U.S. patent number 9,255,292 [Application Number 13/186,353] was granted by the patent office on 2016-02-09 for synthesis of four-color 3'-o-allyl modified photocleavable fluorescent nucleotides and related methods.
This patent grant is currently assigned to THE TRUSTEES OF COLUMBIA UNIVERSITY IN THE CITY OF NEW YORK. The grantee listed for this patent is Xiaopeng Bai, Lanrong Bi, Jingyue Ju, Dae H. Kim, Qinglin Meng, Nicholas J. Turro. Invention is credited to Xiaopeng Bai, Lanrong Bi, Jingyue Ju, Dae H. Kim, Qinglin Meng, Nicholas J. Turro.
United States Patent |
9,255,292 |
Ju , et al. |
February 9, 2016 |
Synthesis of four-color 3'-O-allyl modified photocleavable
fluorescent nucleotides and related methods
Abstract
This invention provides a process for making
3'-O-allyl-dGTP-PC-Biodopy-FL-510, 3'-O-allyl-dATP-PC-ROX,
3'-O-allyl-dCTP-PC-Bodipy-650 and 3'-O-allyl-dUTP-PC-R6G, and
related methods.
Inventors: |
Ju; Jingyue (Englewood Cliffs,
NJ), Meng; Qinglin (Sunnyvale, CA), Kim; Dae H. (New
York, NY), Bi; Lanrong (New York, NY), Bai; Xiaopeng
(Watertown, MA), Turro; Nicholas J. (Tenafly, NJ) |
Applicant: |
Name |
City |
State |
Country |
Type |
Ju; Jingyue
Meng; Qinglin
Kim; Dae H.
Bi; Lanrong
Bai; Xiaopeng
Turro; Nicholas J. |
Englewood Cliffs
Sunnyvale
New York
New York
Watertown
Tenafly |
NJ
CA
NY
NY
MA
NJ |
US
US
US
US
US
US |
|
|
Assignee: |
THE TRUSTEES OF COLUMBIA UNIVERSITY
IN THE CITY OF NEW YORK (New York, NY)
|
Family
ID: |
38006496 |
Appl.
No.: |
13/186,353 |
Filed: |
July 19, 2011 |
Prior Publication Data
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Document
Identifier |
Publication Date |
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US 20120156680 A1 |
Jun 21, 2012 |
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Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
Issue Date |
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12084338 |
Jul 19, 2011 |
7982029 |
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PCT/US2006/042698 |
Oct 31, 2009 |
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60732373 |
Oct 31, 2005 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C07H
19/14 (20130101); C12Q 1/6869 (20130101); C12Q
1/6806 (20130101); C12Q 1/6874 (20130101); C07H
1/04 (20130101); C07H 19/067 (20130101); C07H
19/10 (20130101); C12Q 2563/107 (20130101); C12Q
2521/101 (20130101); C12Q 2525/186 (20130101); C12Q
2525/117 (20130101) |
Current International
Class: |
C12Q
1/68 (20060101); C12P 19/34 (20060101); C07H
19/067 (20060101); C07H 19/04 (20060101) |
Field of
Search: |
;435/6.1,91.1,91.2
;536/26.6 |
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Sep 2014 |
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WO |
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Examination Report Under Section 18(3) issued Oct. 4, 2010 in
connection with United Kingdom Patent Application No. GB0808033.5.
cited by applicant .
Examination Report Under Section 18(3) issued Jan. 7, 2011 in
connection with United Kingdom Patent Application No. GB0808033.5.
cited by applicant .
Examination Report Under Section 18(3) issued Jan. 28, 2010 in
connection with United Kingdom Patent Application No. GB0808034.3.
cited by applicant .
Examination Report Under Section 18(3) issued Oct. 4, 2010 in
connection with United Kingdom Patent Application No. GB0808034.3.
cited by applicant .
Notice of Allowance issued Jan. 28, 2014 in connection with U.S.
Appl. No. 12/084,457. cited by applicant .
Office Action issued Oct. 21, 2014 in connection with U.S. Appl.
No. 14/451,265. cited by applicant .
Oct. 28, 2014 Final Written Decision in connection with
IPR2013-00266. cited by applicant .
Feb. 13, 2014 Decision of Institution of Inter Partes Review
IPR2013-00517. cited by applicant .
May 5, 2014 Patent Owner Response in connection with IPR2013-00517.
cited by applicant .
Exhibit 2005, filed May 5, 2014 in connection with IPR2013-00517:
IBS's Answer, Affirmative Defenses & Counterclaims to Illumina,
Inc. and Illumina Cambridge Ltd.'s Second Amended Counterclaims to
Amended Complaint, Columbia v. Illumina, No. 12-CV-00376 (D. Del).
cited by applicant .
Exhibit 2006, filed May 5, 2014 in connection with IPR2013-00517:
Excerpts from file history of U.S. Appl. No. 13/305,415, filed Nov.
28, 2011, Gordon et al. cited by applicant .
Exhibit 2010, filed May 5, 2014 in connection with IPR2013-00517:
Excerpts from prosecution history of U.S. Pat. No. 7,566,537,
issued Jul. 28, 2009, Barnes et al. cited by applicant .
Exhibit 2011, filed May 5, 2014 in connection with IPR2013-00517:
May 5, 2014 Declaration of Floyd Romesberg, Ph.D. cited by
applicant .
Exhibit 2013, filed May 5, 2014 in connection with IPR2013-00517:
Ranganathan et al., "Facile Conversion of Adenosine into New
2'-Substituted-2'-Deoxy-Arabinofuranosyladenine Derivatives:
Stereospecific Syntheses of 2'-Azido-2'-Deoxy-, 2'-Amino-2'-Deoxy-,
and 2'-Mercapto-2'-Deoxy-.beta.-D- Arabinofuranosyladenines"
Tetrahedron Letters 45:4341-44. cited by applicant .
Exhibit 2014, filed May 5, 2014 in connection with IPR2013-00517:
Mungall et al., "Use of the Azido Group in the Synthesis of
5'Terminal Aminodeoxythymidine Oligonucleotides"J. Org. Chem.,
40:1659-1662 (1975). cited by applicant .
Exhibit 2016, filed May 5, 2014 in connection with IPR2013-00517:
Pilard et al., "A Stereospecific Synthesis OF (+),
.alpha.-Conhydrine and (+) .beta.-Conhydrine)" Tet. Lett.,
25:1555-1556. cited by applicant .
Exhibit 2017, filed May 5, 2014 in connection with IPR2013-00517:
"Synthesis of a Novel Stable GM.sub.3-Lactone Analogue as Hapten
for a Possible Immunization against Cancer" Tietze et al., Angew.
Chem. Int. Ed., 36:1615, 1616 (1997). cited by applicant .
Exhibit 2018, filed May 5, 2014 in connection with IPR2013-00517:
Kit, "Deoxyribonucleic Acids" Annual Rev. Biochem, 32:43 (1963).
cited by applicant .
Exhibit 2019, filed May 5, 2014 in connection with IPR2013-00517:
Canard et al., "Catalytic editing properties of DNA polymerases"
PNAS USA 92:10859 (1995). cited by applicant .
Exhibit 2020, filed May 5, 2014 in connection with IPR2013-00517:
The Merck Index, p. 9815 (entry for Triphenylphosphine) (13.sup.th
Edition, 2001). cited by applicant .
Exhibit 2021, filed May 5, 2014 in connection with IPR2013-00517:
Lee et al., "Unwinding of double-stranded DNA helix by dehydration"
PNAS 78:2838-42 (1981). cited by applicant .
Exhibit 2022, filed May 5, 2014 in connection with IPR2013-00517:
Christensen et al., "Specific Chemical Synthesis of Ribonucleoside
O-Benzyl Ethers" J. Am. Chem. Soc., 37:3398 (1972). cited by
applicant .
Exhibit 2023, filed May 5, 2014 in connection with IPR2013-00517:
Watkins et al., "Synthesis of Oligodeoxyribonucleotides Using
N-Benzyloxycarbonyl-Blocked Nucleosides", J. Am. Chem. Soc.
104:5702-08 (1982). cited by applicant .
Exhibit 2025, filed May 5, 2014 in connection with IPR2013-00517:
Yoshimoto et al., "Tris(2,4,6- trimethoxyphenyl)phosphine (TTMPP):
A Novel Catalyst for Selective Deacetylation" Chemistry Letters
30:934-35 (2001). cited by applicant .
Exhibit 2026, filed May 5, 2014 in connection with IPR2013-00517:
Chapter 3 of Protective Groups in Organic Synthesis (Theodora W.
Greene & Peter G. M. Wuts eds., John Wiley & Sons, Inc. 3rd
ed. 1999) (1991). cited by applicant .
Exhibit 2027, filed May 5, 2014 in connection with IPR2013-00517:
Bentley et al., "Accurate whole human genome sequencing using
reversible terminator chemistry" Nature 456:53-59 (2008). cited by
applicant .
Exhibit 2029, filed May 5, 2014 in connection with IPR2013-00517:
Shendure et al., "Advanced Sequencing Technologies: Methods and
Goals" Nature Reviews Genetics, 5:335-44 (2004). cited by applicant
.
Exhibit 2039, filed May 5, 2014 in connection with IPR2013-00517:
Transcript of Apr. 8, 2014 Deposition of Bruce Branchaud, Ph.D.
cited by applicant .
Exhibit 2044, filed May 5, 2014 in connection with IPR2013-00517:
Excerpts of Transcript of Mar. 20, 2013 Deposition of Dr. Xiaohai
Liu in Columbia v. Illumina, 12-cv-376 (D. Del). cited by applicant
.
Exhibit 2047, filed May 5, 2014 in connection with IPR2013-00517:
Ruparel et al., "Design and synthesis of a 3-O-allyl photocleavable
fluorescent nucleotide as a reversible terminator for DNA
sequencing by synthesis" PNAS 102:5932-5937 (2005). cited by
applicant .
Exhibit 2050, filed May 5, 2014 in connection with IPR2013-00517:
Mardis, "A decade's perspective on DNA sequencing technology"
Nature 470:198-203 (2011). cited by applicant .
Exhibit 2051, filed May 5, 2014 in connection with IPR2013-00517:
Meng et al., "Design and Synthesis of a Photocleavable Fluorescent
Nucleotide 3'-O-Allyl-dGTP-PC-Bodipy-FL-510 as a Reversible
Terminator for DNA Sequencing by Synthesis" J. Org. Chem 71:3248-52
(2006). cited by applicant .
Exhibit 2052, filed May 5, 2014 in connection with IPR2013-00517:
Bi et al., "Design and Synthesis of a Chemically Cleavable
Fluorescent Nucleotide, 3'-O-Allyl-dGTP-allyl-Bodipy-FL-510, as a
Reversible Terminator for DNA Sequencing by Synthesis" J Am Chem
Soc, 128:2542-43 (2006). cited by applicant .
Exhibit 2053, filed May 5, 2014 in connection with IPR2013-00517:
Meng, "Tandem Aldol-Allylation Reactions Promoted by Strained
Silacycles and Design and Synthesis of Modified Flourescent
Nucleotides for DNA Sequencing by Synthesis", Studen Thesis (2006).
cited by applicant .
Exhibit 2054, filed May 5, 2014 in connection with IPR2013-00517:
Wu et al., "3'-O-modified nucleotides as reversible terminators for
pyrosequencing" PNAS, 104:16462-67 (2007). cited by applicant .
Exhibit 2055, filed May 5, 2014 in connection with IPR2013-00517:
Kim, "Four-Color DNA Sequencing by Synthesis on a Chip Using
Cleavable Fluorescent Nucleotide Reversible Terminators", Student
Thesis (2008). cited by applicant .
Exhibit 2056, filed May 5, 2014 in connection with IPR2013-00517:
Wu, "Molecular Engineering of Novel Nucleotide Analogues for DNA
Sequencing by Synthesis", Student Thesis (2008). cited by applicant
.
Exhibit 2057, filed May 5, 2014 in connection with IPR2013-00517:
Zhang, "Development of New DNA Sequencing Approaches and
investigation of Vision-related Proteins Using Synthetic
Chemistry", Student Thesis (2008). cited by applicant .
Exhibit 2058, filed May 5, 2014 in connection with IPR2013-00517:
Guo et al., "Four-color DNA sequencing with 3'-O- modified
nucleotide reversible terminators and chemically cleavable
fluorescent dideoxynucleotides", PNAS 105:9145. cited by applicant
.
Exhibit 2059, filed May 5, 2014 in connection with IPR2013-00517:
Guo, "Molecular Engineering of Novel Nucleotide Analogues for DNA
Sequencing and Analysis", Student Thesis (2009). cited by applicant
.
Exhibit 2060, filed May 5, 2014 in connection with IPR2013-00517:
Yu, "Novel Strategies to Increase Read Length and Accuracy for DNA
Sequencing by Synthesis", Student Thesis (2010). cited by applicant
.
Exhibit 2062, filed May 5, 2014 in connection with IPR2013-00517:
Qui, "Novel Molecular Engineering Approaches for Genotyping and DNA
Sequencing", Student Thesis (2010). cited by applicant .
Exhibit 2073, filed May 5, 2014 in connection with IPR2013-00517:
Kraevskii et al., "Substrate Inhibitors of DNA Biosynthesis",
Molecular Biology 21:25-29 (1987). cited by applicant .
Exhibit 2074, filed May 5, 2014 in connection with IPR2013-00517:
Dantas et al., "Stannous chloride mediates single strand breaks in
plasmid DNA through reactive oxygen species formation", Toxicology
Ltrs. 110:129-36 (1999). cited by applicant .
Exhibit 2077, filed May 5, 2014 in connection with IPR2013-00517:
Burgess et al., "An Approach to Photolabile, Fluorescent Protecting
Groups", J. Org. Chem 62:5165-68 (1997). cited by applicant .
Exhibit 2079, filed May 5, 2014 in connection with IPR2013-00517:
Welch et al., "Syntheses of Nucleosides Designed for Combinatorial
DNA Sequencing", Chem. Eur. J. 5:951-60 (1999). cited by applicant
.
Petitioner Reply to Patent Owner Response, filed Jul. 28, 2014 in
connection with IPR2013-00517. cited by applicant .
Exhibit 1019, filed Jul. 28, 2014 in connection with IPR2013-00517:
Ireland et al., Approach to the Total Synthesis of
Chlorothricolide: Synthesis of
(+)-19,20-Dihydro-24-O-methylchlorothricolide, Methyl Ester, Ethyl
Carbonate, 51 J. Org. Chem. 635 (1986). cited by applicant .
Exhibit 1020, filed Jul. 28, 2014 in connection with IPR2013-00517:
Gordon et al., Abstract, The Relationship of Structure to
Effectiveness of Denaturing Agents for DNA, Biophysical Society 6th
Annual Meeting (Washington, 1962). cited by applicant .
Exhibit 1022, filed Jul. 28, 2014 in connection with IPR2013-00517:
p. 295 from Mar. 20, 2003 deposition of Dr. Xiaohai Liu, The
Trustees of Columbia University and Intelligent Bio-Systems, Inc.
v. Illumina, 12-376 (GMS) (D. Del.). cited by applicant .
Exhibit 1025, filed Jul. 28, 2014 in connection with IPR2013-00517:
Transcript, Jul. 8, 2014 Deposition of Floyd Romesberg, Ph.D. cited
by applicant .
Exhibit 1026, filed Jul. 28, 2014 in connection with IPR2013-00517:
Transcript, Jul. 15, 2014 Deposition of Kevin Burgess, Ph.D. cited
by applicant .
Exhibit 1030, filed Jul. 28, 2014 in connection with IPR2013-00517:
Patent prosecution excerpt from file history of U.S. Pat. No.
7,566,537 (U.S. Appl. No. 11/301,578). cited by applicant .
Exhibit 1031, filed Jul. 28, 2014 in connection with IPR2013-00517:
Second Declaration of Dr. Bruce Branchaud in Support Of Intelligent
Bio-Systems, Inc.'s Reply to Illumina's Patent Owner Response.
cited by applicant .
Exhibit 1032, filed Jul. 28, 2014 in connection with IPR2013-00517:
Gololobov and Kasukhin, Recent advances in the Staudinger reaction,
Tetrahedron 48:1353-1406 (1992). cited by applicant .
Exhibit 1034, filed Jul. 28, 2014 in connection with IPR2013-00517:
Saxon and Bertozzi, Cell Surface Engineering by a Modified
Staudinger Reaction, Science 287:2007-2010 (2000). cited by
applicant .
Exhibit 1036, filed Jul. 28, 2014 in connection with IPR2013-00517:
Faucher and Grand-Maitre, tris(2- Carboxyethyl)phosphine (TCEP) for
the Reduction of Sulfoxides, Sulfonylchlorides, N--Oxides, and
Azides, Synthetic Communications 33:3503-3511 (2003). cited by
applicant .
Exhibits 1037 and 1038, filed Jul. 28, 2014 in connection with
IPR2013-00517: Knouzi et al., Reductions of Azides by
Triphenylphosphine in the presence of water: a General and
chemoselective method of access to primary amines, Bull. Soc. Chim.
Fr., 1-12 (1985), and translation. cited by applicant .
Exhibit 1041, filed Jul. 28, 2014 in connection with IPR2013-00517:
Mag and Engels, Synthesis and selective cleavage of
oligodeoxyribonucleotides containing non-chiral internucleotide
phosphoramidate linkages, Nucleic Acids Research 15:5973-5988
(1989). cited by applicant .
Exhibit 1043, filed Jul. 28, 2014 in connection with IPR2013-00517:
Chang and Bollum, Molecular biology of terminal transferase, CRC
Critical Reviews in Biochemistry 21:27-52.(1986). cited by
applicant .
Exhibit 1044, filed Jul. 28, 2014 in connection with IPR2013-00517:
Chen, DNA polymerases drive DNA sequencing-by-synthesis
technologies: both past and present, Frontiers in Microbiology,
vol. 5, Article 305, 1-11 (2014). cited by applicant .
Exhibit 1046, filed Jul. 28, 2014 in connection with IPR2013-00517:
Declaration of Dr. Michael Metzker in Support of Intelligent
Bio-Systems, Inc's Reply to Illumina's Patent Owner Response. cited
by applicant .
Exhibit 1047, filed Jul. 28, 2014 in connection with IPR2013-00517:
Lebreton et al., Structure-Immunosuppressive Activity Relationships
of New Analogues of 15-Deoxyspergualin. 2. Structural Modifications
of the Spermidine Moiety, Journal of Medicinal Chemistry
42:4749-4763 (1999). cited by applicant .
Exhibit 1048, filed Jul. 28, 2014 in connection with IPR2013-00517:
Levine et al., The Relationship of Structure to the Effectiveness
of Denaturing Agents for Deoxyribonucleic Acid, Biochemistry
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Exhibit 1049, filed Jul. 28, 2014 in connection with IPR2013-00517:
Efimov et al., An azidomethyl protective group in the synthesis of
oligoribonucleotides by the phosphotriester method, 35:250-253
(2009). cited by applicant .
Exhibit 1050, filed Jul. 28, 2014 in connection with IPR2013-00517:
Kirby, A new method for the isolation of deoxyribonucleic acids:
Evidence of the nature of bonds between deoxyribonucleic acids and
proteins, Biochemical Journal 66:495-504 (1957). cited by applicant
.
Exhibit 1051, filed Jul. 28, 2014 in connection with IPR2013-00517:
Bentley et al., Accurate whole human genome sequencing using
reversible terminator chemistry. Nature 456:53
(2008)--Supplementary Information. cited by applicant .
Feb. 13, 2014 Decision of Institution of Inter Partes Review
IPR2013-00518. cited by applicant .
May 5, 2014 Patentee Request for Adverse Judgment in IPR2013-00518.
cited by applicant .
May 6, 2014 Decision of Adverse Judgment in IPR2013-00518. cited by
applicant .
Jun. 4, 2013 Petition for Inter Partes Review of U.S. Pat. No.
7,057,026. cited by applicant .
Exhibit 1004, filed Jun. 4, 2013 in connection with IPR2013-00324:
J. Meinwald, An Approach to the Synthesis of Pederin, 49 Pure and
Appl. Chem. 1275 (1977). cited by applicant .
Exhibit 1005, filed Jun. 4, 2013 in connection with IPR2013-00324:
Takeshi Matsumoto et al., A Revised Structure of Pederin, 60
Tetrahedron Letters 6297 (1968). cited by applicant .
Exhibit 1008, filed Jun. 4, 2013 in connection with IPR2013-00324:
Beckman Coulter CEQTM 2000 DNA Analysis System User's Guide, Jun.
2000. cited by applicant .
Exhibit 1009, filed Jun. 4, 2013 in connection with IPR2013-00324:
Jun. 4, 2013 Declaration of Dr. Bruce Branchaud. cited by applicant
.
Exhibit 1010, filed Jun. 4, 2013 in connection with IPR2013-00324:
Excerpts from the '026 Patent File History. cited by applicant
.
Exhibit 1011, filed Jun. 4, 2013 in connection with IPR2013-00324:
Excerpts from the file history of European Patent Application No:
02781434.2. cited by applicant .
Nov. 21, 2013 Decision Denying Institution of Inter Partes Review
of U.S. Pat. No. 7,057,026 in connection with IPR2013-00324. cited
by applicant .
U.S. Appl. No. 09/684,670, filed Oct. 6, 2000, Ju et al. cited by
applicant .
Aug. 19, 2013 Petition 1 of 2 for Inter Partes Review of U.S. Pat.
No. 7,566,537, issued Jul. 28, 2009. cited by applicant .
Aug. 30, 2013 Revised Petition 1 of 2 for Inter Partes Review of
U.S. Pat. No. 7,566,537, issued Jul. 28, 2009. cited by applicant
.
Exhibit 1004, filed Aug. 19, 2013 in connection with IPR2013-00517:
Zavgorodny et al., 1-Alkylthioalkylation of Nucleoside Hydroxyl
Functions and Its Synthetic Applications: A New Versatile Method in
Nucleoside Chemistry, 32 Tetrahedron Letters 7593 (1991). cited by
applicant .
Exhibit 1005, filed Aug. 19, 2013 in connection with IPR2013-00517:
Protective Groups in Organic Synthesis (Theodora W. Greene &
Peter G. M. Wuts eds., John Wiley & Sons, Inc. 3rd ed. 1999)
(1991). cited by applicant .
Exhibits 1006-1007, filed Aug. 19, 2013 in connection with
IPR2013-00517: English translation of Loubinoux et al., Protection
of Phenols by the Azidomethylene Group Application to the Synthesis
of Unstable Phenols, 44 Tetrahedron 6055 (1988), and Translation
Affidavit. cited by applicant .
Exhibit 1009, filed Aug. 19, 2013 in connection with IPR2013-00517:
Prober et al., A System for Rapid DNA Sequencing with Fluorescent
Chain-Terminating Dideoxynucleotides, 238 Science 336 (1987). cited
by applicant .
Exhibit 1011, filed Aug. 19, 2013 in connection with IPR2013-00517:
Aug. 16, 2013 Declaration of Dr. Bruce Branchaud. cited by
applicant .
Exhibit 1012, filed Aug. 19, 2013 in connection with IPR2013-00517:
Excerpts from the Mar. 20, 2013 Deposition Transcript of Dr.
Xiaohai Liu. cited by applicant .
Exhibit 1013, filed Aug. 19, 2013 in connection with IPR2013-00517:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,713,698. cited by applicant .
Exhibit 1014, filed Aug. 19, 2013 in connection with IPR2013-00517:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,790,869. cited by applicant .
Exhibit 1015, filed Aug. 19, 2013 in connection with IPR2013-00517:
Oct. 3, 2012 Petition for Inter Partes Review of U.S. Pat. No.
8,088,575. cited by applicant .
Record of Dec. 17, 2013 Oral Hearing, entered Feb. 10, 2014 in
connection with IPR2012-00006, IPR2012-00007, and IPR2013-00011.
cited by applicant .
Mar. 6, 2014 Final Written Decision in connection with
IPR2012-00006. cited by applicant .
Mar. 6, 2014 Final Written Decision in connection with
IPR2012-00007. cited by applicant .
Mar. 6, 2014 Final Written Decision in connection with
IPR2013-00011. cited by applicant .
Feb. 19, 2014 Substitute Motion to Amend Under 37 C.F.R.
.sctn.42.121 in connection with IPR2013-00128. cited by applicant
.
Exhibit 2009, filed Feb. 19, 2014 in connection with IPR2013-00128:
Substitute Declaration of Floyd Romesberg, Ph.D., in Support of
Patent Owner's Motion to Amend. cited by applicant .
Exhibit 2028, filed Feb. 19, 2014 in connection with IPR2013-00128:
Substitute Declaration of Eric Vermaas Accompanying Patent Owner's
Motion to Amend. cited by applicant .
Feb. 24, 2014 Patent Owner Illumina's Reply to Petitioner's
Opposition to Illumina's Motion to Amend. cited by applicant .
Exhibit 2029, filed Feb. 24, 2014 in connection with IPR2013-00128:
Supplementary information for Ex. 1032 (Mitra et al., Analytical
Biochem. 320, 55-65, 2003). cited by applicant .
Exhibit 2031, filed Feb. 24, 2014 in connection with IPR2013-00128:
Ju et al., "Four-color DNA 15 Sequencing By Synthesis Using
Cleavable 16 Fluorescent Nucleotide Reversible Terminators," PNAS
USA, 103:19635-19640 (2006). cited by applicant .
Exhibit 2032, filed Feb. 24, 2014 in connection with IPR2013-00128:
ScanArray Express Line of Microarray Scanners. cited by applicant
.
Exhibit 2034, filed Feb. 24, 2014 in connection with IPR2013-00128:
Feb. 11, 2014 Second Deposition Transcript of Bruce Branchaud,
Ph.D. cited by applicant .
Exhibit 2037, filed Feb. 24, 2014 in connection with IPR2013-00128:
Mullis et al., "Specific Synthesis of DNA in Vitro via a
Polymerase-Catalyzed Chain Reaction," pp. 335-350, in Methods in
Enzymology, vol. 155, Recombinant DNA, Part F, ed. Wu, Academic
Press, Inc., San Diego (1987). cited by applicant .
Feb. 14, 2011 Amendment in response to Office Action issued Oct.
14, 2010 in connection with U.S. Appl. No. 12/084,338. cited by
applicant .
Jul. 27, 2010 Response to Examination Report Under Section 18(3)
issued Jan. 28, 2010 in connection with United Kingdom Patent
Application No. GB0808033.5. cited by applicant .
Jan. 4, 2011 Response to Examination Report Under Section 18(3)
issued Oct. 4, 2010 in connection with United Kingdom Patent
Application No. GB0808033.5. cited by applicant .
Jan. 17, 2011 Response to Examination Report Under Section 18(3)
issued Jan. 7, 2011 in connection with United Kingdom Patent
Application No. GB0808033.5. cited by applicant .
Jul. 27, 2010 Response to Examination Report Under Section 18(3)
issued Jan. 28, 2010 in connection with United Kingdom Patent
Application No. GB0808034.3. cited by applicant .
Jan. 4, 2011 Response to Examination Report Under Section 18(3)
issued Oct. 4, 2010 in connection with United Kingdom Patent
Application No. GB0808034.3. cited by applicant .
Jan. 17, 2011 Response to Examination Report Under Section 18(3)
issued Jan. 7, 2011 in connection with United Kingdom Patent
Application No. GB0808034.3. cited by applicant .
Examination Report Under Section 18(3) issued Jan. 7, 2011 in
connection with United Kingdom Patent Application No. GB0808034.3.
cited by applicant .
International Search Report issued by the International Searching
Authority (ISA/US) on Nov. 23, 2007 in connection with
International Application No. PCT/US2006/042698. cited by applicant
.
Written Opinion issued by the International Searching Authority
(ISA/US) on Nov. 23, 2007 in connection with International
Application No. PCT/US2006/042698. cited by applicant .
Meng, Q., et al. "Design and Synthesis of a Photocleavable
Fluorescent Nucleotide 3'-O-Allyl-dGTP-PC-Bodipy-FL-510 as a
Reversible Terminator for DNA Sequencing by Synthesis" J. Org.
Chem. (2006), 71, 3248-3252. cited by applicant .
Ruparel, H., et al. "Design and synthesis of a 3'-O-allyl
photocleavable fluorescent nucleotide as a reversible terminator
for DNA sequencing by synthesis" PNAS, 2005, vol. 102, No. 17,
5932-5937. cited by applicant .
Seo, T.S., et al. "Four-color DNA sequencing by synthesis on a chip
using photocleavable fluorescent nucleotides" PNAS, 2005, vol. 102,
No. 17, 5926-5931. cited by applicant .
Seo, T.S., et al. "Photocleavable fluorescent nucleotides for DNA
sequencing on a chip constructed by site-specific coupling
chemistry" PNAS, 2004, vol. 101, No. 15, 5488-5493. cited by
applicant .
Li, Z., et al. "A photocleavable fluorescent nucleotide for DNA
sequencing and analysis" PNAS, 2003, vol. 100, No. 2, 414-419.
cited by applicant .
Office Action issued Oct. 14, 2010 in connection with U.S. Appl.
No. 12/084,338. cited by applicant .
Notice of Allowance issued Mar. 1, 2011 in connection with U.S.
Appl. No. 12/084,338. cited by applicant .
Issue Notification issued Jun. 29, 2011 in connection with U.S.
Appl. No. 12/084,338. cited by applicant .
Oct. 3, 2012 Petition for Inter Partes Review of U.S. Pat. No.
8,088,575. cited by applicant .
Oct. 3, 2012 Motion to Waive Page Limit and Proposed Petition in
connection with Petition for Inter Partes Review of U.S. Pat. No.
8,088,575. cited by applicant .
Jan. 7, 2013 Preliminary Response under 37 C.F.R. 42.107 in
connection with IPR2013-00011. cited by applicant .
Mar. 12, 2013 Decision on Petition for Inter Partes Review in
connection with IPR2013-00011. cited by applicant .
Mar. 26, 2013 Request for Reconsideration in connection with
IPR2013-00011. cited by applicant .
Mar. 26, 2013 Request for Rehearing under 37 C.F.R. 42.71 of
Decision to Institute Inter Partes Review in connection with
IPR2013-00011. cited by applicant .
Apr. 26, 2013 Opposition to Request for Reconsideration (Rehearing)
Under 37 C.F.R. 42.71.(C) in connection with IPR2013-00011. cited
by applicant .
May 10, 2013 Decision on Request for Rehearing in connection with
IPR2013-00011. cited by applicant .
Jun. 25, 2013 Motion to Amend Under 37 C.F.R. 42.121 in connection
with IPR2013-00011. cited by applicant .
Aug. 30, 2013 Substitute Patent Owner Response Under 37 C.F.R.
42.120 in connection with IPR2013-00011. cited by applicant .
Sep. 27, 2013 Petitioner Opposition to Motion to Amend in
connection with IPR2013-00011. cited by applicant .
Sep. 27, 2013 Petitioner Reply to Response to Petition in
connection with IPR2013-00011. cited by applicant .
Nov. 18, 2013 Substitute Patent Owner Reply on Motion to Amend in
connection with IPR2013-00011. cited by applicant .
Exhibit 1001, filed Oct. 3, 2012 in connection with IPR2013-00011:
U.S. Pat. No. 8,088,575 issued Jan. 3, 2012 to Ju et al. cited by
applicant .
Exhibit 1003, filed Oct. 3, 2012 in connection with IPR2013-00011:
Prober et al. (1987), "A System for Rapid DNA Sequencing with
Fluorescent Chain-Terminating Dideoxynucleotides", Science vol.
238, Oct. 16, 1987, pp. 336-341. cited by applicant .
Exhibit 1021, filed Oct. 3, 2012 in connection with IPR2013-00011:
Oct. 2, 2012 Declaration of George Weinstock Under Rule 37 C.F.R.
.sctn.1.132. cited by applicant .
Exhibit 1022, filed Oct. 3, 2012 in connection with IPR2013-00011:
Excerpts of File History of U.S. Pat. No. 8,088,575. cited by
applicant .
Exhibit 1025, filed Apr. 30, 2013 in connection with IPR2013-00011:
Columbia's Amended Complaint from The Trustees of Columbia
University in the City of New York v. Illumina, Inc., D. Del C.A.
No. 12-376 (GMS), filed Apr. 11, 2012. cited by applicant .
Exhibit 1026, filed Apr. 30, 2013 in connection with IPR2013-00011:
Illumina's Answer to Amended Complaint from The Trustees of
Columbia University in the City of New York v. Illumina, Inc., D.
Del C.A. No. 12-376 (GMS), filed Dec. 21, 2012. cited by applicant
.
Exhibit 1030, filed Jun. 18, 2013 in connection with IPR2013-00011:
Rosenblum et al., "New Dye-Labeled Terminators for Improved DNA
Sequencing Patterns," Nucleic Acid Research, 1997, vol. 25, No. 22,
pp. 4500-4504. cited by applicant .
Exhibit 1034, filed Jun. 18, 2013 in connection with IPR2013-00011:
Jun. 8, 2013 Videotaped Deposition Transcript of George M.
Weinstock, Ph.D. cited by applicant .
Exhibit 1036, filed Sep. 27, 2013 in connection with IPR2013-00011:
"Next Generation Genomics: World Map of High-throughput
Sequencers," Sep. 1, 2013. cited by applicant .
Exhibit 1039, filed Sep. 27, 2013 in connection with IPR2013-00011:
Videotaped Deposition Transcript of Dr. Xiaohai Liu, Mar. 20, 2013.
cited by applicant .
Exhibit 1040, filed Sep. 27, 2013 in connection with IPR2013-00011:
Excerpt from videotaped Deposition Transcript of George M.
Weinstock, Ph.D., Jun. 8, 2013. cited by applicant .
Exhibit 1041, filed Sep. 27, 2013 in connection with IPR2013-00011:
Seela et al., "Oligonucleotide Duplex Stability Controlled by the
7-Substituents of 7-Deazaguanine Bases," Bioorganic & Medical
Chemistry Letters, vol. 5, No. 24, pp. 3049-3052, 1995. cited by
applicant .
Exhibit 1042, filed Sep. 27, 2013 in connection with IPR2013-00011:
Ramzaeva et al., "123. 7-Deazaguanine DNA: Oligonucleotides with
Hydrophobic or Cationic Side Chains," Helvetica Chimica Acta, vol.
80, pp. 1809-1822, 1997. cited by applicant .
Exhibit 1043, filed Sep. 27, 2013 in connection with IPR2013-00011:
Ramzaeva et al., "88. 7-Substituted 7-Deaza- 2'-deoxyguanosines:
Regioselective Halogenation of Pyrrolo[2,3-d]pyrimidine
Nucleosides," Helvetica Chimica Acta, vol. 78, pp. 1083-1090, 1995.
cited by applicant .
Exhibit 1044, filed Sep. 27, 2013 in connection with IPR2013-00011:
Seela et al., "Duplex Stability of Oligonucleoties Containing
7-Substitues 7-Deaza- and 8-Aza-7-Deazapurine Nucleosides,"
Nucleosides & Nucleotides, 16(7-9), pp. 963-966, 1997. cited by
applicant .
Exhibit 1045, filed Sep. 27, 2013 in connection with IPR2013-00011:
Burgess et al., "Syntheses of Nucleosides Designed for
Combinatorial DNA Sequencing," Chemistry--A European Journal, vol.
5, No. 3, pp. 951-960, 1999. cited by applicant .
Exhibit 1049, filed Sep. 27, 2013 in connection with IPR2013-00011:
Jan. 28, 2013 Declaration of Dr. Bruce P. Branchaud in Support of
Petition for Inter Partes Review of U.S. Pat. No. 7,057,026. cited
by applicant .
Exhibit 1050, filed Sep. 27, 2013 in connection with IPR2013-00011:
Lee et al., "DNA sequencing with dye-labeled terminators and T7 DNA
polymerase: effect of dyes and dNTPs on incorporation of
dye-terminators and probability analysis of termination fragments,"
Nucleic Acids Research, vol. 20, No. 10, pp. 2471-2483, 1992. cited
by applicant .
Exhibit 1051, filed Sep. 27, 2013 in connection with IPR2013-00011:
http://www.answers.com/topic/incubate, Accessed Sep. 27, 2013.
cited by applicant .
Exhibit 1052, filed Sep. 27, 2013 in connection with IPR2013-00011:
http://en.wikipedia.org/wiki/Fluorenylmethyloxycarbonyl.sub.--chloride,
Accessed Sep. 27, 2013. cited by applicant .
Exhibit 1053, filed Sep. 27, 2013 in connection with IPR2013-00011:
Sep. 27, 2013 Declaration of Kevin Burgess. cited by applicant
.
Exhibit 1054, filed Sep. 27, 2013 in connection with IPR2013-00011:
Fuji, et al., "An Improved Method for Methoxymethylation of
Alcohols under Mild Acidic Conditions," Synthesis--The Journal of
Synthetic Organic Chemistry, pp. 276-277, Apr. 1975. cited by
applicant .
Exhibit 2001, filed Jan. 7, 2013 in connection with IPR2013-00011:
Composition of a Nucleotide. cited by applicant .
Exhibit 2006, filed Apr. 26, 2013 in connection with IPR2013-00011:
Dower patent with highlights. cited by applicant .
Exhibit 2015, filed Jun. 24, 2013 in connection with IPR2013-00011:
Metzker et al. (1994) Termination of DNA synthesis by novel
3'-modified-deoxyribonucleoside 5'-triphosphates. Nucleic Acids
Res. 22:4259-4267. cited by applicant .
Exhibit 2016, filed Jun. 24, 2013 in connection with IPR2013-00011:
Wu et al. (2007) Termination of DNA synthesis by N6-alkylated, not
3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.
Nucleic Acids Res. 35:6339-6349. cited by applicant .
Exhibit 2017, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sep. 15, 2012 Declaration of George Weinstock Under 37 CFR 1.132
(Exhibit 1021 in IPR2012-00007). cited by applicant .
Exhibit 2018, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sep. 15, 2012 Declaration of George Weinstock Under 37 CFR 1.132
(Exhibit 1021 in IPR2012-00006). cited by applicant .
Exhibit 2019, filed Jun. 24, 2013 in connection with IPR2013-00011:
Definition of "DNA microarray."
http://en/wikipedia.org/wiki/DNA.sub.--microarray. cited by
applicant .
Exhibit 2020, filed Jun. 24, 2013 in connection with IPR2013-00011:
Brettin et al. (2005) Expression capable library for studies of
Neisseria gonorrhoeae, version 1.0 BMC Microbiology. 5:50. cited by
applicant .
Exhibit 2021, filed Jun. 24, 2013 in connection with IPR2013-00011:
George M. Weinstock, Handbook of Molecular Microbial Ecology, vol.
1-Chapter 18: The Impact of Next-Generation Sequencing Technologies
on Metagenomics 141-147 Frans J. de Bruijn ed., John Wiley &
Sons, Inc. (2011). cited by applicant .
Exhibit 2022, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,713,698 (Paper 3 in IPR2012-00006). cited by applicant .
Exhibit 2023, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,790,869 (Paper 5 in IPR2012-00007). cited by applicant .
Exhibit 2024, filed Jun. 24, 2013 in connection with IPR2013-00011:
Maxam and Gilbert (1977) A new method for sequencing DNA, Proc.
Natl. Acad. Sci. USA. 74:560-564. cited by applicant .
Exhibit 2025, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sanger et al. (1977) DNA sequencing with chain-terminating
inhibitors, Proc. Natl. Acad. Sci. USA. 74:5463-5467. cited by
applicant .
Exhibit 2026, filed Jun. 24, 2013 in connection with IPR2013-00011:
Pennisi (2000) DOE Team Sequences Three Chromosomes, Science.
288:417-419. cited by applicant .
Exhibit 2027, filed Jun. 24, 2013 in connection with IPR2013-00011:
Welch and Burgess (1999) Synthesis of Fluorescent, Photolabile
3'-O-Protected nucleoside Triphosphates for the Base Addition
Sequencing Scheme, nucleosides & Nucleotides. 18:197-201. cited
by applicant .
Exhibit 2028, filed Jun. 24, 2013 in connection with IPR2013-00011:
Hyman (1998) A New Method of Sequencing DNA, Analytical
Biochemistry 174:423-436. cited by applicant .
Exhibit 2030, filed Jun. 24, 2013 in connection with IPR2013-00011:
Canard and Sarfati (1994) DNA polymerase fluorescent substrates
with reversible 3'-tags, Gene. 1481-6. cited by applicant .
Exhibit 2032, filed Jun. 24, 2013 in connection with IPR2013-00011:
Sarfati et al. (1987) Synthesis of Fluorescent or Biotinylated
Nucleoside Compounds, Tetrahedron Letters. 43:3491-3497. cited by
applicant .
Exhibit 2033, filed Aug. 30, 2013 in connection with IPR2013-00011:
Jun. 25, 2013 Substitute Declaration of Dr. George L. Trainor
[redacted]. cited by applicant .
Exhibit 2034, filed Jun. 25, 2013 in connection with IPR2013-00011:
Jingyue Ju et. al. (2006) Four-color DNA sequencing by synthesis
using cleavable fluorescent nucleotide reversible terminators,
Proceedings of the National Academy of Sciences. 103: 19635-19640.
cited by applicant .
Exhibit 2035, filed Jun. 25, 2013 in connection with IPR2013-00011:
Batista et al. (2008) PRG-1 and 21U-RNAs Interact to Form the piRNA
Complex Required for Fertility in C. elegans. Molecular Cell
31:1-12. cited by applicant .
Exhibit 2036, filed Jun. 25, 2013 in connection with IPR2013-00011:
Form 7 Review Context and Analysis, Biomedical Engineering and
Research to Aid Persons with Disabilities Programs Dec. 19-20, 2000
Panel Review, Fluorescence Imaging Chip System for Massive Parallel
DNA Sequencing. Proposal No. BES-0097793. cited by applicant .
Exhibit 2037, filed Jun. 25, 2013 in connection with IPR2013-00011:
Oct. 1, 2006 Request for opinion on manuscript by J. Ju et. al.,
Proceedings of National Academy of Sciences, U.S.A. cited by
applicant .
Exhibit 2038, filed Jun. 25, 2013 in connection with IPR2013-00011:
Correspondence between George Rupp, Chancellor, Columbia University
and Richard T. Schlossberg, President, The David and Lucile Packard
Foundation (2001). cited by applicant .
Exhibit 2039, filed Jun. 25, 2013 in connection with IPR2013-00011:
The David and Lucile Packard Foundation, Packard Fellowships for
Science and Engineering,
http://www.packard.org/what-wefund/conservation-and-science/packard-fello-
wships-for-science-andengineering/ (last visited Jun. 25, 2013).
cited by applicant .
Exhibit 2040, filed Jun. 26, 2013 in connection with IPR2013-00011:
"Chemistry for Next-Generation Sequencing."
http://www.illumina.com/technology/sequencing.sub.--technology.ilmn.
cited by applicant .
Exhibit 2041, filed Jun. 26, 2013 in connection with IPR2013-00011:
Chiang et al. (2010) Mammalian microRNAs: experimental evaluation
of novel and previously annotated genes, Genes & Dev. 24:992,
993. cited by applicant .
Exhibit 2042, filed Jun. 26, 2013 in connection with IPR2013-00011:
Seo et al. (2004) Photocleavable fluorescent nucleotides for DNA
sequencing on a chip constructed by site-specific coupling
chemistry, Proc. Natl Acad. Sci. 101(15):5488-5493. cited by
applicant .
Exhibit 2043, filed Jun. 26, 2013 in connection with IPR2013-00011:
Curriculum vitae of Mr. Raymond S. Sims. cited by applicant .
Exhibit 2044, filed Jun. 26, 2013 in connection with IPR2013-00011:
Prior Testimony of Mr. Raymond S. Sims. cited by applicant .
Exhibit 2045, filed Jun. 26, 2013 in connection with IPR2013-00011:
Documents reviewed by Mr. Raymond S. Sims in this Proceeding. cited
by applicant .
Exhibit 2052, filed Jun. 26, 2013 in connection with IPR2013-00011:
Gary Schroth Proof of Chiang Paper. cited by applicant .
Exhibit 2074, filed Jun. 26, 2013 in connection with IPR2013-00011:
Information about Dr. Ju's intellectual property sent to Illumina.
cited by applicant .
Exhibit 2090, filed Jun. 26, 2013 in connection with IPR2013-00011:
IPR Default Protective Order. cited by applicant .
Exhibit 2091, filed Jun. 26, 2013 in connection with IPR2013-00011:
Declaration of Raymond S. Sims. cited by applicant .
Exhibit 2092, filed Oct. 1, 2013 in connection with IPR2013-00011:
Rough transcript of the Sep. 4, 2013 deposition of Dr. George L.
Trainor. cited by applicant .
Exhibit 2093, filed Oct. 1, 2013 in connection with IPR2013-00011:
Excerpt from Protective Groups in Organic Synthesis, 3rd Ed.
(Theodora W. Greene and Peter G.M. Wuts ed., John Wiley & Sons,
Inc. 1999). cited by applicant .
Exhibit 2094, filed Oct. 1, 2013 in connection with IPR2013-00011:
Final transcript of the Sep. 4-6, 2013 deposition of Dr. George L.
Trainor. cited by applicant .
Exhibit 2095, filed Oct. 1, 2013 in connection with IPR2013-00011:
Final transcript of the Sep. 3, 2013 deposition of Ryamond S. Sims.
cited by applicant .
Nov. 12, 2013 Petitioner Motion to Exclude Evidence in connection
with IPR2012-00007. cited by applicant .
Exhibit 1056, filed Nov. 19, 2013 in connection with IPR2012-00007:
Videotaped Deposition Transcript of Kevin Burgess, Ph.D., Oct. 28,
2013, signed with errata. cited by applicant .
Nov. 12, 2013 Patent Owner Motion for Observations on the
Cross-Examination Testimony of Kevin Burgess, Ph.D. in connection
with IPR2012-00007. cited by applicant .
Nov. 12, 2013 Patent Owner Motion to Exclude Evidence in connection
with IPR2012-00007. cited by applicant .
Exhibit 2099, filed Nov. 12, 2013 in connection with IPR2013-00011:
Welch, M., et al (2005) Corrigenda to Syntheses of Nucleosides
Designed for Combinatorial DNA Sequencing Chem. Eur.J., 1999,
951-960. Published in Chem. Eur. J, 2005, 11, 7136-7145. cited by
applicant .
Exhibit 2100, filed Nov. 12, 2013 in connection with IPR2013-00011:
Welch, M (1999) "Base Additions Sequencing Scheme (BASS) and
Studies Toward New Sequencing Methodologies." PhD. Dissertation,
Texas A&M University. cited by applicant .
Exhibit 2101, filed Nov. 12, 2013 in connection with IPR2013-00011:
Lu and Burgess (2006) "A Diversity Oriented Synthesis of
3'-O-modified nucleoside triphosphates for DNA `Sequencing by
Synthesis`." Bioorganic & Medicinal Chemistry Letters, 16,
3902-3905. cited by applicant .
Exhibit 2102, filed Nov. 12, 2013 in connection with IPR2013-00011:
Advanced Sequencing Technology Awards 2004.
http://www.genome.gov/12513162 (accessed Oct. 14, 2013). cited by
applicant .
Exhibit 2103, filed Nov. 12, 2013 in connection with IPR2013-00011:
Welch and Burgess (2006) Erratum to Synthesis of Fluorescent,
Photolabile 3'-O-Protected Nucleoside Triphosphates for the Base
Addition Sequencing Scheme, Nucleosides &
Nucleotides,18:197-201. Published in Nucleosides, Nucleotides and
Nucleic Acids, 25:1, 119. cited by applicant .
Nov. 26, 2013 Petitioner's Response to Motion for Observations in
connection with IPR2013-00011. cited by applicant .
Nov. 26, 2013 Patent Owner's Opposition to Petitioner's Motion to
Exclude in connection with IPR2013-00011. cited by applicant .
Nov. 26, 2013 Petitioner's Opposition to Motion to Exclude in
connection with IPR2013-00011. cited by applicant .
Dec. 3, 2013 Petitioner Reply to Patent Owner's Opposition to
Motion to Exclude in connection with IPR2013-00011. cited by
applicant .
Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in connection
with IPR2013-00011. cited by applicant .
Exhibit 2105, filed Dec. 15, 2013 in connection with IPR2013-00011:
Columbia's Demonstratives Under 42.70(b) for Dec. 17, 2013 Oral
Hearing. cited by applicant .
Exhibit 1057, filed Dec. 16, 2013 in connection with IPR2013-00011:
Illumina's Invalidity Demonstratives for Final Hearing Dec. 17,
2013. cited by applicant .
Record of Dec. 17, 2013 Oral Hearing in connection with
IPR2013-00011. cited by applicant .
U.S. Appl. No. 12/804,025, filed Jul. 13, 2010, Balasubramanian et
al. cited by applicant .
May 4, 2013 Petition for Inter Partes Review of U.S. Pat. No.
8,158,346, issued Apr. 17, 2012. cited by applicant .
Aug. 5, 2013 Patent Owner Preliminary Response to Petition for
Inter Partes Review of U.S. Pat. No. 8,158,246, issued Apr. 17,
2012. cited by applicant .
Exhibit 1004, filed May 4, 2013 in connection with IPR2013-00266:
Kamal et al., A Mild and Rapid Regeneration of Alcohols from their
Allylic Ethers by Chlorotrimethylsilane/Sodium Iodide, 40
Tetrahedron Letters 371 (1999). cited by applicant .
Exhibit 1005, filed May 4, 2013 in connection with IPR2013-00266:
Jung et al., Conversion of Alkyl Carbamates into Amines vie
Treatment with Trimethylsilyl Iodide, 7 J.C.S. Chem. Comm. 315
(1978). cited by applicant .
Exhibit 1011, filed May 4, 2013 in connection with IPR2013-00266:
May 3, 2013 Declaration of Dr. Bruce Branchaud. cited by applicant
.
Exhibit 1012, filed May 4, 2013 in connection with IPR2013-00266:
Excerpts from the '346 Patent File History. cited by applicant
.
Exhibit 1013, filed May 4, 2013 in connection with IPR2013-00266:
Excerpts from the file history of European Patent Application No:
02781434.2. cited by applicant .
Exhibit 1014, filed May 4, 2013 in connection with IPR2013-00266:
Sep. 16, 2013 Petition for Inter Partes Review of U.S. Pat. No.
7,713,698. cited by applicant .
Exhibit 1015, filed May 4, 2013 in connection with IPR2013-00266:
Sep. 16, 2013 Petition for Inter Partes Review of U.S. Pat. No.
7,790,869. cited by applicant .
Exhibit 1016, filed May 4, 2013 in connection with IPR2013-00266:
Oct. 3, 2013 Petition for Inter Partes Review of U.S. Pat. No.
8,088,575. cited by applicant .
Exhibit 2001, filed Aug. 5, 2013 in connection with IPR2013-00266:
Columbia's Apr. 11, 2012 Amended Complaint in connection with case
No. C.A. No. 12-376-GMS. cited by applicant .
Exhibit 2002, filed Aug. 5, 2013 in connection with IPR2013-00266:
Columbia's Jan. 7, 2013 Amended Answer in connection with case No.
C.A. No. 12-376-GMS. cited by applicant .
Oct. 28, 2013 Decision Instituting Inter Partes Review in
connection with IPR2013-00266. cited by applicant .
Dec. 30, 2013 Illumina Motion to Amend Under 37 C.F.R. .sctn.42.121
in connection with IPR2013-00266. cited by applicant .
Exhibits 2004, 2005, and 2028, filed Dec. 30, 2013 in connection
with IPR2013-00266: Floyd Romesburg Declaration, CV, and List of
Documents Considered by Romesburg. cited by applicant .
Exhibit 2008, filed Dec. 30, 2013 in connection with IPR2013-00266:
Maxam & Gilbert, PNAS 74:560-564 (Feb. 1977). cited by
applicant .
Exhibit 2009, filed Dec. 30, 2013 in connection with IPR2013-00266:
Sanger et al., DNA Sequencing, PNAS 74:5463- 5467 (1977). cited by
applicant .
Exhibit 2011, filed Dec. 30, 2013 in connection with IPR2013-00266:
Metzker et al., Nucleic Acids Research, 22:4259-4267 (1994). cited
by applicant .
Exhibit 2012, filed Dec. 30, 2013 in connection with IPR2013-00266:
Welch and Burgess, Nucleosides & Nucleotides, 18:197-201
(1999). cited by applicant .
Exhibit 2013, filed Dec. 30, 2013 in connection with IPR2013-00266:
Bruce P. Branchaud, Ph.D., Jun. 4, 2013 Declaration in
IPR2013-00324. cited by applicant .
Exhibit 2016, filed Dec. 30, 2013 in connection with IPR2013-00266:
Ruby et al., Methods in Enzymology, 181:97-121 (1990). cited by
applicant .
Exhibit 2021, filed Dec. 30, 2013 in connection with IPR2013-00266:
Bystrom, Branchaud et al., Bioorganic & Medicinal Chemistry
Letters, 7:2613-2616 (1997). cited by applicant .
Exhibit 2022, filed Dec. 30, 2013 in connection with IPR2013-00266:
Pages from Handbook of Reagents for Organic Synthesis: Reagents for
Silicon-Mediated Organic Synthesis (Philip L. Fuchs, ed.) (2011).
cited by applicant .
Exhibit 2023, filed Dec. 30, 2013 in connection with IPR2013-00266:
Eric Vermaas Declaration--Redacted version. cited by applicant
.
Exhibit 2024, filed Dec. 30, 2013 in connection with IPR2013-00266:
Excerpts from Oct. 3, 2013 Bruce Branchaud Deposition Transcript in
IPR2013-00128. cited by applicant .
Exhibit 2026, filed Dec. 30, 2013 in connection with IPR2013-00266:
Prober et al., Science 238:336-341 (1987). cited by applicant .
Exhibit 2027, filed Dec. 30, 2013 in connection with IPR2013-00266:
CEQ 2000 DNA Analysis System User's Guide, Beckman Coulter (Jun.
2000). cited by applicant .
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,713,698, issued May 11, 2010. cited by applicant .
Sep. 16, 2012 Motion to Waive Page Limit and Proposed Petition in
connection with Petition for Inter Partes Review of U.S. Pat. No.
7,713,698, issued May 11, 2010. cited by applicant .
Dec. 20, 2012 Preliminary Response under 37 C.F.R. 42.107 in
connection with IPR2012-00006. cited by applicant .
Mar. 12, 2013 Decision on Petition for Inter Partes Review in
connection with IPR2012-00006. cited by applicant .
Mar. 26, 2013 Request for Reconsideration in connection with
IPR2012-00006. cited by applicant .
Apr. 26, 2013 Opposition to Request for Reconsideration (Rehearing)
Under 37 C.F.R. 42.71.(C) in connection with IPR2012-00006. cited
by applicant .
May 10, 2013 Decision on Request for Rehearing in connection with
IPR2012-00006. cited by applicant .
Aug. 30, 2013 Substitute Patent Owner Response Under 37 C.F.R.
42.120 in connection with IPR2012-00006. cited by applicant .
Aug. 30, 2013 Substitute Patent Owner Motion to Amend Under 37
C.F.R. 42.121 in connection with IPR2012-00006. cited by applicant
.
Sep. 27, 2013 Petitioner Opposition to Motion to Amend in
connection with IPR2012-00006. cited by applicant .
Sep. 27, 2013 Petitioner Reply to Response to Petition in
connection with IPR2012-00006. cited by applicant .
Nov. 18, 2013 Patent Owner Substitute Reply on Motion to Amend in
connection with IPR2012-00006. cited by applicant .
Exhibit 1003, filed Sep. 16, 2012 in connection with IPR2012-00006:
Prober et al. (1987), "A System for Rapid DNA Sequencing with
Flourescent Chain-Determining Dideoxynucleotides", Science vol.
238, Oct. 16, 1987, pp. 336-341. cited by applicant .
Exhibit 1021, filed Sep. 16, 2012 in connection with IPR2012-00006:
Sep. 15, 2012 Declaration of George Weinstock Under Rule 37 C.F.R.
.sctn.1.132. cited by applicant .
Exhibit 1022, filed Sep. 16, 2012 in connection with IPR2012-00006:
Excerpts of File History of U.S. Pat. No. 7,713,698. cited by
applicant .
Exhibit 1025, filed Apr. 30, 2013 in connection with IPR2012-00006:
Columbia's Amended Complaint from The Trustees of Columbia
University in the City of New York v. Illumina, Inc., D. Del C.A.
No. 12-376 (GMS), filed Apr. 11, 2012. cited by applicant .
Exhibit 1026, filed Apr. 30, 2013 in connection with IPR2012-00006:
Illumina's Answer to Amended Complaint from The Trustees of
Columbia University in the City of New York v. Illumina, Inc., D.
Del C.A. No. 12-376 (GMS), filed Dec. 21, 2012. cited by applicant
.
Exhibit 1030, filed Jun. 18, 2013 in connection with IPR2012-00006:
Rosenblum et al., "New Dye-Labeled Terminators for Improved DNA
Sequencing Patterns," Nucleic Acid Research, 1997, vol. 25, No. 22,
pp. 4500-4504. cited by applicant .
Exhibit 1034, filed Jun. 18, 2013 in connection with IPR2012-00006:
Jun. 8, 2013 Videotaped Deposition Transcript of George M.
Weinstock, Ph.D. cited by applicant .
Exhibit 1036, filed Sep. 27, 2013 in connection with IPR2012-00006:
"Next Generation Genomics: World Map of High-throughput
Sequencers," Sep. 1, 2013. cited by applicant .
Exhibit 1039, filed Sep. 27, 2013 in connection with IPR2012-00006:
Videotaped Deposition Transcript of Dr. Xiaohai Liu, Mar. 20, 2013.
cited by applicant .
Exhibit 1040, filed Sep. 27, 2013 in connection with IPR2012-00006:
Excerpt from videotaped Deposition Transcript of George M.
Weinstock, Ph.D., Jun. 8, 2013. cited by applicant .
Exhibit 1041, filed Sep. 27, 2013 in connection with IPR2012-00006:
Seela et al., "Oligonucleotide Duplex Stability Controlled by the
7-Substituents of 7-Deazaguanine Bases," Bioorganic & Medical
Chemistry Letters, vol. 5, No. 24, pp. 3049-3052, 1995. cited by
applicant .
Exhibit 1042, filed Sep. 27, 2013 in connection with IPR2012-00006:
Ramzaeva et al., "123. 7-Deazaguanine DNA: Oligonucleotides with
Hydrophobic or Cationic Side Chains," Helvetica Chimica Acta, vol.
80, pp. 1809-1822, 1997. cited by applicant .
Exhibit 1043, filed Sep. 27, 2013 in connection with IPR2012-00006:
Ramzaeva et al., "88. 7-Substituted 7-Deaza-2'-deoxyguanosines:
Regioselective Halogenation of Pyrrolo[2,3-d]pyrimidine
Nucleosides," Helvetica Chimica Acta, vol. 78, pp. 1083-1090, 1995.
cited by applicant .
Exhibit 1044, filed Sep. 27, 2013 in connection with IPR2012-00006:
Seela et al., "Duplex Stability of 7-Substitued 7-Deaza- and
8-Aza-7-Deazapurine Nucleosides," Nucleosides & Nucleotides,
16(7-9), pp. 963-966, 1997. cited by applicant .
Exhibit 1045, filed Sep. 27, 2013 in connection with IPR2012-00006:
Burgess et al., "Syntheses of Nucleosides Designed for
Combinatorial DNA Sequencing," Chemistry--A European Journal, vol.
5, No. 3, pp. 951-960, 1999. cited by applicant .
Exhibit 1049, filed Sep. 27, 2013 in connection with IPR2012-00006:
Jan. 28, 2013 Declaration of Dr. Bruce P. Branchaud in Support of
Petition for Inter Partes Review of U.S. Pat. No. 7,057,026. cited
by applicant .
Exhibit 1050, filed Sep. 27, 2013 in connection with IPR2012-00006:
Lee et al., "DNA sequencing with dye-labeled terminators and T7 DNA
polymerase: effect of dyes and dNTPs on incorporation of
dye-terminators and probability analysis of termination fragments,"
Nucleic Acids Research, vol. 20, No. 10, pp. 2471-2483, 1992. cited
by applicant .
Exhibit 1051, filed Sep. 27, 2013 in connection with IPR2012-00006:
http://www.answers.com/topic/incubate, Accessed Sep. 27, 2013.
cited by applicant .
Exhibit 1052, filed Sep. 27, 2013 in connection with IPR2012-00006:
http://en.wikipedia.org/wiki/Fluorenylmethyloxycarbonyl.sub.--chloride,
Accessed Sep. 27, 2013. cited by applicant .
Exhibit 1053, filed Sep. 27, 2013 in connection with IPR2012-00006:
Sep. 27, 2013 Declaration of Kevin Burgess. cited by applicant
.
Exhibit 1054, filed Sep. 27, 2013 in connection with IPR2012-00006:
Fuji, et al., "An Improved Method for Methoxymethylation of
Alcohols under Mild Acidic Condtions," Synthesis--The Journal of
Synthetic Organic Chemistry, pp. 276-277, Apr. 1975. cited by
applicant .
Exhibit 2006, filed Apr. 26, 2013 in connection with IPR2012-00006:
Dower patent with highlights. cited by applicant .
Exhibit 2013, filed Jun. 24, 2013 in connection with IPR2012-00006:
Oct. 2, 2012 Declaration of George Weinstock Under 37 CFR 1.132
(Exhibit 1021 in IPR2013-00011). cited by applicant .
Exhibit 2014, filed Jun. 24, 2013 in connection with IPR2012-00006:
Petition for Inter Partes Review of U.S. Pat. No. 8,088,575 (Paper
4 in IPR2013-00011). cited by applicant .
Exhibit 2015, filed Jun. 24, 2013 in connection with IPR2012-00006:
Metzker et al. (1994) Termination of DNA synthesis by novel
3'-modified-deoxyribonucleoside 5'-triphosphates. Nucleic Acids
Res. 22:4259-4267. cited by applicant .
Exhibit 2016, filed Jun. 24, 2013 in connection with IPR2012-00006:
Wu et al. (2007) Termination of DNA synthesis by N6-alkylated, not
3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates.
Nucleic Acids Res. 35:6339-6349. cited by applicant .
Exhibit 2017, filed Jun. 24, 2013 in connection with IPR2012-00006:
Sep. 15, 2012 Declaration of George Weinstock Under 37 CFR 1.132
(Exhibit 1021 in IPR2012-00007). cited by applicant .
Exhibit 2019, filed Jun. 24, 2013 in connection with IPR2012-00006:
Definition of "DNA microarray."
http://en/wikipwdia.org/wiki.DNA.sub.--microarray. cited by
applicant .
Exhibit 2020, filed Jun. 24, 2013 in connection with IPR2012-00006:
Brettin et al. (2005) Expression capable library for studies of
Neisseria gonorrhoeae, version 1.0 BMC Microbiology. 5:50. cited by
applicant .
Exhibit 2021, filed Jun. 24, 2013 in connection with IPR2012-00006:
George M. Weinstock, Handbook of Molecular Microbial Ecology, vol.
1-Chapter 18: The Impact of Next-Generation Sequencing Technologies
on Metagenomics 141-147 Frans J. de Bruijn ed., John Wiley &
Sons, Inc. (2011). cited by applicant .
Exhibit 2023, filed Jun. 24, 2013 in connection with IPR2012-00006:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,790,869 (Paper 5 in IPR2012-00007). cited by applicant .
Exhibit 2024, filed Jun. 24, 2013 in connection with IPR2012-00006:
Maxam and Gilbert (1977) A new method for sequencing DNA, Proc.
Natl. Acad. Sci. USA. 74:560-564. cited by applicant .
Exhibit 2025, filed Jun. 24, 2013 in connection with IPR2012-00006:
Sanger et al. (1977) DNA sequencing with chain-terminating
inhibitors, Proc. Natl. Acad. Sci. USA. 74:5463-5467. cited by
applicant .
Exhibit 2026, filed Jun. 24, 2013 in connection with IPR2012-00006:
Pennisi (2000) DOE Team Sequences Three Chromosomes, Science.
288:417-419. cited by applicant .
Exhibit 2027, filed Jun. 24, 2013 in connection with IPR2012-00006:
Welch and Burgess (1999) Synthesis of Fluorescent, Photolabile
3'-O-Protected nucleoside Triphosphates for the Base Addition
Sequencing Scheme, nucleosides & Nucleotides.18:197-201. cited
by applicant .
Exhibit 2028, filed Jun. 24, 2013 in connection with IPR2012-00006:
Hyman (1998) A New Method of Sequencing DNA, Analytical
Biochemistry 174:423-436. cited by applicant .
Exhibit 2030, filed Jun. 24, 2013 in connection with IPR2012-00006:
Canard and Sarfati (1994) DNA polymerase fluorescent substrates
with reversible 3'-tags, Gene. 1481-6. cited by applicant .
Exhibit 2032, filed Jun. 24, 2013 in connection with IPR2012-00006:
Sarfati et al. (1987) Synthesis of Fluorescent or Biotinylated
Nucleoside Compounds, Tetrahedron Letters. 43:3491-3497. cited by
applicant .
Exhibit 2033, filed Aug. 30, 2013 in connection with IPR2012-00006:
Jun. 25, 2013 Substitute Declaration of Dr. George L. Trainor
[redacted]. cited by applicant .
Exhibit 2034, filed Jun. 25, 2013 in connection with IPR2012-00006:
Jingyue Ju et. al. (2006) Four-color DNA sequencing by synthesis
using cleavable fluorescent nucleotide reversible terminators,
Proceedings of the National Academy of Sciences. 103: 19635-19640.
cited by applicant .
Exhibit 2035, filed Jun. 25, 2013 in connection with IPR2012-00006:
Batista et al. (2008) PRG-1 and 21U-RNAs Interact to Form the piRNA
Complex Required for Fertility in C. elegans. Molecular Cell
31:1-12. cited by applicant .
Exhibit 2036, filed Jun. 25, 2013 in connection with IPR2012-00006:
Form 7 Review Context and Analysis, Biomedical Engineering and
Research to Aid Persons with Disabilities Programs Dec. 19-20, 2000
Panel Review, Fluorescence Imaging Chip System for Massive Parallel
DNA Sequencing. Proposal No. BES-0097793. cited by applicant .
Exhibit 2037, filed Jun. 25, 2013 in connection with IPR2012-00006:
Oct. 1, 2006 Request for opinion on manuscript by J. Ju et. al.,
Proceedings of National Academy of Sciences, U.S.A. cited by
applicant .
Exhibit 2038, filed Jun. 25, 2013 in connection with IPR2012-00006:
Correspondence between George Rupp, Chancellor, Columbia University
and Richard T. Schlossberg, President, The David and Lucile Packard
Foundation (2001). cited by applicant .
Exhibit 2039, filed Jun. 25, 2013 in connection with IPR2012-00006:
The David and Lucile Packard Foundation, Packard Fellowships for
Science and Engineering,
http://www.packard.org/what-wefund/conservation-and-science/packard-fello-
wships-for-science-andengineering/ (last visited Jun. 25, 2013).
cited by applicant .
Exhibit 2040, filed Jun. 25, 2013 in connection with IPR2012-00006:
"Chemistry for Next-Generation Sequencing."
http://www.illumina.com/technology/sequencing.sub.--technology.ilmn.
cited by applicant .
Exhibit 2041, filed Jun. 25, 2013 in connection with IPR2012-00006:
Chiang et al. (2010) Mammalian microRNAs: experimental evaluation
of novel and previously annotated genes, Genes & Dev. 24:992,
993. cited by applicant .
Exhibit 2042, filed Jun. 25, 2013 in connection with IPR2012 00006:
Seo et al. (2004) Photocleavable fluorescent nucleotides for DNA
sequencing on a chip constructed by site-specific coupling
chemistry, Proc. Natl Acad. Sci. 101(15):5488-5493. cited by
applicant .
Exhibit 2043, filed Jun. 25, 2013 in connection with IPR2012-00006:
Curriculum vitae of Mr. Raymond S. Sims. cited by applicant .
Exhibit 2044, filed Jun. 25, 2013 in connection with IPR2012-00006:
Prior Testimony of Mr. Raymond S. Sims. cited by applicant .
Exhibit 2045, filed Jun. 25, 2013 in connection with IPR2012-00006:
Documents reviewed by Mr. Raymond S. Sims in this Proceeding. cited
by applicant .
Exhibit 2052, filed Jun. 25, 2013 in connection with IPR2012-00006:
Gary Schroth Proof of Chiang Paper. cited by applicant .
Exhibit 2074, filed Jun. 25, 2013 in connection with IPR2012-00006:
Information about Dr. Ju's intellectual property sent to Illumina.
cited by applicant .
Exhibit 2090, filed Jun. 26, 2013 in connection with IPR2012-00006:
IPR Default Protective Order. cited by applicant .
Exhibit 2091, filed Jun. 26, 2013 in connection with IPR2012-00006:
Declaration of Raymond S. Sims. cited by applicant .
Exhibit 2092, filed Oct. 10, 2013 in connection with IPR2012-00006:
Rough Transcript of the Sep. 4, 2013 deposition of Dr. George L.
Trainor. cited by applicant .
Exhibit 2093, filed Oct. 1, 2013 in connection with IPR2012-00006:
Excerpt from Protective Groups in Organic Synthesis, 3rd Ed.
(Theodora W. Greene and Peter G.M. Wuts ed., John Wiley & Sons,
Inc. 1999). cited by applicant .
Exhibit 2094, filed Oct. 1, 2013 in connection with IPR2012-00006:
Final transcript of the Sep. 4-6, 2013 deposition of Dr. George L.
Trainor. cited by applicant .
Exhibit 2095, filed Oct. 1, 2013 in connection with IPR2012-00006:
Final transcript of the Sep. 3, 2013 deposition of Raymond S. Sims.
cited by applicant .
Nov. 12, 2013 Petitioner Motion to Exclude Evidence in connection
with IPR2012-00006. cited by applicant .
Exhibit 1056, filed Nov. 19, 2013 in connection with IPR2012-00006:
Videotaped Deposition Transcript of Kevin Burgess, Ph.D., Oct. 28,
2013, signed with errata. cited by applicant .
Nov. 12, 2013 Patent Owner Motion for Observations on the
Cross-Examination Testimony of Kevin Burgess, Ph.D. inconnection
with IPR2012-00006. cited by applicant .
Nov. 12, 2013 Patent Owner Motion to Exclude Evidence in connection
with IPR2012-00006. cited by applicant .
Exhibit 2099, filed Nov. 12, 2013 in connection with IPR2012-00006:
Welch, M., et al (2005) Corrigenda to Syntheses of Nucleosides
Designed for Combinatorial DNA Sequencing Chem. Eur.J., 1999,
951-960. Published in Chem. Eur. J, 2005, 11, 7136-7145. cited by
applicant .
Exhibit 2100, filed Nov. 12, 2013 in connection with IPR2012-00006:
Welch, M (1999) "Base Additions Sequencing Scheme (BASS) and
Studies Toward New Sequencing Methodologies." PhD. Dissertation,
Texas A&M University. cited by applicant .
Exhibit 2101, filed Nov. 12, 2013 in connection with IPR2012-00006:
Lu and Burgess (2006) "A Diversity Oriented Synthesis of
3'-O-modified nucleoside triphosphates for DNA `Sequencing by
Synthesis`." Bioorganic & Medicinal Chemistry Letters, 16,
3902-3905. cited by applicant .
Exhibit 2102, filed Nov. 12, 2013 in connection with IPR2012-00006:
Advanced Sequencing Technology Awards 2004.
http://www.genome.gov/12513162 (accessed Oct. 14, 2013). cited by
applicant .
Exhibit 2103, filed Nov. 12, 2013 in connection with IPR2012-00006:
Welch and Burgess (2006) Erratum to Synthesis of Fluorescent,
Photolabile 3'-O-Protected Nucleoside Triphosphates for the Base
Addition Sequencing Scheme, Nucleosides &
Nucleotides,18:197-201. Published in Nucleosides, Nucleotides and
Nucleic Acids, 25:1, 119. cited by applicant .
Nov. 26, 2013 Petitioner Response to Motion for Observations in
connection with IPR2012-00006. cited by applicant .
Nov. 26, 2013 Patent Owner Opposition to Petitioner's Motion to
Exclude in connection with IPR2012-00006. cited by applicant .
Nov. 26, 2013 Petitioner Opposition to Motion to Exclude in
connection with IPR2012-00006. cited by applicant .
Dec. 3, 2013 Petitioner Reply to Patent Owner's Opposition to
Motion to Exclude in connection with IPR2012-00006. cited by
applicant .
Dec. 3, 2013 Patent Owner Reply on Motion to Exclude in connection
with IPR2012-00006. cited by applicant .
Exhibit 2105, filed Dec. 15, 2013 in connection with IPR2012-00006:
Columbia's Demonstratives Under 42.70(b) for Dec. 17, 2013 Oral
Hearing. cited by applicant .
Exhibit 1057, filed Dec. 16, 2013 in connection with IPR2012-00006:
Illumina's Invalidity Demonstratives for Final Hearing Dec. 17,
2013. cited by applicant .
Record of Dec. 17, 2013 Oral Hearing in connection with
IPR2012-00006. cited by applicant .
Aug. 19, 2013 Petition 2 of 2 for Inter Partes Review of U.S. Pat.
No. 7,566,537, issued Aug. 19, 2013. cited by applicant .
Exhibit 1004, filed Aug. 19, 2013 in connection with IPR2013-00518:
Kamal et al., A Mild and Rapid Regeneration of Alcohols from their
Allylic Ethers by Chlorotrimethylsilane/Sodium Iodide, 40
Tetrahedron Letters 371 (1999). cited by applicant .
Exhibit 1005, filed Aug. 19, 2013 in connection with IPR2013-00518:
Jung et al., Conversion of Alkyl Carbamates into Amines via
Treatment with Trimethylsilyl Iodide, 7 J.C.S. Chem. Comm. 315
(1978). cited by applicant .
Exhibit 1007, filed Aug. 19, 2013 in connection with IPR2013-00518:
Prober et al., A System for Rapid DNA Sequencing with Fluorescent
Chain-Terminating Dideoxynucleotides, 238 Science 336 (1987). cited
by applicant .
Exhibit 1015, filed Aug. 19, 2013 in connection with IPR2013-00518:
Aug. 16, 2013 Declaration of Dr. Bruce Branchaud. cited by
applicant .
Exhibit 1016, filed Aug. 19, 2013 in connection with IPR2013-00518:
Excerpts from the '537 Patent File History. cited by applicant
.
Exhibit 1017, filed Aug. 19, 2013 in connection with IPR2013-00518:
Excerpts from the file history of European Patent Application No.
02781434.2. cited by applicant .
Exhibit 1018, filed Aug. 19, 2013 in connection with IPR2013-00518:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,713,698. cited by applicant .
Exhibit 1019, filed Aug. 19, 2013 in connection with IPR2013-00518:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
7,790,869. cited by applicant .
Exhibit 1020, filed Aug. 19, 2013 in connection with IPR2013-00518:
Sep. 16, 2012 Petition for Inter Partes Review of U.S. Pat. No.
8,088,575. cited by applicant .
Petitioner's Feb. 28, 2014 Opposition to Patentee Motion to Amend
in connection with IPR2013-00266. cited by applicant .
Exhibit 1020, filed Feb. 28, 2014 in connection with IPR2013-00266:
Mitra et al, "Fluorescent in situ sequencing on polymerase
colonies" Analytical Biochem. 320:55-65 (2003). cited by applicant
.
Exhibit 1021, filed Feb. 28, 2014 in connection with IPR2013-00266:
Second Declaration of Dr. Bruce Branchaud in support of Intelligent
Bio-Systems, Inc.'s Opposition to Illumina's Motion to Amend, from
Feb. 28, 2014. cited by applicant .
Exhibit 1022, filed Feb. 28, 2014 in connection with IPR2013-00266:
Deposition of Floyd Romesberg, Ph.D., from Jan. 14, 2014. cited by
applicant .
Exhibit 1027, filed Feb. 28, 2014 in connection with IPR2013-00266:
Dawson et al., "Affinity Isolation of Transcriptionally Active
Murine Erythroleukemia Cell DNA Using a Cleavable Biotinylated
Nucleotide Analog" J. of Biol. Chem., 264:12830-37 (1989). cited by
applicant .
Exhibit 1028, filed Feb. 28, 2014 in connection with IPR2013-00266:
Canard et al., "DNA polymerase fluorescent substrates with
reversible 3'-tags" Gene, 148:1-6 (1994). cited by applicant .
Exhibit 1029, filed Feb. 28, 2014 in connection with IPR2013-00266:
Deposition of Eric Vermaas from Jan. 13, 2014. cited by applicant
.
Exhibit 1031, filed Feb. 28, 2014 in connection with IPR2013-00266:
Lukesh et al., "A Potent, Versatile Disulfide-Reducing Agent from
Aspartic Acid" J. Am. Chem. Soc., 134:4057-59 (2012). cited by
applicant .
Exhibit 1032, filed Feb. 28, 2014 in connection with IPR2013-00266:
Prober et al., "A System for Rapid DNA Sequencing with Fluorescent
Chain Terminating Dideoxynucleotides" Science, 238:336-341 (1987).
cited by applicant .
Exhibit 1033, filed Feb. 28, 2014 in connection with IPR2013-00266:
Klausner, Nat. Biotech., "DuPont's New DNA Sequencer Uses New
Chemistry" 5:1111-12 (1987). cited by applicant .
Exhibit 1034, filed Feb. 28, 2014 in connection with IPR2013-00266:
Murakami, et al., "Structure of a Plasmodium yoelii gene-encoded
protein homologous to the Ca.sup.2+-ATPase of rabbit skeletal
muscle sarcoplasmic reticulum" J. Cell Sci., 97, 487-95 (1990).
cited by applicant .
Exhibit 1035, filed Feb. 28, 2014 in connection with IPR2013-00266:
Excerpts from Protective Groups in Organic Synthesis (Theodora W.
Greene & Peter G. M. Wuts eds., John Wiley & Sons, Inc. 3rd
ed. 1999) (1991). cited by applicant .
Exhibit 1036, filed Feb. 28, 2014 in connection with IPR2013-00266:
Letsinger, et al., "2,4-Dinitrobenzenesulfenyl as a Blocking Group
for Hydroxyl Functions in Nucleosides" J. Org. Chem., 29, 2615-2618
(1964). cited by applicant .
Exhibit 1037, filed Feb. 28, 2014 in connection with IPR2013-00266:
Handlon & Oppenheimer, "Thiol Reduction of 3'-Azidothymidine to
3'-Aminothymidine: Kinetics and Biomedical Implications" Pharm.
Res., 5:297-99 (1988). cited by applicant .
Exhibit 1038, filed Feb. 28, 2014 in connection with IPR2013-00266:
Zavgorodny et al., "1-Alkylthioalkylation of Nucleoside Hydroxyl
Functions and Its Synthetic Applications: A New Versatile Method in
Nucleoside Chemistry" 32 Tetrahedron Letters 7593 (1991). cited by
applicant .
Exhibit 1039, filed Feb. 28, 2014 in connection with IPR2013-00266:
Burns, et al., "Selective Reduction of Disulfides by
Tris(2-carboxyethyl)phosphine" J. Org. Chem., 56, 2648-50 (1991).
cited by applicant .
Mar. 21, 2014 Patent Owner's Reply to Petitioner's Opposition to
Patent Owner's Motion to Amend in connection with IPR2013-00266.
cited by applicant .
Exhibit 2030, filed Mar. 21, 2014 in connection with IPR2013-00266:
Mar. 11, 2014 Bruce Branchaud Deposition Transcript. cited by
applicant .
Exhibit 2032, filed Mar. 21, 2014 in connection with IPR2013-00266:
Excerpts from Feb. 11, 2014 Bruce Branchaud Deposition Transcript
in related IPR2013-00128. cited by applicant .
Exhibit 2034, filed Mar. 21, 2014 in connection with IPR2013-00266:
ScanArray Express Line of Microarray Scanners--Brochure. cited by
applicant .
Exhibit 2036, filed Mar. 21, 2014 in connection with IPR2013-00266:
Supplementary information for Ex. 1020 (Mitra et al., Analytical
Biochem. 320, 55-65, 2003). cited by applicant .
Exhibit 2038, filed Mar. 21, 2014 in connection with IPR2013-00266:
Dawson and Herman et al., "Affinity Isolation of Active Murine
Erythroleukemia Cell Chromatin: Uniform Distribution of
Ubiquitinated Histone H2A Between Active and Inactive Fractions"
Journal of Cellular Biochemistry 46:166-173 (1991). cited by
applicant .
Exhibit 2039, filed Mar. 21, 2014 in connection with IPR2013-00266:
Rigas et al., "Rapid plasmid library screening using RecA-coated
biotinylated probes" PNAS USA 83:9591-9595 (1986). cited by
applicant .
Exhibit 2041, filed Mar. 21, 2014 in connection with IPR2013-00266:
Westheimer et al., "Why Nature Chose Phosphates" Science
235:1173-1178 (1987). cited by applicant .
Exhibit 2043, filed Mar. 21, 2014 in connection with IPR2013-00266:
English translation of Loubinoux et al., "Protection Of Phenols By
The Azidomethylene Group Application To The Synthesis Of Unstable
Phenols" Tetrahedron, 44:6055-6064 (1988). cited by applicant .
Exhibit 2044, filed Mar. 21, 2014 in connection with IPR2013-00266:
Excerpts from Oct. 3, 2013 Bruce Branchaud Deposition Transcript in
related Inter Partes Review IPR2013-00128. cited by applicant .
Exhibit 2045, filed Mar. 21, 2014 in connection with IPR2013-00266:
Welch et al., "Syntheses of Nucleosides Designed for Combinatorial
DNA Sequencing" Chem. Eur. J., 5:951-960 (1999). cited by applicant
.
Exhibit 2046, filed Mar. 21, 2014 in connection with IPR2013-00266:
Welch et al., Corrigenda to "Syntheses of Nucleosides Designed for
Combinatorial DNA Sequencing" Chem. Eur. J., 11:8256 (2005). cited
by applicant .
Exhibit 2047, filed Mar. 21, 2014 in connection with IPR2013-00266:
Wu et al., "Termination of DNA synthesis by N.sup.6-alkylated, not
3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates",
Nucleic Acids Research 35:6339-6349 (2007). cited by applicant
.
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Taylor et al., "Rise per base pair in helices of double-stranded
rotavirus RNA determined by electron microscopy" Virus Research,
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Exhibit 2049, filed Mar. 21, 2014 in connection with IPR2013-00266:
Watson et al., Molecular Biology of the Gene, Fifth Edition,
Chapter 6 (2004). cited by applicant .
Exhibit 2050, filed Mar. 21, 2014 in connection with IPR2013-00266:
Shen et al., "RNA structure at high resolution" FASEB J.,
9:1023-1033 (1995). cited by applicant .
Exhibit 2051, filed Mar. 21, 2014 in connection with IPR2013-00266:
Holtzman et al., "Electron microscopy of complexes of isolated
acetylcholine receptor, biotinyl-toxin, and avidin" Proc. Natl.
Acad. Sci. USA, 79:310-314 (1982). cited by applicant .
Exhibit 2052, filed Mar. 21, 2014 in connection with IPR2013-00266:
Pugliese et al., "Three-dimensional Structure of the Tetragonal
Crystal Form of Egg-white Avidin in its Functional Complex with
Biotin at 2.7 Angstrom Resolution" Journal of Molecular Biology,
231:698-710 (1993). cited by applicant .
Exhibit 2053, filed Mar. 21, 2014 in connection with IPR2013-00266:
Fersht, "Fidelity of replication of phage .phi.X174 DNA by DNA
polymerase III holoenzyme: Spontaneous mutation by
misincorporation" Proc. Natl. Acad. Sci. USA, 76:4946-4950 (1979).
cited by applicant .
Exhibit 2054, filed Mar. 21, 2014 in connection with IPR2013-00266:
Fersht et al., "DNA polymerase accuracy and spontaneous mutation
rates: Frequencies of purine-purine, purine-pyrimidine, and
pyrimidine-pyrimidine mismatches during DNA replication" Proc.
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Exhibit 2055, filed Mar. 21, 2014 in connection with IPR2013-00266:
Bebenek et al., "Frameshift errors initiated by nucleotide
misincorporation" Proc. Natl. Acad. Sci. USA, 87:4946-4950 (1990).
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Exhibit 2056, filed Mar. 21, 2014 in connection with IPR2013-00266:
Bebenek et al., "The Effects of dNTP Pool Imbalances on Frameshift
Fidelity during DNA Replication" J. Biol. Chem., 267:3589-3596
(1992). cited by applicant .
Exhibit 2057, filed Mar. 21, 2014 in connection with IPR2013-00266:
Greene and Wuts, Protective Groups in Organic Synthesis, 3rd ed.,
Chapter 1 (1999). cited by applicant .
Apr. 18, 2014 Petitioner Motion for Observations on the
Cross-Examination Testimony of Dr. Romesberg, in connection with
IPR2013-00266. cited by applicant .
Apr. 18, 2014 Petitioner Motion to Exclude Evidence in connection
with IPR2013-00266. cited by applicant .
Exhibit 1042, filed Apr. 18, 2014 in connection with IPR2013-00266:
Apr. 10, 2014 transcript of Deposition of Floyd Romesberg. cited by
applicant .
Apr. 18, 2014 Patentee Motion to Exclude Evidence in connection
with IPR2013-00266. cited by applicant .
May 2, 2014 Patentee Response to Petitioner Motion for Observations
on Romesberg Testimony, in connection with IPR2013-00266. cited by
applicant .
Exhibit 1045, filed May 22, 2014 in connection with IPR2013-00266:
Petitioner Demonstratives for May 28, 2014 Oral Hearing cited by
applicant .
Exhibit 2060, filed May 22, 2014 in connection with IPR2013-00266:
Patentee Demonstratives for May 28, 2014 Oral Hearing. cited by
applicant .
Transcript of May 28, 2014 Oral Hearing in IPR2013-00266, entered
Jul. 8, 2014. cited by applicant .
Petitioner Motion to Exclude Evidence, filed Sep. 2, 2014 in
connection with IPR2013-00517. cited by applicant .
Patent Owner Motion to Exclude Evidence, filed Sep. 2, 2014 in
connection with IPR2013-00517. cited by applicant .
Patent Owner Motion for Observations on the Cross-Examination
Testimony of Bruce Branchaud, Ph.D. and Michael Metzker, Ph.D.,
filed Sep. 2, 2014 in connection with IPR2013-00517. cited by
applicant .
Exhibit 2139, filed Sep. 2, 2014 in connection with IPR2013-00517:
Metzker, "Sequencing Technologies--The Next Generation" Nature
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Exhibit 2140, filed Sep. 2, 2014 in connection with IPR2013-00517:
Tsai et al., "Versatile and Efficient Synthesis of a New Class of
Aza-Based Phosphinic Amide Ligands via Unusual P--C Cleavage"
Helvetica Chimica Acta, 89:3007-3017 (2006). cited by applicant
.
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Treinin, General and Theoretical Aspects, Chapter 1 (pp. 1-55) in
The Chemistry of the Azido Group (Saul Patai, Ed.). cited by
applicant .
Exhibit 2142, filed Sep. 2, 2014 in connection with IPR2013-00517:
Hanlon, "The Importance of London Dispersion Forces in the
Maintenance of the Deoxytibonucleic Acid Helix" Biochemical and
Biophysical Research Communications, 23:861-867 (1966). cited by
applicant .
Exhibit 2144, filed Sep. 2, 2014 in connection with IPR2013-00517:
"Phenol," in The Merck Index, pp. 1299-1300 (13th Ed., 2001). cited
by applicant .
Exhibit 2146, filed Sep. 2, 2014 in connection with IPR2013-00517:
Metzker, "Emerging technologies in DNA sequencing" Genome Research,
15:1767-1776, (2005). cited by applicant .
Exhibit 2147, filed Sep. 2, 2014 in connection with IPR2013-00517:
Gardner et al., "Rapid incorporation kinetics and improved fidelity
of a novel class of 3'-OH unblocked reversible terminators" Nucleic
Acids Research, 40:7404-7415. cited by applicant .
Exhibit 2148, filed Sep. 2, 2014 in connection with IPR2013-00517:
Lander et al., "Initial sequencing and analysis of the human
genome" Nature, 409:860-921 (2001). cited by applicant .
Exhibit 2149, filed Sep. 2, 2014 in connection with IPR2013-00517:
Wu et al., "Termination of DNA synthesis by N.sup.6-alkylated, not
3'-O-alkylated, photocleavable 2'-deoxyadenosine triphosphates"
Nucleic Acids Research, 35:6339-6349 (2007). cited by applicant
.
Exhibit 2150, filed Sep. 2, 2014 in connection with IPR2013-00517:
Aldrich, Fine Chemicals catalogue, p. 1337 (1986). cited by
applicant .
Exhibit 2151, filed Sep. 2, 2014 in connection with IPR2013-00517:
Sebastian et al., "Dendrimers with N,N-Disubstituted Hydrazines as
End Groups, Useful Precursors for the Synthesis of Water-Soluble
Dendrimers Capped with Carbohydrate, Carboxylic or Boronic Acid
Derivatives" Tetrahedron, 56:6269-6277 (2000). cited by applicant
.
Exhibit 2152, filed Sep. 2, 2014 in connection with IPR2013-00517:
Reardon et al., "Reduction of 3'-Azido-3'-deoxythymidine (AZT) and
AZT Nucleotides by Thiols" The Journal of Biological Chemistry,
269:15999-16008 (1994). cited by applicant .
Exhibit 2154, filed Sep. 2, 2014 in connection with IPR2013-00517:
Transcript, Aug. 12, 2014 Deposition of Michael L. Metzker, Ph.D.
cited by applicant .
Exhibit 2155, filed Sep. 2, 2014 in connection with IPR2013-00517:
Transcript, Aug. 26, 2014 Deposition of Bruce P. Branchaud, Ph.D.
cited by applicant .
Petitioner Opposition to Patentee Motion to Exclude Evidence, filed
Sep. 15, 2014 in connection with IPR2013-00517. cited by applicant
.
Office Action issued Feb. 12, 2010 in connection with U.S. Appl.
No. 12/084,457. cited by applicant .
Jun. 10, 2010 Response to Office Action issued Feb. 12, 2010 in
connection with U.S. Appl. No. 12/084,457. cited by applicant .
Office Action issued Aug. 2, 2010 in connection with U.S. Appl. No.
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Feb. 2, 2011 Amendment in response to Office Action issued Aug. 2,
2010 in connection with U.S. Appl. No. 12/084,457. cited by
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Final Office Action issued May 2, 2011 in connection with U.S.
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Nov. 2, 2011 Amendment in response to Final Office Action issued
May 2, 2011 in connection with U.S. Appl. No. 12/084,457. cited by
applicant .
Ex Parte Quayle Action issued Feb. 12, 2013 in connection with U.S.
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Aug. 9, 2013 Response after Ex Parte Quayle Action issued Feb. 12,
2013 in connection with U.S. Appl. No. 12/084,457. cited by
applicant .
Notice of Allowance issued Aug. 29, 2013 in connection with U.S.
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IPR2013-00517. cited by applicant .
U.S. Appl. No. 10/227,131, filed Aug. 23, 2002, Barnes et al. cited
by applicant .
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|
Primary Examiner: Riley; Jezia
Attorney, Agent or Firm: White; John P. Cooper & Dunham
LLP
Government Interests
This invention was made with government support under grant number
IP50 HG002806-01 awarded by the National Institutes of Health. The
government has certain rights in the invention.
Parent Case Text
This application is a continuation of U.S. Ser. No. 12/084,338,
filed Oct. 16, 2009, now U.S. Pat. No. 7,982,029, issued Jul. 19,
2011, a .sctn.371 national stage of PCT International Application
No. PCT/US2006/042698, filed Oct. 31, 2006, which claims the
benefit of U.S. Provisional Application No. 60/732,373, filed Oct.
31, 2005, the contents of all of which are hereby incorporated by
reference into this application.
Claims
What is claimed is:
1. A method for determining the sequence of a single-stranded DNA
template comprising the following steps: (A) contacting the
single-stranded DNA template with 9.degree. N polymerase in the
presence of (i) a primer and (ii) four nucleotide analogues under
conditions such that the 9.degree. N polymerase catalyzes DNA
synthesis of a DNA extension product which has incorporated at its
3' end, a nucleotide analogue complementary to, and base-paired
with, a nucleotide residue which is not base-paired and is located
at the 5' end of the single-stranded DNA template to be sequenced,
wherein each of the four nucleotide analogues comprises: (a) a base
selected from the group consisting of adenine, guanine, cytosine,
thymine, and uracil, (b) a deoxyribose, (c) a unique fluorophore
cleavably attached to each base of the same type base, and (d) a
removable chemical moiety bound to the 3'-oxygen of the deoxyribose
which blocks further DNA synthesis when it is incorporated into the
extension product; and wherein each fluorescent nucleotide analogue
when incorporated into the DNA extension product is characterized
by a predetermined fluorescence emission wavelength different from
the fluorescence emission wavelength of each of the other three
fluorescent nucleotide analogues when incorporated into the DNA
extension product; (B) removing nucleotide analogues not
incorporated into the DNA extension product; (C) determining the
identity of the fluorescent nucleotide analogue incorporated into
the DNA extension product based upon its characteristic
fluorescence emission wavelength; (D) treating the nucleotide
analogue incorporated into the DNA extension product so as to
remove the chemical moiety bound to the 3'-oxygen of the
deoxyribose and cleave the fluorophore from the base; (E) repeating
each of steps (A) to (D) to successively determine the identity of
the nucleotide analogues incorporated at the 3' end of each
succeeding extension product so synthesized so as to thereby
determine the sequence of the single-stranded DNA template.
2. The method of claim 1, wherein the single-stranded DNA template
is bound to a solid substrate.
3. The method of claim 1, wherein the primer in (A) is a
self-priming moiety.
4. The method of claim 1, wherein in (A) the fluorophore is
photocleavably attached to each base of the same type base.
5. The method of claim 4, wherein all the fluorophores are
photocleavably attached to all the bases.
6. The method of claim 1, wherein in (A) the removable chemical
moiety bound to the 3'-oxygen of the deoxyribose is
--CH.sub.2--CH--CH.sub.2 or --CH.sub.2--O--CH.sub.3.
7. The method of claim 1, wherein in (A) the 9.degree. N polymerase
is 9.degree. N polymerase (exo-) A485L/Y409V.
8. The method of claim 1, wherein the treatment in (D) to remove
the chemical moiety from the 3'-oxygen is performed in the presence
of a palladium (Pd) catalyst.
9. The method of claim 8, wherein the palladium catalyst is
Na.sub.2PdCl.sub.4.
10. The method of claim 1, wherein the treatment in (D) to remove
the chemical moiety is performed at about pH 8.8.
11. The method of claim 4, wherein the treatment in (D) to
photocleave the fluorophore from the base comprises light
irradiation.
12. The method of claim 1, wherein the treatment in (D) results in
removal of the chemical moiety from the 3'-oxygen and cleavage of
the fluorophore from the base substantially concurrently.
13. The method of claim 1, wherein the treatment in (D) first
results in removal of the chemical moiety from the 3'-oxygen and
then cleavage of the fluorophore from the base.
14. The method of claim 1, wherein the treatment in (D) first
results in cleavage of the fluorophore from the base and then
removal of the chemical moiety from the 3'-oxygen.
15. A method for determining the sequence of a single-stranded RNA
template comprising the following steps: (A) contacting the
single-stranded RNA template with an RNA polymerase in the presence
of (i) a primer and (ii) four nucleotide analogues under conditions
such that the RNA polymerase catalyzes RNA synthesis of an RNA
extension product which has incorporated at its 3' end, a
nucleotide analogue complementary to, and base-paired with, a
nucleotide residue which is not base-paired and is located at the
5' end of the single-stranded RNA template to be sequenced, wherein
each of the four nucleotide analogues comprises: (a) a base
selected from the group consisting of adenine, guanine, cytosine,
and uracil, (b) a ribose, (c) a unique fluorophore cleavably
attached to each base of the same type base, and (d) a removable
chemical moiety bound to the 3'-oxygen of the ribose which blocks
further RNA synthesis when it is incorporated into the extension
product; and wherein each fluorescent nucleotide analogue when
incorporated into the RNA extension product is characterized by a
predetermined fluorescence emission wavelength different from the
fluorescence emission wavelength of each of the other three
fluorescent nucleotide analogues when incorporated into the RNA
extension product; (B) removing nucleotide analogues not
incorporated into the RNA extension product; (C) determining the
identity of the fluorescent nucleotide analogue incorporated into
the RNA extension product based upon its characteristic
fluorescence emission wavelength; (D) treating the nucleotide
analogue incorporated into the RNA extension product so as to
remove the chemical moiety bound to the 3'-oxygen of the ribose and
cleave the fluorophore from the base; (E) repeating each of steps
(A) to (D) to successively determine the identity of the nucleotide
analogues incorporated at the 3' end of each succeeding extension
product so synthesized so as to thereby determine the sequence of
the single-stranded RNA template.
16. The method of claim 15, wherein the single-stranded RNA
template is bound to a solid substrate.
17. The method of claim 15, wherein the primer in (A) is a
self-priming moiety.
18. The method of claim 15, wherein in (A) the fluorophore is
photocleavably attached to each base of the same type base.
19. The method of claim 18, wherein all the fluorophores are
photocleavably attached to all the bases.
20. The method of claim 15, wherein in (A) the removable chemical
moiety bound to the 3'-oxygen of the ribose is
--CH.sub.2--CH.dbd.CH.sub.2 or --CH.sub.2--O--CH.sub.3.
21. The method of claim 15, wherein the treatment in (D) to remove
the chemical moiety from the 3'-oxygen is performed in the presence
of a palladium (Pd) catalyst.
22. The method of claim 21, wherein the palladium catalyst is
Na.sub.2PdCl.sub.4.
23. The method of claim 15, wherein the treatment in (D) to remove
the chemical moiety is performed at about pH 8.8.
24. The method of claim 18, wherein the treatment in (D) to
photocleave the fluorophore from the base comprises light
irradiation.
25. The method of claim 15, wherein the treatment in (D) results in
removal of the chemical moiety from the 3'-oxygen and cleavage of
the fluorophore from the base substantially concurrently.
26. The method of claim 15, wherein the treatment in (D) first
results in removal of the chemical moiety from the 3'-oxygen and
then cleavage of the fluorophore from the base.
27. The method of claim 15, wherein the treatment in (D) first
results in cleavage of the fluorophore from the base and then
removal of the chemical moiety from the 3'-oxygen.
28. The method of claim 6, wherein if the removable chemical moiety
bound to the 3'-oxygen of the deoxyribose is
--CH.sub.2--CH.dbd.CH.sub.2, then the treatment in (D) to remove
the chemical moiety is performed at about pH 8.8.
Description
Throughout this application, various publications are referenced in
parentheses by number. Full citations for these references may be
found at the end of each experimental section. The disclosures of
these publications in their entireties are hereby incorporated by
reference into this application to more fully describe the state of
the art to which this invention pertains.
BACKGROUND OF THE INVENTION
DNA sequencing is a fundamental tool for biological research and
medical diagnostics, driving disease gene discovery and gene
function studies. DNA sequencing by synthesis (SBS) using
reversible fluorescent nucleotide terminators1 is a potentially
efficient approach to address the limitations of current DNA
sequencing techniques, such as throughput and data accuracy. A
3'-O-allyl photocleavable (PC) fluorescent nucleotide analogue,
3'-O-allyl-dUTP-PC-Bodipy-FL-510, as a reversible terminator for
SBS has previously been reported (2). The nucleotide can be
efficiently incorporated by DNA polymerase into a growing DNA
strand to terminate the polymerase reaction. After that the
fluorophore can be photocleaved quantitatively by irradiation at
355 nm, and the allyl group is rapidly and efficiently removed by
using a Pd-catalyzed reaction in water to regenerate a free 3'-OH
group to reinitiate the polymerase reaction.
SUMMARY
This invention provides a method for making
3'O-allyl-dGTP-PC-Bodipy-FL-510 comprising performing the steps set
forth in FIG. 7. This invention also provides a method for making
3'-O-allyl-dATP-PC-ROX comprising performing the steps set forth in
FIG. 8. This invention also provides a method for making
3'-O-allyl-dCTP-PC-Bodipy-650 comprising performing the steps set
forth in FIG. 9. This invention also provides a method for making
3'-O-allyl-dUTP-PC-R6G comprising performing the steps set forth in
FIG. 10.
This invention also provides a method for making method for
determining the sequence of a DNA comprising performing the
following steps for each residue of the DNA to be sequenced: (a)
contacting the DNA with a DNA polymerase in the presence of (i) a
primer and (ii) four fluorescent nucleotide analogues under
conditions permitting the DNA polymerase to catalyze DNA synthesis,
wherein (1) the nucleotide analogues consist of an analogue of
dGTP, an analogue of dCTP, an analogue of dTTP or dUTP, and an
analogue of dATP, (2) each nucleotide analogue comprises (i) a base
selected from the group consisting of adenine, guanine, cytosine,
thymine or uracil, and analogues thereof, (ii) a deoxyribose, (iii)
a fluorophore photocleavably attached to the base, and (iv) an
allyl moiety bound to the 3'-oxygen of the deoxyribose, so that a
nucleotide analogue complementary to the residue being sequenced is
bound to the DNA by the DNA polymerase, and (3) each of the four
analogues has a predetermined fluorescence wavelength which is
different than the fluorescence wavelengths of the other three
analogues; (b) removing unbound nucleotide analogues; (c)
determining the identity of the bound nucleotide analogues; and (d)
following step (c), except with respect to the final DNA residue to
be sequenced, (i) chemically cleaving from the bound nucleotide
analogue the allyl moiety bound to the 3'-oxygen atom of the
deoxyribose and (ii) photocleaving the fluorophore from the bound
nucleotide analogue, wherein steps (d)(i) and (d)(ii) can be
performed concurrently or in any order, and step (d) (i) is
performed using a Pd catalyst at a pH of about 8.8, thereby
determining the sequence of the DNA.
This invention also provides a method for removing an allyl moiety
from the 3'-oxygen of a nucleotide analogue's deoxyribose moiety
comprising the step of contacting the nucleotide analogue with a Pd
catalyst at a pH of about 8.8.
BRIEF DESCRIPTION OF THE FIGURES
FIG. 1: Synthesis of a 3'-O-allyl modified 19-mer
oligonucleotide.
FIG. 2: Synthesis of 3'-O-allyl-dUTP-PC-Bodipy-FL-510.
FIG. 3: Schematic representation (left) and step-by-step MALDI-TOF
MS results (right) for the deallylation of a 3'-O-allyl-modified
oligonucleotide and the use of the deallylated oligonucleotide as a
primer in a polymerase extension reaction. (A) Peak at m/z 5871
corresponding to the HPLC-purified 3'-O-allyl modified 19-mer
oligonucleotide. (B) Peak at m/z 5831 corresponding to the above
oligonucleotide without the allyl group, obtained after 30 sec of
incubation with Na.sub.2PdCl.sub.4 and TPPTS
[P(PhSO.sub.3Na).sub.3] at 70.degree. C. (C) Peak at m/z 6535
corresponding to the extension of the deallylated oligonucleotide
by Biotin-11-ddGTP using Thermo Sequenase DNA polymerase.
FIG. 4: One entire polymerase reaction cycle using
3'-O-allyl-dUTP-PC-Bodipy-FL-510 as a reversible terminator.
FIG. 5: MALDI-TOF MS results for each step of a polymerase reaction
cycle using 3'-O-allyl-dUTP-PC-Bodipy-FL-510 as a reversible
terminator. (A) Peak at m/z 6787 corresponding to the primer
extension product 11 obtained using
3'-O-allyl-dUTP-PC-Bodipy-FL-510 and the 9.degree. N Polymerase
(exo-) A485L/Y409V. (B) Peak at m/z 6292 corresponding to the
photocleavage product 12. (C) Peak at m/z 6252 corresponding to the
photocleavage product without the allyl group 13 obtained after 90
secs of incubation with the catalyst and ligand at 70.degree. C.
(D) Peak at m/z 7133 corresponding to the extension product 14 from
the purified deallylated product using dGTP-PC-Bodipy-FL-510 and
Thermo Sequenase DNA Polymerase. (E) Peak at m/z 6637 corresponding
to the photocleavage product 15.
FIG. 6: Structures of four-color 3'-O-allyl modified photocleavable
fluorescent nucleotides.
FIG. 7: Synthesis of 3'-O-allyl-dGTP-PC-Bodipy-FL-510 10.
FIG. 8. Synthesis of 3'-O-allyl-dATP-PC-ROX 19.
FIG. 9: Synthesis of 3'-O-allyl-dCTP-PC-Bodipy-650 26.
FIG. 10. Synthesis of 3'-O-allyl-dUTP-PC-R6G 33.
FIG. 11. Polymerase DNA extension reaction using
3'-O-allyl-dGTP-PC-Bodipy-FL-510 10 as a reversible terminator.
FIG. 12. A continuous polymerase extension using 10 as a reversible
terminator (left) and MALDI-TOF MS spectra of consecutive extension
photocleavage and deallylation products (right).
FIG. 13. (Left) Scheme showing 3'-O-allyl-dATP-PC-ROX 19 as a base
specific reversible terminator for DNA primer extension,
photocleavage and deallylation; (right) MALDI-TOF MS spectra for
incorporation, photocleavage and deallylation products.
FIG. 14. (Left) Scheme showing 3'-O-allyl-dCTP-PC-Bodipy-650 26 as
a base specific reversible terminator for DNA primer extension,
photocleavage and deallylation; (right) MALDI-TOF MS spectra for
incorporation, photocleavage and deallylation products.
FIG. 15. (Left) Scheme showing 3'-O-allyl-dUTP-PC-R6G 33 as a base
specific reversible terminator for DNA primer extension,
photocleavage and deallylation; (right) MALDI-TOF MS spectra for
incorporation, photocleavage and deallylation products.
FIG. 16: Structures of dGTP-PC-Bodipy-FL-510 (.lamda..sub.abs
(max)=502 nm; .lamda..sub.em (max).about.510 nm), dUTP-PC-R6G
(.lamda..sub.abs (max)=525 nm; .lamda..sub.em (max)=550 nm),
dATP-PC-ROX (.lamda..sub.abs (max)=575 nm; .lamda..sub.em (max)=602
nm), and dCTP-PC-Bodipy-650 (.lamda..sub.em (max)=630 nm;
.lamda..sub.em (max)=650 nm).
FIG. 17: Synthesis of photocleavable fluorescent nucleotides. (a)
acetonitrile or DMF/1 M NaHCO.sub.3 solution; (b)
N,N'-disuccinimidyl carbonate (DSC), triethylamine; (c) 0.1 M
Na.sub.2CO.sub.3/NaHCO.sub.3 aqueous buffer (pH 8.5-8.7).
FIG. 18: DNA extension reaction performed in solution phase to
characterize the 4 different photocleavable fluorescent nucleotide
analogues (dUTP-PC-R6G, dCTP-PC-Bodipy-FL-510, dATP-PC-ROX,
dCTP-PC-Bodipy-650). After each extension reaction, the DNA
extension product is purified by HPLC for MALDI-TOF MS measurement,
to verify that it is the correct extension product. Photolysis is
performed to produce a DNA product that is used as a primer for the
next DNA extension reaction.
FIG. 19: The polymerase extension scheme (left) and MALDI-TOF MS
spectra of the four consecutive extension products and their
photocleavage products (right). Primer extended with dUTP-PC-R6G
(1), and its photocleavage product 2; Product 2 extended with
dGTP-PC-Bodipy-FL-510 (3), and its photocleavage product 4; Product
4 extended with dATP-PC-ROX (5), and its photocleavage product 6;
Product 6 extended with dCTP-PC-Bodipy-650 (7), and its
photocleavage product 8. After 10 seconds of irradiation with a
laser at 355 nm, photocleavage is complete with all the
fluorophores cleaved from the extended DNA products.
FIG. 20: Immobilization of an azido-labeled PCR product on an
alkynyl-functionalized surface and a ligation reaction between the
immobilized single-stranded DNA template and a loop primer to form
a self-priming DNA moiety on the chip. The sequence of the loop
primer is shown in (A).
FIG. 21: Schematic representation of SBS on a chip using four PC
fluorescent nucleotides (Upper panel) and the scanned fluorescence
images for each step of SBS on a chip (Lower panel). (1)
Incorporation of dATP-PC-ROX; (2) Photocleavage of PC-ROX; (3)
Incorporation of dGTP-PC-Bodipy-FL-510; (4) Photocleavage of
PC-Bodipy-FL-510; (5) Incorporation of dATP-PC-ROX; (6)
Photocleavage of PC-ROX; (7) Incorporation of dCTP-PC-Bodipy-650;
(8) Photocleavage of PC-Bodipy-650; (9) Incorporation of
dUTP-PC-R6G; (10) Photocleavage of PC-R6G; (11) Incorporation of
dATP-PC-ROX; (12) Photocleavage of PC-ROX; (13) Incorporation of
dUTP-PC-R6G; (14) Photocleavage of PC-R6G; (15) Incorporation of
dATP-PC-ROX; (16) Photocleavage of PC-ROX; (17) Incorporation of
dGTP-PC-Bodipy-FL-510; (18) Photocleavage of PC-Bodipy-FL-510; (19)
Incorporation of dUTP-PC-R6G; (20) Photocleavage of PC-R6G; (21)
Incorporation of dCTP-PC-Bodipy-650; (22) Photocleavage of
PC-Bodipy-650; (23) Incorporation of dATP-PC-ROX; (24)
Photocleavage of PC-ROX.
FIG. 22: 4-Color DNA sequencing data using
3'-.beta.-allyl-dGTP-PC-Bodipy-FL-510, 3'-O-allyl-dATP-PC-ROX,
3'-O-allyl-dUTP-PC-R6G and 3'-O-allyl-dCTP-PC-Bodipy-650 as
reversible terminators and a 4-color Laser Scanner. Scanned
fluorescence images for each step of SBS on a DNA chip to sequence
a DNA template with homopolymeric regions.
DETAILED DESCRIPTION OF THE INVENTION
Terms
The following definitions are presented as an aid in understanding
this invention:
A--Adenine;
C--Cytosine;
DNA--Deoxyribonucleic acid;
G--Guanine;
PC--Photocleavable
RNA--Ribonucleic acid;
SBS--Sequencing by synthesis;
T--Thymine; and
U--Uracil.
"Nucleic acid" shall mean any nucleic acid, including, without
limitation, DNA, RNA and hybrids thereof. The nucleic acid bases
that form nucleic acid molecules can be the bases A, C, G, T and U,
as well as derivatives thereof. Derivatives of these bases are well
known in the art, and are exemplified in PCR Systems, Reagents and
Consumables (Perkin Elmer Catalogue 1996 1997, Roche Molecular
Systems, Inc., Branchburg, N.J., USA).
As used herein, "self-priming moiety" shall mean a nucleic acid
moiety covalently bound to a nucleic acid to be transcribed,
wherein the bound nucleic acid moiety, through its proximity with
the transcription initiation site of the nucleic acid to be
transcribed, permits transcription of the nucleic acid under
nucleic acid polymerization-permitting conditions (e.g. the
presence of a suitable polymerase, nucleotides and other reagents).
That is, the self-priming moiety permits the same result (i.e.
transcription) as does a non-bound primer. In one embodiment, the
self-priming moiety is a single stranded nucleic acid having a
hairpin structure. Examples of such self-priming moieties are shown
in the Figures.
"Hybridize" shall mean the annealing of one single-stranded nucleic
acid to another nucleic acid based on sequence complementarity. The
propensity for hybridization between nucleic acids depends on the
temperature and ionic strength of their milieu, the length of the
nucleic acids and the degree of complementarity. The effect of
these parameters on hybridization is well known in the art (see
Sambrook J, Fritsch E F, Maniatis T. 1989. Molecular cloning: a
laboratory manual. Cold Spring Harbor Laboratory Press, New
York.)
As used herein, "nucleotide analogue" shall mean an analogue of A,
G, C, T or U (that is, an analogue of a nucleotide comprising the
base A, G, C, T or U) which is recognized by DNA or RNA polymerase
(whichever is applicable) and incorporated into a strand of DNA or
RNA (whichever is appropriate). Examples of nucleotide analogues
include, without limitation 7-deaza-adenine, 7-deaza-guanine, the
analogues of deoxynucleotides shown in FIG. 6, analogues in which a
label is attached through a cleavable linker to the 5-position of
cytosine or thymine or to the 7-position of deaza-adenine or
deaza-guanine, analogues in which a small chemical moiety such as
--CH.sub.2CH.dbd.CH.sub.2 is used to cap the --OH group at the
3'-position of deoxyribose, and analogues of related
dideoxynucleotides. Nucleotide analogues, including
dideoxynucleotide analogues, and DNA polymerase-based DNA
sequencing are also described in U.S. Pat. No. 6,664,079.
1,3 dipolar azide-alkyne cycloaddition chemistry is described in WO
2005/084367 and PCT/US03/39354, the contents of each of which are
hereby incorporated by reference.
All embodiments of U.S. Pat. No. 6,664,079 (the contents of which
are hereby incorporated by reference) with regard to sequencing a
nucleic acid are specifically envisioned here.
With regard to the synthesis of the nucleotide analogues disclosed
herein, other fluorophores or chromophores to be photocleavably
attached to the base of the analogue are envisioned. In addition,
combinatorial fluorescence energy tags as described in U.S. Pat.
No. 6,627,748 (the contents of which are hereby incorporated by
reference) may be used in place of the fluorophores described
herein.
Embodiments of the Invention
This invention provides a method for making
3'O-allyl-dGTP-PC-Bodipy-FL-510 comprising performing the steps set
forth in FIG. 7. This invention also provides a method for making
3'-O-allyl-dATP-PC-ROX comprising performing the steps set forth in
FIG. 8. This invention also provides a method for making
3'-O-allyl-dCTP-PC-Bodipy-650 comprising performing the steps set
forth in FIG. 9. This invention also provides a method for making
3'-O-allyl-dUTP-PC-R6G comprising performing the steps set forth in
FIG. 10.
This invention also provides a method for making method for
determining the sequence of a DNA comprising performing the
following steps for each residue of the DNA to be sequenced: (a)
contacting the DNA with a DNA polymerase in the presence of (i) a
primer and (ii) four fluorescent nucleotide analogues under
conditions permitting the DNA polymerase to catalyze DNA synthesis,
wherein (1) the nucleotide analogues consist of an analogue of
dGTP, an analogue of dCTP, an analogue of dTTP or dUTP, and an
analogue of dATP, (2) each nucleotide analogue comprises (i) a base
selected from the group consisting of adenine, guanine, cytosine,
thymine or uracil, and analogues thereof, (ii) a deoxyribose, (iii)
a fluorophore photocleavably attached to the base, and (iv) an
allyl moiety bound to the 3'-oxygen of the deoxyribose, so that a
nucleotide analogue complementary to the residue being sequenced is
bound to the DNA by the DNA polymerase, and (3) each of the four
analogues has a predetermined fluorescence wavelength which is
different than the fluorescence wavelengths of the other three
analogues; (b) removing unbound nucleotide analogues; (c)
determining the identity of the bound nucleotide analogues; and (d)
following step (c), except with respect to the final DNA residue to
be sequenced, (i) chemically cleaving from the bound nucleotide
analogue the allyl moiety bound to the 3'-oxygen atom of the
deoxyribose and (ii) photocleaving the fluorophore from the bound
nucleotide analogue, wherein steps (d)(i) and (d)(ii) can be
performed concurrently or in any order, and step (d) (i) is
performed using a Pd catalyst at a pH of about 8.8, thereby
determining the sequence of the DNA.
In one embodiment of the instant method, chemically cleaving the
allyl moiety bound to the 3'-oxygen atom is performed using
Na.sub.2PdCl.sub.4.
In one embodiment of the instant method, the primer is a
self-priming moiety.
In one embodiment of the instant method, the DNA is bound to a
solid substrate. In one embodiment of the instant method, the DNA
is bound to the solid substrate via 1,3-dipolar azide-alkyne
cycloaddition chemistry. In one embodiment of the instant method,
about 1000 or fewer copies of the DNA are bound to the solid
substrate.
In one embodiment of the instant method, the four fluorescent
nucleotide analogues are, 3'-O-allyl-dGTP-PC-Bodipy-FL-510,
3'-O-allyl-dATP-PC-ROX, 3'-O-allyl-dCTP-PC-Bodipy-650 and
3'-O-allyl-dUTP-PC-R6G.
In one embodiment of the instant method, the DNA polymerase is a
9.degree. N polymerase.
This invention also provides a method for removing an allyl moiety
from the 3'-oxygen of a nucleotide analogue's deoxyribose moiety
comprising the step of contacting the nucleotide analogue with a Pd
catalyst at a pH of about 8.8. In one embodiment of the instant
method, the Pd catalyst is Na.sub.2PdCl.sub.4.
In embodiments of this invention the sequencing methods described
can be applied, mutatis mutandis, to sequencing an RNA molecule or
an RNA/DNA hybrid molecule.
This invention will be better understood by reference to the
Experimental Details which follow, but those skilled in the art
will readily appreciate that the specific experiments detailed are
only illustrative of the invention as described more fully in the
claims which follow thereafter.
EXPERIMENTAL DETAILS
The design and synthesis of a complete set of four-color 3'-O-allyl
modified photocleavable fluorescent nucleotides as reversible
terminators for SBS is disclosed herein.
Example 1
Synopsis
DNA sequencing by synthesis (SBS) offers a new approach for
potential high-throughput sequencing applications. In this method,
the ability of an incoming nucleotide to act as a reversible
terminator for a DNA polymerase reaction is an important
requirement to unambiguously determine the identity of the
incorporated nucleotide before the next nucleotide is added. A free
3'-OH group on the terminal nucleotide of the primer is necessary
for the DNA polymerase to incorporate an incoming nucleotide.
Therefore, if the 3'-OH group of an incoming nucleotide is capped
by a chemical moiety, it will cause the polymerase reaction to
terminate after the nucleotide is incorporated into the DNA strand.
If the capping group is subsequently removed to generate a free
3'-OH, the polymerase reaction will reinitialize. Here, the design
and synthesis of a 3'-modified photocleavable fluorescent
nucleotide, 3'-O-allyl-dUTP-PC-Bodipy-FL-510, as a reversible
terminator for SBS is disclosed. This nucleotide analogue contains
an allyl moiety capping the 3'-OH group and a fluorophore
Bodipy-FL-510 linked to the 5 position of the uracil through a
photocleavable 2-nitrobenzyl linker. In addition, it is shown that
this nucleotide is a good substrate for a DNA polymerase. After the
nucleotide was successfully incorporated into a growing DNA strand
and the fluorophore photocleaved, the allyl group was removed using
a Pd catalyzed reaction to reinitiate the polymerase reaction,
thereby establishing the feasibility of using such nucleotide
analogues as reversible terminators for SBS.
Introduction
The completion of the Human Genome Project (1, 2) has led to an
increased demand for high-throughput and rapid DNA sequencing
methods to identify genetic variants for applications in
pharmacogenomics (3), disease gene discovery (4, 5) and gene
function studies (6). Current state-of-the-art DNA sequencing
technologies (7-11) to some extent address the accuracy and
throughput requirements but suffer limitations with respect to cost
and data quality. Thus, new DNA sequencing approach is required to
broaden the applications of genomic information in medical research
and health care. In this regard, DNA sequencing by synthesis (SBS)
offers an alternative approach to possibly address the limitations
of current DNA sequencing techniques. The design of a parallel chip
based SBS system, which uses a self-priming DNA template covalently
linked to the glass surface of a chip and four modified nucleotides
has previously been described (12-14). The nucleotides are modified
such that they have a photocleavable fluorescent moiety attached to
the base (5 position of pyrimidines, 7 position of purines) and a
chemically cleavable group to cap the 3'-OH. When the correct
nucleotide is incorporated in a DNA polymerase reaction, specific
to the template sequence, the reaction is temporarily terminated
because of the lack of a free 3'-OH group. After the fluorescent
signal is detected and the nucleotide identified, the 3'-OH needs
to be regenerated in order to continue incorporating the next
nucleotide. In Example 3 hereinbelow, it is demonstrated that 4
photocleavable fluorescent nucleotides can be efficiently
incorporated by DNA polymerase into a growing DNA strand base
specifically in a polymerase extension reaction, and the
fluorophores can be completely removed by photocleavage under near
UV irradiation (.lamda..about.355 nm) with high efficiency (15).
Using this system in a four-color sequencing assay, accurate
identification of multiple bases in a self-priming DNA template
covalently attached to a glass surface can be achieved.
Another important requirement for this approach to sequence DNA
unambiguously is a suitable chemical moiety to cap the 3'-OH of the
nucleotide such that it terminates the polymerase reaction to allow
the identification of the incorporated nucleotide. The capping
group then needs to be efficiently removed to regenerate the 3'-OH
thereby allowing the polymerase reaction to continue. Thus, the
photocleavable fluorescent nucleotides used in SBS must be
reversible terminators of the DNA polymerase reaction to allow the
detection of the fluorescent signal such that the complementary DNA
synthesis and sequence identification can be efficiently performed
in tandem. The principal challenge posed by this requirement is the
incorporation ability of the 3'-modified nucleotide by DNA
polymerase into the growing DNA strand. The 3'-position on the
sugar ring of a nucleotide is very close to the amino acid residues
in the active site of the DNA polymerase. This is supported by the
3-D structure of the previously determined ternary complexes of rat
DNA polymerase, a DNA template-primer, and dideoxycytidine
triphosphate (16). Thus, any bulky modification at this position
provides steric hindrance to the DNA polymerase and prevents the
nucleotide from being incorporated. A second challenge is the
efficient removal of the capping group once the fluorescence signal
is detected. Thus, it is important to use a functional group small
enough to present no hindrance to DNA polymerase, stable enough to
withstand DNA extension reaction conditions, and able to be removed
easily and rapidly to regenerate a free 3'-OH under specific
conditions.
Results
Numerous studies have previously been undertaken to identify a
3'-modified nucleotide as a substrate for DNA polymerase.
3'-O-methyl-nucleotides have been shown to be good substrates for
several polymerases (17). However, the procedure to chemically
cleave the methyl group is stringent and requires anhydrous
conditions. Thus, it is not practical to use a methyl group to cap
the 3''-OH group for SBS. It has been reported that nucleotides
with ether linkages at the 3' position can be incorporated by some
DNA polymerases, while those with ester linkages are not generally
accepted by most of the polymerases tested (18). Significant
efforts have been dedicated to evaluate a wide variety of
3'-modified nucleotides to be used as terminators for various DNA
polymerases and reverse transcriptases but none of the functional
groups tested have had established methods to regenerate a free
3'-OH (19-22).
It is known that stable chemical functionalities such as allyl
(--CH.sub.2--CH.dbd.CH.sub.2) and methoxymethyl (--CH.sub.2--O--CH)
groups can be used to cap an OH group, and can be cleaved
chemically with high yield (23, 24). Use of such groups as
reversible caps for the 3'-OH of the nucleotide for SBS (12) is
investigated here, and the establishment of the allyl group as a
3'-OH capping moiety for the nucleotide analogues that can be used
in SBS is revealed. The choice of this group was based on the fact
that the allyl moiety, being relatively small, would not provide
significant hindrance for the polymerase reaction, and therefore
allow the incoming 3'-O-allyl modified nucleotide analogue to be
accepted by DNA polymerase. Furthermore, it was proposed to remove
this group using catalytic deallylation. Here, the synthesis of a
photocleavable fluorescent nucleotide analogue,
3'-O-allyl-dUTP-PC-Bodipy-FL-510, that can be efficiently
incorporated by DNA polymerase into a growing DNA strand is shown.
The allyl group can be rapidly and completely removed by a Pd
catalyzed reaction to regenerate a 3'-OH group and the deallylated
DNA can then allow reinitiation of the polymerase reaction to
incorporate the subsequent nucleotide analogue.
Materials and Methods
All chemicals were purchased from Sigma-Aldrich unless otherwise
indicated. Oligonucleotides used as primers or templates were
synthesized on an EXPEDITE Nucleic Acid Synthesizer (Applied
Biosystems). .sup.1H NMR spectra were recorded on a Bruker 400
spectrometer, while .sup.13C and .sup.31P NMR spectra were recorded
on a Bruker 300 spectrometer. High-resolution MS (HRMS) data were
obtained by using a JEOL JHS HX 110A mass spectrometer. Mass
measurement of DNA was made on a Voyager DE matrix-assisted laser
desorption ionization time-of-flight (MALDI-TOF) mass spectrometer
(Applied Biosystems). Photolysis was performed using a Spectra
Physics GCR-150-30 Nd-YAG laser that generates light pulses at 355
nm (ca. 50 mJ/pulse, pulse length ca. 7 ns) at a frequency of 30 Hz
with a light intensity at ca. 1.5 Ware. Thermo Sequenase DNA
Polymerase, HIV-1 and RAV2 Reverse Transcriptases were obtained
from Amersham Biosciences. Therminator, Vent (exo-), Deep Vent
(exo-), Bst and Klenow (exo-) fragment DNA Polymerases were
obtained from New England Biolabs. 9.degree. N Polymerase (exo-)
A485L/Y409V was generously provided by New England Biolabs.
Sequenase V2 DNA Polymerase, M-MulV and AMV Reverse Transcriptases
were obtained from USB Corporation (Cleveland, Ohio). Tfl and Tth
DNA Polymerases were obtained from Promega Corporation (Madison,
Wis.). Pfu (exo-) DNA Polymerase was obtained from Stratagene, Inc.
(La Jolla, Calif.). Phosphoramidites and columns for nucleic acid
synthesis were obtained from Glen Research (Sterling, Va.).
Synthesis of a 3'-O-allyl Modified 19-mer Oligonucleotide.
3'-O-allyl-thymidine phosphoramidite 3, prepared according to FIG.
1 was used to synthesize a 19-mer oligonucleotide
5'-AGA-GGA-TCC-AAC-CGA-GAC-T(allyl)-3' 4 (SEQ ID NO:1)(MW=5871).
The synthesis was carried out in the 5' to 3' direction using 3
along with dA-5'-CE, dC-5'-CE, dG-5'-CE and dT-5'-CE
phosphoramidites and a dA-5'-CPG column. The oligonucleotide was
purified by HPLC using an Xterra MS C18 (4.6.times.50 mm) column
(Waters). The elution was performed over 90 min at a flow rate of
0.5 ml/min and a fixed temperature of 50.degree. C. using a linear
gradient (12-34.5%) of methanol in a buffer containing 8.6 mM
triethylamine and 100 mM hexafluoroisopropyl alcohol (pH=8.1). The
product was characterized using MALDI-TOF MS.
Deallylation Reaction Performed Using the 3'-O-allyl Modified
19-mer Oligonucleotide.
For the deallylation reaction, 55 equivalents of Na.sub.2PdCl.sub.4
and 440 equivalents of a trisodium triphenylphosphinetrisulfonate
(TPPTS) ligand were used in water at 70.degree. C.
Na.sub.2PdCl.sub.4 in degassed water (0.7 .mu.l, 2.2 nmol) was
added to a solution of TPPTS in degassed water (1 .mu.l, 17.6 nmol)
and mixed well. After 5 min, a solution of 3'-O-allyl modified
oligonucleotide 4 (1 .mu.l, 40 pmol) was added. The reaction
mixture was then placed in a heating block at 70.degree. C. and
incubated for 30 seconds. The resulting deallylated product was
desalted by Zip Tip (Millipore Corporation) and analyzed using
MALDI-TOF MS.
Primer Extension Reaction Performed with the Deallylated DNA
Product.
The 10 .mu.l extension reaction mixture consisted of 45 pmol of the
deallylated DNA product as a primer, 100 pmol of a single-stranded
synthetic 100-mer DNA template (sequence shown in reference 15)
corresponding to a portion of exon 7 of the p53 gene, 100 pmol of
Biotin-11-2',3'-dideoxyguanosine-5'-triphosphate (Biotin-11-ddGTP)
terminator (Perkin Elmer), 1.times. Thermo Sequenase reaction
buffer and 4 U of Thermo Sequenase DNA Polymerase. The extension
reaction consisted of 15 cycles at 94.degree. C. for 20 sec,
48.degree. C. for 30 sec and 60.degree. C. for 60 sec. The product
was purified using solid phase capture on streptavidin-coated
magnetic beads (25), desalted using Zip Tip and analyzed using
MALDI-TOF MS.
Synthesis of 3'-O-allyl-dUTP-PC-Bodipy-FL-510.
3'-O-allyl-dUTP-PC-Bodipy-FL-510 10 was synthesized as shown in
FIG. 2. Detailed synthesis procedures and characterization data for
all intermediate compounds (6-9) are described in the supporting
information.
PC-Bodipy-FL-510 NHS ester (13) (7.2 mg, 12 mmol) in 300 .mu.l of
acetonitrile was added to a solution of
3'-.beta.-allyl-5-(3-aminoprop-1-ynyl)-2'-deoxyuridine-5'-triphosphate
9 (2 mg, 4 mmol) in 300 .mu.l of Na.sub.2CO.sub.3--NaHCO.sub.3
buffer (0.1 M, pH 8.7). The reaction mixture was stirred at room
temperature for 3 h. A preparative silica-gel TLC plate was used to
separate the unreacted PC-Bodipy-FL-510 NHS ester from the
fractions containing 10 (CHCl.sub.3/CH.sub.3OH, 85/15). The product
was concentrated further under vacuum and purified with
reverse-phase HPLC on a 150 4.6-mm C18 column to obtain the pure
product 10 (retention time .about.35 min). Mobile phase: A, 8.6 mM
triethylamine/100 mM hexafluoroisopropyl alcohol in water (pH 8.1);
8, methanol. Elution was performed with 100% A isocratic over 10
min followed by a linear gradient of 0-50% B for 20 min and then
50% .beta. isocratic over another 20 min.
3'-O-allyl-dUTP-PC-Bodipy-FL-510 10 was characterized by the
following single base extension reaction and MALDI-TOF MS.
Primer Extension Using 3'-O-allyl-dUTP-PC-Bodipy-PL-510 and
Photocleavage of the Extension Product.
An 18-mer oligonucleotide 5'-AGA-GGA-TCC-AAC-CGA-GAC-3' (SEQ ID NO:
2) (MW==5907) was synthesized using dA-CE, dC-CE, dG-CE and
Biotin-dT phosphoramidites. A primer extension reaction was
performed using a 15 (1 reaction mixture consisting of 50 pmol of
primer, 100 pmol of single-stranded synthetic 100-mer DNA template
corresponding to a portion of exon 7 of the p53 gene (15), 200 pmol
of 3'-O-allyl-dUTP-PC-Bodipy-FL-510, 1.times. Thermopol reaction
buffer (New England Biolabs) and 15 U of 9(N Polymerase (exo-)
A485L/Y409V. The extension reaction consisted of 15 cycles of 94 (C
for 20 sec, 48 (C for 30 sec and 60 (C for 60 sec. A small portion
of the DNA extension product 11 was desalted using Zip Tip and
analyzed using MALDI-TOF MS. The rest of the product was
freeze-dried, resuspended in 200 (1 of deionized water and
irradiated for 10 sec in a quartz cell with path lengths of 1.0 cm
employing an Nd-YAG laser ((.about.355 nm) to cleave the
fluorophore from the DNA, yielding product 12.
Deallylation of the DNA Extension Product Generated by the
Incorporation of 3'-O-allyl-dUTP-PC-Bodipy-FL-510.
The above photocleaved 3'-O-allyl modified DNA product 12 (180 pmol
produced in multiple reactions) was dried and resuspended in 1 (1
of deionized H2O. Na2PdCl4 in degassed H2O (4.1 (1, 72 nmol) was
added to a solution of TPPTS in degassed H2O (2.7 (l, 9 nmol) and
mixed well. After 5 min, the above DNA product (1 (1, 180 pmol) was
added. The reaction mixture was then placed in a heating block,
incubated at 70.degree. C. for 90 sec to yield deallylated product
13, and then cooled to room temperature for analysis by MALDI-TOF
MS.
Polymerase Extension and Photocleavage Using the Deallylated DNA
Product as a Primer.
The above deallylated DNA product 13 was used as a primer in a
single base extension reaction. The 10 (l reaction mixture
consisted of 50 pmol of the above deallylated product 13, 125 pmol
of dGTP-PC-Bodipy-FL-510 (14), 4 U of Thermo Sequenase DNA
Polymerase and 1.times. reaction buffer. The extension reaction
consisted of 15 cycles of 94 (C for 20 sec, 48 (C for 30 sec and 60
(C for 60 sec. The DNA extension product 14 was desalted using the
Zip Tip protocol and a small portion was analyzed using MALDI-TOF
MS. The remaining product was then irradiated with near UV light
for 10 sec to cleave the fluorophore from the extended DNA product.
The resulting photocleavage product 15 was desalted and analyzed
using MALDI-TOF MS.
Discussion
It is shown here that an allyl moiety can be successfully used as a
blocking group for the 3'-OH of a photocleavable fluorescent
nucleotide analogue in SBS to prevent the DNA polymerase reaction
from continuing after the incorporation of the 3'-O-allyl modified
nucleotide analogue. Furthermore, it is demonstrated that the allyl
group can be efficiently removed to generate a free 3'-OH group and
allow the DNA polymerase reaction to continue to the subsequent
cycle.
Conventional methods for cleavage of the allyl group combine a
transition metal-catalyzed isomerization of the double bond to the
enol ether and subsequent hydrolysis of the latter to produce the
corresponding alcohol (26, 27). For application in SBS, it is
important to ensure that complete chemical cleavage of the
3'-O-allyl group can be rapidly and specifically carried out while
leaving the DNA intact. Trisodium triphenylphosphinetrisulfonate
(TPPTS) has been widely used as a ligand for Pd mediated
deallylation under aqueous conditions (28-30), while an active Pd
catalyst can be generated from Na2PdCl4 and an appropriate ligand
(31, 32). Thus, a water-soluble Pd catalyst system generated from
Na.sub.2PdCl.sub.4 and TPPTS was investigated for deallylation of
the 3'-O-allyl modified DNA product.
To evaluate the cleavage conditions of the allyl group capping the
3'-OH of DNA, first a 19-mer oligonucleotide
[5'-AGAGGATCCAACCGAGAC-T(allyl)-3'] (SEQ ID NO:3) was synthesized
using 3'-O-allyl-thymidine phosphoramidite (FIG. 3). The identity
of the purified oligonucleotide was established using MALDI-TOF
mass spectrometry. Then the above Na.sub.2PdCl.sub.4/TPPTS catalyst
system was tested for the deallylation of the oligonucleotide. In
FIG. 3A, the mass peak at m/z 5871 corresponds to the mass of the
purified oligonucleotide bearing the allyl group. FIG. 3B shows a
single mass peak at m/z 5831 indicating that near complete
deallylation was achieved with a DNA/Na.sub.2PdCl.sub.4/TPPTS ratio
of 1/55/440 in a reaction time of 30 seconds. The next step was to
prove that the above deallylated DNA product could be used as a
primer in a polymerase extension reaction. A single base extension
reaction was performed using the deallylated DNA product as a
primer, a synthetic template and a Biotin-11-ddGTP nucleotide
terminator which was complementary to the base immediately adjacent
to the priming site on the template. The DNA extension product was
isolated using solid phase capture purification and analyzed using
MALDI-TOF MS (25). The mass spectrum in FIG. 3C shows a clear peak
at m/z 6535 corresponding to the extension product indicating that
the deallylated product can be successfully used as a primer in a
polymerase reaction.
The above experiments established that Na.sub.2PdCl.sub.4 and TPPTS
could be used to efficiently carry out deallylation on DNA in an
aqueous environment. Our next step was to investigate if a
3'-O-allyl-modified nucleotide could be incorporated in a DNA
polymerase reaction. For this purpose, a nucleotide analogue
3'-O-allyl-thymidine triphosphate (3'-O-allyl-dTTP) was synthesized
which was tested with 15 different polymerases for incorporation.
The tested enzymes included Therminator, Thermo Sequenase, Vent
(exo-), Deep Vent (exo-), Tth, Tfl, Bat, Pfu (exo-), Klenow (exo-)
fragment and Sequenase DNA Polymerases, AMV, RAV2, M-MulV, HIV
reverse transcriptases and a 9.degree. N Polymerase (exo-) bearing
the mutations A485L and Y409V. Our preliminary results showed that
9.degree. N DNA polymerase (exo-) A485L/Y409V could efficiently
incorporate 3'-O-allyl-dTTP in an extension reaction, consistent
with results reported recently (31).
After confirming the incorporation ability of 3'-.beta.-allyl-dTTP
into a growing DNA strand by DNA polymerase, a new 3'-modified
photocleavable fluorescent nucleotide analogue was synthesized,
3'-O-allyl-dUTF-PC-Bodipy-FL-510, according to FIG. 2, and it was
established that the analogue can also can be efficiently
incorporated by the above polymerase. The aim was to evaluate that
the presence of the bulky photocleavable fluorescent moiety on the
base and the allyl group on the 3' end of the nucleotide analogue
would not affect the polymerase extension reaction. Furthermore,
demonstration of an entire cycle of primer extension was desirable,
photocleavage of the fluorophore, deallylation followed by
extension with another photocleavable fluorescent nucleotide
complementary to the next base on the template and photocleavage
once again. This experiment will thus test the feasibility of using
3'-O-allyl-dUTP-PC-Bodipy-FL-510 as a reversible terminator for
SBS.
The entire cycle of a polymerase reaction using
3'-O-allyl-dUTP-PC-Bodipy-FL-510 as a reversible terminator is
depicted in FIG. 5. The extension product 11 obtained using
3'-O-allyl-dUTP-PC-Bodipy-FL-510 and 9.degree. N DNA Polymerase
(exo-) A485L/Y409V was purified using HPLC and analyzed using
MALDI-TOF MS. The base in the template immediately adjacent to the
priming site was `A`. Thus, if 3'-O-allyl-dUTP-PC-Bodipy-FL-510 was
accepted by the polymerase as a terminator, the primer would extend
by one base and then the reaction would terminate. Our results
indicate that this was indeed the case. After confirming that the
extension reaction was successful, it was irradiated with near UV
light at 355 nm for 10 seconds to cleave the fluorophore from the
DNA, generating product 12. In an SBS system, this step would
ensure that there would be no carryover of the fluorescence signal
into the next incorporation cycle so as to prevent the generation
of ambiguous data at each step, as shown in the accompanying paper
(15). The photocleavage product 12 was then incubated with a
Na.sub.2PdCl.sub.4/TPPTS catalyst system at 70.degree. C. for 90
seconds to perform deallylation. The deallylated DNA product 13 was
purified by reverse phase HPLC and then used as a primer in a
second DNA extension reaction to prove that the regenerated 3'-OH
was capable of allowing the polymerase reaction to continue. For
the extension reaction, a photocleavable fluorescent nucleotide
dGTP-PC-Bodipy-FL-510 was used and Thermo Sequenase DNA polymerase.
The extension product 14 was irradiated as above, for 10 seconds to
generate photocleavage product 15 and hence complete an entire
reversible termination cycle.
After each step in the above cycle, a portion of the product was
purified and analyzed using MALDI-TOF MS to confirm its identity
and the successful completion of that step. Each product was
desalted using the Zip Tip desalting protocol to ensure the
generation of sharp and well-resolved data free from salt peaks.
The MALDI-TOF MS data for each step are shown in FIG. 5. FIG. 5A
shows the primer extension product 11 at m/z 6787 generated using
3'-O-allyl-dUTP-PC-Bodipy-FL-510. The peak at m/z 6292 corresponds
to the photocleavage product that was generated by the partial
photocleavage of the extension product due to the nitrogen laser
(.lamda..about.337 nm) used for ionization of the analyte in
MALDI-TOF MS. FIG. 5B shows the photocleavage result after the
10-second irradiation of the extension product at 355 nm. It can be
seen from the data that the peak at m/z 6787, corresponding to the
extension product has completely vanished and only a single peak
corresponding to 12 remains at m/z 6292, which proves that
photocleavage was efficiently achieved. FIG. 5C shows a similar
single peak at m/z 6252, which corresponds to the deallylated
photocleavage product 13. The absence of a significant peak at m/z
6292 proves that deallylation was completed with high efficiency.
FIG. 5D shows the MALDI-TOF MS data for the extension product
obtained using the above deallylated DNA product 13 as a primer and
nucleotide analogue dGTP-PC-Bodipy-FL-510. A dominant peak is seen
at m/z 7133 corresponding to the extension product 14. Finally,
FIG. 5E shows a clear peak at m/z 6637 corresponding to the
photocleavage product 15 and no significant peak at m/z 7133
indicating that complete photocleavage had occurred.
The results of the above experiments provide sufficient proof of
the feasibility of using the allyl group as a reversible capping
moiety for the 3'-OH of the photocleavable nucleotide analogues for
SBS. It is shown that a 3'-O-allyl modified nucleotide bearing a
photocleavable fluorophore is an excellent substrate for 9.degree.
N DNA polymerase A485L/Y409V and can be incorporated with high
efficiency in a polymerase extension reaction. It is also
demonstrated that complete photocleavage is achieved in .about.10
seconds on these DNA products. Furthermore, it is shown that
deallylation can be swiftly achieved to near completion under mild
reaction conditions in an aqueous environment using a palladium
catalyst. Finally, it is have established that the deallylated DNA
product can be used as a primer to continue the polymerase reaction
and that extension and photocleavage can be performed with high
efficiency. These findings confirm that an allyl moiety protecting
the 3'-OH group indeed bestows the capability of reversible
terminating abilities to photocleavable nucleotide analogues, which
can be used for SBS. Further efforts are being focused on
generating four nucleotide analogues (A, C, G and T), each with a
distinct photocleavable fluorophore and with a 3'-O-allyl capping
group. These nucleotides will facilitate the development of SBS for
high-throughput DNA sequencing and genotyping applications.
Example 2
Synopsis
DNA sequencing by synthesis (SBS) using reversible fluorescent
nucleotide terminators is a potentially efficient approach to
address the limitations of current DNA sequencing techniques. Here,
the design and synthesis of a complete set of four-color 3'-O-allyl
modified photocleavable fluorescent nucleotides as reversible
terminators for SBS is described. The nucleotides are efficiently
incorporated by DNA polymerase into a growing DNA strand to
terminate the polymerase reaction. After that the fluorophore is
photocleaved quantitatively by irradiation at 355 nm, and the allyl
group is rapidly and efficiently removed by using a Pd-catalyzed
reaction under DNA compatible conditions to regenerate a free 3'-OH
group to reinitiate the polymerase reaction. A homopolymeric region
of a DNA template was successfully sequenced using these 3'-O-allyl
modified nucleotide analogues, facilitating the development of SBS
as a viable approach for high-throughput DNA sequencing
Introduction
The design and synthesis of a complete set of four-color 3'-O-allyl
modified photocleavable fluorescent nucleotides,
3'-O-allyl-dGTP-PC-Bodipy-FL-510, 3'-O-allyl-dCTP-PC-Bodipy-650,
3'-O-allyl-dUTP-PC-R6G and 3'-O-allyl-dATP-PC-ROX, is disclosed
here, as shown in FIG. 6. Their applications as reversible
terminators for SBS are also described here, demonstrating the
base-specific incorporation of these nucleotide analogues by DNA
polymerase, the highly efficient photocleavage of the fluorescent
dye, and the rapid and complete removal of 3'-O-allyl group in a
Pd-catalyzed reaction under DNA compatible conditions. Previously,
the Pd-catalyzed deallylation to regenerate a free 3'-OH of the DNA
extension product was carried out in pure water (34) which can
destabilize the primer-template duplex. A new condition for rapid
quantitative deallylation in a buffer solution at pH 8.8 has been
identified here, which is commonly used in a polymerase reaction.
The successful synthesis of these 3'-O-allyl modified
photocleavable fluorescent nucleotides as reversible terminators to
sequence through a homopolymer sequence, and the identification of
the new deallylation condition will facilitate the development of
SOS as a viable approach for de novo DNA sequencing.
As an example, 3'-O-allyl-dGTP-PC-Bodipy-FL-510 (10) is used here
to illustrate the detailed synthesis strategy and procedures. To
the applicants' knowledge, using 3'-modified dGTP as a reversible
terminator for SBS has not been reported, partly due to the
difficulty of modifying 3'-OH of guanosine by a suitable capping
group without protecting the guanine base. Structure 10 was
prepared following a synthesis route as shown in FIG. 7.
2-amino-4-methoxy-7-(.beta.-D-2-deoxyribofuranosyl)pyrrolo[2,3-d]-pyrimid-
ine 1 was chosen as the starting material for the synthesis of
3'-O-allyl-dGTP 9 (FIG. 7) (see (35)). Structure 1 was first
protected by isobutyryl chloride to form 2 quantitatively (4).
Structure 2 was iodinized with NIS to afford a single iodo product
3 in 84% yield, as the protected 2-amino group in the heterocyclic
ring promotes the formation of 7-substituted product (5). Structure
3 was deprotected to afford 4 in 91% yield by sodium methoxide. The
5'-OH of 4 was protected by tert-butyldimethylsilyl chloride to
yield 5 in 88% yield (6). The 3'-OH of 5 was subsequently allylated
in CH.sub.2Cl.sub.2 and 40% aqueous NaOH solution using
tetrabutylammonium bromide as phase-transfer catalyst to give a 92%
yield of 6 without 2-N-allylated product. Cross-coupling reaction
of 6 with the terminal alkyne catalyzed by Pd(0)/Cu(I) formed 7 in
94% yield (7). Next, a one-pot procedure of demethylation (8) and
desilylation of 7 gave a moderate 34% yield of 8. Finally structure
8 was transformed into the corresponding triphosphate 9 following
established procedures (9). Coupling 9 with PC-Bodipy-FL-510 NHS
ester (2) yielded the target compound,
3'-O-allyl-dGTP-PC-Bodipy-FL-510, structure 10.
3'-O-allyl-dATP-PC-ROX 19 was also prepared, as were
3'-O-allyl-dCTP-PC-Bodipy-650 26 and 3'-O-allyl-dUTP-PC-R6G 33, as
shown in FIGS. 8, 9, and 10, respectively.
For 3'-O-allyl modified PC fluorescent nucleotides to act as
reversible terminators for SBS, it is important to establish that
they can be used to determine a repeated DNA sequence in a
polymerase reaction. To this end, polymerase DNA extension
reactions were performed using these nucleotides as substrates in
solution. This allows the isolation of the DNA product at each step
of SBS for detailed molecular structure characterization by using
MALDI-TOF mass spectrometry (MS).
3'-O-allyl-dGTP-PC-Bodipy-FL-510 (structure 10) was used as a
substrate in a DNA extension reaction as shown in FIG. 11. A
synthetic 100-mer DNA corresponding to a portion of exon 7 of the
human p53 gene was used as a template to perform the extension. The
sequence in the template immediately adjacent to the annealing site
of the primer had a repeating sequence of 3'-CC-5'. First, a
polymerase extension reaction using 10 as a terminator along with a
primer and the above template was performed. After the reaction, a
small portion of the DNA extension product was characterized by
MALDI-TOF MS. The rest of the product was irradiated at 355 nm for
10 sec to cleave the fluorophore from the DNA and then analyzed by
MALDI-TOF MS. After photocleavage, the DNA product was added to a
deallylation cocktail [1.times. Thermopol reaction
buffer/Na.sub.2PdCl.sub.4/--P(PhSO.sub.3Na).sub.3] to remove the
3'-Allyl group in 30 sec to yield quantitatively deallylated DNA
product. The deallylated DNA product with a free 3'-OH group
regenerated was then used as a primer to incorporate 10 in a
subsequent second polymerase extension reaction.
FIG. 12 (right panel) shows sequential mass spectrum at each step
of DNA sequencing by synthesis using 10 as a reversible terminator.
As can be seen from FIG. 12, panel (A), the MALDI-TOF MS spectrum
consists of a distinct peak at m/z 7,052 corresponding to the
single base DNA extension product 34 with 100% incorporation
efficiency, confirming that the reversible terminator can be
incorporated base-specifically by DNA polymerase into a growing DNA
strand. The small peak at m/z 6,556 corresponding to the
photocleavage product is due to the partial cleavage caused by the
nitrogen laser pulse (337 nm) used in MALDI ionization. FIG. 12,
panel (B) shows the photocleavage result after 10 sec irradiation
of the DNA extension product at 355 nm. The peak at m/z 7,052 has
completely disappeared, whereas the peak corresponding to the
photocleavage product 35 appears as the sole dominant peak at m/z
6,556. FIG. 12, panel (C) shows a single peak at m/z 6,516, which
corresponds to a deallylated photocleavage product 36. The absence
of a peak at m/z 6,556 proves that the deallylation reaction was
completed with high efficiency. The next extension reaction was
carried out by using this deallylated photocleavage product 36 as a
primer along with 3'-O-allyl-dGTP-PC-Bodipy-FL-510 (10) to yield an
extension product 37 (FIG. 12, panel D). DNA products (38 and 39)
from photocleavage (FIG. 12, panel E) and deallylation (FIG. 12,
panel F) respectively were obtained in similar manner as described
previously, thereby completing two entire polymerase extension
cycles to sequence a homopolymeric region of a template using 10 as
a reversible terminator.
3'-O-allyl-dATP-PC-ROX 19, mixed together with
3'-D-allyl-dGTP-PC-Bodipy-FL-510 10/3'-O-allyl-dCTP-PC-Bodipy-650
26/3'-O-allyl-dUTP-PC-R6G 33, was used as a reversible terminator
in a primer extension reaction as shown in FIG. 13 (left panel).
After the incorporation, photocleavage and deallylation reactions
were performed on the DNA extension product, following a similar
procedure as for 10. FIG. 13 (right panel, A) shows the MOLDI-TOF
MS results for the characterization of the product from each step.
In the extension reaction, all four 3'-O-allyl modified
photocleavable fluorescent nucleotides were added simultaneously
instead of using only the correct one. The MS showed that only
3'-.beta.-allyl-dATP-PC-ROX 19, the one complementary with the
template sequence, was successfully incorporated in this extension
reaction, as demonstrated by the single major peak at m/z 7,228 and
a partial photocleavage peak at m/z 6,495. There is no other DNA
extension product observed, indicating a faithful incorporation of
the 3'-O-allyl modified nucleotide. The MS results also
demonstrated that the photocleavage and deallylation steps were
successfully conducted as shown in FIG. 13 (right panel, B and C)
with peaks at m/z 6,495 and 6,455.
3'-O-allyl-dCTP-PC-Bodipy-650 26, mixed together with
3'-O-allyl-dGTP-PC-Bodipy-FL-510 10/3'-O-allyl-dATP-PC-ROX
19/3'-O-allyl-dUTP-PC-R6G 33, was used in a primer extension
reaction and then photocleavage and deallyation reactions were
performed on the DNA extension product, as shown in FIG. 14 (left
panel). FIG. 14 (right panel, A) shows the successful incorporation
of 26, among the four nucleotide analogues, by the DNA polymerase
to generate a single DNA extension product 43 at m/z 8,532.
Subsequently, photocleavage was conducted to generate a
photocleavage product 44 at m/z 7,762, and deallyation product 45
was observed at m/z 7,722, as shown in FIG. 14 (right panel, B and
C), respectively.
Similarly, 3'-O-allyl-dUTP-PC-R6G 33, mixed together with
3'-O-allyl-dGTP-PC-Bodipy-FL-510 10/3'-O-allyl-dATP-PC-ROX
19/3'-O-allyl-dCTP-PC-Bodipy-650 26, also showed successful
incorporation by a DNA polymerase in a primer extension reaction,
as indicated by the single extension product (46) peak at m/z 6,210
in MALDI-TOF MS spectrum in FIG. 15 (right panel, A). The
fluorescent dye was then photocleaved to generate a photocleavage
product 47 at m/z 5,552, and 3'-O-allyl was removed in a
Pd-catalyzed reaction to generate a deallylated product 48 at m/z
5,512, as shown in FIG. 15 (right panel, B and C),
respectively.
Material and Methods
General Information .sup.1H NMR spectra were recorded on Brucker
DPX-400 (400 MHz) and Brucker DPX-300 spectrometers and are
reported in ppm from CD.sub.3OD or DMSO-d6 internal standard (3.31
or 2.50 ppm respectively). Data are reported as follows:
(s=singlet, d=doublet, t=triplet, q=quartet, m=multiplet,
dd=doublet of doublets, ddd=doublet of doublets of doublets;
coupling constant(s) in Hz; integration; assignment). Proton
decoupled .sup.13C NMR spectra were recorded on a Brucker DPX-400
(100 MHz) spectrometer and are reported in ppm from CD.sub.3OD,
DMSO-d6, or CDCl.sub.3 internal standard (49.0, 39.5, or 77.0 ppm
respectively). Proton decoupled .sup.31P NMR spectra were recorded
on a Brucker DPX-300 (121.4 MHz) spectrometer without calibration.
High Resolution Mass Spectra (HRMS) were obtained on a JEOL JMS HX
110A mass spectrometer. Mass measurement of DNA was made on a
Voyager DE MALDI-TOF mass spectrometer (Applied Biosystems).
Photolysis was performed by using a Spectra Physics GCR-150-30
Nd-yttrium/aluminum garnet laser that generates light pulses at 355
nm. Compounds 1 and 11 were purchased from Berry & Associates
(Dexter, Mich.). Bodipy-FL-510 NHS ester, ROX NHS ester, Bodipy-650
NHS ester and R6G NHS ester were purchased from Invitrogen
(Carlsbad, Calif.). All other chemicals were purchased from
Sigma-Aldrich. 9.degree. N polymerase (exo-) A485L/Y409V was
generously provided by New England Biolabs.
I. Synthesis of 3'-O-allyl Modified Photocleavable Fluorescent
Nucleotides.
1) Synthesis of 3'-O-allyl-dGTP-PC-Bodipy-FL-510 as shown in FIG.
7.
2-(2-Methylpropanoyl)amino-7-[3',5'-bis-O-(2-methylpropanoyl)-.beta.-D-2'-
-deoxyribofuranosyl]-4-methoxypyrrolo[2,3-d]pyrimidine (2): To a
stirred suspension of 1 (1.00 g; 3.57 mmol) in anhydrous pyridine
(35 mL) was added slowly isobutyryl chloride (3.40 mL; 32.2 mmol)
at 0.degree. C. The reaction mixture was stirred at 0.degree. C.
for 1 h. Methanol (2 mL) was then added and the reaction mixture
was stirred for another 10 min. Then most solvent was removed under
vacuum. Ethyl acetate (200 mL) and saturated aqueous NaHCO.sub.3
(50 mL) were added to the residue. The organic layer was separated
and washed by saturated aqueous NaHCO.sub.3 and NaCl respectively,
and dried over anhydrous Na.sub.2SO.sub.4. After evaporation of the
solvent, the residue was purified by flash column chromatography
over silica gel using ethyl acetate-hexane (1:3.about.2) as the
eluent to afford 2 as white foam (1.75 g; 99% yield): .sup.1H NMR
(400 MHz, CD.sub.3OD) .delta. 7.28 (d, J=3.7 Hz, 1H, 6-H), 6.66
(dd, J=5.9, 8.6 Hz, 1H, 1'-H), 6.51 (d, J=3.7 Hz, 1H, 5-H), 5.41
(m, 1H, 3'-H), 4.33-4.36 (m, 2H, 5'-H), 4.22 (m, 1H, 4'-H), 4.08
(s, 3H, 4-OCH.sub.3), 2.83-2.96 (m, 2H, one of CH(CH.sub.3).sub.2
and one of 2'-H), 2.54-2.70 (m, 2H, two of CH(CH.sub.3).sub.2),
2.48-2.54 (ddd, J=2.0, 5.9, 14.2 Hz, one of 2'-H), 1.15-1.23 (m,
18H, CH(CH.sub.3).sub.2); .sup.13C NMR (100 MHz, CD.sub.3OD)
.delta. 178.2, 177.7, 177.4, 164.2, 153.4, 152.5, 123.4, 103.5,
100.7, 85.2, 83.0, 75.9, 65.0, 54.4, 37.9, 36.6, 35.0, 34.9, 19.9
(two CH.sub.3), 19.3-19.4 (four peaks for four CH.sub.3); HRMS
(FAB+) calcd for C.sub.24H.sub.35O.sub.7N.sub.4 (M+H.sup.+):
491.2506. found: 491.2503.
2-(2-Methylpropenoyl)amino-7-[3',5'-bis-O-(2-methylpropanoyl)-.beta.-D-2'-
-deoxyribo-furanosyl]-5-iodo-4-methoxypyrrolo[2,3-d]pyrimidine (3):
To a vigorously stirred solution of 2 (1.75 g; 3.57 mmol) in
anhydrous DMF (27 mL) was added 95% N-iodosuccimide (NIS) (866 mg;
3.66 mmol). The reaction mixture was stirred at room temperature
for 22 h, and then most solvent was removed under vacuum. Diethyl
ether (200 mL) and saturated aqueous NaHCO.sub.3 (50 mL) were
added. The organic layer was separated and washed by saturated
aqueous NaCl, and dried over anhydrous Na.sub.2SO.sub.4. After
evaporation of the solvent, the residue was purified by flash
column chromatography over silica gel using ethyl acetate-hexane
(1:3) as the eluent to afford 3 as white solid (1.98 g; 90% yield):
.sup.1H NMR (400 MHz, CD.sub.3OD) .delta. 7.43 (s, 1H, 6-H), 6.63
(dd, J 6.0, 8.2 Hz, 1H, 1'-H), 5.41 (m, 1H, 3'-H), 4.33-4.36 (m,
2H, 5'-H), 4.23 (m, 1H, 4'-H), 4.09 (s, 3H, 4-OCH.sub.3), 2.78-2.94
(m, 2H, one of CH(CH.sub.3).sub.2 and one of 2'-H), 2.57-2.70 (m,
2H, two of CH(CH.sub.3).sub.2), 2.50-2.57 (ddd, J=2.3, 6.0, 14.2
Hz, one of 2'-H), 1.17-1.24 (m, 18H, CH(CH.sub.3).sub.2); .sup.13C
NMR (100 MHz, CD.sub.3OD) .delta. 178.3, 177.8, 177.5, 164.3,
153.3, 152.8, 128.6, 105.2, 85.3, 83.3, 75.8, 65.0, 54.4, 51.8,
38.2, 36.8, 35.2, 35.1, 19.9 (two CH.sub.3), 19.3-19.5 (four peaks
for four CH.sub.3); HRMS (FAB+) calcd for
C.sub.24H.sub.34O.sub.7N.sub.4I (M+H.sup.+): 617.1472. found:
617.1464.
2-Amino-7-(.beta.-D-2'-deoxyribofuranosyl)-5-iodo-4-methoxypyrrolo[2,3-d]-
pyrimidine (4): 3 (1.98 g; 3.21 mmol) was dissolved in 0.5 M
methanolic CH.sub.3ONa (50 mL) and stirred at 65.degree. C. for 12
h. Saturated aqueous NaHCO.sub.3 (20 mL) was added and the mixture
was stirred for 10 min. Then most of methanol was evaporated and
the residue was extracted by ethyl acetate (150 mL). The organic
layer was washed by saturated aqueous NaHCO.sub.3 and Had
respectively, and dried over anhydrous Na.sub.2SO.sub.4. After
evaporation of the solvent, the residue was purified by flash
column chromatography over silica gel using
CH.sub.3OH--CH.sub.2Cl.sub.2 (1:30-15) as the eluent to afford 4 as
white solid (1.23 g; 94% yield): .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 7.17 (s, 1H, 6-H), 6.36 (dd, J=6.0, 8.4 Hz, 1H, 1'-H), 4.47
(m, 1H, 3'-H), 3.99 (s, 3H, 4-OCH.sub.3), 3.96 (m, 1H, 4'-H), 3.77
(dd, J=3.4, 12.0 Hz, 1H, one of 5'-H), 3.70 (dd, J=3.7, 12.0 Hz,
1H, one of 5'-H), 2.55-2.64 (ddd, J=6.0, 8.4, 13.4 Hz, one of
2'-H), 2.20-2.26 (ddd, J=2.4, 5.9, 13.4 Hz, one of 2'-H); .sup.13C
NMR (100 MHz, CD.sub.3OD) .delta. 164.7, 160.6, 154.3, 126.5,
101.6, 88.7, 86.0, 73.0, 63.7, 53.7, 51.3, 41.1; HRMS (FAB+) calcd
for C.sub.12H.sub.16O.sub.4O.sub.4N.sub.4I (M+H.sup.+): 407.0216.
found: 407.0213.
2-Amino-7-[.beta.-D-5'-O-(tert-butyldimethylsilyl)-2'-deoxyribofuranosyl]-
-5-iodo-4-methoxypyrrolo[2,3-d]pyrimidine (5): To a stirred
solution of 4 (1.23 g; 3.02 mmol) and imidazole (494 mg; 7.24 mmol)
in anhydrous DMF (15 mL) was added tert-butyldimethylsilyl chloride
(TBDMSCl) (545 mg; 3.51 mmol). The reaction mixture was stirred at
room temperature for 20 h. Then most solvent was removed under
vacuum, and the residue was purified by flash column chromatography
over silica gel using ethyl acetate-hexane (1:2.about.0.5) as the
eluent to afford 5 as white foam (1.38 g; 88% yield): .sup.1H NMR
(400 MHz, CD.sub.3OD) .delta. 7.23 (s, 1H, 6-H), 6.49 (dd, J=6.1,
7.7 Hz, 1H, 1'-H), 4.46 (m, 1H, 3'-H), 3.99 (s, 3H, 4-OCH.sub.3),
3.94 (m, 1H, 4'-H), 3.79-3.87 (m, 2H, 5'-H), 2.36-2.44 (ddd, J=5.8,
7.7, 13.3 Hz, one of 2'-H), 2.24-2.31 (ddd, J=3.1, 6.0, 13.3 Hz,
one of 2'-H), 0.96 (s, 9H, C(CH.sub.3).sub.3), 0.14 (s, 3H, one of
SiCH.sub.3), 0.13 (s, 3H, one of SiCH.sub.3); .sup.13C NMR (100
MHz, CD.sub.3OD) .delta. 164.6, 160.7, 154.7, 125.1, 101.0, 88.2,
84.2, 72.7, 64.7, 53.7, 51.7, 41.9, 26.7, 19.4, -5.0, -5.1; HRMS
(FAB+) calcd for C.sub.18H.sub.30O.sub.4N.sub.4SiI (M+H.sup.+):
521.1081. found: 521.1068.
7-[.beta.-D-3'-O-Allyl-5'-O-(tert-butyldimethylsilyl)-2'-deoxyribofuranos-
yl]-2-amino-5-iodo-4-methoxypyrrolo[2,3-d]pyrimidine (6): To a
stirred solution of 5 (1.38 g; 2.66 mmol) in CH.sub.2Cl.sub.2 (80
mL) were added tetrabutylammonium bromide (TBAB) (437 mg; 1.33
mmol), allyl bromide (1.85 mL, 21.4 mmol) and 40% aqueous NaOH
solution (40 mL). The reaction mixture was stirred at room
temperature for 1 h. Ethyl acetate (200 mL) was added and the
organic layer was separated. The aqueous layer was extracted with
ethyl acetate (2.times.50 mL). The combined organic layer was
washed by saturated aqueous NaHCO.sub.3 and NaCl respectively, and
dried over anhydrous Na.sub.2SO.sub.4. After evaporation of the
solvent, the residue was purified by flash column chromatography
over silica gel using ethyl acetate-hexane (1:3) as the eluent to
afford 6 as white solid (1.37 g; 92% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 7.20 (s, 1H, 6-H), 6.43 (dd, J=6.2, 7.9 Hz, 1H,
1'-H), 5.89-5.99 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.29-5.35 (dm,
J=17.3 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm,
J=10.5 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.24 (m, 1H, 3'-H),
4.01-4.11 (m, 3H, 4'-H and CH.sub.2CH.dbd.CH.sub.2), 3.99 (s, 3H,
4-OCH.sub.3), 3.76-3.84 (m, 2H, 5'-H), 2.32-2.44 (m, 2H, 2'-H),
0.95 (s, 9H, C(CH.sub.3).sub.3), 0.14 (s, 3H, one of SiCH.sub.3),
0.13 (s, 3H, one of SiCH.sub.3); .sup.13C NMR (100 MHz, CDCl.sub.3)
.delta. 163.3, 158.6, 153.6, 134.1, 123.7, 116.9, 100.6, 84.4,
83.0, 79.1, 70.0, 63.6, 53.3, 51.1, 38.1, 26.1, 18.5, -5.1, -5.3;
HRMS (FAS+) calcd for C.sub.21H.sub.34O.sub.4N.sub.4SiI
(M+H.sup.+): 561.1394. found: 561.1390.
7-[.beta.-D-3'-O-Allyl-5'-O-(tert-butyldimethylsilyl)-2'-deoxyribofuranos-
yl]-2-amino-5-[3-[(trifluoroacetyl)amino]-prop-1-ynyl]-4-methoxypyrrolo[2,-
3-d]pyrimidine (7): To a stirred solution of 6 (1.37 g; 2.45 mmol)
in anhydrous DMF (11 mL) were added
tetrakis(triphenylphosphine)palladium(0) (286 mg; 0.245 mmol) and
CuI (101 mg; 0.532 mmol). The solution was stirred at room
temperature for 10 min. Then N-propargyltrifluoroacetamide (1.12 g;
7.43 mmol) and triethylamine (0.68 mL; 4.90 mmol) were added. The
reaction was stirred at room temperature for 13 h with exclusion of
air and light. Most DMF was removed under vacuum and the residue
was dissolved in ethyl acetate (100 mL). The solution was washed by
saturated aqueous NaHCO.sub.3 and NaCl respectively, and dried over
anhydrous Na.sub.2SO.sub.4. After evaporation of the solvent, the
residue was purified by flash column chromatography over silica gel
using ethyl acetate-hexane (1:3.about.1.5) and
CH.sub.3OH--CH.sub.2Cl.sub.2 (1:30) respectively as the eluent to
afford 7 as yellow solid (1.34 g; 94% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 7.34 (s, 1H, 6-H), 6.42 (dd, J=6.2, 7.7 Hz, 1H,
1'-H), 5.88-5.99 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.28-5.35 (dm,
J=17.3 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm,
J=10.5 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.29 (s, 2H,
C.ident.CCH.sub.2), 4.24 (m, 1H, 3'-H), 4.00-4.09 (m, 3H, 4'-H and
CH.sub.2CH.dbd.CH.sub.2), 3.98 (s, 3H, 4-OCH.sub.3), 3.76-3.84 (m,
2H, 5'-H), 2.32-2.45 (m, 2H, 2'-H), 0.94 (s, 9H,
C(CH.sub.3).sub.3), 0.12 (s, 3H, one of SiCH.sub.3), 0.11 (s, 3H,
one of SiCH.sub.3); .sup.13C NMR (100 MHz, CD.sub.3OD) .delta.
165.0, 161.2, 158.1 (q, J=36 Hz, COCF.sub.3), 154.2, 135.6, 125.0,
117.2 (q, J=284 Hz, COCF.sub.3), 117.0, 99.2, 97.3, 86.0, 84.6,
84.5, 80.3, 78.0, 71.0, 64.8, 53.8, 39.0, 30.9, 26.5, 19.3, -5.1,
-5.2; HRMS (FAB+) calculated for
C.sub.26H.sub.37O.sub.5N.sub.5F.sub.3Si (M+H.sup.+): 584.2516.
found: 584.2491.
3'-O-Allyl-7-deaza-7-[3-[(trifluoroacetyl)amino]-prop-1-ynyl]-2'-deoxygua-
nosine (8): To a stirred solution of 7 (1.34 g; 2.30 mmol) in
anhydrous CH.sub.3CN (86 mL) were added NaI (363 mg; 2.42 mmol) and
chlorotrimethylsilane (TMSCl) (0.306 mL; 2.42 mmol). The reaction
was stirred at room temperature for 1 h and then at 50.degree. C.
for 12 h. The solvent was evaporated and the residue was dissolved
in anhydrous THF (76 mL). 1 tetrabutylammonium fluoride (TBAF) in
THF solution (4.80 mL; 4.80 mmol) was added and the reaction was
stirred at room temperature for 1 h. The solvent was evaporated and
the residue was dissolved in ethyl acetate (150 mL). The solution
was washed by saturated aqueous NaCl and dried over anhydrous
Na.sub.2SO.sub.4. After evaporation of the solvent, the residue was
purified by flash column chromatography over silica gel using
CH.sub.3OH-ethyl acetate (1:30) as the eluent to afford 8 as yellow
solid (356 mg; 34% yield): .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 7.21 (s, 1H, 6-H), 6.30 (dd, J=6.0, 8.4 Hz, 1H, 1'-H),
5.88-5.99 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.28-5.35 (dm, J=17.3
Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.15-5.20 (dm, J=10.5 Hz,
1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.29 (s, 2H,
C.ident.CCH.sub.2), 4.23 (m, 1H, 3'-H), 4.00-4.10 (m, 3H, 4'-H and
CH.sub.2CH.dbd.CH.sub.2), 3.65-3.75 (m, 2H, 5'-H), 2.41-2.49 (ddd,
J=5.8, 8.4, 13.6 Hz, 1H, one of 2'-H), 2.34-2.40 (ddd, J=2.3, 6.0,
13.6 Hz, 1H, one of 2'-H); .sup.13C NMR (100 MHz, CD.sub.3OD)
.delta. 160.9, 158.0 (q, J=36 Hz, COCF.sub.3), 154.1, 151.8, 135.6,
124.4, 117.2 (q, J=284 Hz, COCF.sub.3), 117.0, 101.4, 99.7, 86.4,
85.5, 84.8, 80.7, 78.0, 71.0, 63.7, 38.5, 31.2; HRMS (FAB+) calcd
for C.sub.19H.sub.21O.sub.5N.sub.5F.sub.3 (M+H.sup.+): 456.1495.
found: 456.1493.
3'-O-Allyl-7-deaza-7-(3-aminoprop-1-ynyl)-2'-deoxyguanosine-5'-triphospha-
te (9): The procedure is the same as that of preparing
3'-O-allyl-5-(3-aminoprop-1-ynyl)-2'-deoxyuridine-5'-triphosphate
in Ref. 34a to yield 9 as colorless syrup: .sup.1H NMR (300 MHz,
D.sub.2O) .delta. 7.56 (s, 1H, 6-H), 6.37 (t, J=7.3 Hz, 1H, 1'-H),
5.89-6.02 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.31-5.39 (dm, J=17.3
Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.21-5.28 (dm, J=10.5 Hz,
1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.49 (s, 2H,
C.ident.CCH.sub.2), 4.32 (m, 1H, 3'-H), 4.06-4.18 (m, 3H, 4'-H and
CH.sub.2CH.dbd.CH.sub.2), 3.92-3.99 (m, 2H, 5'-H), 2.44-2.60 (m,
2H, 2'-H); .sup.31P NMR (121.4 MHz, D.sub.2O) .delta. -6.1 (d,
J=20.8 Hz, 1P, .gamma.-P), -10.8 (d, J=18.9 Hz, 1P, .alpha.-P),
-21.9 (t, J=19.8 Hz, 1P, .beta.-P).
3'-O-Allyl-dGTP-PC-Bodipy-FL-510 (10): PC-Bodipy-FL-510 NHS ester
(prepared by the same procedure in Ref. 34a) (7.2 mg, 12 .mu.mol)
in 300 .mu.l, of acetonitrile was added to a solution of 9 (2 mg,
3.4 .mu.mol) in 300 .mu.L of Na.sub.2CO.sub.3--NaHCO.sub.3 aqueous
buffer (0.1 M, pH 8.5). The reaction mixture was stirred at room
temperature for 3 h. A preparative silica-gel TLC plate was used to
separate the unreacted PC-Bodipy-FL-510 NHS ester from the fraction
containing 10 with CHCl.sub.3--CH.sub.3OH (85:15) as the eluent.
The product was concentrated further under vacuum and purified with
reverse-phase HPLC on a 150.times.4.6-mm C18 column to obtain the
pure product 10 (retention time of 34 min). Mobile phase: A, 8.6 mM
triethylamine/100 mM hexafluoroisopropyl alcohol in water (pH 8.1);
B, methanol. Elution was performed with 100% A isocratic over 10
min, followed by a linear gradient of 0-50% B for 20 min and then
50% .beta. isocratic over another 20 min.
3'-O-allyl-dGTP-PC-Bodipy-FL-510 10 was characterized by primer
extension reaction and MALDI-TOF MS.
2) Synthesis of 3'-O-Allyl-dATP-PC-ROX as shown in FIG. 8.
4-Chloro-5-iodopyrrolo[2,3-d]pyrimidine (12): To a vigorously
stirred solution of 11 (1.0 g; 6.51 mmol) in CH.sub.2Cl.sub.2 (55
mL) was added 95% N-iodosuccimide (1.70 g; 7.18 mmol). The reaction
mixture was stirred at room temperature for 1 h, during which time
more precipitate appeared. The solid was filtered and
recrystallized in hot methanol to afford 12 as slightly grey
crystals, (1.49 g; 82% yield): .sup.1H NMR (400 MHz, DMSO-d6)
.delta. 12.96 (s br, 1H, NH), 8.59 (s, 1H, 2-H), 7.94 (s, 1H, 6-H);
.sup.13C NMR (100 MHz, DMSO-d6) .delta. 151.2, 150.4, 150.2, 133.6,
115.5, 51.7; HRMS (FAB+) calcd for C.sub.6H.sub.4N.sub.3ClI
(M+H.sup.+): 279.9139. found: 279.9141.
4-Chloro-7-O-D-2'-deoxyribofuranoeyl)-5-iodopyrrolo[2,3-d]pyrimidine
(13): To a stirred solution of 12 (597 mg; 2.14 mmol) in CH.sub.3CN
(36 mL) were added KOH powder (0.30 g; 5.36 mmol) and
tris[2-(2-methoxyethoxy)ethyl]amine (44 .mu.L, 0.14 mmol). The
mixture was stirred at room temperature for 10 min and then 90%
3,5-di-O-(p-toluoyl)-2-deoxy-D-ribofuranosyl chloride (1.00 g; 2.31
mmol) was added. The reaction was stirred vigorously at room
temperature for 1 h, and the insoluble material was filtered and
washed by hot acetone. The combined solution was evaporated and
dissolved in 7M methanolic ammonia (72 mL). The solution was
stirred at room temperature for 24 h. After evaporation of the
solvent, the residue was purified by flash column chromatography
over silica gel using CH.sub.3OH--CH.sub.2Cl.sub.2 (0.about.1:20)
as the eluent to afford 13 as white solid (711 mg; 84% yield):
.sup.1H NMR (400 MHz, CD.sub.3OD) .delta. 8.57 (s, 1H, 2-H), 8.08
(s, 1H, 6-H), 6.72 (dd, J=6.3, 7.5 Hz, 1H, 1'-H), 4.53 (m, 1H,
3'-H), 4.00 (m, 1H, 4'-H), 3.80 (dd, J=3.6, 12.0 Hz, 1H, one of
5'-H), 3.74 (dd, J=3.6, 12.0 Hz, 1H, one of 5'-H), 2.56-2.64 (ddd,
J=6.1, 7.5, 13.5 Hz, 1H, one of 2'-H), 2.36-2.43 (ddd, J=3.3, 6.2,
13.5 Hz, 1H, one of 2'-H); .sup.13C NMR (100 MHz, CD.sub.3OD)
.delta. 152.9, 151.7, 151.3, 134.7, 118.5, 89.0, 85.7, 72.6, 63.2,
52.6, 41.7; HRMS (FAB+) calcd for C.sub.11H.sub.12O.sub.3N.sub.3ClI
(M+H.sup.+): 395.9612. found: 395.9607.
7-[.beta.-D-5'-O-(tart-Butyldimethylsilyl)-2'-deoxyribofuranosyl]-4-chlor-
o-5-iodopyrro-lo[2,3-d]pyrimidine (14): The procedure is the same
as that of and the crude was purified by flash column
chromatography over silica gel using ethyl acetate-hexane
(1:3.about.2) as the eluent to afford 14 as white solid (65% yield)
and 30% of the starting material 13: .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 8.56 (s, 1H, 2-H), 7.99 (s, 1H, 6-H), 6.73 (t,
J=6.7 Hz, 1H, 1'-H), 4.52 (m, 1H, 3'-H), 4.02 (m, 1H, 4'-H), 3.92
(dd, J=3.0, 11.4 Hz, 1H, one of 5'-H), 3.86 (dd, J=3.1, 11.4 Hz,
1H, one of 5'-H), 2.47-2.55 (ddd, J=5.8, 7.1, 13.4 Hz, 1H, one of
2'-H), 2.40-2.47 (ddd, J=3.6, 6.3, 13.4 Hz, 1H, one of 2'-H), 0.94
(s, 9H, C(CH.sub.3).sub.3), 0.14 (s, 3H, one of SiCH.sub.3), 0.13
(s, 3H, one of SiCH.sub.3); .sup.13C NMR (100 MHz, CD.sub.3OD)
.delta. 152.8, 151.5, 151.3, 133.8, 118.2, 88.9, 85.4, 72.5, 64.6,
52.6, 42.4, 26.7, 19.5, -4.9, -5.0; HRMS (FAB+) calcd for
C.sub.17H.sub.26O.sub.3N.sub.3ClSiI (M+H.sup.+): 510.0477. found:
510.0487.
7-[.beta.-D-3'-O-Allyl-5'-O-(tert-butyldimethylsilyl)-2'-deoxyribofuranos-
yl]-4-chloro-5-iodopyrrolo[2,3-d]pyrimidine (15): The procedure is
the same as that of 6 and the crude was purified by flash column
chromatography over silica gel using ethyl acetate-hexane (1:6) as
the eluent to afford 15 as yellow oil (752 mg; 95% yield): .sup.1H
NMR (400 MHz, CD.sub.3OD) .delta. 8.52 (s, 1H, 2-H), 7.94 (s, 1H,
6-H), 6.64 (dd, J=6.1, 7.6 Hz, 1H, 1'-H), 5.88-5.99 (m, 1H,
CH.sub.2CH.dbd.CH.sub.2), 5.28-5.34 (dm, J=17.3 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm, J=10.4 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 4.28 (m, 1H, 3'-H), 4.13 (m, 1H, 4'-H),
4.01-4.11 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.88 (dd, J=3.6, 11.2
Hz, 1H, one of 5'-H), 3.80 (dd, J=3.1, 11.3 Hz, 1H, one of 5'-H),
2.51-2.57 (ddd, J=2.7, 6.0, 13.5 Hz, 1H, one of 2'-H), 2.42-2.50
(ddd, J=5.7, 7.7, 13.5 Hz, 1H, one of 2'-H), 0.93 (s, 9H,
C(CH.sub.3).sub.3), 0.13 (s, 3H, one of SiCH.sub.3), 0.12 (s, 3H,
one of SiCH.sub.3); .sup.13C NMR (100 MHz, CD.sub.3OD) .delta.
152.8, 151.4, 151.3, 135.5, 133.6, 118.2, 117.2, 86.5, 85.6, 80.2,
71.0, 64.8, 52.8, 39.7, 26.7, 19.4, -4.8, -5.0; HRMS (FAB+) calcd
for C.sub.20H.sub.30O.sub.3N.sub.3ClSiI (M+H.sup.+): 550.0790.
found: 550.0773.
3'-O-Allyl-7-deaza-7-iodo-2'-deoxyadenosine (16): To a stirred
solution of 15 (752 mg; 1.37 mmol) in anhydrous THF (32 mL) was
added 1 M THAF in THF solution (1.50 mL; 1.50 mmol) and the
reaction was stirred at room temperature for 1 h. The solvent was
evaporated and the residue was dissolved in 7 M methanolic ammonia
(22 mL). The solution was stirred in an autoclave at
115-120.degree. C. for 17 h. After evaporation of the solvent, the
residue was purified by flash column chromatography over silica gel
using CH.sub.3OH--CH.sub.2Cl.sub.2 (1:20) as the eluent to afford
16 as white solid (479 mg; 84% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 8.08 (s, 1H, 2-H), 7.56 (s, 1H, 6-H), 6.45 (dd,
J=5.8, 8.6 Hz, 1H, 1'-H), 5.90-6.00 (m, 1H,
CH.sub.2CH.dbd.CH.sub.2), 5.29-5.35 (dm, J=17.2 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm, J=10.5 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 4.28 (m, 1H, 3'-H), 4.12 (m, 1H, 4'-H),
4.02-4.12 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.78 (dd, J=3.7, 12.1
Hz, 1H, one of 5'-H), 3.70 (dd, J=3.6, 12.1 Hz, 1H, one of 5'-H),
2.53-2.61 (ddd, J 5.8, 8.6, 13.6 Hz, 1H, one of 2'-H), 2.41-2.47
(ddd, J=2.0, 5.8, 13.5 Hz, 1H, one of 2'-H); .sup.13C NMR (100 MHz,
CD.sub.3OD) .delta. 158.5, 152.3, 150.3, 135.7, 128.8, 117.0,
105.3, 86.8, 86.4, 80.7, 71.0, 63.7, 51.3, 38.8; HRMS (FAB+) calcd
for C.sub.24H.sub.18O.sub.3N.sub.4I (M+H.sup.+): 417.0424. found:
417.0438.
3'-O-Allyl-7-deaza-7-[3-[(trifluoroacetyl)amino]-prop-1-ynyl]-2'-deoxyade-
nosine (17): The procedure is the same as that of 7 and the crude
product was purified by flash column chromatography over silica gel
using ethyl acetate-hexane (1:1.about.0) as the eluent to afford 17
as yellow solid (455 mg; 90% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 8.08 (s, 1H, 2-H), 7.60 (s, 1H, 6-H), 6.41 (dd,
J=5.8, 8.6 Hz, 1H, 5.89-6.00 (m, 1H, CH.sub.2CH.dbd.CH.sub.2),
5.29-5.35 (dm, J=17.3 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2),
5.16-5.21 (dm, J=10.4 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.31
(s, 2H, C.ident.CCH.sub.2), 4.29 (m, 1H, 3'-H), 4.13 (m, 1H, 4'-H),
4.01-4.11 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.79 (dd, J=3.6, 12.1
Hz, 1H, one of 5'-H), 3.71 (dd, J=3.5, 12.1 Hz, 1H, one of 5'-H),
2.54-2.62 (ddd, J=5.8, 8.6, 13.6 Hz, 1H, one of 2'-H), 2.42-2.48
(ddd, J=1.9, 5.8, 13.6 Hz, 1H, one of 2'-H); .sup.13C NMR (100 MHz,
CD.sub.3OD) .delta. 158.8, 158.6 (q, J=38 Hz, COCF.sub.3), 152.9,
149.6, 135.6, 128.1, 117.1 (q, J=284 Hz, COCF.sub.3), 117.0, 104.5,
96.3, 87.3, 86.9, 86.8, 80.7, 77.0, 71.0, 63.8, 38.7, 31.1; HRMS
(FAB+) calcd for C.sub.19H.sub.21O.sub.4N.sub.5F.sub.3 (M+H.sup.+):
440.1546. found: 440.1544.
3'-O-Allyl-7-deaza-7-(3-aminoprop-1-ynyl)-2'-deoxyadenosine-5'-triphospha-
te (18): The procedure is the same as that of preparing 9 to yield
17 as colorless syrup: .sup.1H NMR (300 MHz, D.sub.2O) .delta. 8.02
(s, 1H, 2-H), 7.89 (s, 1H, 6-H), 6.54 (t, J=6.6 Hz, 1H, 1'-H),
5.89-6.02 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.30-5.39 (dm, J=17.3
Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.20-5.27 (dm, J=10.4 Hz,
1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.48 (s, 2H,
C.ident.CCH.sub.2), 4.35 (m, 1H, 3'-H), 4.05-4.17 (m, 4H,
CH.sub.2CH.dbd.CH.sub.2 and 5'-H), 3.99 (m, 1H, 4'-H), 2.50-2.59
(m, 2H, 2'-H); .sup.31P NMR (121.4 MHz, D.sub.2O) .delta. -6.1 (d,
J=21.1 Hz, 1P, .gamma.-P), -10.8 (d, J=18.8 Hz, 1P, .alpha.-P),
-21.9 (t, J=19.9 Hz, 1P, .beta.-P).
3'-O-allyl-dATP-ROX (19): The coupling reaction of 18 with
PC-ROX-NHS ester (Ref. 2b) afforded 19, following a similar
procedure as the preparation of 10. 3'-O-allyl-dATP-PC-ROX 19 was
characterized by the primer extension reaction and MALDI-TOF
MS.
3) Synthesis of 3'-O-Allyl-dCTP-PC-Bodipy-650 as shown in FIG.
9.
5'-O-(tert-Butyldimethylsilyl)-5-iodo-2'-deoxycytidine (21): The
procedure is the same as that of 5 and the crude product was
purified by flash column chromatography over silica gel using
CH.sub.3OH--CH.sub.2Cl.sub.2 (1:20) as the eluent to afford 21 as
white solid (1.18 g; 89% yield): .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 8.18 (s, 1H, 6-H), 6.17 (dd, J=5.8, 7.5 Hz, 1H, 1'-H), 4.34
(m, 1H, 3'-H), 4.04 (m, 1H, 4'-H), 3.93 (dd, J=2.5, 11.6 Hz, 1H,
one of 5'-H), 3.84 (dd, J=2.9, 11.6 Hz, 1H, one of 5'-H), 2.41-2.48
(ddd, J=2.5, 5.8, 13.5 Hz, 1H, one of 2'-H), 2.01-2.08 (ddd, J=5.9,
7.6, 13.5 Hz, 1H, one of 2'-H), 0.95 (s, 9H, C(CH.sub.3).sub.3),
0.17 (s, 3H, one of SiCH.sub.3), 0.16 (s, 3H, one of SiCH.sub.3);
.sup.13C NMR (100 MHz, CD.sub.3OD) .delta. 165.5, 156.8, 147.8,
89.4, 88.3, 72.8, 64.6, 57.1, 43.1, 26.7, 19.4, -4.8, -4.9; HRMS
(FAB+) calcd for C.sub.15H.sub.27O.sub.4N.sub.3SiI (M+H.sup.+):
468.0816. found: 468.0835.
3'-O-Allyl-5'-O-(text-butyldimethylsilyl)-5-iodo-2'-deoxycytidine
(22): To a stirred solution of 21 (1.18 g; 2.52 mmol) in anhydrous
THF (43 mL) was added 95% NaH powder (128 mg; 5.07 mmol). The
suspension was stirred at room temperature for 45 min. Allyl
bromide (240 .mu.L, 2.79 mmol) was then added at 0.degree. C. and
the reaction was stirred at room temperature for 14 h with
exclusion of moisture. Saturated aqueous NaHCO.sub.3 (10 mL) was
added at 0.degree. C. and stirred for 10 min. Most THF was
evaporated and the residue was dissolved in ethyl acetate (150 mL).
The solution was washed by saturated aqueous NaHCO.sub.3 and NaCl
respectively, and dried over anhydrous Na.sub.2SO.sub.4. After
evaporation of the solvent, the residue was purified by flash
column chromatography over silica gel using ethyl acetate as the
eluent to afford 22 as white solid (537 mg; 42% yield): .sup.1H NMR
(400 MHz, CD.sub.3OD) .delta. 8.15 (s, 1H, 6-H), 6.12 (dd, J 5.6,
8.0 Hz, 1H, 1'-H), 4.17 (m, 1H, 4'-H), 4.14 (m, 1H, 3'-H),
3.98-4.10 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.93 (dd, J 2.8, 11.5
Hz, 1H, one of 5'-H), 3.83 (dd, J=2.8, 11.5 Hz, 1H, one of 5'-H),
2.53-2.60 (ddd, J=1.7, 5.6, 13.6 Hz, 1H, one of 2'-H), 1.94-2.02
(ddd, J=5.9, 8.0, 13.6 Hz, 1H, one of 2'-H), 0.94 (s, 9H,
C(CH.sub.3).sub.3), 0.17 (s, 3H, one of SiCH.sub.3), 0.16 (s, 3H,
one of SiCH.sub.3); .sup.13C NMR (100 MHz, CD.sub.3OD) .delta.
165.4, 156.7, 147.7, 135.5, 117.2, 88.2, 87.0, 80.4, 70.9, 64.8,
57.3, 40.1, 26.7, 19.4, -4.7, -4.9; HRMS (FAB+) calcd for
C.sub.18H.sub.31O.sub.4N.sub.3SiI (M+H.sup.+): 508.1129. found:
508.1123.
3'-O-allyl-5-iodo-2'-deoxycytidine (23): To a stirred solution of
22 (537 mg; 1.06 mmol) in anhydrous THF (25 mL) was added 1 M TBAF
in THF solution (1.17 mL; 1.17 mmol) and the reaction was stirred
at room temperature for 1 h. The solvent was evaporated and the
residue was dissolved in ethyl acetate (100 mL). The solution was
washed by saturated aqueous NaCl and dried over anhydrous
Na.sub.2SO.sub.4. After evaporation of the solvent, the residue was
purified by flash column chromatography over silica gel using
CH.sub.3OH--CH.sub.3Cl.sub.2 (1:10) as the eluent to afford 23 as
white crystals (287 mg; 69% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 8.47 (s, 1H, 6-H), 6.15 (dd, J=6.2, 6.7 Hz, 1H,
1'-H), 5.87-5.98 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.26-5.33 (dm,
J=17.2 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.14-5.19 (dm,
J=10.5 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.18 (m, 1H, 3'-H),
4.08 (m, 1H, 4'-H), 3.98-4.10 (m, 2H, CH.sub.2CH.dbd.CH.sub.2),
3.82 (dd, J=3.2, 13.0 Hz, 1H, one of 5'-H), 3.72 (dd, J=3.3, 13.0
Hz, 1H, one of 5'-H), 2.44-2.51 (ddd, J=3.2, 6.0, 13.6 Hz, 1H, one
of 2'-H), 2.07-2.15 (m, 1H, one of 2'-H); .sup.13C NMR (100 MHz,
CD.sub.3OD) .delta. 165.4, 156.9, 148.8, 135.6, 117.0, 87.9, 86.9,
79.6, 71.2, 62.7, 57.2, 39.7; HAMS (FAB+) calcd for
C.sub.22H.sub.17O.sub.4N.sub.3I (M+H.sup.+): 394.0264. found:
394.0274.
3'-O-Allyl-5-[3-[(trifluoroacetyl)amino]-prop-1-ynyl]-2'-deoxycytidine
(24): The procedure is the same as that of 7 and the crude product
was purified by flash column chromatography over silica gel using
CH.sub.3OH--CH.sub.2Cl.sub.2 (0.about.1:10) as the eluent to afford
24 as yellow crystals (252 mg; 83% yield): .sup.1H NMR (400 MHz,
CD.sub.3OD) .delta. 8.31 (5, 1H, 6-H), 6.17 (dd, J=6.0, 7.3 Hz, 1H,
1'-H), 5.87-5.97 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.26-5.33 (dm,
J=17.3 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.15-5.19 (dm,
J=10.4 Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.31 (s, 2H,
C.ident.CCH.sub.2), 4.17 (m, 1H, 3'-H), 4.09 (m, 1H, 4'-H),
3.98-4.10 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.80 (dd, J=3.4, 12.0
Hz, 1H, one of 5'-H), 3.72 (dd, J=3.6, 12.0 Hz, 1H, one of 5'-H),
2.46-2.53 (ddd, J=2.9, 5.3, 13.6 Hz, 1H, one of 2'-H), 2.04-2.12
(m, 1H, one of 2'-H); .sup.13C NMR (100 MHz, CD.sub.3OD) .delta.
166.0, 158.4 (q, J=38 Hz, COCF.sub.3), 156.3, 145.8, 135.6, 117.1
(q, J=284 Hz, COCF.sub.3), 117.0, 91.9, 90.7, 88.0, 87.0, 79.8,
75.5, 71.2, 62.8, 39.6, 31.0; HRMS (FAB+) calcd for
C.sub.17H.sub.20O.sub.5N.sub.4F.sub.3 (M+H.sup.+): 417.1386. found:
417.1377.
3'-O-Allyl-5-(3-aminoprop-1-ynyl)-2'-deoxycytidine-5'-triphosphate
(25): The procedure is the same as that of preparing 9 to yield 25
as colorless syrup: .sup.1H NMR (300 MHz, D.sub.2O) .delta. 8.43
(s, 1H, 6-H), 6.21 (t, J=6.7 Hz, 1H, 1'-H), 5.85-6.00 (m, 1H,
CH.sub.2CH.dbd.CH.sub.2), 5.28-5.38 (dm, J=17.3 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 5.19-5.27 (dm, J=10.4 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 4.22-4.41 (m, 3H, 3'-H and
C.ident.CCH.sub.2), 4.05-4.18 (m, 3H, 4'-H and
CH.sub.2CH.dbd.CH.sub.2), 3.94-4.01 (m, 2H, 5'-H), 2.47-2.59 (m,
1H, one of 2'-H), 2.20-2.32 (m, 1H, one of 2'-H); .sup.31P NMR
(121.4 MHz, D.sub.2O) .delta. -7.1 (d, J=19.8 Hz, 1P, .gamma.-P),
-11.1 (d, J=19.1 Hz, 1P, .alpha.-P), -21.9 (t, J=19.5 Hz, 1P,
.beta.-P).
3'O-allyl-dCTP-PC-Bodipy-650 (26): The coupling reaction of 25 with
PC-Bodipy-650-NHS ester (Ref. 34b) afforded 26, following a similar
procedure as the preparation of 10. 3'-O-allyl-dCTP-PC-Bodipy-650
26 was characterized by the primer extension reaction and MALDI-TOF
MS.
4) Synthesis of 3'-O-allyl-dUTP-PC-R6G as shown in FIG. 10.
5'-O-(tert-butyldimethylsilyl)-5-iodo-2'-deoxyuridine (28): The
procedure is the same as that of 5 and the crude product was
purified by flash column chromatography over silica gel using
CH.sub.3OH--CH.sub.2Cl.sub.2 (1:20) as the eluent to afford 28 as
white solid (1.18 g; 89% yield): .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 8.17 (s, 1H, 6-H), 6.21 (dd, J=5.9, 7.9 Hz, 1H, 1'-H), 4.36
(m, 1H, 3'-H), 4.02 (m, 1H, 4'-H), 3.93 (dd, J=2.4, 11.5 Hz, 1H,
one of 5'-H), 3.85 (dd, J=2.9, 11.5 Hz, 1H, one of 5'-H), 2.30-2.37
(ddd, J=2.3, 5.8, 13.4 Hz, 1H, one of 2'-H), 2.08-2.15 (ddd, J=5.9,
7.9, 13.4 Hz, 1H, one of 2'-H), 0.96 (s, 9H, C(CH.sub.3).sub.3),
0.19 (s, 3H, one of SiCH.sub.3), 0.17 (s, 3H, one of SiCH.sub.3).
.sup.13C NMR (100 MHz, CD.sub.3OD) .delta. 162.4, 151.5, 145.8,
89.3, 87.2, 72.8, 68.7, 64.6, 42.3, 26.8, 19.5, -4.8, -4.9. HRMS
(FAB+) Calcd for C.sub.15H.sub.26O.sub.5N.sub.2SiI (M+H.sup.+):
469.0656. found: 469.0672.
3'-O-allyl-5'-O-(tert-butyldimethylsilyl)-5-iodo-2'-deoxyuridine
(29): The procedure is the same as that of 22 and the crude product
was purified by flash column chromatography over silica gel using
ethyl acetate-hexane (1:2.5) as the eluent to afford 29 as white
solid (1.03 g; 80% yield). .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 8.15 (s, 1H, 6-H), 6.15 (dd, J=5.6, 8.3 Hz, 1H, 1'-H),
5.87-5.97 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.27-5.33 (dm, J=17.3
Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm, J=10.4 Hz,
1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.13-4.18 (m, 2H, 3'-H and
4'-H), 3.99-4.10 (m, 2H, CH.sub.2CH.dbd.CH.sub.2), 3.92 (dd, J=2.7,
11.5 Hz, 1H, one of 5'-H), 3.84 (dd, J=2.7, 11.5 Hz, 1H, one of
5'-H), 2.43-2.49 (ddd, J=1.7, 5.6, 13.6 Hz, 1H, one of 2'-H),
2.02-2.10 (ddd, J=5.6, 8.4, 13.6 Hz, 1H, one of 2'-H), 0.96 (s, 9H,
C(CH.sub.3).sub.3), 0.18 (s, 3H, one of SiCH.sub.3), 0.17 (s, 3H,
one of SiCH.sub.3). .sup.13C NMR (100 MHz, CD.sub.3OD) .delta.
162.3, 151.4, 145.5, 135.5, 117.2, 87.0, 86.8, 80.3, 70.9, 69.0,
64.8, 39.4, 26.8, 19.4, -4.7, -4.8. HRMS (FAB+) Calcd for
C.sub.18H.sub.30O.sub.5N.sub.2SiI (M+H.sup.+): 509.0969. found:
509.0970.
3'-O-allyl-5'-O-(tert-butyldimethylsilyl)-5-[3-[(trifluoroacetyl)amino]-p-
rop-1-ynyl]-2'-deoxyuridine (30): The procedure is the same as that
of 7 and the crude product was purified by flash column
chromatography over silica gel using CH.sub.3OH--CH.sub.2Cl.sub.2
(0.about.1:40) as the eluent to afford 30 as yellow crystals (786
mg; 73% yield). .sup.1H NMR (400 MHz, CD.sub.3OD) .delta. 8.11 (s,
1H, 6-H), 6.18 (dd, J=5.8, 7.9 Hz, 1H, 1'-H), 5.87-5.97 (m, 1H,
CH.sub.2CH.dbd.CH.sub.2), 5.27-5.33 (dm, J=17.2 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 5.16-5.21 (dm, J=10.4 Hz, 1H, one of
CH.sub.2CH.dbd.CH.sub.2), 4.27-4.32 (dd, J=17.7 Hz, 1H, one of
C.ident.CCH.sub.2), 4.21-4.27 (dd, J=17.7 Hz, 1H, one of
C.ident.CCH.sub.2), 4.14-4.18 (m, 2H, 3'-H and 4'-H), 3.98-4.10 (m,
2H, CH.sub.2CH.dbd.CH.sub.2), 3.93 (dd, J 2.4, 11.5 Hz, 1H, one of
5'-H), 3.84 (dd, J=2.2, 11.5 Hz, 1H, one of 5'-H), 2.44-2.50 (ddd,
J=1.8, 5.7, 13.5 Hz, 1H, one of 2'-H), 2.04-2.12 (ddd, J=5.6, 8.0,
13.5 Hz, 1H, one of 2'-H), 0.94 (s, 9H, C(CH.sub.3).sub.3), 0.16
(s, 3H, one of SiCH.sub.3), 0.15 (s, 3H, one of SiCH.sub.3).
.sup.13C NMR (100 MHz, CD.sub.3OD) .delta. 164.1, 158.0 (q, J=37
Hz, COCF.sub.2), 150.6, 144.3, 135.5, 117.3, 117.1 (q, J=284 Hz,
COCF.sub.2), 99.5, 88.9, 87.2, 86.9, 80.3, 76.0, 71.0, 64.7, 39.6,
30.7, 26.6, 19.3, -5.0, -5.2. HRMS (FAB+) m/z: anal. Calcd for
C.sub.22H.sub.33O.sub.6N.sub.3F.sub.3Si (M+H.sup.+): 532.2091.
found: 532.2074.
3'-O-allyl-5-[3-[(trifluoroacetyl)amino]-prop-1-ynyl]-2'-deoxyuridine
(31): The procedure is the same as that of 23 and the crude product
was purified by flash column chromatography over silica gel using
ethyl acetate-hexane (3:1) as the eluent to afford 31 as yellow
solid (302 mg; 49% yield). .sup.1H NMR (400 MHz, CD.sub.3OD)
.delta. 8.29 (s, 1H, 6-H), 6.19 (dd, J=6.1, 7.4 Hz, 1H, 1'-H),
5.87-5.99 (m, 1H, CH.sub.2CH.dbd.CH.sub.2), 5.27-5.33 (dm, J=17.2
Hz, 1H, one of CH.sub.2CH.dbd.CH.sub.2), 5.15-5.20 (dm, J=10.4 Hz,
1H, one of CH.sub.2CH.dbd.CH.sub.2), 4.27 (s, 2H,
C.ident.CCH.sub.2), 4.20 (m, 1H, 3'-H), 3.99-4.09 (m, 3H, 4'-H and
CH.sub.2CH.dbd.CH.sub.2), 3.80 (dd, J=3.3, 12.0 Hz, 1H, one of
5'-H), 3.72 (dd, J=3.4, 12.0 Hz, 1H, one of 5'-H), 2.39-2.46 (ddd,
J=2.6, 5.9, 13.7 Hz, 1H, one of 2'-H), 2.14-2.22 (ddd, J=6.3, 7.5,
13.7 Hz, 1H, one of 2'-H). .sup.13C NMR (100 MHz, CD.sub.3OD)
.delta. 164.2, 158.0 (q, J=38 Hz, COCF.sub.3), 150.8, 145.3, 135.6,
117.2 (q, J=285 Hz, COCF.sub.3), 117.1, 99.5, 88.3, 87.1, 87.0,
79.9, 75.9, 71.2, 62.9, 39.0, 30.8. HRMS (FAB+) Calcd for
C.sub.17H.sub.19O.sub.6N.sub.3F.sub.3 (M+H.sup.+): 418.1226. found:
418.1213.
3'-O-allyl-5-(3-aminoprop-1-ynyl)-2'-deoxyuridine-5'-triphosphate
(32): The procedure is the same as that of preparing 9 to yield 32
as colorless syrup: .sup.1H NMR (300 MHz, D.sub.2O) .delta. 8.31
(s, 1H), 6.17 (t, 1H), 5.81-5.90 (m, 1H), 5.18 (d, 1H), 5.14 (d,
1H), 4.34 (m, 2H), 4.03-4.15 (m, 2H), 4.00 (d, 2H), 3.93 (s, 2H),
2.44-2.47 (m, 1H), 2.22-2.24 (m, 1H). .sup.31P NMR (121.4 MHz,
D.sub.2O) .delta. -5.90 (d, J=19.0 Hz, 1P, .gamma.-P), -11.43 (d,
J=20.0 Hz, 1P, .alpha.-P), -22.25 (t, J=19.8 Hz, 1P, .beta.-P).
3'-O-allyl-dUTP-PC-R6G (33): The coupling reaction of 32 with
PC-R6G-NHS ester (Ref. 34b) afforded 33, following a similar
procedure as the preparation of 10. 3'-O-allyl-dCTP-PC-Bodipy-650
33 was characterized by the primer extension reaction and MALDI-TOF
MS.
II. 3'-O-allyl Modified Photocleavable Fluorescent Nucleotides as
Reversible Terminators for Primer Extension Reactions.
1) Primer Extension by Using 3'-O-Allyl-dGTP-PC-Bodipy-FL-510 (10)
and Photocleavage of the Extension Product 34. The polymerase
extension reaction mixture consisted of 60 pmol of primer
(5'-GTTGATGTACACATTGTCAA-3') (SEQ ID NO:4), 80 pmol of 100-mer
template
(5'-TACCCGGAGGCCAAGTACGGCGGGTACGTCC-TTGACAATGTGTACATCAACATCACCTACCACCATGT-
CAGTCTCGGTTGGATCCT CTATTGTGTCCGGG-3') (SEQ ID NO:5), 120 pmol of
3'-O-allyl-dGTP-PC-Bodipy-FL-510, 1.times. Thermopol reaction
buffer (20 mM Tris-HCl/10 mM (NH.sub.4).sub.2SO.sub.4/10 mM KCl/2
mM-MgSO.sub.4/0.1% Triton X-100, pH 8.8, New England Biolabs), and
6 units of 9.degree. N Polymerase (exo-)A485L/Y409V in a total
volume of 20 .mu.l. The reaction consisted of 20 cycles at
94.degree. C. for 20 sec, 46.degree. C. for 40 sec, and 60.degree.
C. for 90 sec. After the reaction, a small portion of the DNA
extension product was desalted by using ZipTip and analyzed by
MALDI-TOF MS, which shows a dominant peak at m/z 7,052
corresponding to the DNA product 34. The rest of the product
mixture was freeze-dried, resuspended in 200 .mu.l of deionized
water, and irradiated at 355 nm for 10 sec to cleave the
fluorophore from the DNA to yield product 35 and then analyzed by
MALDI-TOF MS.
Deallyation of photocleaved DNA extension product 35. DNA product
35 (20 pmol) was added to a mixture of degassed 1.times. Thermopol
reaction buffer (20 mM Tris-HCl/10 mM (NH.sub.4).sub.2SO.sub.4/10
mM KCl/2 mM MgSO.sub.4/0.1% Triton X-100, pH 8.8, 1 .mu.l),
Na.sub.2PdCl.sub.4 in degassed H.sub.2O (7 .mu.l, 23 nmol) and
P(PhSO.sub.3Na).sub.3 in degassed H.sub.2O (10 .mu.l, 176 nmol) to
perform deallylation. The reaction mixture was then placed in a
heating block and incubated at 70.degree. C. for 30 seconds to
yield quantitatively deallylated DNA product 36 and analyzed by
MALDI-TOF MS.
Primer Extension Reaction Performed with the deallylated DNA
Product. The deallylated DNA product 36 was used as a primer in a
single-base extension reaction. The 20 .mu.l reaction mixture
consisted of 60 pmol of the deallylated product 36, 80 pmol of the
100-mer template
(5'-TACCCGGAGGCCAAGTACGGCGGGTACGTCC-TTGACAATGTGTACATCAACATCACCTACCACCATGT-
CAGTCTCGGTTGGATCCT CTATTGTGTCCGGG-3') (SEQ ID NO:6), 120 pmol of
3'-O-allyl-dGTP-PC-Bodipy-FL-510 (10), 6 units of 9.degree. N
Polymerase (exo-)A485L/Y409V in a total volume of 20 .mu.l. The
reaction consisted of 20 cycles at 94.degree. C. for 20 sec,
46.degree. C. for 40 sec, and 60.degree. C. for 90 sec. The DNA
extension product 37 was desalted by using the ZipTip protocol, and
a small portion was analyzed by using MALDI-TOF MS. The remaining
product was then irradiated with near-UV light (355 nm) for 10 sec
to cleave the fluorophore from the extended DNA product. The
resulting photocleavage product 38 was analyzed by using MALDI-TOF
MS. Finally, deallylation of the photocleavage product 38 was
performed using a Pd-catalyzed deallylation reaction resulting in a
deallylated DNA product 39, which was then analyzed by MALDI-TOF
MS.
2) Primer Extension with 3'-O-Allyl-dATP-PC-ROX (19), followed by
Photocleavage and Deallylation of the Extension Product. The
polymerase extension reaction mixture consisted of 60 pmol of
primer (5'-TAGATGACCCTGCCTTGTCG-3') (SEQ ID NO:7), 80 pmol of
100-mer template
(5'-GAAGGAGACACGCGGCCAGAGAGGGT-CCTGTCCGTGTTTGTGCGTGGAGTTCGACAAGGCAGGGTCAT-
CTAATGGTGATGA GTCCTATCCTTTTCTCTTCGTTCTCCGT-3') (SEQ ID NO:8), 120
pmol of 3'-O-allyl-dUTP-PC-R6G, 120 pmol of 3'-O-allyl-dATP-PC-ROX,
120 pmol of 3'-O-allyl-dGTP-PC-Bodipy-FL-510, 120 pmol of
3'-O-allyl-dCTP-PC-Bodipy-650, 1.times. Thermopol reaction buffer
(20 mM Tris-HCl/10 mM (NH.sub.4).sub.2SO.sub.4/10 mM KCl/2 mM
MgSO.sub.4/0.1% Triton X-100, pH 8.8, New England Biolabs), and 6
units of 9.degree. N Polymerase (exo-)A485L/Y409V in a total volume
of 20 .mu.l. The reaction consisted of 20 cycles at 94.degree. C.
for 20 sec, 55.degree. C. for 40 sec, and 68.degree. C. for 90 sec,
which yielded DNA extension product 40. DNA extension product
mixture was freeze-dried, resuspended in 200 .mu.l of deionized
water, and irradiated at 355 nm for 10 sec to cleave the
fluorophore from the DNA to yield DNA product 41 and then analyzed
by MALDI-TOF MS. Finally, deallylation of the photocleavage product
was performed using a Pd-catalyzed deallylation reaction resulting
in a deallylated DNA product 42, which was then analyzed by
MALDI-TOF MS.
3) Primer Extension with 3'-O-Allyl-dCTP-PC-Bodipy-650 (26),
followed by Photocleavage and Deallylation of the Extension
Product. The polymerase extension reaction mixture consisted of 60
pmol of primer (5'-ACACAATAGAGGATCCAACCG AGA-3') (SEQ ID NO:9), 80
pmol of 100-mer template (5'-TACCCGGAGGCCAAGTACGGCGGGT
ACGTCCTTGACAATGTGTACATCAACATCACCTACCACCATGTCAGTCTCGGTTG
GATCCTCTATTGTGTCCGGG-3') (SEQ ID NO:10), 120 pmol of
3'-O-allyl-dUTP-PC-R6G, 120 pmol of 3'-O-allyl-dATP-PC-ROX, 120
pmol of 3'-O-allyl-dGTP-PC-Bodipy-FL-510, 120 pmol of
3'-O-allyl-dCTP-PC-Bodipy-650, 1.times. Thermopol reaction buffer
(20 mM Tris-HCl/10 mM (NH.sub.4).sub.2SO.sub.4/10 mM KCl/2 mM
MgSO.sub.4/0.1% Triton X-100, pH 8.8, New England Biolabs), and 6
units of 9.degree. N Polymerase (exo-)A485L/Y409V in a total volume
of 20 .mu.l. The reaction consisted of 20 cycles at 94.degree. C.
for 20 sec, 64.degree. C. for 40 sec, and 72.degree. C. for 90 sec,
which yielded DNA extension product 43. DNA extension product
mixture was freeze-dried, resuspended in 200 .mu.l of deionized
water, and irradiated at 355 nm for 10 sec to cleave the
fluorophore from the DNA to yield DNA product 44 and then analyzed
by MALDI-TOF MS. Finally, deallylation of the photocleavage product
was performed using a Pd-catalyzed deallylation reaction resulting
in a deallylated DNA product 45, which was then analyzed by
MALDI-TOF MS.
4) Primer Extension with 3'-O-Allyl-dUTP-PC-R6G (33), followed by
Photocleavage and Deallylation of the Extension Product. The
polymerase extension reaction mixture consisted of 60 pmol of
primer (5'-GATAGGACTCATCACCA-3') (SEQ ID NO:11), 80 pmol of 100-mer
template (5'-GAAGGAGACACGCGGCCAGAGAGGGTCCTGTCCGTGTTTGT GCG
TGGAGTTCGACAAGGCAGGGTCATCTAATGGTGATGAGTCCTATCCTTT
TCTCTTCGTTCTCCGT-3') (SEQ ID NO:12), 120 pmol of
3'-.beta.-allyl-dUTP-PC-R6G, 120 pmol of 3'-O-allyl-dATP-PC-ROX,
120 pmol of 3'-O-allyl-dGTP-PC-Bodipy-FL-510, 120 pmol of
3'-O-allyl-dCTP-PC-Bodipy-650, 1.times. Thermopol reaction buffer
(20 mM Tris-HCl/10 mM (NH.sub.4).sub.2SO.sub.4/10 mM KCl/2 mM
MgSO.sub.4/0.1% Triton X-100, pH 8.8, New England Biolabs), and 6
units of 9.degree. N Polymerase (exo-)A485L/Y409V in a total volume
of 20 .mu.l. The reaction consisted of 20 cycles at 94.degree. C.
for 20 sec, 46.degree. C. for 40 sec, and 60.degree. C. for 90 sec,
which yielded DNA extension product 46. DNA extension product
mixture was freeze-dried, resuspended in 200 .mu.l of deionized
water, and irradiated at 355 nm for 10 sec to cleave the
fluorophore from the DNA to yield DNA product 47 and then analyzed
by MALDI-TOF MS. Finally, deallylation of the photocleavage product
was performed using a Pd-catalyzed deallylation reaction resulting
in a deallylated DNA product 48, which was then analyzed by
MALDI-TOF MS.
Example 3
Four-Color DNA Sequencing by Synthesis on a Chip Using
Photocleavable Fluorescent Nucleotides
Synopsis
In this example, 4-color DNA sequencing by synthesis (SBS) on a
chip using four photocleavable fluorescent nucleotide analogues
(dGTP-PC-Bodipy-FL-510, dUTP-PC-R6G, dATP-PC-ROX, and
dCTP-PC-Bodipy-650) is demonstrated. Each nucleotide analogue
consists of a different fluorophore attached to the 5-position of
the pyrimidines (C and U) and the 7-position of the purines (G and
A) through a photocleavable 2-nitrobenzyl linker. After verifying
that these nucleotides could be successfully incorporated into a
growing DNA strand in a solution-phase polymerase reaction and the
fluorophore could be cleaved using laser irradiation
(.lamda..about.355 nm) in 10 seconds, an SEE reaction was then
performed on a chip which contains a self-priming DNA template
covalently immobilized using 1,3-dipolar azide-alkyne
cycloaddition. The DNA template was produced by a polymerase chain
reaction using an azido-labeled primer and the self-priming moiety
was attached to the immobilized DNA template by enzymatic ligation.
Each cycle of SBS consists of the incorporation of the
photocleavable fluorescent nucleotide into the DNA, detection of
the fluorescent signal and photocleavage of the fluorophore. The
entire process was repeated to identify 12 continuous bases in the
DNA template. These results demonstrate that photocleavable
fluorescent nucleotide analogues can be incorporated accurately
into a growing-DNA strand during a polymerase reaction in solution
phase as well as on a chip. Moreover, all 4 fluorophores can be
detected and then efficiently cleaved using near-UV irradiation,
thereby allowing continuous identification of the DNA template
sequence. Optimization of the steps involved increases the
readlength.
Results
DNA sequencing is a fundamental tool for biological science. The
completion of the Human Genome Project has set the stage for
screening genetic mutations to identify disease genes on a
genome-wide scale (42). Accurate high-throughput DNA sequencing
methods are needed to explore the complete human genome sequence
for applications in clinical medicine and health care. Recent
studies have indicated that an important route for identifying
functional elements in the human genome involves sequencing the
genomes of many species representing a wide sampling of the
evolutionary tree (43). To overcome the limitations of the current
electrophoresis-based sequencing technology (44-47), a variety of
new DNA-sequencing methods have been investigated. Such approaches
include sequencing by hybridization (48), mass spectrometry based
sequencing (49-51), sequence-specific detection of single-stranded
DNA using engineered nanopores (52). More recently, DNA sequencing
by synthesis (SBS) approaches such as pyrosequencing (53),
sequencing of single DNA molecules (54) and polymerase colonies
(55) have been widely explored.
The concept of DNA sequencing by synthesis was revealed in 1988
(56). This approach involves detection of the identity of each
nucleotide immediately after its incorporation into a growing
strand of DNA in a polymerase reaction. Thus far, no complete
success has been reported in using such a system to sequence DNA
unambiguously. An SBS approach was proposed using photocleavable
fluorescent nucleotide analogues on a surface in 2000 (57). In this
approach, modified nucleotides are used as reversible terminators,
in which a different fluorophore with a distinct fluorescent
emission is linked to each of the 4 bases through a photocleavable
linker and the 3'-OH group is capped by a small chemical moiety.
DNA polymerase incorporates only a single nucleotide analogue
complementary to the base on a DNA template covalently linked to a
surface. After incorporation, the unique fluorescence emission is
detected to identify the incorporated nucleotide and the
fluorophore is subsequently removed photochemically. The 3'-OH
group is then chemically regenerated, which allows the next cycle
of the polymerase reaction to proceed. Since the large surface on a
DNA chip can have a high density of different DNA templates
spotted, each cycle can identify many bases in parallel, allowing
the simultaneous sequencing of a large number of DNA molecules. The
advantage of using photons as reagents for initiating
photoreactions to cleave the fluorophore is that no additional
chemical reagents are required to be introduced into the system and
clean products can be generated with no need for subsequent
purification. It has previously been established the feasibility of
performing SBS on a chip using a synthetic DNA template and
photocleavable pyrimidine nucleotides (C and U) (58). As further
development of this approach, here the design and synthesis of 4
photocleavable nucleotide analogues (A, C, G, U) is reported, each
of which contains a unique fluorophore with a distinct fluorescence
emission. Initially, it is established that these nucleotides are
good substrates for DNA polymerase in a solution-phase DNA
extension reaction and that the fluorophore can be removed with
high speed and efficiency by laser irradiation (D-355 nm).
Subsequently, SBS was performed using these 4 photocleavable
nucleotide analogues to identify the sequence of a DNA template
immobilized on a chip. The DNA template was produced by PCR using
an azido-labeled primer, and was immobilized on the surface of the
chip with 1,3-dipolar azide-alkyne cycloaddition chemistry. A
self-priming moiety was then covalently attached to the DNA
template by enzymatic ligation to allow the polymerase reaction to
proceed on the DNA immobilized on the surface.
Materials and Methods
All chemicals were purchased from Sigma-Aldrich unless otherwise
indicated. 1H NMR spectra were recorded on a Bruker 400
spectrometer. High-resolution MS (HRMS) data were obtained by using
a JEOL JMS HX 110A mass spectrometer. Mass measurement of DNA was
made on a Voyager DE matrix-assisted laser desorption
ionization-time-of-flight (MALDI-TOF) mass spectrometer (Applied
Biosystems). Photolysis was performed using a Spectra Physics
GCR-150-30 Nd-YAG laser that generates light pulses at 355 nm (ca.
50 mJ/pulse, pulse length ca. 7 ns) at a frequency of 30 Hz with a
light intensity at ca. 1.5 W/cm2. The scanned fluorescence emission
images were obtained by using a ScanArray Express scanner
(Perkin-Elmer Life Sciences) equipped with four lasers with
excitation wavelengths of 488, 543, 594, and 633 nm and emission
filters centered at 522, 570, 614, and 670 nm.
Synthesis of Photocleavable Fluorescent Nucleotides.
Photocleavable fluorescent nucleotides dGTP-PC-Bodipy-FL-510,
dUTP-PC-R6G, dATP-PC-ROX and dCTP-PC-Bodipy-650 (FIG. 16) were
synthesized according to FIG. 17 using a similar method as reported
previously (57). A photocleavable linker (PC-Linker)
1-[5-(aminomethyl)-2-nitrophenyl]ethanol was reacted with the NHS
ester of the corresponding fluorescent dye to produce an
intermediate PC-Dye, which was converted to a PC-Dye NHS ester by
reacting with N,N'-disuccinimidyl carbonate. The coupling reaction
between the different PC-Dye NHS esters and the amino nucleotides
(dATP-NH2 and dGTP-NH2 from Perkin-Elmer; dUTP-NH2 from Sigma;
dCTP-NH2 from TriLink BioTechnologies) produced the 4
photocleavable fluorescent nucleotides.
DNA polymerase reaction using 4 photocleavable fluorescent
nucleotide analogues in solution.
Four nucleotide analogues were characterized,
dGTP-PC-Bodipy-FL-510, dUTP-PC-R6G, dATP-PC-ROX and
dCTP-PC-Bodipy-650 by performing four continuous DNA-extension
reactions sequentially using a primer (5'-AGAGGATCCAACCGAGAC-3')
(SEQ ID NO:13) and a synthetic DNA template
(5'-GTGTACATCAACATCACCTACCACCATGTCAGTCTCGGTTGGAT-CCTCTATTGTGTCCGG-3')
(SEQ ID NO:14) corresponding to a portion of exon 7 of the human
p53 gene (FIG. 18). The four nucleotides in the template
immediately adjacent to the annealing site of the primer were
3'-ACTG-5'. First, a polymerase extension reaction using
dUTP-PC-R6G along with the primer and the template was performed
producing a single base extension product. The reaction mixture for
this, and all subsequent extension reactions, consisted of 80 pmol
of template, 50 pmol of primer, 80 pmol of the particular
photocleavable fluorescent nucleotide, 1.times. Thermo Sequenase
reaction buffer, and 4 U of Thermo Sequenase DNA polymerase
(Amersham Biosciences) in a total volume of 20 .mu.L. The reaction
consisted of 25 cycles at 94.degree. C. for 20 sec, 48.degree. C.
for 40 sec, and 60.degree. C. for 75 sec. Subsequently, the
extension product was purified by using reverse-phase HPLC. An
Xterra MS C18 (4.6.times.50-mm) column (Waters) was used for the
HPLC purification. Elution was performed over 120 minutes at a flow
rate of 0.5 mL/min with the temperature set at 50.degree. C. by
using a linear gradient (12-34.5%) of methanol in a buffer
consisting of 8.6 mM triethylamine and 100 mM hexafluoroisopropyl
alcohol (pH 8.1). The fraction containing the desired DNA product
was collected and freeze-dried for analysis using MALDI-TOF mass
spectrometry. For photocleavage, the purified DNA extension product
bearing the fluorescent nucleotide analogue was resuspended in 200
.mu.L of deionized water. The mixture was irradiated for 10 seconds
in a quartz cell with path lengths of 1.0 cm employing a Nd-YAG
laser at 355 nm and then analyzed by MALDI-TOF MS. After
photocleavage, the DNA product with the fluorophore removed was
used as a primer for a second extension reaction using
dGTP-PC-Bodipy-FL-510. The second extended product was then
purified by HPLC and photolyzed. The third extension using
dATP-PC-ROX and the fourth extension using dCTP-PC-Bodipy-650 were
carried out in a similar manner using the previously extended and
photocleaved product as the primer.
PCR amplification to produce azido-labeled DNA template.
An azido-labeled PCR product was obtained using a 100-bp template
(5'-AGCGACTGCTATCATGTCATATCGACGTGCTCACTAGCTCTACATATGCGTGCGT
GATCAGATGACGTATCGATGCTGACTATAGTCTCCCATGCGAGTG-3') (SEQ ID NO:15), a
24-bp azido-labeled forward primer
(5'-N3-AGCGACTGCTATCATGTCATATCG-3') (SEQ ID NO:16), and a 24-bp
unlabeled reverse primer (5'-CACTCGCATGGGAGACTATAGTCA-3') (SEQ ID
NO:17). In a total reaction volume of 50 .mu.L, 1 pmol of template
and 30 pmol of forward and reverse primers were mixed with 1 U of
AccuPrime Pfx DNA polymerase and 5 .mu.L of 10.times. AccuPrime Pfx
reaction mix (Invitrogen) containing 1 mM of MgSO.sub.4 and 0.3 mM
of dNTP. The PCR reaction consisted of an initial denaturation step
at 95.degree. C. for 1 min, followed by 38 cycles at 94.degree. C.
for 15 sec, 63.degree. C. for 30 sec, 68.degree. C. for 30 sec. The
product was purified using a 96 Q1Aquick multiwell PCR purification
kit (Qiagen) and the quality was checked using 2% agarose gel
electrophoresis in 1.times.TAE buffer. The concentration of the
purified PCR product was measured using a Perkin-Elmer Lambda 40
UV-Vis spectrophotometer.
Construction of a self-priming DNA template on a chip by enzymatic
ligation.
The amino-modified glass slide (Sigma) was functionalized to
contain a terminal alkynyl group as described previously (57). The
azido-labeled DNA product generated by PCR was dissolved in
DMSO/H.sub.2O (1/3, v/v) to obtain a 20 .mu.M solution. 5 .mu.L of
the DNA solution was mixed with CuI (10 nmol, 100 eq.) and
N,N-diisopropyl-ethylamine (DIPEA) (10 nmol, 100 eq.) and then
spotted onto the alkynyl-modified glass surface in the form of 6
.mu.L drops. The glass slide was incubated in a humid chamber at
room temperature for 24 hr, washed with deionized water (dH.sub.2O)
and SPSC buffer (50 mM sodium phosphate, 1 M NaCl, pH 6.5) for 1 hr
(57), and finally rinsed with dH.sub.2O. To denature the double
stranded PCR-amplified DNA to remove the non-azido-labeled strand,
the glass slide was immersed into 0.1 M NaOH solution for 10 min
and then washed with 0.1 M NaOH and dH.sub.2O, producing a single
stranded DNA template that is immobilized on the chip. For the
enzymatic ligation of a self-priming moiety to the immobilized DNA
template on the chip, a 5'-phosphorylated 40-bp loop primer
(5'-PO3-GCTGAATTCCGCGTTCGCGGAATTCAGCCACTCGCATGGG-3') (SEQ ID NO:18)
was synthesized. This primer contained a thermally stable loop
sequence 3'-G(CTTG)C-5.degree., a 12-bp stem, and a 12-bp
overhanging end that would be annealed to the immobilized single
stranded template at its 3'-end. A 10 .mu.L solution consisting of
100 pmol of the primer, 10 U of Taq DNA ligase, 0.1 mM NAD, and
1.times. reaction buffer (New England Biolabs) was spotted onto a
location of the chip containing the immobilized DNA and incubated
at 45.degree. C. for 4 hr. The glass slide was washed with
dH.sub.2O, SPSC buffer, and again with dH.sub.2O. The formation of
a stable hairpin was ascertained by covering the entire surface
with 1.times. reaction buffer (26 mM Tris HCl/6.5 mM MgCl.sub.2, pH
9.3), incubating it in a humid chamber at 94.degree. C. for 5 min
to dissociate any partial hairpin structure, and then slowly
cooling down to room temperature for reannealing.
SBS reaction on a chip with four photocleavable fluorescent
nucleotide analogues.
One microliter of a solution consisting of dATP-PC-ROX (60 pmol), 2
U of Thermo Sequenase DNA polymerase, and 1.times. reaction buffer
was spotted on the surface of the chip, where the self-primed DNA
moiety was immobilized. The nucleotide analogue was allowed to
incorporate into the primer at 72.degree. C. for 5 min. After
washing with a mixture of SPSC buffer, 0.1% SDS, and 0.1% Tween 20
for 10 min, the surface was rinsed with dH.sub.2O and ethanol
successively, and then scanned with a ScanArray Express scanner to
detect the fluorescence signal. To perform photocleavage, the glass
chip was placed inside a chamber (50.times.50.times.50 mm) filled
with acetonitrile/water (1/1, v/v) solution and irradiated for 1
min with the Nd-YAG laser at 355 nm. The light intensity applied on
the glass surface was ca. 1.5 W/cm.sup.2. After washing the surface
with dH.sub.2O and ethanol, the surface was scanned again to
compare the intensity of fluorescence after photocleavage with the
original fluorescence intensity. This process was followed by the
incorporation of dGTP-PC-Bodipy-FL-510, with the subsequent
washing, fluorescence detection, and photocleavage processes
performed as described above. The same cycle was repeated 10 more
times using each of the four photocleavable fluorescent nucleotide
analogues complementary to the base on the template. For a negative
control experiment, 1 .mu.L solution containing dATP-PC-ROX (60
pmol), and 1.times. reaction buffer was added on to the DNA
immobilized on the chip in the absence of DNA polymerase and then
incubated at 72.degree. C. for 5 min, followed by the same washing
and detection steps as above.
Results and Discussion
To demonstrate the feasibility of carrying out DNA sequencing by
synthesis on a chip, four photocleavable fluorescent nucleotide
analogues (dGTP-PC-Bodipy-FL-510, dUTP-PC-R6G, dATP-PC-ROX, and
dCTP-PC-Bodipy-650) (FIG. 16) were synthesized according to FIG. 17
using a similar procedure as reported previously (57). Modified DNA
polymerases have been shown to be highly tolerant to nucleotide
modifications with bulky groups at the 5-position of pyrimidines (C
and U) and the 7-position of purines (A and G) (59, 60). Thus, each
unique fluorophore was attached to the 5 position of C/U and the 7
position of A/G through a photocleavable 2-nitrobenzyl linker.
In order to verify that these fluorescent nucleotides are
incorporated accurately in a base-specific manner in a polymerase
reaction, four continuous steps of DNA extension and photocleavage
by near UV irradiation were carried out in solution as shown in
FIG. 18. This allows the isolation of the DNA product at each step
for detailed molecular structure characterization as shown in FIG.
19. The first extension product 5'-U(PC-R6G)-3' 1 was purified by
HPLC and analyzed using MALDI-TOF MS [FIG. 19(1)]. This product was
then irradiated at 355 nm using an Nd-YAG laser for 10 seconds and
the photocleavage product 2 was also analyzed using MALDI-TOF MS
[FIG. 19(2)]. Near UV light absorption by the aromatic
2-nitrobenzyl linker causes reduction of the 2-nitro group to a
nitroso group and an oxygen insertion into the carbon-hydrogen bond
followed by cleavage and decarboxylation (61). As can be seen from
FIG. 19(1), the MALDI-TOF MS spectrum consists of a distinct peak
at m/z 6536 corresponding to the DNA extension product
5'-U(PC-R6G)-3' (1), which confirms that the nucleotide analogue
can be incorporated base specifically by DNA polymerase into a
growing DNA strand. The small peak at m/z 5872 corresponding to the
photocleavage product is due to the partial cleavage caused by the
nitrogen laser pulse (337 nm) used in MALDI ionization. For
photocleavage, a Nd-YAG laser was used to irradiate the DNA product
carrying the fluorescent nucleotide for 10 seconds at 355 nm to
cleave the fluorophore from the DNA extension product. FIG. 19(2)
shows the photocleavage result of the above DNA product. The peak
at m/z 6536 has completely disappeared while the peak corresponding
to the photocleavage product 5'-U (2) appears as the sole dominant
peak at m/z 5872, which establishes that laser irradiation
completely cleaves the fluorophore with high speed and efficiency
without damaging the DNA. The next extension reaction was carried
out using this photocleaved DNA product as a primer along with
dGTP-PC-Bodipy-FL-510 to yield an extension product
5'-UG(PC-Bodipy-FL-510)-3' (3). As described above, the extension
product 3 was purified, analyzed by MALDI-TOF MS producing a
dominant peak at m/z 6751 [FIG. 19(3)], and then photocleaved for
further MS analysis yielding a single peak at m/z 6255 (product 4)
[FIG. 19(4)]. The third extension using dATP-PC-ROX to yield
5'-UGA(PC-ROX)-3' (5), the fourth extension using
dCTP-PC-Bodipy-650 to yield 5'-UGAC(PC-Bodipy-650)-3' (7) and their
photocleavage to yield products 6 and 8 were similarly carried out
and analyzed by MALDI-TOF MS as shown in FIGS. 19(5), 19(6), 19(7)
and 19(8). These results demonstrate that the above-synthesized
four photocleavable fluorescent nucleotide analogues can
successfully incorporate into the growing DNA strand in a
polymerase reaction, and the fluorophore can be efficiently cleaved
by near UV irradiation, which makes it feasible to use them for SBS
on a chip.
The photocleavable fluorescent nucleotide analogues were then used
in an SBS reaction to identify the sequence of the DNA template
immobilized on a solid surface as shown in FIG. 20. A site-specific
1,3-dipolar cycloaddition coupling chemistry was used to covalently
immobilize the azido-labeled double-stranded PCR products on the
alkynyl-functionalized surface in the presence of a Cu(I) catalyst.
Previously, it has shown have shown that DNA is successfully
immobilized on the glass surface by this chemistry and evaluated
the functionality of the surface-bound DNA and the stability of the
array using a primer extension reaction (57). The
surface-immobilized double stranded PCR product was denatured using
a 0.1 M NaOH solution to remove the complementary strand without
the azido group, thereby generating a single-stranded PCR template
on the surface. Then, a 5'-phosphorylated self-priming moiety (loop
primer) was ligated to the 3'-end of the above single stranded DNA
template using Taq DNA ligase (21). The structure of the loop
primer was designed to bear a thermally stable loop (22) and stem
sequence with a melting temperature of 89.degree. C. The 12-bp
overhanging portion of the loop primer was made complementary to
the 12-bp sequence of the template at its 3' end to allow the Taq
DNA ligase to seal the nick between the 5'-phosphate group of the
loop primer and the 3'-hydroxyl group of the single-stranded DNA
template. This produces a unique DNA moiety that can self-prime for
the synthesis of a complementary strand. The ligation was found to
be in quantitative yield in a parallel solution-phase reaction
using the same primer and single-stranded DNA template.
The principal advantage offered by the use of a self-priming moiety
as compared to using separate primers and templates is that the
covalent linkage of the primer to the template in the self-priming
moiety prevents any possible dissociation of the primer from the
template under vigorous washing conditions. Furthermore, the
possibility of mispriming is considerably reduced and a universal
loop primer can be used for all the templates allowing enhanced
accuracy and ease of operation. SBS was performed on the
chip-immobilized DNA template using the 4 photocleavable
fluorescent nucleotide analogues and the results are shown in FIG.
21. The structure of the self-priming DNA moiety is shown
schematically in the upper panel, with the first 12 nucleotide
sequence immediately after the priming site. The sequencing
reaction on the chip was initiated by extending the self-priming
DNA using dATP-PC-ROX (complementary to the T on the template), and
Thermo Sequenase DNA polymerase. After washing, the extension of
the primer by a single fluorescent nucleotide was confirmed by
observing an orange signal (the emission signal from ROX) in a
microarray scanner [FIG. 21(1)]. After detection of the fluorescent
signal, the surface was irradiated at 355 nm for 1 min using an
Nd-YAG laser to cleave the fluorophore. The surface was then
washed, and a negligible residual fluorescent signal was detected
to confirm complete photocleavage of the fluorophore [FIG. 21(2)].
This was followed by incorporation of the next fluorescent
nucleotide complementary to the subsequent base on the template.
The entire process of incorporation, detection and photocleavage
was performed multiple times using the four photocleavable
fluorescent nucleotide analogues to identify 12 successive bases in
the DNA template. The integrated fluorescence intensity on the
spot, obtained from the scanner software, indicated that the
incorporation efficiency was over 90% and more than 97% of the
original fluorescence signal was removed by photocleavage. A
negative control experiment consisting of incubating the
self-priming DNA moiety with dATP-PC-ROX in the absence of DNA
polymerase and washing the surface showed that negligible
fluorescence remained as compared to that of FIG. 21(1).
In summary, synthesis and characterization of four photocleavable
fluorescent nucleotide analogues are disclosed here, and their use
to produce 4-color DNA sequencing data on a chip. These nucleotides
have been shown to be excellent substrates for the DNA polymerase
and the fluorophore could be cleaved efficiently using near UV
irradiation. This is important with respect to enhancing the speed
of each cycle in SBS for high throughput DNA analysis. It has also
been demonstrated that a PCR-amplified DNA template can be ligated
with a self-priming moiety and its sequence can be accurately
identified in a DNA polymerase reaction on a chip, indicating that
a PCR product from any organism can be potentially used as a
template for the SBS system in the future. The modification of the
3'-OH of the photocleavable fluorescent nucleotide with a small
chemical group to allow reversible termination is reported in (58).
The library of photocleavable fluorescent nucleotides reported here
should also facilitate the development of single molecule DNA
sequencing approaches. Thus, by further improving the readlength
and incorporation efficiency, this approach potentially can be
developed into a high-throughput DNA-analysis system for biological
research and medical applications.
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SEQUENCE LISTINGS
1
18119DNAArtificial Sequenceprimer directed to Human p53 1agaggatcca
accgagact 19218DNAHomo sapiens 2agaggatcca accgagac
18319DNAArtificial Sequencechemically synthesized 3agaggatcca
accgagact 19420DNAArtificial Sequenceprimer directed to Human p53
4gttgatgtac acattgtcaa 205100DNAHomo sapiens 5tacccggagg ccaagtacgg
cgggtacgtc cttgacaatg tgtacatcaa catcacctac 60caccatgtca gtctcggttg
gatcctctat tgtgtccggg 1006100DNAHomo sapiens 6tacccggagg ccaagtacgg
cgggtacgtc cttgacaatg tgtacatcaa catcacctac 60caccatgtca gtctcggttg
gatcctctat tgtgtccggg 100720DNAArtificial Sequenceprimer directed
to Human p53 7tagatgaccc tgccttgtcg 208109DNAHomo sapiens
8gaaggagaca cgcggccaga gagggtcctg tccgtgtttg tgcgtggagt tcgacaaggc
60agggtcatct aatggtgatg agtcctatcc ttttctcttc gttctccgt
109924DNAArtificial Sequenceprimer directed to Human p53
9acacaataga ggatccaacc gaga 2410100DNAHomo sapiens 10tacccggagg
ccaagtacgg cgggtacgtc cttgacaatg tgtacatcaa catcacctac 60caccatgtca
gtctcggttg gatcctctat tgtgtccggg 1001117DNAArtificial
Sequenceprimer directed to Human p53 11gataggactc atcacca
1712109DNAHomo sapiens 12gaaggagaca cgcggccaga gagggtcctg
tccgtgtttg tgcgtggagt tcgacaaggc 60agggtcatct aatggtgatg agtcctatcc
ttttctcttc gttctccgt 1091318DNAArtificial Sequenceprimer directed
to Human p53 13agaggatcca accgagac 181460DNAHomo sapiens
14gtgtacatca acatcaccta ccaccatgtc agtctcggtt ggatcctcta ttgtgtccgg
6015100DNAHomo sapiens 15agcgactgct atcatgtcat atcgacgtgc
tcactagctc tacatatgcg tgcgtgatca 60gatgacgtat cgatgctgac tatagtctcc
catgcgagtg 1001624DNAArtificial Sequenceforward primer directed to
Human p53 16agcgactgct atcatgtcat atcg 241724DNAArtificial
Sequencereverse primer directed to Human p53 17cactcgcatg
ggagactata gtca 241840DNAArtificial Sequenceprimer directed to
Human p53 18gctgaattcc gcgttcgcgg aattcagcca ctcgcatggg 40
* * * * *
References