAGCUCAACCCCUCUGG 297 5349 CCAGAGGGGUUGAGCUUCC 608 5349 GGCACCAACCCUGCAUUGC 298 5349 GGCACCAACCCUGCAUUGC 298 5367 GCAAUGCAGGGUUGGUGCC 609 5367 CAGGUUGGCACCUUACUUC 299 5367 CAGGUUGGCACCUUACUUC 299 5385 GAAGUAAGGUGCCAACCUG 610 5385 CCCUGGGAUCCCCAGAGUU 300 5385 CCCUGGGAUCCCCAGAGUU 300 5403 AACUCUGGGGAUCCCAGGG 611 5403 UGGUCCAAGGAGGGAGAGU 301 5403 UGGUCCAAGGAGGGAGAGU 301 5421 ACUCUCCCUCCUUGGACCA 612 5421 UGGGUUCUCAAUACGGUAC 302 5421 UGGGUUCUCAAUACGGUAC 302 5439 GUACCGUAUUGAGAACCCA 613 5439 CCAAAGAUAUAAUCACCUA 303 5439 CCAAAGAUAUAAUCACCUA 303 5457 UAGGUGAUUAUAUCUUUGG 614 5457 AGGUUUACAAAUAUUUUUA 304 5457 AGGUUUACAAAUAUUUUUA 304 5475 UAAAAAUAUUUGUAAACCU 615 5475 AGGACUCACGUUAACUCAC 305 5475 AGGACUCACGUUAACUCAC 305 5493 GUGAGUUAACGUGAGUCCU 616 5493 CAUUUAUACAGCAGAAAUG 306 5493 CAUUUAUACAGCAGAAAUG 306 5511 CAUUUCUGCUGUAUAAAUG 617 5511 GCUAUUUUGUAUGCUGUUA 307 5511 GCUAUUUUGUAUGCUGUUA 307 5529 UAACAGCAUACAAAAUAGC 618 5529 AAGUUUUUCUAUCUGUGUA 308 5529 AAGUUUUUCUAUCUGUGUA 308 5547 UACACAGAUAGAAAAACUU 619 5547 ACUUUUUUUUAAGGGAAAG 309 5547 ACUUUUUUUUAAGGGAAAG 309 5565 CUUUCCCUUAAAAAAAAGU 620 5565 GAUUUUAAUAUUAAACCUG 310 5565 GAUUUUAAUAUUAAACCUG 310 5583 CAGGUUUAAUAUUAAAAUC 621 5578 AACCUGGUGCUUCUCACUC 311 5578 AACCUGGUGCUUCUCACUC 311 5596 GAGUGAGAAGCACCAGGUU 622 The 3'-ends of the Upper sequence and the Lower sequence of the siNA construct can include an overhang sequence, for example about 1, 2, 3, or 4 nucleotides in length, preferably 2 nucleotides in length, wherein the overhanging sequence of the lower sequence is optionally complementary to a portion of the target sequence. The upper sequence is also referred to as the sense strand, whereas the lower sequence is also referred to as the antisense strand. The upper and lower sequences in the Table can further comprise a chemical modification having Formulae I-VII, such as exemplary siNA constructs shown in FIGS. 4 and 5, or having modifications described in Table IV or any combination thereof.

TABLE-US-00003 TABLE III PDGFRB Synthetic Modified siNA Constructs Target Seq Seq Pos Target ID Cmpd# Aliases Sequence ID 422 UGCCUGUCCUUCUACUCAGCUGU 623 31910 PDGFRB:208U21 sense siNA CCUGUCCUUCUACUCAGCUTT 631 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:949U21 sense siNA AGGUGGAUUCUGAUGCCUATT 632 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1325U21 sense siNA CACACUACAAUUUGCUGAGTT 633 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1610U21 sense siNA AGUGCUGGAGCUAAGUGAGTT 634 616 CUCGAAUUACAUCUCCAAAGGCA 627 31911 PDGFRB:2920U21 sense siNA CGAAUUACAUCUCCAAAGGTT 635 681 CUGCUAUGAGGCUUUGGAGGAAU 628 31912 PDGFRB:4569U21 sense siNA GCUAUGAGGCUUUGGAGGATT 636 751 GACAAAGAGGGCAAAUGAGAUCA 629 31913 PDGFRB:4985U21 sense siNA CAAAGAGGGCAAAUGAGAUTT 637 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5415U21 sense siNA GGAGAGUGGGUUCUCAAUATT 638 422 UGCCUGUCCUUCUACUCAGCUGU 623 31914 PDGFRB:226L21 antisense siNA AGCUGAGUAGAAGGACAGGTT 639 (208C) 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA UAGGCAUCAGAAUCCACCUTT 640 (949C) 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA CUCAGCAAAUUGUAGUGUGTT 641 (1325C) 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA CUCACUUAGCUCCAGCACUTT 642 (1610C) 616 CUCGAAUUAGAUCUCCAAAGGCA 627 31915 PDGFRB:2938L21 antisense siNA CCUUUGGAGAUGUAAUUCGTT 643 (2920C) 681 CUGCUAUGAGGCUUUGGAGGAAU 628 31916 PDGFRB:4587L21 antisense siNA UCCUCCAAAGCCUCAUAGCTT 644 (4569C) 751 GACAAAGAGGGCAAAUGAGAUCA 629 31917 PDGFRB:5003L21 antisense siNA AUCUCAUUUGCCCUCUUUGTT 645 (4985C) 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA UAUUGAGAACCCACUCUCCTT 646 (5415C) 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:208U21 sense siNA stab04 B ccuGuccuucuAcucAGcuTT B 647 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:949U21 sense siNA stab04 B AGGuGGAuucuGAuGccuATT B 648 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1325U21 sense siNA stab04 B cAcAcuAcAAuuuGcuGAGTT B 649 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1610U21 sense siNA stab04 B AGuGcuGGAGcuAAGuGAGTT B 650 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2920U21 sense siNA stab04 B cGAAuuAcAucuccAAAGGTT B 651 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4569U21 sense siNA stab04 B GcuAuGAGGcuuuGGAGGATT B 652 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:4985U21 sense siNA stab04 B cAAAGAGGGcAAAuGAGAuTT B 653 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5415U21 sense siNA stab04 B GGAGAGuGGGuucucAAuATT B 654 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:226L21 antisense siNA AGcuGAGuAGAAGGAcAGGTsT 655 (208C) stab05 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA uAGGcAucAGAAuccAccuTsT 656 (949C) stab05 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA cucAGcAAAuuGuAGuGuGTsT 657 (1325C) stab05 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA cucAcuuAGcuccAGcAcuTsT 658 (1610C) stab05 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2938L21 antisense siNA ccuuuGGAGAuGuAAuucGTsT 659 (2920C) stab05 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4587L21 antisense siNA uccuccAAAGccucAuAGcTsT 660 (4569C) stab05 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:5003L21 antisense siNA AucucAuuuGcccucuuuGTsT 661 (4985C) stab05 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA uAuuGAGAAcccAcucuccTsT 662 (5415C) stab05 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:208U21 sense siNA stab07 B ccuGuccuucuAcucAGcuTT B 663 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:949U21 sense siNA stab07 B AGGuGGAuucuGAuGccuATT B 664 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1325U21 sense siNA stab07 B cAcAcuAcAAuuuGcuGAGTT B 665 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1610U21 sense siNA stab07 B AGuGcuGGAGcuAAGuGAGTT B 666 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2920U21 sense siNA stab07 B cGAAuuAcAucuccAAAGGTT B 667 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4569U21 sense siNA stab07 B GcuAuGAGGcuuuGGAGGATT B 668 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:4985U21 sense siNA stab07 B cAAAGAGGGcAAAuGAGAuTT B 669 815 AGGGAGAGUGGGUUGUCAAUACG 630 PDGFRB:5415U21 sense siNA stab07 B GGAGAGuGGGuucucAAuATT B 670 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:226L21 antisense siNA AGcuGAGuAGAAGGAcAGGTsT 671 (208C) stab11 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA uAGGcAucAGAAuccAccuTsT 672 (949C) stab11 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA cucAGcAAAuuGuAGuGuGTsT 673 (1325C) stab11 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA cucAcuuAGcuccAGcAcuTsT 674 (1610C) stab11 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2938L21 antisense siNA ccuuuGGAGAuGuAAuucGTsT 675 (2920C) stab11 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4587L21 antisense siNA uccuccAAAGccucAuAGcTsT 676 (4569C) stab11 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:5003L21 antisense siNA AucucAuuuGcccucuuuGTsT 677 (4985C) stab11 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA uAuuGAGAAcccAcucuccTsT 678 (5415C) stab11 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:208U21 sense siNA stab18 B ccuGuccuucuAcucAGcuTT B 679 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:949U21 sense siNA stab18 B AGGuGGAuucuGAuGccuATT B 680 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1325U21 sense siNA stab18 B cAcAcuAcAAuuuGcuGAGTT B 681 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1610U21 sense siNA stab18 B AGuGcuGGAGcuAAGuGAGTT B 682 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2920U21 sense siNA stab18 B cGAAuuAcAucuccAAAGGTT B 683 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4569U21 sense siNA stab18 B GcuAuGAGGcuuuGGAGGATT B 684 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:4985U21 sense siNA stab18 B cAAAGAGGGcAAAuGAGAuTT B 685 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5415U21 sense siNA stab18 B GGAGAGuGGGuucucAAuATT B 686 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:226L21 antisense siNA AGcuGAGuAGAAGGAcAGGTsT 687 (208C) stab08 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA uAGGcAucAGAAuccAccuTsT 688 (949C) stab08 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA cucAGcAAAuuGuAGuGuGTsT 689 (1325C) stab08 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA cucAcuuAGcuccAGcAcuTsT 690 (1610C) stab08 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2938L21 antisense siNA ccuuuGGAGAuGuAAuucGTsT 691 (2920C) stab08 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4587L21 antisense siNA uccuccAAAGccucAuAGcTsT 692 (4569C) stab08 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:5003L21 antisense siNA AucucAuuuGcccucuuuGTsT 693 (4985C) stab08 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA uAuuGAGAAcccAcucuccTsT 694 (5415C) stab08 422 UGCCUGUCCUUCUACUCAGCUGU 623 37092 PDGFRB:208U21 sense siNA stab09 B CCUGUCCUUCUACUCAGCUTT B 695 427 GGAGGUGGAUUCUGAUGCCUACU 624 37093 PDGFRB:949U21 sense siNA stab09 B AGGUGGAUUCUGAUGCCUATT B 696 506 GGCACACUACAAUUUGCUGAGCU 625 37094 PDGFRB:1325U21 sense siNA stab09 B CACACUACAAUUUGCUGAGTT B 697 511 CGAGUGCUGGAGCUAAGUGAGAG 626 37095 PDGFRB:1610U21 sense siNA stab09 B AGUGCUGGAGCUAAGUGAGTT B 698 616 CUCGAAUUACAUCUCCAAAGGCA 627 37096 PDGFRB:2920U21 sense siNA stab09 B CGAAUUACAUCUCCAAAGGTT B 699 681 CUGCUAUGAGGCUUUGGAGGAAU 628 37097 PDGFRB:4569U21 sense siNA stab09 B GCUAUGAGGCUUUGGAGGATT B 700 751 GACAAAGAGGGCAAAUGAGAUCA 629 37098 PDGFRB:4985U21 sense siNA stab09 B CAAAGAGGGCAAAUGAGAUTT B 701

815 AGGGAGAGUGGGUUCUCAAUACG 630 37099 PDGFRB:5415U21 sense siNA stab09 B GGAGAGUGGGUUCUCAAUATT B 702 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:226L21 antisense siNA AGCUGAGUAGAAGGACAGGTsT 703 (208C) stab10 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA UAGGCAUCAGAAUCCACCUTsT 704 (949C) stab10 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA CUCAGCAAAUUGUAGUGUGTsT 705 (1325C) stab10 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA CUCACUUAGCUCCAGCACUTsT 706 (1610C) stab10 616 CUCGAAUUACAUCUC0AAAGGCA 627 PDGFRB:2938L21 antisense siNA CCUUUGGAGAUGUAAUUCGTsT 707 (2920C) stab10 681 CUGCUAUGAGGCUUUGGAGGAAU 626 PDGFRB:4587L21 antisense siNA UCCUCCAAAGCCUCAUAGCTsT 708 (4569C) stab10 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:5003L21 antisense siNA AUCUCAUUUGCCCUCUUUGTsT 709 (4985C) stab10 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA UAUUGAGAACCCACUCUCCTsT 710 (5415C) stab10 422 UGCCUGUCCUUCUACUCAGCUGU 623 PDGFRB:226L21 antisense siNA AGcuGAGuAGAAGGAcAGGTT B 711 (208C) stab19 427 GGAGGUGGAUUCUGAUGCCUACU 624 PDGFRB:967L21 antisense siNA uAGGcAucAGAAuCcAccuTT B 712 (949C) stab19 506 GGCACACUACAAUUUGCUGAGCU 625 PDGFRB:1343L21 antisense siNA cucAGcAAAuuGuAGuGuGTT B 713 (1325C) stab19 511 CGAGUGCUGGAGCUAAGUGAGAG 626 PDGFRB:1628L21 antisense siNA cucAcuuAGcuccAGcAcuTT B 714 (1610C) stab19 616 CUCGAAUUACAUCUCCAAAGGCA 627 PDGFRB:2938L21 antisense siNA ccuuuGGAGAuGuAAuucGTT B 715 (2920C) stab19 681 CUGCUAUGAGGCUUUGGAGGAAU 628 PDGFRB:4587L21 antisense siNA uccuccAAAGccucAuAGcTT B 716 (4569C) stab19 751 GACAAAGAGGGCAAAUGAGAUCA 629 PDGFRB:5003L21 antisense siNA AucucAuuuGcccucuuuGTT B 717 (4985C) stab19 815 AGGGAGAGUGGGUUCUCAAUACG 630 PDGFRB:5433L21 antisense siNA uAuuGAGAAcccAcucuccTT B 718 (5415C) stab19 422 UGCCUGUCCUUCUACUCAGCUGU 623 37100 PDGFRB:226L21 antisense siNA AGCUGAGUAGAAGGACAGGTT B 719 (208C) stab22 427 GGAGGUGGAUUCUGAUGCCUACU 624 37101 PDGFRB:967L21 antisense siNA UAGGCAUCAGAAUCCACCUTT B 720 (949C) stab22 506 GGCACACUACAAUUUGCUGAGCU 625 37102 PDGFRB:1343121 antisense siNA CUCAGCAAAUUGUAGUGUGTT B 721 (1325C) stab22 511 CGAGUGCUGGAGCUAAGUGAGAG 626 37103 PDGFRB:1628L21 antisense siNA CUCACUUAGCUCCAGCACUTT B 722 (1610C) stab22 616 CUCGAAUUACAUCUCCAAAGGCA 627 37104 PDGFRB:2938L21 antisense siNA CCUUUGGAGAUGUAAUUCGTT B 723 (2920C) stab22 681 CUGCUAUGAGGCUUUGGAGGAAU 628 37105 PDGFRB:4587L21 antisense siNA UCCUCCAAAGCCUCAUAGCTT B 724 (4569C) stab22 751 GACAAAGAGGGCAAAUGAGAUCA 629 37106 PDGFRB:5003L21 antisense siNA AUCUCAUUUGCCCUCUUUGTT B 725 (4985C) stab22 815 AGGGAGAGUGGGUUCUCAAUACG 630 37107 PDGFRB:5433L21 antisense siNA UAUUGAGAACCCACUCUCCTT B 726 (5415C) stab22 Uppercase = ribonucleotide u,c = 2'-deoxy-2'-fluoro U,C T = thymidine B = inverted deoxy abasic s = phosphorothioate linkage A = deoxy Adenosine G = deoxy Guanosine G = 2'-O-methyl Guanosine A = 2'-O-methyl Adenosine

TABLE-US-00004 TABLE IV Non-limiting examples of Stabilization Chemistries for chemically modified siNA constructs Chemistry pyrimidine Purine cap p = S Strand "Stab 00" Ribo Ribo S/AS "Stab 1" Ribo Ribo -- 5 at 5'-end S/AS 1 at 3'-end "Stab 2" Ribo Ribo -- All Usually AS linkages "Stab 3" 2'-fluoro Ribo -- 4 at 5'-end Usually S 4 at 3'-end "Stab 4" 2'-fluoro Ribo 5' and 3'- -- Usually S ends "Stab 5" 2'-fluoro Ribo -- 1 at 3'-end Usually AS "Stab 6" 2'-O- Ribo 5' and 3'- -- Usually S Methyl ends "Stab 7" 2'-fluoro 2'-deoxy 5' and 3'- -- Usually S ends "Stab 8" 2'-fluoro 2'-O- -- 1 at 3'-end S/AS Methyl "Stab 9" Ribo Ribo 5' and 3'- -- Usually S ends "Stab 10" Ribo Ribo -- 1 at 3'-end Usually AS "Stab 11" 2'-fluoro 2'-deoxy -- 1 at 3'-end Usually AS "Stab 12" 2'-fluoro LNA 5' and 3'- Usually S ends "Stab 13" 2'-fluoro LNA 1 at 3'-end Usually AS "Stab 14" 2'-fluoro 2'-deoxy 2 at 5'-end Usually AS 1 at 3'-end "Stab 15" 2'-deoxy 2'-deoxy 2 at 5'-end Usually AS 1 at 3'-end "Stab 16" Ribo 2'-O- 5' and 3'- Usually S Methyl ends "Stab 17" 2'-O- 2'-O- 5' and 3'- Usually S Methyl Methyl ends "Stab 18" 2'-fluoro 2'-O- 5' and 3'- Usually S Methyl ends "Stab 19" 2'-fluoro 2'-O- 3'-end S/AS Methyl "Stab 20" 2'-fluoro 2'-deoxy 3'-end Usually AS "Stab 21" 2'-fluoro Ribo 3'-end Usually AS "Stab 22" Ribo Ribo 3'-end Usually AS "Stab 23" 2'-fluoro* 2'-deoxy* 5' and 3'- Usually S ends "Stab 24" 2'-fluoro* 2'-O- -- 1 at 3'-end S/AS Methyl* "Stab 25" 2'-fluoro* 2'-O- -- 1 at 3'-end S/AS Methyl* "Stab 26" 2'-fluoro* 2'-O- -- S/AS Methyl* "Stab 27" 2'-fluoro* 2'-O- 3'-end S/AS Methyl* "Stab 28" 2'-fluoro* 2'-O- 3'-end S/AS Methyl* "Stab 29" 2'-fluoro* 2'-O- 1 at 3'-end S/AS Methyl* "Stab 30" 2'-fluoro* 2'-O- S/AS Methyl* "Stab 31" 2'-fluoro* 2'-O- 3'-end S/AS Methyl* "Stab 32" 2'-fluoro 2'-O- S/AS Methyl CAP = any terminal cap, see for example FIG. 10. All Stab 00-32 chemistries can comprise 3'-terminal thymidine (TT) residues All Stab 00-32 chemistries typically comprise about 21 nucleotides, but can vary as described herein. S = sense strand AS = antisense strand *Stab 23 has a single ribonucleotide adjacent to 3'-CAP *Stab 24 and Stab 28 have a single ribonucleotide at 5'-terminus *Stab 25, Stab 26, and Stab 27 have three ribonucleotides at 5'-terminus *Stab 29, Stab 30, and Stab 31, any purine at first three nucleotide positions from 5'-terminus are ribonucleotides p = phosphorothioate linkage

TABLE-US-00005 TABLE V Reagent Equivalents Amount Wait Time* DNA Wait Time* 2'-O-methyl Wait Time*RNA A. 2.5 .mu.mol Synthesis Cycle ABI 394 Instrument Phosphoramidites 6.5 163 .mu.L 45 sec 2.5 min 7.5 min S-Ethyl Tetrazole 23.8 238 .mu.L 45 sec 2.5 min 7.5 min Acetic Anhydride 100 233 .mu.L 5 sec 5 sec 5 sec N-Methyl 186 233 .mu.L 5 sec 5 sec 5 sec Imidazole TCA 176 2.3 mL 21 sec 21 sec 21 sec Iodine 11.2 1.7 mL 45 sec 45 sec 45 sec Beaucage 12.9 645 .mu.L 100 sec 300 sec 300 sec Acetonitrile NA 6.67 mL NA NA NA B. 0.2 .mu.mol Synthesis Cycle ABI 394 Instrument Phosphoramidites 15 31 .mu.L 45 sec 233 sec 465 sec S-Ethyl Tetrazole 38.7 31 .mu.L 45 sec 233 min 465 sec Acetic Anhydride 655 124 .mu.L 5 sec 5 sec 5 sec N-Methyl 1245 124 .mu.L 5 sec 5 sec 5 sec Imidazole TCA 700 732 .mu.L 10 sec 10 sec 10 sec Iodine 20.6 244 .mu.L 15 sec 15 sec 15 sec Beaucage 7.7 232 .mu.L 100 sec 300 sec 300 sec Acetonitrile NA 2.64 mL NA NA NA C. 0.2 .mu.mol Synthesis Cycle 96 well Instrument Equivalents: DNA/ Amount: DNA/2'-O- Wait Time* Reagent 2'-O-methyl/Ribo methyl/Ribo Wait Time* DNA 2'-O-methyl Wait Time* Ribo Phosphoramidites 22/33/66 40/60/120 .mu.L 60 sec 180 sec 360 sec S-Ethyl Tetrazole 70/105/210 40/60/120 .mu.L 60 sec 180 min 360 sec Acetic Anhydride 265/265/265 50/50/50 .mu.L 10 sec 10 sec 10 sec N-Methyl 502/502/502 50/50/50 .mu.L 10 sec 10 sec 10 sec Imidazole TCA 238/475/475 250/500/500 .mu.L 15 sec 15 sec 15 sec Iodine 6.8/6.8/6.8 80/80/80 .mu.L 30 sec 30 sec 30 sec Beaucage 34/51/51 80/120/120 100 sec 200 sec 200 sec Acetonitrile NA 1150/1150/1150 .mu.L NA NA NA Wait time does not include contact time during delivery. Tandem synthesis utilizes double coupling of linker molecule

Sequence CWU 1

1

749119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 1ccccucagcc cugcugccc 19219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 2cagcacgagc cugugcucg 19319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 3gcccugccca acgcagaca 19419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 4agccagaccc agggcggcc 19519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 5cccucuggcg gcucugcuc 19619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 6ccucccgaag gaugcuugg 19719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 7gggagugagg cgaagcugg 19819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 8ggcgcuccuc uccccuaca 19919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 9agcagccccc uuccuccau 191019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 10ucccucuguu cuccugagc 191119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 11ccuucaggag ccugcacca 191219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 12aguccugccu guccuucua 191319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 13acucagcugu uacccacuc 191419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 14cugggaccag cagucuuuc 191519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 15cugauaacug ggagagggc 191619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 16caguaaggag gacuuccug 191719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 17ggagggggug acuguccag 191819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 18gagccuggaa cugugccca 191919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 19acaccagaag ccaucagca 192019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 20agcaaggaca ccaugcggc 192119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 21cuuccgggug cgaugccag 192219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 22gcucuggccc ucaaaggcg 192319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 23gagcugcugu ugcugucuc 192419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 24cuccuguuac uucuggaac 192519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 25ccacagaucu cucagggcc 192619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 26cuggucguca cacccccgg 192719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 27gggccagagc uuguccuca 192819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 28aaugucucca gcaccuucg 192919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 29guucugaccu gcucggguu 193019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 30ucagcuccgg ugguguggg 193119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 31gaacggaugu cccaggagc 193219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 32cccccacagg aaauggcca 193319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 33aaggcccagg auggcaccu 193419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 34uucuccagcg ugcucacac 193519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 35cugaccaacc ucacugggc 193619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 36cuagacacgg gagaauacu 193719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 37uuuugcaccc acaaugacu 193819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 38ucccguggac uggagaccg 193919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 39gaugagcgga aacggcucu 194019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 40uacaucuuug ugccagauc 194119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 41cccaccgugg gcuuccucc 194219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 42ccuaaugaug ccgaggaac 194319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 43cuauucaucu uucucacgg 194419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 44gaaauaacug agaucacca 194519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 45auuccaugcc gaguaacag 194619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 46gacccacagc uggugguga 194719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 47acacugcacg agaagaaag 194819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 48ggggacguug cacugccug 194919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 49guccccuaug aucaccaac 195019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 50cguggcuuuu cugguaucu 195119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 51uuugaggaca gaagcuaca 195219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 52aucugcaaaa ccaccauug 195319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 53ggggacaggg agguggauu 195419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 54ucugaugccu acuaugucu 195519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 55uacagacucc aggugucau 195619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 56uccaucaacg ucucuguga 195719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 57aacgcagugc agacugugg 195819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 58guccgccagg gugagaaca 195919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 59aucacccuca ugugcauug 196019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 60gugaucggga augaggugg 196119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 61gucaacuucg aguggacau 196219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 62uacccccgca aagaaagug 196319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 63gggcggcugg uggagccgg 196419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 64gugacugacu uccucuugg 196519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 65gauaugccuu accacaucc 196619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 66cgcuccaucc ugcacaucc 196719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 67cccagugccg aguuagaag 196819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 68gacucgggga ccuacaccu 196919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 69ugcaauguga cggagagug 197019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 70gugaaugacc aucaggaug 197119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 71gaaaaggcca ucaacauca 197219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 72accgugguug agagcggcu 197319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 73uacgugcggc uccugggag 197419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 74gaggugggca cacuacaau 197519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 75uuugcugagc ugcaucgga 197619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 76agccggacac ugcagguag 197719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 77guguucgagg ccuacccac 197819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 78ccgcccacug uccuguggu 197919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 79uucaaagaca accgcaccc 198019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 80cugggcgacu ccagcgcug 198119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 81ggcgaaaucg cccugucca 198219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 82acgcgcaacg ugucggaga 198319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 83acccgguaug ugucagagc 198419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 84cugacacugg uucgcguga 198519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 85aagguggcag aggcuggcc 198619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 86cacuacacca ugcgggccu 198719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 87uuccaugagg augcugagg 198819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 88guccagcucu ccuuccagc 198919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 89cuacagauca augucccug 199019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 90guccgagugc uggagcuaa 199119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 91agugagagcc acccugaca 199219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 92aguggggaac agacagucc 199319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 93cgcugucgug gccggggca 199419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 94augccccagc cgaacauca 199519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 95aucuggucug ccugcagag 199619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 96gaccucaaaa gguguccac 199719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 97cgugagcugc cgcccacgc 199819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 98cugcugggga acaguuccg 199919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 99gaagaggaga gccagcugg 1910019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 100gagacuaacg ugacguacu 1910119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 101ugggaggagg agcaggagu 1910219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 102uuugaggugg ugagcacac 1910319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 103cugcgucugc agcacgugg 1910419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 104gaucggccac ugucggugc 1910519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 105cgcugcacgc ugcgcaacg 1910619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 106gcugugggcc aggacacgc 1910719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 107caggagguca ucguggugc 1910819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 108ccacacuccu ugcccuuua 1910919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 109aagguggugg ugaucucag 1911019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 110gccauccugg cccuggugg 1911119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 111gugcucacca ucaucuccc 1911219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 112cuuaucaucc ucaucaugc 1911319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 113cuuuggcaga agaagccac 1911419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 114cguuacgaga uccgaugga 1911519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 115aaggugauug agucuguga 1911619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 116agcucugacg gccaugagu 1911719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 117uacaucuacg uggacccca 1911819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 118augcagcugc ccuaugacu 1911919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 119uccacguggg agcugccgc 1912019RNAArtificial SequenceSynthetic Target Sequence/siNA

sense region 120cgggaccagc uugugcugg 1912119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 121ggacgcaccc ucggcucug 1912219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 122ggggccuuug ggcaggugg 1912319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 123guggaggcca cggcucaug 1912419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 124ggccugagcc auucucagg 1912519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 125gccacgauga aaguggccg 1912619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 126gucaagaugc uuaaaucca 1912719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 127acagcccgca gcagugaga 1912819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 128aagcaagccc uuaugucgg 1912919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 129gagcugaaga ucaugaguc 1913019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 130caccuugggc cccaccuga 1913119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 131aacgugguca accuguugg 1913219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 132ggggccugca ccaaaggag 1913319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 133ggacccaucu auaucauca 1913419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 134acugaguacu gccgcuacg 1913519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 135ggagaccugg uggacuacc 1913619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 136cugcaccgca acaaacaca 1913719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 137accuuccugc agcaccacu 1913819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 138uccgacaagc gccgcccgc 1913919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 139cccagcgcgg agcucuaca 1914019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 140agcaaugcuc ugcccguug 1914119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 141gggcuccccc ugcccagcc 1914219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 142cauguguccu ugaccgggg 1914319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 143gagagcgacg guggcuaca 1914419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 144auggacauga gcaaggacg 1914519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 145gagucggugg acuaugugc 1914619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 146cccaugcugg acaugaaag 1914719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 147ggagacguca aauaugcag 1914819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 148gacaucgagu ccuccaacu 1914919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 149uacauggccc cuuacgaua 1915019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 150aacuacguuc ccucugccc 1915119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 151ccugagagga ccugccgag 1915219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 152gcaacuuuga ucaacgagu 1915319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 153ucuccagugc uaagcuaca 1915419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 154auggaccucg ugggcuuca 1915519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 155agcuaccagg uggccaaug 1915619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 156ggcauggagu uucuggccu 1915719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 157uccaagaacu gcguccaca 1915819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 158agagaccugg cggcuagga 1915919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 159aacgugcuca ucugugaag 1916019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 160ggcaagcugg ucaagaucu 1916119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 161ugugacuuug gccuggcuc 1916219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 162cgagacauca ugcgggacu 1916319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 163ucgaauuaca ucuccaaag 1916419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 164ggcagcaccu uuuugccuu 1916519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 165uuaaagugga uggcuccgg 1916619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 166gagagcaucu ucaacagcc 1916719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 167cucuacacca cccugagcg 1916819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 168gacguguggu ccuucggga 1916919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 169auccugcucu gggagaucu 1917019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 170uucaccuugg guggcaccc 1917119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 171ccuuacccag agcugccca 1917219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 172augaacgagc aguucuaca 1917319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 173aaugccauca aacgggguu 1917419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 174uaccgcaugg cccagccug 1917519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 175gcccaugccu ccgacgaga 1917619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 176aucuaugaga ucaugcaga 1917719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 177aagugcuggg aagagaagu 1917819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 178uuugagauuc ggccccccu 1917919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 179uucucccagc uggugcugc 1918019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 180cuucucgaga gacuguugg 1918119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 181ggcgaagguu acaaaaaga 1918219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 182aaguaccagc agguggaug 1918319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 183gaggaguuuc ugaggagug 1918419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 184gaccacccag ccauccuuc 1918519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 185cggucccagg cccgcuugc 1918619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 186ccuggguucc auggccucc 1918719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 187cgaucucccc uggacacca 1918819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 188agcuccgucc ucuauacug 1918919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 189gccgugcagc ccaaugagg 1919019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 190ggugacaacg acuauauca 1919119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 191aucccccugc cugacccca 1919219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 192aaacccgagg uugcugacg 1919319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 193gagggcccac uggaggguu 1919419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 194ucccccagcc uagccagcu 1919519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 195uccacccuga augaaguca 1919619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 196aacaccuccu caaccaucu 1919719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 197uccugugaca gcccccugg 1919819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 198gagccccagg acgaaccag 1919919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 199gagccagagc cccagcuug 1920019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 200gagcuccagg uggagccgg 1920119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 201gagccagagc uggaacagu 1920219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 202uugccggauu cggggugcc 1920319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 203ccugcgccuc gggcggaag 1920419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 204gcagaggaua gcuuccugu 1920519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 205uagggggcug gccccuacc 1920619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 206ccugcccugc cugaagcuc 1920719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 207cccccccugc cagcaccca 1920819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 208agcaucuccu ggccuggcc 1920919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 209cugaccgggc uuccuguca 1921019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 210agccaggcug cccuuauca 1921119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 211agcugucccc uucuggaag 1921219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 212gcuuucugcu ccugacgug 1921319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 213guugugcccc aaacccugg 1921419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 214gggcuggcuu aggaggcaa 1921519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 215agaaaacugc aggggccgu 1921619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 216ugaccagccc ucugccucc 1921719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 217cagggaggcc aacugacuc 1921819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 218cugagccagg guuccccca 1921919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 219agggaacuca guuuuccca 1922019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 220auauguaaga ugggaaagu 1922119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 221uuaggcuuga ugacccaga 1922219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 222aaucuaggau ucucucccu 1922319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 223uggcugacag guggggaga 1922419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 224accgaauccc ucccuggga 1922519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 225aagauucuug gaguuacug 1922619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 226gaggugguaa auuaacuuu 1922719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 227uuuucuguuc agccagcua 1922819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 228accccucaag gaaucauag 1922919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 229gcucucuccu cgcacuuuu 1923019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 230uuauccaccc aggagcuag 1923119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 231gggaagagac ccuagccuc 1923219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 232cccuggcugc uggcugagc 1923319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 233cuagggccua gccuugagc 1923419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 234caguguugcc ucauccaga 1923519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 235aagaaagcca gucuccucc 1923619RNAArtificial SequenceSynthetic

Target Sequence/siNA sense region 236ccuaugaugc cagucccug 1923719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 237gcguucccug gcccgagcu 1923819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 238uggucugggg ccauuaggc 1923919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 239cagccuaauu aaugcugga 1924019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 240aggcugagcc aaguacagg 1924119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 241gacaccccca gccugcagc 1924219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 242cccuugccca gggcacuug 1924319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 243ggagcacacg cagccauag 1924419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 244gcaagugccu gugucccug 1924519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 245guccuucagg cccaucagu 1924619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 246uccuggggcu uuuucuuua 1924719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 247aucacccuca gucuuaauc 1924819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 248ccauccacca gagucuaga 1924919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 249aaggccagac gggccccgc 1925019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 250caucugugau gagaaugua 1925119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 251aaaugugcca guguggagu 1925219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 252uggccacgug ugugugcca 1925319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 253aguauauggc ccuggcucu 1925419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 254ugcauuggac cugcuauga 1925519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 255aggcuuugga ggaaucccu 1925619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 256ucacccucuc ugggccuca 1925719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 257aguuuccccu ucaaaaaau 1925819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 258ugaauaaguc ggacuuauu 1925919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 259uaacucugag ugccuugcc 1926019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 260cagcacuaac auucuagag 1926119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 261guauuccagg ugguugcac 1926219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 262cauuugucca gaugaagca 1926319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 263aaggccauau acccuaaac 1926419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 264cuuccauccu gggggucag 1926519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 265gcugggcucc ugggagauu 1926619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 266uccagaucac acaucacac 1926719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 267cucuggggac ucaggaacc 1926819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 268caugccccuu ccccaggcc 1926919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 269ccccagcaag ucucaagaa 1927019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 270acacagcugc acaggccuu 1927119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 271ugacuuagag ugacagccg 1927219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 272gguguccugg aaagcccca 1927319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 273aagcagcugc cccagggac 1927419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 274caugggaaga ccacgggac 1927519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 275ccucuuucac uacccacga 1927619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 276augaccuccg gggguaucc 1927719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 277cugggcaaaa gggacaaag 1927819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 278gagggcaaau gagaucacc 1927919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 279cuccugcagc ccaccacuc 1928019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 280ccagcaccug ugccgaggu 1928119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 281ucugcgucga agacagaau 1928219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 282uggacaguga ggacaguua 1928319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 283augucuugua aaagacaag 1928419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 284gaagcuucag augguaccc 1928519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 285ccaagaagga ugugagagg 1928619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 286guggccgcuu ggaguuugc 1928719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 287ccccucaccc accagcugc 1928819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 288ccccaucccu gaggcagcg 1928919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 289gcuccauggg gguaugguu 1929019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 290uuugucacug cccagaccu 1929119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 291uagcagugac aucucauug 1929219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 292guccccagcc cagugggca 1929319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 293auuggaggug ccaggggag 1929419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 294gucaggguug uagccaaga 1929519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 295acgcccccgc acggggagg 1929619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 296gguugggaag ggggugcag 1929719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 297ggaagcucaa ccccucugg 1929819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 298ggcaccaacc cugcauugc 1929919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 299cagguuggca ccuuacuuc 1930019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 300cccugggauc cccagaguu 1930119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 301ugguccaagg agggagagu 1930219RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 302uggguucuca auacgguac 1930319RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 303ccaaagauau aaucaccua 1930419RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 304agguuuacaa auauuuuua 1930519RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 305aggacucacg uuaacucac 1930619RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 306cauuuauaca gcagaaaug 1930719RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 307gcuauuuugu augcuguua 1930819RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 308aaguuuuucu aucugugua 1930919RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 309acuuuuuuuu aagggaaag 1931019RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 310gauuuuaaua uuaaaccug 1931119RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 311aaccuggugc uucucacuc 1931219RNAArtificial SequencesiNA antisense region 312gggcagcagg gcugagggg 1931319RNAArtificial SequencesiNA antisense region 313cgagcacagg cucgugcug 1931419RNAArtificial SequencesiNA antisense region 314ugucugcguu gggcagggc 1931519RNAArtificial SequencesiNA antisense region 315ggccgcccug ggucuggcu 1931619RNAArtificial SequencesiNA antisense region 316gagcagagcc gccagaggg 1931719RNAArtificial SequencesiNA antisense region 317ccaagcaucc uucgggagg 1931819RNAArtificial SequencesiNA antisense region 318ccagcuucgc cucacuccc 1931919RNAArtificial SequencesiNA antisense region 319uguaggggag aggagcgcc 1932019RNAArtificial SequencesiNA antisense region 320auggaggaag ggggcugcu 1932119RNAArtificial SequencesiNA antisense region 321gcucaggaga acagaggga 1932219RNAArtificial SequencesiNA antisense region 322uggugcaggc uccugaagg 1932319RNAArtificial SequencesiNA antisense region 323uagaaggaca ggcaggacu 1932419RNAArtificial SequencesiNA antisense region 324gaguggguaa cagcugagu 1932519RNAArtificial SequencesiNA antisense region 325gaaagacugc uggucccag 1932619RNAArtificial SequencesiNA antisense region 326gcccucuccc aguuaucag 1932719RNAArtificial SequencesiNA antisense region 327caggaagucc uccuuacug 1932819RNAArtificial SequencesiNA antisense region 328cuggacaguc acccccucc 1932919RNAArtificial SequencesiNA antisense region 329ugggcacagu uccaggcuc 1933019RNAArtificial SequencesiNA antisense region 330ugcugauggc uucuggugu 1933119RNAArtificial SequencesiNA antisense region 331gccgcauggu guccuugcu 1933219RNAArtificial SequencesiNA antisense region 332cuggcaucgc acccggaag 1933319RNAArtificial SequencesiNA antisense region 333cgccuuugag ggccagagc 1933419RNAArtificial SequencesiNA antisense region 334gagacagcaa cagcagcuc 1933519RNAArtificial SequencesiNA antisense region 335guuccagaag uaacaggag 1933619RNAArtificial SequencesiNA antisense region 336ggcccugaga gaucugugg 1933719RNAArtificial SequencesiNA antisense region 337ccgggggugu gacgaccag 1933819RNAArtificial SequencesiNA antisense region 338ugaggacaag cucuggccc 1933919RNAArtificial SequencesiNA antisense region 339cgaaggugcu ggagacauu 1934019RNAArtificial SequencesiNA antisense region 340aacccgagca ggucagaac 1934119RNAArtificial SequencesiNA antisense region 341cccacaccac cggagcuga 1934219RNAArtificial SequencesiNA antisense region 342gcuccuggga cauccguuc 1934319RNAArtificial SequencesiNA antisense region 343uggccauuuc cuguggggg 1934419RNAArtificial SequencesiNA antisense region 344aggugccauc cugggccuu 1934519RNAArtificial SequencesiNA antisense region 345gugugagcac gcuggagaa 1934619RNAArtificial SequencesiNA antisense region 346gcccagugag guuggucag 1934719RNAArtificial SequencesiNA antisense region 347aguauucucc cgugucuag 1934819RNAArtificial SequencesiNA antisense region 348agucauugug ggugcaaaa 1934919RNAArtificial SequencesiNA antisense region 349cggucuccag uccacggga 1935019RNAArtificial SequencesiNA antisense region 350agagccguuu ccgcucauc 1935119RNAArtificial SequencesiNA antisense region 351gaucuggcac aaagaugua 1935219RNAArtificial SequencesiNA antisense region 352ggaggaagcc cacgguggg 1935319RNAArtificial SequencesiNA antisense region 353guuccucggc aucauuagg 1935419RNAArtificial SequencesiNA antisense region 354ccgugagaaa gaugaauag 1935519RNAArtificial SequencesiNA antisense region 355uggugaucuc

aguuauuuc 1935619RNAArtificial SequencesiNA antisense region 356cuguuacucg gcauggaau 1935719RNAArtificial SequencesiNA antisense region 357ucaccaccag cuguggguc 1935819RNAArtificial SequencesiNA antisense region 358cuuucuucuc gugcagugu 1935919RNAArtificial SequencesiNA antisense region 359caggcagugc aacgucccc 1936019RNAArtificial SequencesiNA antisense region 360guuggugauc auaggggac 1936119RNAArtificial SequencesiNA antisense region 361agauaccaga aaagccacg 1936219RNAArtificial SequencesiNA antisense region 362uguagcuucu guccucaaa 1936319RNAArtificial SequencesiNA antisense region 363caaugguggu uuugcagau 1936419RNAArtificial SequencesiNA antisense region 364aauccaccuc ccugucccc 1936519RNAArtificial SequencesiNA antisense region 365agacauagua ggcaucaga 1936619RNAArtificial SequencesiNA antisense region 366augacaccug gagucugua 1936719RNAArtificial SequencesiNA antisense region 367ucacagagac guugaugga 1936819RNAArtificial SequencesiNA antisense region 368ccacagucug cacugcguu 1936919RNAArtificial SequencesiNA antisense region 369uguucucacc cuggcggac 1937019RNAArtificial SequencesiNA antisense region 370caaugcacau gagggugau 1937119RNAArtificial SequencesiNA antisense region 371ccaccucauu cccgaucac 1937219RNAArtificial SequencesiNA antisense region 372auguccacuc gaaguugac 1937319RNAArtificial SequencesiNA antisense region 373cacuuucuuu gcgggggua 1937419RNAArtificial SequencesiNA antisense region 374ccggcuccac cagccgccc 1937519RNAArtificial SequencesiNA antisense region 375ccaagaggaa gucagucac 1937619RNAArtificial SequencesiNA antisense region 376ggauguggua aggcauauc 1937719RNAArtificial SequencesiNA antisense region 377ggaugugcag gauggagcg 1937819RNAArtificial SequencesiNA antisense region 378cuucuaacuc ggcacuggg 1937919RNAArtificial SequencesiNA antisense region 379agguguaggu ccccgaguc 1938019RNAArtificial SequencesiNA antisense region 380cacucuccgu cacauugca 1938119RNAArtificial SequencesiNA antisense region 381cauccugaug gucauucac 1938219RNAArtificial SequencesiNA antisense region 382ugauguugau ggccuuuuc 1938319RNAArtificial SequencesiNA antisense region 383agccgcucuc aaccacggu 1938419RNAArtificial SequencesiNA antisense region 384cucccaggag ccgcacgua 1938519RNAArtificial SequencesiNA antisense region 385auuguagugu gcccaccuc 1938619RNAArtificial SequencesiNA antisense region 386uccgaugcag cucagcaaa 1938719RNAArtificial SequencesiNA antisense region 387cuaccugcag uguccggcu 1938819RNAArtificial SequencesiNA antisense region 388guggguaggc cucgaacac 1938919RNAArtificial SequencesiNA antisense region 389accacaggac agugggcgg 1939019RNAArtificial SequencesiNA antisense region 390gggugcgguu gucuuugaa 1939119RNAArtificial SequencesiNA antisense region 391cagcgcugga gucgcccag 1939219RNAArtificial SequencesiNA antisense region 392uggacagggc gauuucgcc 1939319RNAArtificial SequencesiNA antisense region 393ucuccgacac guugcgcgu 1939419RNAArtificial SequencesiNA antisense region 394gcucugacac auaccgggu 1939519RNAArtificial SequencesiNA antisense region 395ucacgcgaac cagugucag 1939619RNAArtificial SequencesiNA antisense region 396ggccagccuc ugccaccuu 1939719RNAArtificial SequencesiNA antisense region 397aggcccgcau gguguagug 1939819RNAArtificial SequencesiNA antisense region 398ccucagcauc cucauggaa 1939919RNAArtificial SequencesiNA antisense region 399gcuggaagga gagcuggac 1940019RNAArtificial SequencesiNA antisense region 400cagggacauu gaucuguag 1940119RNAArtificial SequencesiNA antisense region 401uuagcuccag cacucggac 1940219RNAArtificial SequencesiNA antisense region 402ugucagggug gcucucacu 1940319RNAArtificial SequencesiNA antisense region 403ggacugucug uuccccacu 1940419RNAArtificial SequencesiNA antisense region 404ugccccggcc acgacagcg 1940519RNAArtificial SequencesiNA antisense region 405ugauguucgg cuggggcau 1940619RNAArtificial SequencesiNA antisense region 406cucugcaggc agaccagau 1940719RNAArtificial SequencesiNA antisense region 407guggacaccu uuugagguc 1940819RNAArtificial SequencesiNA antisense region 408gcgugggcgg cagcucacg 1940919RNAArtificial SequencesiNA antisense region 409cggaacuguu ccccagcag 1941019RNAArtificial SequencesiNA antisense region 410ccagcuggcu cuccucuuc 1941119RNAArtificial SequencesiNA antisense region 411aguacgucac guuagucuc 1941219RNAArtificial SequencesiNA antisense region 412acuccugcuc cuccuccca 1941319RNAArtificial SequencesiNA antisense region 413gugugcucac caccucaaa 1941419RNAArtificial SequencesiNA antisense region 414ccacgugcug cagacgcag 1941519RNAArtificial SequencesiNA antisense region 415gcaccgacag uggccgauc 1941619RNAArtificial SequencesiNA antisense region 416cguugcgcag cgugcagcg 1941719RNAArtificial SequencesiNA antisense region 417gcguguccug gcccacagc 1941819RNAArtificial SequencesiNA antisense region 418gcaccacgau gaccuccug 1941919RNAArtificial SequencesiNA antisense region 419uaaagggcaa ggagugugg 1942019RNAArtificial SequencesiNA antisense region 420cugagaucac caccaccuu 1942119RNAArtificial SequencesiNA antisense region 421ccaccagggc caggauggc 1942219RNAArtificial SequencesiNA antisense region 422gggagaugau ggugagcac 1942319RNAArtificial SequencesiNA antisense region 423gcaugaugag gaugauaag 1942419RNAArtificial SequencesiNA antisense region 424guggcuucuu cugccaaag 1942519RNAArtificial SequencesiNA antisense region 425uccaucggau cucguaacg 1942619RNAArtificial SequencesiNA antisense region 426ucacagacuc aaucaccuu 1942719RNAArtificial SequencesiNA antisense region 427acucauggcc gucagagcu 1942819RNAArtificial SequencesiNA antisense region 428ugggguccac guagaugua 1942919RNAArtificial SequencesiNA antisense region 429agucauaggg cagcugcau 1943019RNAArtificial SequencesiNA antisense region 430gcggcagcuc ccacgugga 1943119RNAArtificial SequencesiNA antisense region 431ccagcacaag cuggucccg 1943219RNAArtificial SequencesiNA antisense region 432cagagccgag ggugcgucc 1943319RNAArtificial SequencesiNA antisense region 433ccaccugccc aaaggcccc 1943419RNAArtificial SequencesiNA antisense region 434caugagccgu ggccuccac 1943519RNAArtificial SequencesiNA antisense region 435ccugagaaug gcucaggcc 1943619RNAArtificial SequencesiNA antisense region 436cggccacuuu caucguggc 1943719RNAArtificial SequencesiNA antisense region 437uggauuuaag caucuugac 1943819RNAArtificial SequencesiNA antisense region 438ucucacugcu gcgggcugu 1943919RNAArtificial SequencesiNA antisense region 439ccgacauaag ggcuugcuu 1944019RNAArtificial SequencesiNA antisense region 440gacucaugau cuucagcuc 1944119RNAArtificial SequencesiNA antisense region 441ucaggugggg cccaaggug 1944219RNAArtificial SequencesiNA antisense region 442ccaacagguu gaccacguu 1944319RNAArtificial SequencesiNA antisense region 443cuccuuuggu gcaggcccc 1944419RNAArtificial SequencesiNA antisense region 444ugaugauaua gaugggucc 1944519RNAArtificial SequencesiNA antisense region 445cguagcggca guacucagu 1944619RNAArtificial SequencesiNA antisense region 446gguaguccac caggucucc 1944719RNAArtificial SequencesiNA antisense region 447uguguuuguu gcggugcag 1944819RNAArtificial SequencesiNA antisense region 448aguggugcug caggaaggu 1944919RNAArtificial SequencesiNA antisense region 449gcgggcggcg cuugucgga 1945019RNAArtificial SequencesiNA antisense region 450uguagagcuc cgcgcuggg 1945119RNAArtificial SequencesiNA antisense region 451caacgggcag agcauugcu 1945219RNAArtificial SequencesiNA antisense region 452ggcugggcag ggggagccc 1945319RNAArtificial SequencesiNA antisense region 453ccccggucaa ggacacaug 1945419RNAArtificial SequencesiNA antisense region 454uguagccacc gucgcucuc 1945519RNAArtificial SequencesiNA antisense region 455cguccuugcu cauguccau 1945619RNAArtificial SequencesiNA antisense region 456gcacauaguc caccgacuc 1945719RNAArtificial SequencesiNA antisense region 457cuuucauguc cagcauggg 1945819RNAArtificial SequencesiNA antisense region 458cugcauauuu gacgucucc 1945919RNAArtificial SequencesiNA antisense region 459aguuggagga cucgauguc 1946019RNAArtificial SequencesiNA antisense region 460uaucguaagg ggccaugua 1946119RNAArtificial SequencesiNA antisense region 461gggcagaggg aacguaguu 1946219RNAArtificial SequencesiNA antisense region 462cucggcaggu ccucucagg 1946319RNAArtificial SequencesiNA antisense region 463acucguugau caaaguugc 1946419RNAArtificial SequencesiNA antisense region 464uguagcuuag cacuggaga 1946519RNAArtificial SequencesiNA antisense region 465ugaagcccac gagguccau 1946619RNAArtificial SequencesiNA antisense region 466cauuggccac cugguagcu 1946719RNAArtificial SequencesiNA antisense region 467aggccagaaa cuccaugcc 1946819RNAArtificial SequencesiNA antisense region 468uguggacgca guucuugga 1946919RNAArtificial SequencesiNA antisense region 469uccuagccgc caggucucu 1947019RNAArtificial SequencesiNA antisense region 470cuucacagau gagcacguu 1947119RNAArtificial SequencesiNA antisense region 471agaucuugac cagcuugcc 1947219RNAArtificial SequencesiNA antisense region 472gagccaggcc aaagucaca 1947319RNAArtificial SequencesiNA antisense region 473agucccgcau gaugucucg 1947419RNAArtificial SequencesiNA antisense region 474cuuuggagau guaauucga 1947519RNAArtificial SequencesiNA antisense region 475aaggcaaaaa ggugcugcc 1947619RNAArtificial SequencesiNA antisense region 476ccggagccau ccacuuuaa 1947719RNAArtificial SequencesiNA antisense region 477ggcuguugaa gaugcucuc 1947819RNAArtificial SequencesiNA antisense region 478cgcucagggu gguguagag 1947919RNAArtificial SequencesiNA antisense region 479ucccgaagga ccacacguc 1948019RNAArtificial SequencesiNA antisense region 480agaucuccca gagcaggau

1948119RNAArtificial SequencesiNA antisense region 481gggugccacc caaggugaa 1948219RNAArtificial SequencesiNA antisense region 482ugggcagcuc uggguaagg 1948319RNAArtificial SequencesiNA antisense region 483uguagaacug cucguucau 1948419RNAArtificial SequencesiNA antisense region 484aaccccguuu gauggcauu 1948519RNAArtificial SequencesiNA antisense region 485caggcugggc caugcggua 1948619RNAArtificial SequencesiNA antisense region 486ucucgucgga ggcaugggc 1948719RNAArtificial SequencesiNA antisense region 487ucugcaugau cucauagau 1948819RNAArtificial SequencesiNA antisense region 488acuucucuuc ccagcacuu 1948919RNAArtificial SequencesiNA antisense region 489aggggggccg aaucucaaa 1949019RNAArtificial SequencesiNA antisense region 490gcagcaccag cugggagaa 1949119RNAArtificial SequencesiNA antisense region 491ccaacagucu cucgagaag 1949219RNAArtificial SequencesiNA antisense region 492ucuuuuugua accuucgcc 1949319RNAArtificial SequencesiNA antisense region 493cauccaccug cugguacuu 1949419RNAArtificial SequencesiNA antisense region 494cacuccucag aaacuccuc 1949519RNAArtificial SequencesiNA antisense region 495gaaggauggc ugggugguc 1949619RNAArtificial SequencesiNA antisense region 496gcaagcgggc cugggaccg 1949719RNAArtificial SequencesiNA antisense region 497ggaggccaug gaacccagg 1949819RNAArtificial SequencesiNA antisense region 498ugguguccag gggagaucg 1949919RNAArtificial SequencesiNA antisense region 499caguauagag gacggagcu 1950019RNAArtificial SequencesiNA antisense region 500ccucauuggg cugcacggc 1950119RNAArtificial SequencesiNA antisense region 501ugauauaguc guugucacc 1950219RNAArtificial SequencesiNA antisense region 502uggggucagg cagggggau 1950319RNAArtificial SequencesiNA antisense region 503cgucagcaac cucggguuu 1950419RNAArtificial SequencesiNA antisense region 504aacccuccag ugggcccuc 1950519RNAArtificial SequencesiNA antisense region 505agcuggcuag gcuggggga 1950619RNAArtificial SequencesiNA antisense region 506ugacuucauu cagggugga 1950719RNAArtificial SequencesiNA antisense region 507agaugguuga ggagguguu 1950819RNAArtificial SequencesiNA antisense region 508ccagggggcu gucacagga 1950919RNAArtificial SequencesiNA antisense region 509cugguucguc cuggggcuc 1951019RNAArtificial SequencesiNA antisense region 510caagcugggg cucuggcuc 1951119RNAArtificial SequencesiNA antisense region 511ccggcuccac cuggagcuc 1951219RNAArtificial SequencesiNA antisense region 512acuguuccag cucuggcuc 1951319RNAArtificial SequencesiNA antisense region 513ggcaccccga auccggcaa 1951419RNAArtificial SequencesiNA antisense region 514cuuccgcccg aggcgcagg 1951519RNAArtificial SequencesiNA antisense region 515acaggaagcu auccucugc 1951619RNAArtificial SequencesiNA antisense region 516gguaggggcc agcccccua 1951719RNAArtificial SequencesiNA antisense region 517gagcuucagg cagggcagg 1951819RNAArtificial SequencesiNA antisense region 518ugggugcugg caggggggg 1951919RNAArtificial SequencesiNA antisense region 519ggccaggcca ggagaugcu 1952019RNAArtificial SequencesiNA antisense region 520ugacaggaag cccggucag 1952119RNAArtificial SequencesiNA antisense region 521ugauaagggc agccuggcu 1952219RNAArtificial SequencesiNA antisense region 522cuuccagaag gggacagcu 1952319RNAArtificial SequencesiNA antisense region 523cacgucagga gcagaaagc 1952419RNAArtificial SequencesiNA antisense region 524ccaggguuug gggcacaac 1952519RNAArtificial SequencesiNA antisense region 525uugccuccua agccagccc 1952619RNAArtificial SequencesiNA antisense region 526acggccccug caguuuucu 1952719RNAArtificial SequencesiNA antisense region 527ggaggcagag ggcugguca 1952819RNAArtificial SequencesiNA antisense region 528gagucaguug gccucccug 1952919RNAArtificial SequencesiNA antisense region 529ugggggaacc cuggcucag 1953019RNAArtificial SequencesiNA antisense region 530ugggaaaacu gaguucccu 1953119RNAArtificial SequencesiNA antisense region 531acuuucccau cuuacauau 1953219RNAArtificial SequencesiNA antisense region 532ucugggucau caagccuaa 1953319RNAArtificial SequencesiNA antisense region 533agggagagaa uccuagauu 1953419RNAArtificial SequencesiNA antisense region 534ucuccccacc ugucagcca 1953519RNAArtificial SequencesiNA antisense region 535ucccagggag ggauucggu 1953619RNAArtificial SequencesiNA antisense region 536caguaacucc aagaaucuu 1953719RNAArtificial SequencesiNA antisense region 537aaaguuaauu uaccaccuc 1953819RNAArtificial SequencesiNA antisense region 538uagcuggcug aacagaaaa 1953919RNAArtificial SequencesiNA antisense region 539cuaugauucc uugaggggu 1954019RNAArtificial SequencesiNA antisense region 540aaaagugcga ggagagagc 1954119RNAArtificial SequencesiNA antisense region 541cuagcuccug gguggauaa 1954219RNAArtificial SequencesiNA antisense region 542gaggcuaggg ucucuuccc 1954319RNAArtificial SequencesiNA antisense region 543gcucagccag cagccaggg 1954419RNAArtificial SequencesiNA antisense region 544gcucaaggcu aggcccuag 1954519RNAArtificial SequencesiNA antisense region 545ucuggaugag gcaacacug 1954619RNAArtificial SequencesiNA antisense region 546ggaggagacu ggcuuucuu 1954719RNAArtificial SequencesiNA antisense region 547cagggacugg caucauagg 1954819RNAArtificial SequencesiNA antisense region 548agcucgggcc agggaacgc 1954919RNAArtificial SequencesiNA antisense region 549gccuaauggc cccagacca 1955019RNAArtificial SequencesiNA antisense region 550uccagcauua auuaggcug 1955119RNAArtificial SequencesiNA antisense region 551ccuguacuug gcucagccu 1955219RNAArtificial SequencesiNA antisense region 552gcugcaggcu ggggguguc 1955319RNAArtificial SequencesiNA antisense region 553caagugcccu gggcaaggg 1955419RNAArtificial SequencesiNA antisense region 554cuauggcugc gugugcucc 1955519RNAArtificial SequencesiNA antisense region 555cagggacaca ggcacuugc 1955619RNAArtificial SequencesiNA antisense region 556acugaugggc cugaaggac 1955719RNAArtificial SequencesiNA antisense region 557uaaagaaaaa gccccagga 1955819RNAArtificial SequencesiNA antisense region 558gauuaagacu gagggugau 1955919RNAArtificial SequencesiNA antisense region 559ucuagacucu gguggaugg 1956019RNAArtificial SequencesiNA antisense region 560gcggggcccg ucuggccuu 1956119RNAArtificial SequencesiNA antisense region 561uacauucuca ucacagaug 1956219RNAArtificial SequencesiNA antisense region 562acuccacacu ggcacauuu 1956319RNAArtificial SequencesiNA antisense region 563uggcacacac acguggcca 1956419RNAArtificial SequencesiNA antisense region 564agagccaggg ccauauacu 1956519RNAArtificial SequencesiNA antisense region 565ucauagcagg uccaaugca 1956619RNAArtificial SequencesiNA antisense region 566agggauuccu ccaaagccu 1956719RNAArtificial SequencesiNA antisense region 567ugaggcccag agaggguga 1956819RNAArtificial SequencesiNA antisense region 568auuuuuugaa ggggaaacu 1956919RNAArtificial SequencesiNA antisense region 569aauaaguccg acuuauuca 1957019RNAArtificial SequencesiNA antisense region 570ggcaaggcac ucagaguua 1957119RNAArtificial SequencesiNA antisense region 571cucuagaaug uuagugcug 1957219RNAArtificial SequencesiNA antisense region 572gugcaaccac cuggaauac 1957319RNAArtificial SequencesiNA antisense region 573ugcuucaucu ggacaaaug 1957419RNAArtificial SequencesiNA antisense region 574guuuagggua uauggccuu 1957519RNAArtificial SequencesiNA antisense region 575cugaccccca ggauggaag 1957619RNAArtificial SequencesiNA antisense region 576aaucucccag gagcccagc 1957719RNAArtificial SequencesiNA antisense region 577gugugaugug ugaucugga 1957819RNAArtificial SequencesiNA antisense region 578gguuccugag uccccagag 1957919RNAArtificial SequencesiNA antisense region 579ggccugggga aggggcaug 1958019RNAArtificial SequencesiNA antisense region 580uucuugagac uugcugggg 1958119RNAArtificial SequencesiNA antisense region 581aaggccugug cagcugugu 1958219RNAArtificial SequencesiNA antisense region 582cggcugucac ucuaaguca 1958319RNAArtificial SequencesiNA antisense region 583uggggcuuuc caggacacc 1958419RNAArtificial SequencesiNA antisense region 584gucccugggg cagcugcuu 1958519RNAArtificial SequencesiNA antisense region 585gucccguggu cuucccaug 1958619RNAArtificial SequencesiNA antisense region 586ucguggguag ugaaagagg 1958719RNAArtificial SequencesiNA antisense region 587ggauaccccc ggaggucau 1958819RNAArtificial SequencesiNA antisense region 588cuuugucccu uuugcccag 1958919RNAArtificial SequencesiNA antisense region 589ggugaucuca uuugcccuc 1959019RNAArtificial SequencesiNA antisense region 590gagugguggg cugcaggag 1959119RNAArtificial SequencesiNA antisense region 591accucggcac aggugcugg 1959219RNAArtificial SequencesiNA antisense region 592auucugucuu cgacgcaga 1959319RNAArtificial SequencesiNA antisense region 593uaacuguccu cacugucca 1959419RNAArtificial SequencesiNA antisense region 594cuugucuuuu acaagacau 1959519RNAArtificial SequencesiNA antisense region 595ggguaccauc ugaagcuuc 1959619RNAArtificial SequencesiNA antisense region 596ccucucacau ccuucuugg 1959719RNAArtificial SequencesiNA antisense region 597gcaaacucca agcggccac 1959819RNAArtificial SequencesiNA antisense region 598gcagcuggug ggugagggg 1959919RNAArtificial SequencesiNA antisense region 599cgcugccuca gggaugggg 1960019RNAArtificial SequencesiNA antisense region 600aaccauaccc ccauggagc 1960119RNAArtificial SequencesiNA antisense region 601aggucugggc agugacaaa 1960219RNAArtificial SequencesiNA antisense region 602caaugagaug ucacugcua 1960319RNAArtificial SequencesiNA antisense region 603ugcccacugg gcuggggac 1960419RNAArtificial SequencesiNA antisense region 604cuccccuggc accuccaau 1960519RNAArtificial SequencesiNA antisense region 605ucuuggcuac aacccugac 1960619RNAArtificial SequencesiNA antisense region 606ccuccccgug

cgggggcgu 1960719RNAArtificial SequencesiNA antisense region 607cugcaccccc uucccaacc 1960819RNAArtificial SequencesiNA antisense region 608ccagaggggu ugagcuucc 1960919RNAArtificial SequencesiNA antisense region 609gcaaugcagg guuggugcc 1961019RNAArtificial SequencesiNA antisense region 610gaaguaaggu gccaaccug 1961119RNAArtificial SequencesiNA antisense region 611aacucugggg aucccaggg 1961219RNAArtificial SequencesiNA antisense region 612acucucccuc cuuggacca 1961319RNAArtificial SequencesiNA antisense region 613guaccguauu gagaaccca 1961419RNAArtificial SequencesiNA antisense region 614uaggugauua uaucuuugg 1961519RNAArtificial SequencesiNA antisense region 615uaaaaauauu uguaaaccu 1961619RNAArtificial SequencesiNA antisense region 616gugaguuaac gugaguccu 1961719RNAArtificial SequencesiNA antisense region 617cauuucugcu guauaaaug 1961819RNAArtificial SequencesiNA antisense region 618uaacagcaua caaaauagc 1961919RNAArtificial SequencesiNA antisense region 619uacacagaua gaaaaacuu 1962019RNAArtificial SequencesiNA antisense region 620cuuucccuua aaaaaaagu 1962119RNAArtificial SequencesiNA antisense region 621cagguuuaau auuaaaauc 1962219RNAArtificial SequencesiNA antisense region 622gagugagaag caccagguu 1962323RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 623ugccuguccu ucuacucagc ugu 2362423RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 624ggagguggau ucugaugccu acu 2362523RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 625ggcacacuac aauuugcuga gcu 2362623RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 626cgagugcugg agcuaaguga gag 2362723RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 627cucgaauuac aucuccaaag gca 2362823RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 628cugcuaugag gcuuuggagg aau 2362923RNAArtificial SequenceSynthetic Target Sequence/siNA sense region 629gacaaagagg gcaaaugaga uca 2363023DNAArtificial SequenceSynthetic Target Sequence/siNA sense region 630agggagagug gguucucaau acg 2363121DNAArtificial SequencesiNA sense region 631ccuguccuuc uacucagcut t 2163221DNAArtificial SequencesiNA sense region 632agguggauuc ugaugccuat t 2163321DNAArtificial SequencesiNA sense region 633cacacuacaa uuugcugagt t 2163421DNAArtificial SequencesiNA sense region 634agugcuggag cuaagugagt t 2163521DNAArtificial SequencesiNA sense region 635cgaauuacau cuccaaaggt t 2163621DNAArtificial SequencesiNA sense region 636gcuaugaggc uuuggaggat t 2163721DNAArtificial SequencesiNA sense region 637caaagagggc aaaugagaut t 2163821DNAArtificial SequencesiNA sense region 638ggagaguggg uucucaauat t 2163921DNAArtificial SequencesiNA antisense region 639agcugaguag aaggacaggt t 2164021DNAArtificial SequencesiNA antisense region 640uaggcaucag aauccaccut t 2164121DNAArtificial SequencesiNA antisense region 641cucagcaaau uguagugugt t 2164221DNAArtificial SequencesiNA antisense region 642cucacuuagc uccagcacut t 2164321DNAArtificial SequencesiNA antisense region 643ccuuuggaga uguaauucgt t 2164421DNAArtificial SequencesiNA antisense region 644uccuccaaag ccucauagct t 2164521DNAArtificial SequencesiNA antisense region 645aucucauuug cccucuuugt t 2164621DNAArtificial SequencesiNA antisense region 646uauugagaac ccacucucct t 2164721DNAArtificial SequencesiNA sense region 647ccuguccuuc uacucagcut t 2164821DNAArtificial SequencesiNA sense region 648agguggauuc ugaugccuat t 2164921DNAArtificial SequencesiNA sense region 649cacacuacaa uuugcugagt t 2165021DNAArtificial SequencesiNA sense region 650agugcuggag cuaagugagt t 2165121DNAArtificial SequencesiNA sense region 651cgaauuacau cuccaaaggt t 2165221DNAArtificial SequencesiNA sense region 652gcuaugaggc uuuggaggat t 2165321DNAArtificial SequencesiNA sense region 653caaagagggc aaaugagaut t 2165421DNAArtificial SequencesiNA sense region 654ggagaguggg uucucaauat t 2165521DNAArtificial SequencesiNA antisense region 655agcugaguag aaggacaggt t 2165621DNAArtificial SequencesiNA antisense region 656uaggcaucag aauccaccut t 2165721DNAArtificial SequencesiNA antisense region 657cucagcaaau uguagugugt t 2165821DNAArtificial SequencesiNA antisense region 658cucacuuagc uccagcacut t 2165921DNAArtificial SequencesiNA antisense region 659ccuuuggaga uguaauucgt t 2166021DNAArtificial SequencesiNA antisense region 660uccuccaaag ccucauagct t 2166121DNAArtificial SequencesiNA antisense region 661aucucauuug cccucuuugt t 2166221DNAArtificial SequencesiNA antisense region 662uauugagaac ccacucucct t 2166321DNAArtificial SequencesiNA sense region 663ccuguccuuc uacucagcut t 2166421DNAArtificial SequencesiNA sense region 664agguggauuc ugaugccuat t 2166521DNAArtificial SequencesiNA sense region 665cacacuacaa uuugcugagt t 2166621DNAArtificial SequencesiNA sense region 666agugcuggag cuaagugagt t 2166721DNAArtificial SequencesiNA sense region 667cgaauuacau cuccaaaggt t 2166821DNAArtificial SequencesiNA sense region 668gcuaugaggc uuuggaggat t 2166921DNAArtificial SequencesiNA sense region 669caaagagggc aaaugagaut t 2167021DNAArtificial SequencesiNA sense region 670ggagaguggg uucucaauat t 2167121DNAArtificial SequencesiNA antisense region 671agcugaguag aaggacaggt t 2167221DNAArtificial SequencesiNA antisense region 672uaggcaucag aauccaccut t 2167321DNAArtificial SequencesiNA antisense region 673cucagcaaau uguagugugt t 2167421DNAArtificial SequencesiNA antisense region 674cucacuuagc uccagcacut t 2167521DNAArtificial SequencesiNA antisense region 675ccuuuggaga uguaauucgt t 2167621DNAArtificial SequencesiNA antisense region 676uccuccaaag ccucauagct t 2167721DNAArtificial SequencesiNA antisense region 677aucucauuug cccucuuugt t 2167821DNAArtificial SequencesiNA antisense region 678uauugagaac ccacucucct t 2167921DNAArtificial SequencesiNA sense region 679ccuguccuuc uacucagcut t 2168021DNAArtificial SequencesiNA sense region 680agguggauuc ugaugccuat t 2168121DNAArtificial SequencesiNA sense region 681cacacuacaa uuugcugagt t 2168221DNAArtificial SequencesiNA sense region 682agugcuggag cuaagugagt t 2168321DNAArtificial SequencesiNA sense region 683cgaauuacau cuccaaaggt t 2168421DNAArtificial SequencesiNA sense region 684gcuaugaggc uuuggaggat t 2168521DNAArtificial SequencesiNA sense region 685caaagagggc aaaugagaut t 2168621DNAArtificial SequencesiNA sense region 686ggagaguggg uucucaauat t 2168721DNAArtificial SequencesiNA antisense region 687agcugaguag aaggacaggt t 2168821DNAArtificial SequencesiNA antisense region 688uaggcaucag aauccaccut t 2168921DNAArtificial SequencesiNA antisense region 689cucagcaaau uguagugugt t 2169021DNAArtificial SequencesiNA antisense region 690cucacuuagc uccagcacut t 2169121DNAArtificial SequencesiNA antisense region 691ccuuuggaga uguaauucgt t 2169221DNAArtificial SequencesiNA antisense region 692uccuccaaag ccucauagct t 2169321DNAArtificial SequencesiNA antisense region 693aucucauuug cccucuuugt t 2169421DNAArtificial SequencesiNA antisense region 694uauugagaac ccacucucct t 2169521DNAArtificial SequencesiNA sense region 695ccuguccuuc uacucagcut t 2169621DNAArtificial SequencesiNA sense region 696agguggauuc ugaugccuat t 2169721DNAArtificial SequencesiNA sense region 697cacacuacaa uuugcugagt t 2169821DNAArtificial SequencesiNA sense region 698agugcuggag cuaagugagt t 2169921DNAArtificial SequencesiNA sense region 699cgaauuacau cuccaaaggt t 2170021DNAArtificial SequencesiNA sense region 700gcuaugaggc uuuggaggat t 2170121DNAArtificial SequencesiNA sense region 701caaagagggc aaaugagaut t 2170221DNAArtificial SequencesiNA sense region 702ggagaguggg uucucaauat t 2170321DNAArtificial SequencesiNA antisense region 703agcugaguag aaggacaggt t 2170421DNAArtificial SequencesiNA antisense region 704uaggcaucag aauccaccut t 2170521DNAArtificial SequencesiNA antisense region 705cucagcaaau uguagugugt t 2170621DNAArtificial SequencesiNA antisense region 706cucacuuagc uccagcacut t 2170721DNAArtificial SequencesiNA antisense region 707ccuuuggaga uguaauucgt t 2170821DNAArtificial SequencesiNA antisense region 708uccuccaaag ccucauagct t 2170921DNAArtificial SequencesiNA antisense region 709aucucauuug cccucuuugt t 2171021DNAArtificial SequencesiNA antisense region 710uauugagaac ccacucucct t 2171121DNAArtificial SequencesiNA antisense region 711agcugaguag aaggacaggt t 2171221DNAArtificial SequencesiNA antisense region 712uaggcaucag aauccaccut t 2171321DNAArtificial SequencesiNA antisense region 713cucagcaaau uguagugugt t 2171421DNAArtificial SequencesiNA antisense region 714cucacuuagc uccagcacut t 2171521DNAArtificial SequencesiNA antisense region 715ccuuuggaga uguaauucgt t 2171621DNAArtificial SequencesiNA antisense region 716uccuccaaag ccucauagct t 2171721DNAArtificial SequencesiNA antisense region 717aucucauuug cccucuuugt t 2171821DNAArtificial SequencesiNA antisense region 718uauugagaac ccacucucct t 2171921DNAArtificial SequencesiNA antisense region 719agcugaguag aaggacaggt t 2172021DNAArtificial SequencesiNA antisense region 720uaggcaucag aauccaccut t 2172121DNAArtificial SequencesiNA antisense region 721cucagcaaau uguagugugt t 2172221DNAArtificial SequencesiNA antisense region 722cucacuuagc uccagcacut t 2172321DNAArtificial SequencesiNA antisense region 723ccuuuggaga uguaauucgt t 2172421DNAArtificial SequencesiNA antisense region 724uccuccaaag ccucauagct t 2172521DNAArtificial SequencesiNA antisense region 725aucucauuug cccucuuugt t 2172621DNAArtificial SequencesiNA antisense region 726uauugagaac ccacucucct t 2172721DNAArtificial SequencesiNA sense region 727nnnnnnnnnn nnnnnnnnnn 2172821DNAArtificial SequencesiNA antisense region 728nnnnnnnnnn nnnnnnnnnn 2172921DNAArtificial SequencesiNA sense region 729nnnnnnnnnn nnnnnnnnnn 2173021DNAArtificial SequencesiNA antisense region 730nnnnnnnnnn nnnnnnnnnn 2173121DNAArtificial SequencesiNA sense region 731nnnnnnnnnn nnnnnnnnnn 2173221DNAArtificial SequencesiNA antisense region 732nnnnnnnnnn nnnnnnnnnn 2173321DNAArtificial SequencesiNA sense region 733nnnnnnnnnn nnnnnnnnnn 2173421DNAArtificial SequencesiNA sense region 734nnnnnnnnnn nnnnnnnnnn 2173521DNAArtificial SequencesiNA antisense region 735nnnnnnnnnn nnnnnnnnnn 2173621DNAArtificial SequencesiNA sense region 736ucugaugccu acuaugucut t 2173721DNAArtificial SequencesiNA antisense region 737agacauagua ggcaucagat 2173821DNAArtificial SequencesiNA sense region 738ucugaugccu acuaugucut t 2173921DNAArtificial SequencesiNA antisense region 739agacauagua ggcaucagat 2174021DNAArtificial SequencesiNA sense region 740ucugaugccu acuaugucut t 2174121DNAArtificial

SequencesiNA antisense region 741agacauagua ggcaucagat 2174221DNAArtificial SequencesiNA sense region 742ucugaugccu acuaugucut 2174321DNAArtificial SequencesiNA sense region 743ucugaugccu acuaugucut 2174421DNAArtificial SequencesiNA antisense region 744agacauagua ggcaucagat 2174514RNAArtificial SequenceSynthetic Target Sequence 745auauaucuau uucg 1474614RNAArtificial SequenceSynthetic Complement to Synthetic Target Sequence 746cgaaauagua uaua 1474722RNAArtificial SequenceSynthetic appended target/complement 747cgaaauagau auaucuauuu cg 2274824DNAArtificial SequenceSynthetic duplex forming oligonucleotide 748cgaaauagau auaucuauuu cgtt 247495598RNAHomo sapiens 749ggccccucag cccugcugcc cagcacgagc cugugcucgc ccugcccaac gcagacagcc 60agacccaggg cggccccucu ggcggcucug cuccucccga aggaugcuug gggagugagg 120cgaagcuggg cgcuccucuc cccuacagca gcccccuucc uccaucccuc uguucuccug 180agccuucagg agccugcacc aguccugccu guccuucuac ucagcuguua cccacucugg 240gaccagcagu cuuucugaua acugggagag ggcaguaagg aggacuuccu ggagggggug 300acuguccaga gccuggaacu gugcccacac cagaagccau cagcagcaag gacaccaugc 360ggcuuccggg ugcgaugcca gcucuggccc ucaaaggcga gcugcuguug cugucucucc 420uguuacuucu ggaaccacag aucucucagg gccuggucgu cacacccccg gggccagagc 480uuguccucaa ugucuccagc accuucguuc ugaccugcuc ggguucagcu ccgguggugu 540gggaacggau gucccaggag cccccacagg aaauggccaa ggcccaggau ggcaccuucu 600ccagcgugcu cacacugacc aaccucacug ggcuagacac gggagaauac uuuugcaccc 660acaaugacuc ccguggacug gagaccgaug agcggaaacg gcucuacauc uuugugccag 720aucccaccgu gggcuuccuc ccuaaugaug ccgaggaacu auucaucuuu cucacggaaa 780uaacugagau caccauucca ugccgaguaa cagacccaca gcugguggug acacugcacg 840agaagaaagg ggacguugca cugccugucc ccuaugauca ccaacguggc uuuucuggua 900ucuuugagga cagaagcuac aucugcaaaa ccaccauugg ggacagggag guggauucug 960augccuacua ugucuacaga cuccaggugu cauccaucaa cgucucugug aacgcagugc 1020agacuguggu ccgccagggu gagaacauca cccucaugug cauugugauc gggaaugagg 1080uggucaacuu cgaguggaca uacccccgca aagaaagugg gcggcuggug gagccgguga 1140cugacuuccu cuuggauaug ccuuaccaca uccgcuccau ccugcacauc cccagugccg 1200aguuagaaga cucggggacc uacaccugca augugacgga gagugugaau gaccaucagg 1260augaaaaggc caucaacauc accgugguug agagcggcua cgugcggcuc cugggagagg 1320ugggcacacu acaauuugcu gagcugcauc ggagccggac acugcaggua guguucgagg 1380ccuacccacc gcccacuguc cugugguuca aagacaaccg cacccugggc gacuccagcg 1440cuggcgaaau cgcccugucc acgcgcaacg ugucggagac ccgguaugug ucagagcuga 1500cacugguucg cgugaaggug gcagaggcug gccacuacac caugcgggcc uuccaugagg 1560augcugaggu ccagcucucc uuccagcuac agaucaaugu cccuguccga gugcuggagc 1620uaagugagag ccacccugac aguggggaac agacaguccg cugucguggc cggggcaugc 1680cccagccgaa caucaucugg ucugccugca gagaccucaa aaggugucca cgugagcugc 1740cgcccacgcu gcuggggaac aguuccgaag aggagagcca gcuggagacu aacgugacgu 1800acugggagga ggagcaggag uuugaggugg ugagcacacu gcgucugcag cacguggauc 1860ggccacuguc ggugcgcugc acgcugcgca acgcuguggg ccaggacacg caggagguca 1920ucguggugcc acacuccuug cccuuuaagg ugguggugau cucagccauc cuggcccugg 1980uggugcucac caucaucucc cuuaucaucc ucaucaugcu uuggcagaag aagccacguu 2040acgagauccg auggaaggug auugagucug ugagcucuga cggccaugag uacaucuacg 2100uggaccccau gcagcugccc uaugacucca cgugggagcu gccgcgggac cagcuugugc 2160ugggacgcac ccucggcucu ggggccuuug ggcagguggu ggaggccacg gcucauggcc 2220ugagccauuc ucaggccacg augaaagugg ccgucaagau gcuuaaaucc acagcccgca 2280gcagugagaa gcaagcccuu augucggagc ugaagaucau gagucaccuu gggccccacc 2340ugaacguggu caaccuguug ggggccugca ccaaaggagg acccaucuau aucaucacug 2400aguacugccg cuacggagac cugguggacu accugcaccg caacaaacac accuuccugc 2460agcaccacuc cgacaagcgc cgcccgccca gcgcggagcu cuacagcaau gcucugcccg 2520uugggcuccc ccugcccagc cauguguccu ugaccgggga gagcgacggu ggcuacaugg 2580acaugagcaa ggacgagucg guggacuaug ugcccaugcu ggacaugaaa ggagacguca 2640aauaugcaga caucgagucc uccaacuaca uggccccuua cgauaacuac guucccucug 2700ccccugagag gaccugccga gcaacuuuga ucaacgaguc uccagugcua agcuacaugg 2760accucguggg cuucagcuac cagguggcca auggcaugga guuucuggcc uccaagaacu 2820gcguccacag agaccuggcg gcuaggaacg ugcucaucug ugaaggcaag cuggucaaga 2880ucugugacuu uggccuggcu cgagacauca ugcgggacuc gaauuacauc uccaaaggca 2940gcaccuuuuu gccuuuaaag uggauggcuc cggagagcau cuucaacagc cucuacacca 3000cccugagcga cguguggucc uucgggaucc ugcucuggga gaucuucacc uuggguggca 3060ccccuuaccc agagcugccc augaacgagc aguucuacaa ugccaucaaa cgggguuacc 3120gcauggccca gccugcccau gccuccgacg agaucuauga gaucaugcag aagugcuggg 3180aagagaaguu ugagauucgg ccccccuucu cccagcuggu gcugcuucuc gagagacugu 3240ugggcgaagg uuacaaaaag aaguaccagc agguggauga ggaguuucug aggagugacc 3300acccagccau ccuucggucc caggcccgcu ugccuggguu ccauggccuc cgaucucccc 3360uggacaccag cuccguccuc uauacugccg ugcagcccaa ugagggugac aacgacuaua 3420ucaucccccu gccugacccc aaacccgagg uugcugacga gggcccacug gaggguuccc 3480ccagccuagc cagcuccacc cugaaugaag ucaacaccuc cucaaccauc uccugugaca 3540gcccccugga gccccaggac gaaccagagc cagagcccca gcuugagcuc cagguggagc 3600cggagccaga gcuggaacag uugccggauu cggggugccc ugcgccucgg gcggaagcag 3660aggauagcuu ccuguagggg gcuggccccu acccugcccu gccugaagcu cccccccugc 3720cagcacccag caucuccugg ccuggccuga ccgggcuucc ugucagccag gcugcccuua 3780ucagcugucc ccuucuggaa gcuuucugcu ccugacgugu ugugccccaa acccuggggc 3840uggcuuagga ggcaagaaaa cugcaggggc cgugaccagc ccucugccuc cagggaggcc 3900aacugacucu gagccagggu ucccccaggg aacucaguuu ucccauaugu aagaugggaa 3960aguuaggcuu gaugacccag aaucuaggau ucucucccug gcugacaggu ggggagaccg 4020aaucccuccc ugggaagauu cuuggaguua cugagguggu aaauuaacuu uuuucuguuc 4080agccagcuac cccucaagga aucauagcuc ucuccucgca cuuuuuaucc acccaggagc 4140uagggaagag acccuagccu cccuggcugc uggcugagcu agggccuagc cuugagcagu 4200guugccucau ccagaagaaa gccagucucc ucccuaugau gccagucccu gcguucccug 4260gcccgagcug gucuggggcc auuaggcagc cuaauuaaug cuggaggcug agccaaguac 4320aggacacccc cagccugcag cccuugccca gggcacuugg agcacacgca gccauagcaa 4380gugccugugu cccuguccuu caggcccauc aguccugggg cuuuuucuuu aucacccuca 4440gucuuaaucc auccaccaga gucuagaagg ccagacgggc cccgcaucug ugaugagaau 4500guaaaugugc caguguggag uggccacgug ugugugccag uauauggccc uggcucugca 4560uuggaccugc uaugaggcuu uggaggaauc ccucacccuc ucugggccuc aguuuccccu 4620ucaaaaaaug aauaagucgg acuuauuaac ucugagugcc uugccagcac uaacauucua 4680gaguauucca ggugguugca cauuugucca gaugaagcaa ggccauauac ccuaaacuuc 4740cauccugggg gucagcuggg cuccugggag auuccagauc acacaucaca cucuggggac 4800ucaggaacca ugccccuucc ccaggccccc agcaagucuc aagaacacag cugcacaggc 4860cuugacuuag agugacagcc gguguccugg aaagccccaa gcagcugccc cagggacaug 4920ggaagaccac gggaccucuu ucacuaccca cgaugaccuc cggggguauc cugggcaaaa 4980gggacaaaga gggcaaauga gaucaccucc ugcagcccac cacuccagca ccugugccga 5040ggucugcguc gaagacagaa uggacaguga ggacaguuau gucuuguaaa agacaagaag 5100cuucagaugg uaccccaaga aggaugugag agguggccgc uuggaguuug ccccucaccc 5160accagcugcc ccaucccuga ggcagcgcuc caugggggua ugguuuuguc acugcccaga 5220ccuagcagug acaucucauu guccccagcc cagugggcau uggaggugcc aggggaguca 5280ggguuguagc caagacgccc ccgcacgggg aggguuggga agggggugca ggaagcucaa 5340ccccucuggg caccaacccu gcauugcagg uuggcaccuu acuucccugg gauccccaga 5400guugguccaa ggagggagag uggguucuca auacgguacc aaagauauaa ucaccuaggu 5460uuacaaauau uuuuaggacu cacguuaacu cacauuuaua cagcagaaau gcuauuuugu 5520augcuguuaa guuuuucuau cuguguacuu uuuuuuaagg gaaagauuuu aauauuaaac 5580cuggugcuuc ucacucac 5598

Claims

1. A chemically modified nucleic acid molecule, wherein: (a) the nucleic acid molecule comprises a sense strand and a separate antisense strand, each strand having one or more pyrimidine nucleotides and one or more purine nucleotides; (b) each strand of the nucleic acid molecule is independently 18 to 27 nucleotides in length; (c) an 18 to 27 nucleotide sequence of the antisense strand is complementary to a human Platelet Derived Growth Factor Receptor (PDGFr) RNA sequence comprising SEQ ID NO: 749; (d) an 18 to 27 nucleotide sequence of the sense strand is complementary to the antisense strand and comprises an 18 to 27 nucleotide sequence of the human PDGFr RNA sequence; and (e) 50 percent or more of the nucleotides in at least one strand comprise a 2-sugar modification, wherein the 2'-sugar modification of any of the pyrimidine nucleotides differs from the 2'-sugar modification of any of the purine nucleotides.

2. The nucleic acid molecule of claim 1, wherein 50 percent or more of the nucleotides in each strand comprise a 2'-sugar modification.

3. The nucleic acid molecule of claim 1, wherein the 2'-sugar modification is selected from the group consisting of 2'-deoxy-2'-fluoro, 2'-O-methyl, and 2'-deoxy.

4. The nucleic acid of claim 3, wherein the 2'-deoxy-2'-fluoro sugar modification is a pyrimidine modification.

5. The nucleic acid of claim 3, wherein the 2'-deoxy sugar modification is a pyrimidine modification.

6. The nucleic acid of claim 3, wherein the 2'-O-methyl sugar modification is a pyrimidine modification.

7. The nucleic acid molecule of claim 4, wherein said pyrimidine modification is in the sense strand, the antisense strand, or both the sense strand and antisense strand.

8. The nucleic acid molecule of claim 6, wherein said pyrimidine modification is in the sense strand, the antisense strand, or both the sense strand and antisense strand.

9. The nucleic acid molecule of claim 3, wherein the 2'-deoxy sugar modification is a purine modification.

10. The nucleic acid molecule of claim 3, wherein the 2'-O-methyl sugar modification is a purine modification.

11. The nucleic acid molecule of claim 9, wherein the purine modification is in the sense strand.

12. The nucleic acid molecule of claim 10, wherein the purine modification is in the antisense strand.

13. The nucleic acid molecule of claim 1, wherein the nucleic acid molecule comprises ribonucleotides.

14. The nucleic acid molecule of claim 1, wherein the sense strand includes a terminal cap moiety at the 5'-end, the 3'-end, or both of the 5'- and 3'-ends.

15. The nucleic acid molecule of claim 14, wherein the terminal cap moiety is an inverted deoxy abasic moiety.

16. The nucleic acid molecule of claim 1, wherein said nucleic acid molecule includes one or more phosphorothioate internucleotide linkages.

17. The nucleic acid molecule of claim 16, wherein one of the phosphorothioate internucleotide linkages is at the 3'-end of the antisense strand.

18. The nucleic acid molecule of claim 1, wherein the 5'-end of the antisense strand includes a terminal phosphate group.

19. The nucleic acid molecule of claim 1, wherein the sense strand, the antisense strand, or both the sense strand and the antisense strand include a 3'-overhang.

20. A composition comprising the nucleic acid molecule of claim 1, in a pharmaceutically acceptable carrier or diluent.