U.S. patent application number 17/327002 was filed with the patent office on 2022-02-03 for crispr oligoncleotides and gene editing.
The applicant listed for this patent is LIFE TECHNOLOGIES CORPORATION, THERMO FISHER SCIENTIFIC GENEART GMBH. Invention is credited to Yizhu GUO, Korbinian HEIL, Sanjay KUMAR, Xiquan LIANG, Robert POTTER, Namritha RAVINDER.
Application Number | 20220033858 17/327002 |
Document ID | / |
Family ID | 54356656 |
Filed Date | 2022-02-03 |
United States Patent
Application |
20220033858 |
Kind Code |
A1 |
RAVINDER; Namritha ; et
al. |
February 3, 2022 |
CRISPR OLIGONCLEOTIDES AND GENE EDITING
Abstract
The present disclosure generally relates to compositions and
methods for the genetic modification of cells. In particular, the
disclosure relates to CRISPR reagents and the use of such
reagents.
Inventors: |
RAVINDER; Namritha; (San
Diego, CA) ; HEIL; Korbinian; (Munich, DE) ;
GUO; Yizhu; (Chatsworth, CA) ; LIANG; Xiquan;
(Escondido, CA) ; POTTER; Robert; (San Marcos,
CA) ; KUMAR; Sanjay; (Carlsbad, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
LIFE TECHNOLOGIES CORPORATION
THERMO FISHER SCIENTIFIC GENEART GMBH |
Carlsbad
Regensburg |
CA |
US
DE |
|
|
Family ID: |
54356656 |
Appl. No.: |
17/327002 |
Filed: |
May 21, 2021 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
15842664 |
Dec 14, 2017 |
|
|
|
17327002 |
|
|
|
|
14879872 |
Oct 9, 2015 |
9879283 |
|
|
15842664 |
|
|
|
|
62218826 |
Sep 15, 2015 |
|
|
|
62101787 |
Jan 9, 2015 |
|
|
|
62061961 |
Oct 9, 2014 |
|
|
|
Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12Q 1/686 20130101;
C12N 9/22 20130101; C12N 2310/3519 20130101; C12P 19/34 20130101;
C12N 15/102 20130101; C12N 15/11 20130101; C12N 2330/30 20130101;
C12N 2310/20 20170501; C12N 15/907 20130101; C12N 15/902 20130101;
C12Q 1/686 20130101; C12Q 2525/143 20130101 |
International
Class: |
C12N 15/90 20060101
C12N015/90; C12Q 1/686 20060101 C12Q001/686; C12N 15/10 20060101
C12N015/10; C12N 15/11 20060101 C12N015/11; C12P 19/34 20060101
C12P019/34 |
Claims
1. A method for producing a nucleic acid molecule, the method
comprising performing polymerase chain reaction (PCR) in a reaction
mixture containing (i) a double-stranded nucleic acid segment and
(ii) at least one oligonucleotide capable of hybridizing to nucleic
acid at one terminus of the double-stranded nucleic acid segment,
wherein the nucleic acid molecule is produced by the PCR reaction,
and wherein the product nucleic acid molecule contains at or near
one terminus a promoter suitable for in vitro transcription.
2. The method of claim 1, wherein the nucleic acid molecule
produced by the PCR reaction encodes an RNA molecule from 35 to 150
nucleotides in length.
3. The method of claim 1, wherein the nucleic acid molecule
produced by the PCR reaction is from 70 to 150 base pairs in
length.
4. The method of claim 1, wherein the nucleic acid molecule is
produced by the PCR reaction encodes an RNA molecule with at least
two hairpin turns.
5. The method of claim 1, wherein the nucleic acid molecule is
produced by the PCR reaction encodes a CRISPR RNA.
6. The method of claim 5, wherein the nucleic acid molecule is
produced by the PCR reaction encodes a guide RNA.
7.-26. (canceled)
27. A ligated RNA molecule comprising two RNA regions that differ
in nucleotide sequence connected by a ligation group, wherein the
ligated RNA molecule is capable of binding to a Cas9 protein and
has a region of sequence complementarity of at least 10 nucleotides
to a target locus.
28. The ligated RNA molecule of claim 27, wherein one region is
composed of a crRNA molecule and the other region is a tracrRNA
molecule.
29. A method of making the ligated RNA molecule of claim 27, the
method comprising covalently linking a crRNA molecule and a
tracrRNA molecule.
30. A method for gene editing at a target locus within a cell, the
method comprising forming an intracellular complex comprising a
Cas9 protein and the ligated RNA molecule of claim 27, under
conditions that allow for cleavage of the target locus.
31. A method for performing homologous recombination in a cell, the
method comprising: (a) introducing into the cell a nucleic acid
cutting entity capable of generating a double-stranded break at a
specified location in a nucleic acid molecule present inside a cell
to produce a cleaved nucleic acid molecule, and (b) introducing a
donor nucleic acid molecule into the cell, wherein step (a) is
performed before step (b) or wherein step (b) is performed before
step (a).
32. The method of claim 31, wherein the introduction of the nucleic
acid cutting entity or the donor nucleic acid molecule into the
cell is mediated by electroporation.
33. The method of claim 31, wherein the donor nucleic acid molecule
is double-stranded and has either blunt termini or 5'
overhangs.
34. The method of claim 31, wherein the donor nucleic acid molecule
is single stranded.
35. The method of claim 31, wherein the donor nucleic acid molecule
contains one or more nuclease resistant group at one or both
termini.
Description
PRIORITY
[0001] This application is a continuation of U.S. patent
application Ser. No. 15/842,664 filed Dec. 14, 2017, which is a
divisional of U.S. patent application Ser. No. 14/879,872, filed
Oct. 9, 2015, now U.S. Pat. No. 9,879,283 issued Jan. 30, 2018,
which application claims the benefit of priority to U.S.
Provisional Application No. 62/061,961, filed Oct. 9, 2014, U.S.
Provisional Application No. 62/101,787, filed Jan. 9, 2015 and U.S.
Provisional Application No. 62/218,826 filed Sep. 15, 2015, whose
disclosures are incorporated by reference in their entirety.
SEQUENCE LISTING
[0002] The instant application contains a Sequence Listing which
has been submitted electronically in ASCII format and is hereby
incorporated by reference in its entirety. Said ASCII copy, created
on Oct. 7, 2015, is named LT00948_SL.txt and is 98,513 bytes in
size.
FIELD
[0003] The present disclosure generally relates to compositions and
methods for the genetic modification of cells. In particular, the
disclosure relates to CRISPR reagents and the use of such
reagents.
BACKGROUND
[0004] A number of genome-editing systems, such as designer zinc
fingers, transcription activator-like effectors (TALEs), CRISPRs,
and homing meganucleases, have been developed. One issue with these
systems is that they require a both the identification of target
sites for modification and the designing of a reagents specific for
those sites, which is often laborious and time consuming. In one
aspect, the invention allows for the efficient design, preparation,
and use of genome editing reagents.
SUMMARY
[0005] The present disclosure relates, in part, to compositions and
methods for editing of nucleic acid molecules. There exists a
substantial need for efficient systems and techniques for modifying
genomes. This invention addresses this need and provides related
advantages.
[0006] CRISPR systems do not require the generation of customized
proteins to target specific sequences but rather a single Cas
enzyme that can be directed to a target nucleotide sequence (a
target locus) by a short RNA molecule with sequence complementarity
to the target.
[0007] The present disclosure is directed, in part, to CRISPR
editing system modifications that increase the usefulness of these
systems. One problem associated with gene editing systems is the
amount of time and labor required to design and produce target
locus specific gene editing reagents. The invention provides, in
part, compositions and methods for the efficient, cost-effective
production of CRISPR components.
[0008] In some specific aspects, the invention is directed to three
types of sequence specific nucleic acid binding activities. Using
the Cas9 proteins as an example, these three systems include those
where Cas9 proteins are employed with (1) double-stranded cutting
activity (e.g., one Cas9 protein gene editing systems), (2) nickase
activity (e.g., two Cas9 protein gene editing systems, referred to
as "dual nickase" systems), and (3) no cutting activity but with
the retention of nucleic acid binding activity (e.g., "dead" Cas9,
referred to as dCas9, useful, for example, for gene repression,
gene activation, DNA methylation, etc.).
[0009] In some aspects, the invention provides methods for
producing nucleic acid molecules, including methods comprising
performing polymerase chain reactions (PCR) in reaction mixtures
containing (i) a double-stranded nucleic acid segment and (ii) at
least one oligonucleotide capable of hybridizing to nucleic acid at
one terminus of the double-stranded nucleic acid segment, wherein
the nucleic acid molecule is produced by the PCR reaction, and
wherein the product nucleic acid molecule contains at or near one
terminus a promoter suitable for in vitro transcription. In some
instances, nucleic acid molecules produced by PCR reaction encode
RNA molecules of lengths from about 20 to about 300 (e.g., from
about 20 to about 250, from about 20 to about 200, from about 35 to
about 150, from about 70 to about 150, from about 40 to about 200,
from about 50 to about 200, from about 60 to about 200, from about
60 to about 125, etc.) nucleotides.
[0010] RNA molecules generated by methods of the invention (e.g.,
ligation) or encoded by nucleic acid molecules produced by methods
of the invention may contain a region (e.g., from about 10 to about
50, from about 20 to about 50, from about 30 to about 50, from
about 15 to about 40, from about 15 to about 30, etc. nucleotides)
of sequence complementarity to a target locus. Such RNA molecules
may also form one or more (e.g., two, three, four, five, etc.)
hairpin turn under physiological conditions (e.g., 37.degree. C.,
10 mM Tris-HCl, pH 7.0, 0.9% sodium chloride). Further, such RNA
molecules may be a CRISPR RNA such as a guide RNA molecule.
[0011] In additional aspects, the invention includes methods for
producing nucleic acid molecules, these methods comprising
performing polymerase chain reactions (PCR) in reaction mixtures
comprising (i) a double-stranded nucleic acid segment comprising a
first terminus and a second terminus, (ii) a first oligonucleotide
comprising a first terminus and a second terminus, wherein the
second terminus of the first oligonucleotide is capable of
hybridizing to the first terminus of the double-stranded nucleic
acid segment, and (iii) a second oligonucleotide comprising a first
terminus and a second terminus, wherein the second terminus of the
second oligonucleotide is capable of hybridizing to the first
terminus of the first oligonucleotide, to produce the nucleic acid
molecule. In some instances, the product nucleic acid molecule will
contains one or more (e.g., one, two, three, etc.) promoter
suitable for in vitro transcription at or near one terminus. Also,
in some instances, the product nucleic acid molecule will encode
one or more CRISPR RNA (e.g., a crRNA molecule, a tracrRNA
molecule, a guide RNA molecule, etc.). In some instances, reaction
mixtures further comprises a first primer and a second primer,
wherein the first primer is capable of hybridizing at or near the
first terminus of the second oligonucleotide and the second primer
is capable of hybridizing at or near the second terminus of the
double-stranded nucleic acid segment.
[0012] The invention also includes methods for producing nucleic
acid molecules, the methods comprising performing polymerase chain
reactions in reaction mixtures containing (i) a first
double-stranded nucleic acid segment comprising a first terminus
and a second terminus, (ii) a second double-stranded nucleic acid
segment comprising a first terminus and a second terminus, and
(iii) at least one oligonucleotide comprising a first terminus and
a second terminus, wherein the first terminus of the
oligonucleotide is capable of hybridizing to nucleic acid at the
first terminus of the first double-stranded nucleic acid segment to
produce the nucleic acid molecule, and wherein the second terminus
of the oligonucleotide is capable of hybridizing to nucleic acid at
the second terminus of the second double-stranded nucleic acid
segment to produce the nucleic acid molecule. In some instances,
the product nucleic acid molecule will contain one or more promoter
suitable for in vitro transcription at or near one terminus.
[0013] The invention further includes methods for producing nucleic
acid molecules, these method comprising performing polymerase chain
reactions in reaction mixtures containing (i) a first
double-stranded nucleic acid segment comprising a first terminus
and a second terminus, (ii) a second double-stranded nucleic acid
segment comprising a first terminus and a second terminus, (iii) a
first oligonucleotide comprising a first terminus and a second
terminus, and (iv) a second oligonucleotide comprising a first
terminus and a second terminus, wherein the second terminus of the
first oligonucleotide is capable of hybridizing to nucleic acid at
the first terminus of the second double-stranded nucleic acid
segment, wherein the second terminus of the second oligonucleotide
is capable of hybridizing to the first terminus of the first
oligonucleotide, wherein the second terminus of the second
oligonucleotide is capable of hybridizing to the first terminus of
the second double-stranded nucleic acid segment. In some instances,
the product nucleic acid molecules contain one or more promoter
suitable for in vitro transcription at or near (e.g., within 10
base pairs) one terminus.
[0014] The invention also includes methods for producing CRISPR RNA
molecules, these methods comprise contacting two or more linear RNA
segments with each other under conditions that allow for the 5'
terminus of a first RNA segment to be covalently linked with the 3'
terminus of a second RNA segment to form the CRISPR RNA. In some
instances, the CRISPR RNA molecules are separated from reaction
mixture components (e.g., by column chromatography, such as by
high-performance liquid chromatography).
[0015] The invention additionally includes methods for producing a
guide RNA molecules, these method comprise: (a) separately
producing a crRNA molecule and a tracrRNA molecule and (b)
contacting the crRNA molecule and the tracrRNA molecule with each
other under conditions that allow for the covalently linking of the
3' terminus of the crRNA to the 5' terminus of the tracrRNA to
produce the guide RNA molecule. Guide RNA molecules may have a
region of sequence complementarity of at least 10 (e.g., from about
10 to about 50, from about 10 to about 40, from about 10 to about
35, from about 10 to about 30, from about 10 to about 25, from
about 15 to about 25, from about 17 to about 22, etc.) nucleotides
to a target locus. In many instances, the target locus is a
naturally occurring chromosomal locus in a eukaryotic cell.
[0016] The invention also includes compositions comprising two RNA
molecules connected by a triazole group, wherein one of the RNA
molecules has a region of sequence complementarity of at least 10
nucleotides to a target locus.
[0017] In some aspects, the invention is directed to methods for
gene editing at a target locus within a cell, these methods
comprise introducing into the cell at least one CRISPR protein and
at least one CRISPR RNA, wherein the at least one CRISPR RNA has a
region of sequence complementarity of at least 10 base pairs to the
target locus. In some instances, a linear DNA segment that has
sequence homology at both termini to the target locus is also
introduced into the cell. In some instances, one of the at least
one CRISPR proteins is a Cas9 protein. This Cas9 protein may have
the ability to make a double-stranded cut in DNA or to nick
double-stranded DNA. In some instances, two Cas9 proteins are
introduced into the cells, where one Cas9 protein has a mutation
that renders to HNH domain inactive and the other Cas9 protein has
a mutation that renders to RuvC domain rendering that domain
inactive. In some instances, two RNA molecules (e.g., CRISPR RNA
molecules), each with sequence complementarity to different target
sequences, are introduced into the cell. Further, these different
target sequences may be located within forty (e.g., from about 2 to
about 40, from about 2 to about 25, from about 2 to about 20, from
about 2 to about 15, from about 2 to about 10, from about 2 to
about 8, from about 4 to about 20, from about 4 to about 15, from
about 4 to about 10, from about 6 to about 20, etc.) base pairs of
each other. Distances between sequences may be measured in
reference to the double-stranded cut or nick site. In such
instances, target sequences may overlap.
[0018] The invention further includes cells containing one or more
CRISPR system components and cells made by methods set out herein.
For example, the invention includes cells into which CRISPR
complexes have been introduced (e.g., cells that contain (1)
plasmids encoding Cas9 and guide RNA, (2) Cas9 mRNA and guide RNA,
etc.). The invention further includes cells containing mRNA
encoding dCas9 and fusion proteins thereof, as well as cells that
have been modified by methods of the invention (e.g., cells that
have undergone cleavage and relegation of cellular DNA with and
without inserts at the cleavage site) that either contain or no
longer contain one or more CRISPR system component.
BRIEF DESCRIPTION OF THE DRAWINGS
[0019] For a more complete understanding of the principles
disclosed herein, and the advantages thereof, reference is now made
to the following descriptions taken in conjunction with the
accompanying drawings, in which:
[0020] FIG. 1 is a representative diagram of a naturally occurring
CRISPR system. In addition to the "Target DNA", three additional
components are required: Cas9 protein (shaded rectangle), crRNA
(CRISPR RNA), and tracrRNA (trans-activating crRNA). The arrows
labeled "RuvC and "HNH" indicate cutting locations in the Target
DNA. The dashed box labeled "PAM" refers to protospacer adjacent
motif.
[0021] FIG. 2 shows the association between a crRNA molecule (SEQ
ID NO: 56) and a tracrRNA molecule (SEQ ID NO: 57). Hybridization
Region 1 (19 nucleotides, in this instance) is complementary to the
target site. Hybridization Region 2 is a region of sequence
complementarity between the crRNA (41 nucleotides) and the tracrRNA
(85 nucleotides). The tracrRNA 3' region is the 3' region of the
tracrRNA molecule that extends beyond Hybridization Region 2. The
Loop Replaceable Region is roughly defined by the closed box and
may be replaced with a hairpin loop to connect crRNA and tracrRNA
molecules into a single entity, typically referred to as a guide
RNA (see FIG. 3).
[0022] FIG. 3 is a schematic of a guide RNA molecule (104
nucleotides) showing the guide RNA bound to both Cas9 protein and a
target genomic locus. Hairpin Region 1 is formed by the
hybridization of complementary crRNA and tracrRNA regions joined by
the nucleotides GAAA. Hairpin Region 2 is formed by a complementary
region in the 3' portion of the tracrRNA. FIG. 3 discloses SEQ ID
NOS 58-60, respectively, in order of appearance.
[0023] FIG. 4 is a schematic showing a nicking based nucleic acid
cleavage strategy using a CRISPR system. In the top portion of the
figure, two lines represent double-stranded nucleic acid. Two nick
sites are indicated by Site 1 and Site 2. These sites are located
within a solid or dashed box indicating the region of the nucleic
acid that interacts with the CRISPR/Cas9 complex. The lower portion
of the figure show nicking actions that result in two closely
positioned nicks in both strands.
[0024] FIG. 5 is a schematic showing some methodologies for
transient CRISPR activity within cells. The introduction of Cas9
proteins and/or nucleic acid encoding Cas9 is shown on the left.
The introduction of guide RNA, crRNA plus tracrRNA, or crRNA alone
is shown on the right. The middle shows the introduction of linear
DNA encoding Cas9 or Cas9 plus tracrRNA. This DNA is designed to be
stably maintained in the cell.
[0025] FIG. 6 shows a workflow for synthesizing guide RNA using DNA
oligo templates. Guide RNA encoding DNA template is generated using
assembly PCR. Components of this assembly reaction include 1) a
target specific DNA oligo (encodes the crRNA region), 2) DNA oligo
specific to the bacterial promoter used for in vitro transcription
(in this case T7 promoter), and 3) overlapping PCR products
encoding tracrRNA region. A fill in reaction followed by PCR
amplification is performed in a Thermo cycler using DNA polymerase
enzyme (in this case high fidelity PHUSION.RTM. Taq DNA polymerase)
to generate full length gRNA encoding templates. Following PCR
assembly the resulting DNA template is transcribed at 37.degree. C.
to generate target specific gRNA using in vitro transcription
reagents for non-coding RNA synthesis (in this case
MEGASHORTSCRIPT.TM. T7 kit). Following synthesis the resulting gRNA
is purified using a column or magnetic bead based method. Purified
in vitro transcribed guide RNA is ready for co-transfection with
Cas9 protein or mRNA delivery in a host system or cell line of
interest. FIG. 6 guide RNA disclosed as SEQ ID NO: 58.
[0026] FIG. 7 shows overlapping DNA oligos as template for gRNA
synthesis. The T7 promoter sequence and the overlap region are each
about 20 nucleotides in length. Further, the box labeled "20 bp
crRNA" is the target recognition component of the crRNA. Guide RNA
is synthesized using 2 overlapping DNA oligonucleotides. 1) The
forward DNA oligo contains the T7 promoter region (or other
relevant in vitro transcription promoter), followed by target
specific crRNA encoding region and a region that overlaps with the
reverse oligonucleotide 2) Reverse DNA oligo encodes a tracrRNA
sequence that is the constant component. These two overlapping
oligonucleotides are annealed and extended to generate a DNA
template for gRNA in vitro transcription (IVT) using high fidelity
DNA polymerase enzyme (example PHUSION.RTM. Taq DNA polymerase).
The assembly reaction also includes a 2-3 PCR cycling condition to
enrich for the full length templates. The assembled DNA template is
then used to generate guide RNA at 37.degree. C. using in vitro
transcription reagents for non-coding RNA synthesis (in this case
MEGASHORTSCRIPT.TM. T7 kit was used). Following gRNA synthesis the
product is purified using a column or, alternatively, using bead
based purification methods.
[0027] FIG. 8 shows a PCR assembly based method for producing DNA
molecules that encode guide RNA molecules. In this schematic,
"Oligo 1" encodes a T7 promoter and part of Hybridization Region 1
and "Oligo 2" encode part of Hybridization Region 1 and has
overlapping sequence with the "3' PCR Segment". PCR is then used
for assembly of these overlapping fragments, followed by
amplification using the 5' and 3' primers, resulting in a
double-stranded DNA molecule containing a T7 promoter operably
connected to a target specific guide RNA coding sequence. RNA may
be produced from this double-stranded DNA molecule by in vitro
transcription. FIG. 8 guide RNA disclosed as SEQ ID NO: 58.
[0028] FIG. 9 shows PCR assembly method for synthesizing guide RNA
expressing templates by PCR assembly. This method can be used to
introduce other promoters and terminators in the context of the
guide RNA. In this schematic, the overlap region between "First
Oligo" and "Second Oligo" encode "Hybridization Region 1". The
.about. in the RNA polymerase III promoter region represents an
unrepresented segment of the nucleic acid molecule because these
promoters can be several hundred bases in length. The RNA
polymerase III terminator sequence is not shown in this figure. The
5' primer and 3' primer sequences extend beyond termini the nucleic
acid segments that they hybridize to indicate that primers may be
used to add additional functionalities to the amplified nucleic
acid molecules.
[0029] FIG. 10 shows a collection of variable crRNA molecules and a
constant tracrRNA molecule. A specific crRNA molecule (crRNA3 in
this instance) may be selected and then linked to a tracrRNA
molecule.
[0030] FIG. 11 shows an exemplary method for linking two RNA
segments. The linking reaction shown in this figure using propargyl
on one terminus and azide on the other terminus is unidirectional
in that the termini with the chemical modifications are the only
one that can link with each other.
[0031] FIGS. 12A-12F shows an alignment of Cas9 proteins of from
five Streptococcus species (SEQ ID NOS 61-63, 1 and 64,
respectively, in order of appearance). Identical amino acids are
shown as white characters on a black background. Conservative amino
acid alterations are shown as black letters on a gray
background.
[0032] FIG. 13 shows oligonucleotide designs for a one-step
synthesis of gRNA template workflow. Sequence validated PCR
fragment refers to a PCR fragment of a sequence validated
plasmid.
[0033] FIG. 14 shows data from in vivo genome cleavage and
detection assays. Gel Image A: Original cleavage assay with gRNA
amplified from a plasmid versus gRNA assembled from 6 overlapping
oligos. Less than 50% cleavage activity compared to plasmid is
seen. This is due to incorrect assembly. Gel Image B: New assembly
method as outlined in FIG. 13, with either a 20 bp overlap or 15 bp
overlap. An equivalent cleavage activity compared to the plasmid
control is seen.
[0034] FIG. 15 shows data derived from synthetic gRNA templates
that were cloned into a ZERO BLUNT.RTM. TOPO vector. Ninety-six
colonies were randomly picked for sequencing analysis. The
percentage of incorrect clones was calculated.
[0035] FIG. 16 shows data showing the effect of deletions of G's
from the 3' terminus of a T7 promoter on in vitro
transcription.
[0036] FIG. 17 shows an "all-in-one" vector containing a CD4 coding
region. The nucleotide sequence for the vector is set out in Table
9.
[0037] FIG. 18 shows an "all-in-one" vector containing an orange
fluorescent protein (OFP) coding region. The nucleotide sequence
for the vector is set out in Table 10.
[0038] FIG. 19. Cell engineering workflow. On day 1, the researcher
designs CRISPR targets and seeds cells. Synthesis of gRNA and cell
transfection with Cas9 protein/gRNA complex (Cas9 RNP) are
performed on day 2. Genome cleavage assays carried out on days 3-4.
FIG. 19 discloses SEQ ID NO: 65.
[0039] FIGS. 20A-20D. Design and synthesis of gRNA. (FIG. 20A)
Design of oligonucleotide pool. The pool consists of one 80
nucleotide tracerRNA PCR fragment, two end primers, and two 34 bp
oligonucleotides with 15 bp overlap. (FIG. 20B) One-step synthesis
of gRNA template. Four DNA oligonucleotides and one PCR fragment
were assembled in a single tube and the PCR product was analyzed by
agarose gel electrophoresis (Lanes 2 and 3). A gRNA template
prepared from all-in-one plasmid served as control (Lane 1). (FIG.
20C) In vitro transcription. Aliquots of PCR product (Lanes 2 and
3) along with the control (Lane 1) were subjected to in vitro
transcription. The resulting product was analyzed by denaturing
gel. (FIG. 20D: Error rates in synthetic gRNA templates) The DNA
template of gRNA was synthesized using the standard gene synthesis
approach with a set of short oligonucleotides (GS). Alternatively,
the oligonucleotide pool described above was used for PCR assembly.
Two standard desalted end primers (15 bp) and HPLC or PAGE-purified
end primers (15 bp*) were tested in assembly PCR reaction. The
synthetic gRNA templates as well as control gRNA template from the
`all-in-one` plasmid (plasmid) were cloned into a TOPO vector. For
each individual template, 96 colonies were randomly picked for
sequencing.
[0040] FIGS. 21A-21D. Lipid-mediated transfection. (FIG. 21A: DNA
vs. mRNA vs. Protein) Three separate genomic loci (HPRT, AAVS or
RelA) were edited via Cas9 plasmid DNA, mRNA or protein
transfection of HEK293FT cells. For the HPRT target, transfection
was performed in the presence or absence of serum. The efficiency
of genome modification was determined by Genomic Cleavage assay.
(FIG. 21B: Time course of editing) HEK293FT cells were transfected
with either plasmid DNA, Cas9 mRNA/gRNA or Cas9 RNPs directed to
the HPRT loci. Cell samples were taken at different time points and
analyzed by genomic cleavage assays. (FIG. 21C) Western Blot
analysis of samples taken at different time points. (FIG. 21D)
Off-target mutation of VEGFA T3 target caused by Cas9 plasmid DNA,
mRNA or protein transfection. Percentages of on-target mutation as
well as OT3-2 and OT3-18 off-target mutations were determined by
DNA sequencing.
[0041] FIGS. 22A-22B. Electroporation-mediated transfection. (FIG.
22A: Electroporation-mediated transfection) Mastermixes of plasmid
DNA, Cas9 mRNA/gRNA or Cas9 protein/gRNA were used to electroporate
Jurkat T cells using the Neon 24 optimized protocol, which varies
in pulse voltage, pulse width and number of pulses. The percentage
of locus-specific genome cleavage was estimated 48-hour post
transfection using a genomic cleavage assay. The letter "P" has
been positioned at the top of each protein lane for ease of data
review. The two bars to the right of each "P" are DNA and mRNA,
respectively. (FIG. 22B: Electroporation-mediated transfection)
Dose-dependent effect of genome editing. While keeping the ratio of
Cas9 protein/gRNA constant, different amounts of Cas9 RNPs were
used for electroporation using protocol 5. Experiments were done in
triplicate. The percentage of cleavage was confirmed by
sequencing.
[0042] FIGS. 23A-23D. Multiple gene editing in the human genome.
Jurkat T cells were cotransfected with either a Cas9 plasmid pool,
a Cas9 mRNA/gRNA pool or Cas9 RNP complexes targeting AAVS1 and
HPRT targets (FIG. 23A) or AAVS, RelA and HPRT gene targets (FIG.
23C). Genomic cleavage assays were performed for each locus at 48
hours post transfection. Cell aliquots were then subjected to
clonal isolation by serial dilution. After clonal expansion, each
locus was PCR-amplified from each clonal cell line. The PCR product
was then cloned into a plasmid vector and the percentage of indel
mutation was determined by sequencing of eight individual E. coli
colonies. Quantitation of double mutants for AAVS1 and HPRT was
based on 16 clonal cell lines (FIG. 23B: Efficiency of double
mutant production), whereas quantitation of triple mutants of AAVS,
RelA and HPRT was based on a total of 53 clonal cell lines derived
from three independent experiments (FIG. 23D: Efficiency of triple
mutant production).
[0043] FIG. 24 shows a workflow for sequential delivery of CRISPR
components and donor DNA into HEK293 cells and cell enrichment
wherein donor DNA was labeled with Alexa647 dye and Cas9 was fused
to GFP.
[0044] FIG. 25 shows a workflow for sequential delivery of CRISPR
components and donor DNA and cell enrichment. In this work flow,
cells are subjected to electroporation twice with donor DNA or Cas9
RNP introduced into the cells with each electroporation.
[0045] FIG. 26 shows data derived from two series of experiments
using HEK293 cells involving either co-delivery of CRISPR system
components and donor DNA or sequential delivery of CRISPR system
components and donor DNA. In brief, 2 .mu.g of Cas9 protein and 500
ng of the corresponding T1, T2 and/or T8 gRNA were added to
Suspension Buffer R (Thermo Fisher Scientific, DPBS, cat no.
#14287) to prepare the Cas9 RNP complexes. For co-delivery, 1 .mu.l
of 50 .mu.M donor DNA with either blunt end (B) or 5' protrusion
(50) was added to the 10 .mu.l reaction at this point.
Alternatively, 1 .mu.g of single strand (ss) DNA oligonucleotide
and 500 ng double stranded DNA fragment was added. The mixture was
then electroporated into a cell line having a disrupted GFP coding
sequence using 1150 volts, 20 ms and 2 pulses. The cells were
immediately transferred to a 24-well containing 500 .mu.l medium,
followed by incubation for 48 hours prior to flow cytometric
analysis. For sequential electroporation, Cas9 RNP was delivered
first into the cells, followed by a quick wash with 500 .mu.l
Suspension Buffer R. Upon centrifugation, the cell pellets were
resuspended in 10 .mu.l Suspension Buffer R. After addition of the
corresponding donor DNA molecule, the cells were electroporated
again using the same electroporation condition. The nucleotides
sequences of nucleic acid molecules used in these experiment series
are set out in Table 12.
[0046] Oligonucleotides were designed in a manner to correct an
alteration in nucleic acid encoding GFP resulting in the generation
of fluorescence upon correction. Thus, homologous recombination
corrects the alteration resulting in expression active GFP. "% of
GFP+ cells" refers to the percentage of cells that were found to
contain functionally active GFP. The same assay was used to score
homologous recombination in a number of additional experiments set
out herein.
[0047] FIG. 27 shows data for the effect of the amount of
oligonucleotide on homologous recombination. Under the conditions
tested, the optimal amount of oligonucleotide is between 0.2 to 0.5
.mu.g of single-stranded donor DNA in 10 .mu.l of Suspension Buffer
R.
[0048] FIG. 28 shows data for the effect of oligonucleotide length
and phosphorothioate modifications on homologous recombination. The
amount of oligonucleotide for the equal mass experiments was 0.33
.mu.g per 10 .mu.l reaction. For equal molarity experiments, 10
pmoles per 10 .mu.l reaction (1 .mu.M final concentration) was
used. "N" refers to no chemical modifications. "PS" refers to
phosphorothioate chemical modifications at both termini.
[0049] FIG. 29 shows a number of electroporation conditions and
data resulting from their use. The data was generated using
sequential delivery in the HEK 293 cells, first using Pstd
electroporation conditions to deliver Cas9 RNP and the second using
the indicated conditions for delivery of donor DNA. The data for
Pstd with 0.2 .mu.g of antisense donor DNA shows about a 147-fold
induction of homologous recombination over the HR background
induced by Cas9/donor without gRNA and about 47-fold induction over
Cas9 RNP background. The data for Pstd with 0.5 .mu.g of antisense
donor DNA shows about a 126-fold induction of homologous
recombination over Cas9/donor background and about 40-fold
induction over Cas9 RNP background.
[0050] FIG. 30 shows the results of an experiment to determine
gRNA/Cas9 complex stability. 50 .mu.g of gRNA was combined with 150
.mu.g of Cas9 protein, left at room temperature for 5 minutes, and
then samples were stored either at 4.degree. C. or frozen at
-20.degree. C. for the following lengths of time: 1 week (A), 2
weeks (B), 1 month (C), 2 months (D), 3 months (E), or 6 months
(F). After the designated length of time, the samples were then
screened using 293FT cells for cleavage activity using GENEART.RTM.
Genomic Cleavage Detection Kits (Thermo Fisher Scientific, Cat. No.
A24372). Cleavage activity was compared to freshly prepared
gRNA/Cas9 complexes and relative activity was calculated with 1
being the same activity for both the stored sample and the freshly
prepared sample. The errors bars indicated one standard
deviation.
[0051] FIG. 31 shows the results of an experiment to determine
gRNA/Cas9 complex stability and OPTI-MEM.RTM. culture medium
(Thermo Fisher Scientific, cat. no. 31985-070) Complex preparation
and storage conditions were as set out in the legend to FIG. 30
with 50 .mu.g of gRNA was combined with 150 .mu.g of Cas9 protein
and 10 .mu.l of OPTI-MEM.RTM..
[0052] FIG. 32 shows the results of an experiment to determine Cas9
protein and LIPOFECTAMINE.RTM. RNAiMax transfection reagent (Thermo
Fisher Scientific, cat. no. 13778-150) stability Complex
preparation and storage conditions were as set out in the legend to
FIG. 30 with 150 ng of Cas9 protein and 1.5 .mu.l of
LIPOFECTAMINE.RTM. RNAiMax at stored at 4 C or -20.degree. C. 50 ng
of gRNA mix with Opti-MEM.
DETAILED DESCRIPTION
Definitions
[0053] As used herein the term "CRISPR activity" refers to an
activity associated with a CRISPR system. Examples of such
activities are double-stranded nuclease, nickase, transcriptional
activation, transcriptional repression, nucleic acid methylation,
nucleic acid demethylation, and recombinase.
[0054] As used herein the term "CRISPR system" refers to a
collection of CRISPR proteins and nucleic acid that, when combined,
result in at least CRISPR associated activity (e.g., the target
locus specific, double-stranded cleavage of double-stranded
DNA).
[0055] As used herein the term "CRISPR complex" refers to the
CRISPR proteins and nucleic acid (e.g., RNA) that associate with
each other to form an aggregate that has functional activity. An
example of a CRISPR complex is a wild-type Cas9 (sometimes referred
to as Csn1) protein that is bound to a guide RNA specific for a
target locus.
[0056] As used herein the term "CRISPR protein" refers to a protein
comprising a nucleic acid (e.g., RNA) binding domain nucleic acid
and an effector domain (e.g., Cas9, such as Streptococcus pyogenes
Cas9). The nucleic acid binding domains interact with a first
nucleic acid molecules either having a region capable of
hybridizing to a desired target nucleic acid (e.g., a guide RNA) or
allows for the association with a second nucleic acid having a
region capable of hybridizing to the desired target nucleic acid
(e.g., a crRNA). CRISPR proteins can also comprise nuclease domains
(i.e., DNase or RNase domains), additional DNA binding domains,
helicase domains, protein-protein interaction domains, dimerization
domains, as well as other domains.
[0057] CRISPR protein also refers to proteins that form a complex
that binds the first nucleic acid molecule referred to above. Thus,
one CRISPR protein may bind to, for example, a guide RNA and
another protein may have endonuclease activity. These are all
considered to be CRISPR proteins because they function as part of a
complex that performs the same functions as a single protein such
as Cas9.
[0058] In many instances, CRISPR proteins will contain nuclear
localization signals (NLS) that allow them to be transported to the
nucleus.
[0059] The amino acid sequence of a representative Cas9 protein is
set out below in Table 1.
TABLE-US-00001 TABLE 1 Streptococcus pyogenes Cas9 (GenBank
Accession No. WP_010922251) (SEQ ID NO: 1) 1 MDKKYSIGLD IGTNSVGWAV
ITDEYKVPSK KFKVLGNTDR HSIKKNLIGA LLFDSGETAE 61 ATRLKRTARR
RYTRRKNRIC YLQEIFSNEM AKVDDSFFHR LEESFLVEED KKHERHPIFG 121
NIVDEVAYHE KYPTIYHLRK KLVDSTDKAD LRLIYLALAH MIKFRGHFLI EGDLNPDNSD
181 VDKLFIQLVQ TYNQLFEENP INASGVDAKA ILSARLSKSR RLENLIAQLP
GEKKNGLFGN 241 LIALSLGLTP NFKSNFDLAE DAKLQLSKDT YDDDLDNLLA
QIGDQYADLF LAAKNLSDAI 301 LLSDILRVNT EITKAPLSAS MIKRYDEHHQ
DLTLLKALVR QQLPEKYKEI FFDQSKNGYA 361 GYIDGGASQE EFYKFIKPIL
EKMDGTEELL VKLNREDLLR KQRTFDNGSI PHQIHLGELH 421 AILRRQEDFY
PFLKDNREKI EKILTFRIPY YVGPLARGNS RFAWMTRKSE ETITPWNFEE 481
VVDKGASAQS FIERMTNFDK NLPNEKVLPK HSLLYEYFTV YNELTKVKYV TEGMRKPAFL
541 SGEQKKAIVD LLFKTNRKVT VKQLKEDYFK KIECFDSVEI SGVEDRFNAS
LGTYHDLLKI 601 IKDKDFLDNE ENEDILEDIV LTLTLFEDRE MIEERLKTYA
HLFDDKVMKQ LKRRRYTGWG 661 RLSRKLINGI RDKQSGKTIL DFLKSDGFAN
RNFMQLIHDD SLTFKEDIQK AQVSGQGDSL 721 HEHIANLAGS PAIKKGILQT
VKVVDELVKV MGRHKPENIV IEMARENQTT QKGQKNSRER 781 MKRIEEGIKE
LGSQILKEHP VENTQLQNEK LYLYYLQNGR DMYVDQELDI NRLSDYDVDH 841
IVPQSFLKDD SIDNKVLTRS DKNRGKSDNV PSEEVVKKMK NYWRQLLNAK LITQRKFDNL
901 TKAERGGLSE LDKAGFIKRQ LVETRQITKH VAQILDSRMN TKYDENDKLI
REVKVITLKS 961 KLVSDFRKDF QFYKVREINN YHHAHDAYLN AVVGTALIKK
YPKLESEFVY GDYKVYDVRK 1021 MIAKSEQEIG KATAKYFFYS NIMNFFKTEI
TLANGEIRKR PLIETNGETG EIVWDKGRDF 1081 ATVRKVLSMP QVNIVKKTEV
QTGGFSKESI LPKRNSDKLI ARKKDWDPKK YGGFDSPTVA 1141 YSVLVVAKVE
KGKSKKLKSV KELLGITIME RSSFEKNPID FLEAKGYKEV KKDLIIKLPK 1201
YSLFELENGR KRMLASAGEL QKGNELALPS KYVNFLYLAS HYEKLKGSPE DNEQKQLFVE
1261 QHKHYLDEII EQISEFSKRV ILADANLDKV LSAYNKHRDK PIREQAENII
HLFTLTNLGA 1321 PAAFKYFDTT IDRKRYTSTK EVLDATLIHQ SITGLYETRI
DLSQLGGD
[0060] As used herein, the term "transcriptional regulatory
sequence" refers to a functional stretch of nucleotides contained
on a nucleic acid molecule, in any configuration or geometry, that
act to regulate the transcription of (1) one or more structural
genes (e.g., two, three, four, five, seven, ten, etc.) into
messenger RNA or (2) one or more genes into untranslated RNA.
Examples of transcriptional regulatory sequences include, but are
not limited to, promoters, enhancers, repressors, and the like.
[0061] As used herein, the term "promoter" is an example of a
transcriptional regulatory sequence, and is specifically a nucleic
acid generally described as the 5' region of a gene located
proximal to the start codon or nucleic acid which encodes
untranslated RNA. The transcription of an adjacent nucleic acid
segment is initiated at the promoter region. A repressible
promoter's rate of transcription decreases in response to a
repressing agent. An inducible promoter's rate of transcription
increases in response to an inducing agent. A constitutive
promoter's rate of transcription is not specifically regulated,
though it can vary under the influence of general metabolic
conditions.
[0062] As used herein, the terms "vector" refers to a nucleic acid
molecule (e.g., DNA) that provides a useful biological or
biochemical property to an insert. Examples include plasmids,
phages, autonomously replicating sequences (ARS), centromeres, and
other sequences which are able to replicate or be replicated in
vitro or in a host cell, or to convey a desired nucleic acid
segment to a desired location within a host cell. A vector can have
one or more restriction endonuclease recognition sites (e.g., two,
three, four, five, seven, ten, etc.) at which the sequences can be
cut in a determinable fashion without loss of an essential
biological function of the vector, and into which a nucleic acid
fragment can be spliced in order to bring about its replication and
cloning. Vectors can further provide primer sites (e.g., for PCR),
transcriptional and/or translational initiation and/or regulation
sites, recombinational signals, replicons, selectable markers, etc.
Clearly, methods of inserting a desired nucleic acid fragment which
do not require the use of recombination, transpositions or
restriction enzymes (such as, but not limited to, uracil N
glycosylase (UDG) cloning of PCR fragments (U.S. Pat. Nos.
5,334,575 and 5,888,795, both of which are entirely incorporated
herein by reference), T:A cloning, and the like) can also be
applied to clone a fragment into a cloning vector to be used
according to the present invention. The cloning vector can further
contain one or more selectable markers (e.g., two, three, four,
five, seven, ten, etc.) suitable for use in the identification of
cells transformed with the cloning vector.
[0063] As used herein the term "nucleic acid targeting capability"
refers to the ability of a molecule or a complex of molecule to
recognize and/or associate with nucleic acid on a sequence specific
basis. As an example, Hybridization Region 1 on a crRNA molecule
confers nucleic acid targeting capability upon a CRISPR
complex.
[0064] As used herein the term "target locus" refers to a site
within a nucleic acid molecule for CRISPR system interaction (e.g.,
binding and cleavage). When a single CRISPR complex is designed to
cleave double-stranded nucleic acid, then the target locus is the
cut site and the surrounding region recognized by the CRISPR
complex. When two CRISPR complexes are designed to nick
double-stranded nucleic acid in close proximity to create a
double-stranded break, then the region surrounding and including
the break point is referred to as the target locus.
[0065] A "counter selectable" marker (also referred to herein a
"negative selectable marker") or marker gene as used herein refers
to any gene or functional variant thereof that allows for selection
of wanted vectors, clones, cells or organisms by eliminating
unwanted elements. These markers are often toxic or otherwise
inhibitory to replication under certain conditions which often
involve exposure to a specific substrates or shift in growth
conditions. Counter selectable marker genes are often incorporated
into genetic modification schemes in order to select for rare
recombination or cloning events that require the removal of the
marker or to selectively eliminate plasmids or cells from a given
population. One example of a negative selectable marker system
widely used in bacterial cloning methods is the ccdA/ccdB
toxin-antitoxin system.
[0066] Overview:
[0067] The invention relates, in part, to compositions and methods
for the preparation of nucleic acid molecules. In particular, the
invention relates to combinations of proteins and nucleic acid
molecules designed to interact with other nucleic acid molecules.
More specifically, the invention relates to protein nucleic acid
complexes, where the nucleic acid component has sequence
complementarity to a target nucleic acid molecule. In these
systems, sequence complementarity between the complexed nucleic
acid and the target nucleic acid molecule is the used to bring the
complex into association with the target nucleic acid. Once this
occurs, functional activities associated with the complex may be
used to modify the target nucleic acid molecule.
[0068] The invention is exemplified by CRISPR systems. The term
"CRISPR" is a general term that applies to three type of systems,
and system sub-types. In general, the term CRISPR refers to the
repetitive regions that encode CRISPR system components (e.g.,
encoded crRNAs). Three types of CRISPR systems (see Table 2) have
been identified, each with differing features.
TABLE-US-00002 TABLE 2 CRISPR System Types Overview System Features
Example Type I Multiple proteins (5-7 proteins S. epidermidis (Type
IA) typical), crRNA, requires PAM. DNA Cleavage is catalyzed by
Cas3. Type II 3-4 proteins (one protein (Cas9) has Streptococcus
pyogenes nuclease activity) two RNAs, CRISPR/Cas9 requires PAMs.
Target DNA cleavage catalyzed by Cas9 and RNA components. Type III
Five or six proteins required for S. epidermidis cutting, number of
required RNAs (Type IIIA); unknown but expected to be 1, P.
furiosus PAMs not required. Type IIIB (Type IIIB); systems have the
ability to target RNA.
[0069] While the invention has numerous aspects and variations
associated with it, the Type II CRISPR/Cas9 system has been chosen
as a port of reference for explanation herein.
[0070] In certain aspects, the invention provides: [0071] 1.
Individual oligonucleotides to make crRNA/tracrRNAs and collections
of such oligonucleotides, as well as methods for generating and
using such oligonucleotides. [0072] 2. Compositions and methods for
introducing CRISPR complex components into cells.
[0073] FIG. 1 shows components and molecular interactions
associated with a Type II CRISPR system. In this instance, the Cas9
mediated Streptococcus pyogenes system is exemplified.
[0074] A crRNA is shown in FIG. 1 hybridizing to both target DNA
(Hybridization Region 1) and tracrRNA (Hybridization Region 2). In
this system, these two RNA molecules serve to bring the Cas9
protein to the target DNA sequence is a manner that allows for
cutting of the target DNA. The target DNA is cut at two sites, to
form a double-stranded break.
[0075] There appears to be substantial sequence variation in
tracrRNA sequence. It has been postulated that tracrRNA function
relates more to RNA structure, than RNA sequence.
[0076] The Cas9 protein of Streptococcus pyogenes is 1368 amino
acids in length (NCBI Reference Sequence: WP_030126706.1) and
contains a number of domains for the binding and cutting of nucleic
acid molecules. This protein has two domains (RuvC and HNH), each
of which has DNA nickase activity. When this protein nicks DNA on
both strands, the nicks are in close enough proximity to result in
the formation of a double-stranded break.
[0077] In some instances, CRISPR proteins will contain one or more
of the following amino acid sequences: (1) YSIGLDIGTNSVG (SEQ ID
NO: 2), (2) PTIYHLR (SEQ ID NO: 3), (3) RGHFLIE (SEQ ID NO: 4), (4)
TKAPLSASM (SEQ ID NO: 5), (5) LRKQRTFDNG (SEQ ID NO: 6), (6)
LTFRIPYYVGPLAR (SEQ ID NO: 7), (7) TLTLFEDREMI (SEQ ID NO: 8), (8)
AGSPAIKKGILQ (SEQ ID NO: 9), (9) RQLVETRQITKHVA (SEQ ID NO: 10)
and/or (10) QTGGFSKESIL (SEQ ID NO: 11).
[0078] While not wishing to be bound by theory, in brief, as shown
in FIG. 1, crRNA hybridizes to target DNA, referred to as
"Hybridization Region 1". Hybridization region 1 is typically in
the range of 18 to 22 base pairs but can be longer or shorter. The
crRNA thus "indentifies" the target DNA sequence. The crRNA also
hybridizes to the tracrRNA, referred to as "Hybridization Region
2". Hybridization Region 1 is typically in the range of 15 to 25
base pairs but can be longer or shorter and often there is not have
full sequence complementarity between the hybridized strands. The
tracrRNA is believed to associate with the Cas9 protein, bringing
the RuvC and HNH cleavage domains in contact with the target
DNA.
[0079] A number of features of the CRISPR/Cas9 system, any or all
of which may be used in the practice of the invention, have been
identified: [0080] 1. crRNA and tracrRNA may be combined to form a
guide RNA (gRNA). [0081] 2. Mutations may be introduced into Cas9
proteins that inactivate either the RuvC or HNH domains resulting
in proteins with strand specific nickase activity. [0082] 3.
Mutations may be introduced into Cas9 proteins that inactivate all
nucleic acid cleavage activities but allow for these proteins to
retain nucleic acid binding activity. [0083] 4. Sequence
alterations, including truncations and multi-nucleotide deletions,
can be made to the CRISPR system RNA components.
[0084] One limitation on Type II CRISPR systems is the requirement
of a protospacer adjacent motif (PAM) for high level activity.
Efficient binding and cleavage of DNA by Cas9-RNA requires
recognition of a PAM. Typically, PAMs are three nucleotides in
length.
[0085] In many instances, it will be desirable to make two nicks in
close proximity to each other when cleaving nucleic acid using
methods of the invention. This is especially so when the target
locus is in a cellular genome. The use of CRISPR system components
that nick nucleic acid is believed to limit "off-target effects" in
that a single nick at a location other than the target locus is
unlikely to result in single-stranded cleavage of the nucleic
acid.
[0086] FIG. 4 shows the selection of two closely associated sites
that form a target locus. Each of the sites (Site 1 and Site 2)
binds a CRISPR complex with nickase activity.
[0087] The two sites exemplified in FIG. 4 will generally be
located sufficiently close to each other so that the
double-stranded nucleic acid containing the nick breaks. While this
distance will vary with factors such as the AT/CG content of the
region, the nick sites will generally be within 200 base pairs of
each other (e.g., from about 1 to about 200, from about 10 to about
200, from about 25 to about 200, from about 40 to about 200, from
about 50 to about 200, from about 60 to about 200, from about 1 to
about 100, from about 10 to about 100, from about 20 to about 100,
from about 30 to about 100, from about 40 to about 100, from about
50 to about 100, from about 1 to about 60, from about 10 to about
60, from about 20 to about 60, from about 30 to about 60, from
about 40 to about 60, from about 1 to about 35, from about 5 to
about 35, from about 10 to about 35, from about 20 to about 35,
from about 25 to about 35, from about 1 to about 25, from about 10
to about 25, from about 15 to about 25, from about 2 to about 15,
from about 5 to about 15, etc. base pairs).
[0088] In many instances, CRISPR complexes bind with high affinity
to the target locus. In many such instances, when double-stranded
breaks at the target locus are desired CRISPR complexes will be
directed to the target locus in a manner such that they do not
strictly interfere with each other. Thus, the invention includes
methods in which CRISPR complex binding sites at a target locus are
selected such that nicking activity on each strand is not
significantly altered by the binding of a CRISPR complex directed
to the nicking of the other strand. The invention further includes
compositions for performing such methods.
TABLE-US-00003 TABLE 3 Predicted S. pyogenes Cas9 Functional
Regions Description Positions Length RuvC-I 1-62 62 Recognition
lobe 60-718 659 RuvC-II 718-765 48 HNH 810-872 63 RuvC-III 925-1102
178 PAM-interacting domain 1099-1368 270 PAM substrate binding
1125-1127 3
[0089] S. pyogenes Cas9 protein has a number of domains (see Table
3), two of which are nuclease domains. The discontinuous RuvC-like
domain is encompassed by approximately amino acids 1-62, 718-765
and 925-1102. The HNH nuclease domain is encompassed by
approximately amino acids residues 810-872. The recognition lobe,
approximately amino acids 60-718, recognizes and binds regions of
guide RNAs in a sequence-independent manner. Deletions of some
parts of this lobe abolishes CRISPR activity. The PAM-interacting
domain, approximately amino acids 1099-1368, recognizes the PAM
motif.
[0090] The nicking activity may be accomplished in a number of
ways. For example, the Cas9 protein has two domains, termed RuvC
and HNH, that nick different strands of double-stranded nucleic
acid. Cas9 proteins may be altered to inactivate one domain or the
other. The result is that two Cas9 proteins are required to nick
the target locus in order for a double-stranded break to occur. For
example, an aspartate-to-alanine substitution (D10A) in the RuvC
catalytic domain of Cas9 from S. pyogenes converts Cas9 from a
nuclease that cleaves both strands to a nickase (cleaves a single
strand). Other examples of mutations that render Cas9 a nickase
include H840A, N854A, and N863A.
[0091] CRISPR proteins (e.g., Cas9) with nickase activities may be
used in combination with guide sequences (e.g., two guide
sequences) which target respectively sense and antisense strands of
the DNA target.
[0092] Another way to generate double-stranded breaks in nucleic
acid using nickase activity is by using CRISPR proteins that lack
nuclease activity linked to a heterologous nuclease domain. One
example of this is a mutated form of Cas9, referred to as dCas9,
linked to FokI domain. FokI domains require dimerization for
nuclease activity. Thus, in such instances, CRISPR RNA molecules
are used to bring two dCas9-FokI fusion proteins into sufficiently
close proximity to generate nuclease activity that results in the
formation of a double-stranded cut. Methods of this type are set
out in Tsai et al., "Dimeric CRISPR RNA-guided FokI nucleases for
highly specific genome editing," Nature Biotech., 32:569-576 (2014)
and Guilinger et al., "Fusion of catalytically inactive Cas9 to
FokI nuclease improves the specificity of genome modification,"
Nature Biotech., 32:577-582 (2014).
[0093] Transient Activity
[0094] One need is for a genome editing system having transient or
highly regulatable activity. Transient activity is important for a
number of applications. For example, for construction of cells
lines involving one or more nuclease activity. Once a cellular
nucleic acid, for example, has been effectively exposed to a
nuclease and appropriately cut, repair of the nucleic acid (e.g.,
via non-homologous end-joining) normally takes place. Repair of the
cellular nucleic acid is generally required for the cell to remain
viable. In many cases, the cell will either integrate nucleic acid
into the repaired nucleic acid molecule or nucleic acid will be
removed (e.g., from 1 base pair to about 100 base pairs) for the
repaired nucleic acid molecule. In either instance, a heritable
change occurs within the genome of the cell. Cells with genetic
changes can then be screened to identify ones with a desired
alteration. Once cells with desired changes are identified, for
most applications, it is beneficial to maintain the cells without
further nuclease induced genetic change. Thus, it is generally
desirable that the nuclease activity used to facilitate the genetic
changes not be active within the cells.
[0095] Transient activity can be achieved in a number of ways, some
of which are represented in FIG. 5. CRISPR systems typically
require that all necessary components be present for activity.
Using a CRISPR/Cas9 system for reference, a target nucleic acid
molecule must be contacted with a Cas9 protein and one or more
CRISPR nucleic acid molecules (e.g., either (1) a crRNA molecule
and a tracrRNA molecule or (2) a guide RNA molecule).
[0096] The invention thus includes compositions and methods for
transient CRISPR mediate activities (e.g., nuclease activity).
Transient activity may be the generated in any number of ways. One
feature of CRISPR systems is that all components typically need to
come together for activity. These components are (1) one or more
CRISPR proteins (e.g., Cas9), (2) Hybridization Region 1 (e.g.,
crRNA), and (3) nucleic acid that associates with both
Hybridization Region 1 and the one or more CRISPR proteins. Thus,
if one or more components required for CRISPR mediate activity is
removed, then the activity is inhibited.
[0097] Using the Cas9 based CRISPR system for purposes of
illustration, three components are required for CRISP mediated
activity: (1) Cas9 protein, (2) crRNA, and (3) tracrRNA. Thus,
transient systems can be generated by the time limited presence of
any one of these components. A number of variations are represented
in FIG. 5.
TABLE-US-00004 TABLE 4 Exemplary CRISPR Components Format 1 Format
2 Row Cas9 Protein crRNA tracrRNA Guide RNA No. (Col. A) (Col. B)
(Col. C) (Col. D) 1 Integrated Integrated Integrated Integrated
Coding Seq. Coding Seq. Coding Seq. Coding Seq. 2 Protein crRNA
tracrRNA Guide RNA 3 Linear Linear Linear Linear Coding Seq. Coding
Seq. Coding Seq. Coding Seq. 4 Vector Vector Vector Vector 5 mRNA
-- -- --
[0098] As noted above, in Cas9 mediated system, Cas9 protein must
be present for activity. Further, proteins normally are fairly
stable molecules within cells. Cas9 proteins may be modified to
enhance intracellular degradation (e.g., proteosome mediated
degradation) by, for example, ubiquitination.
[0099] Cas9 protein may be either introduced into cells (Row 2,
Column A) or produced intracellularly (Rows 1, 3, 4, and 5, Column
A). Further, the duration of time that Cas9 protein is taken up or
produced intracellularly and the amount that is present
intracellularly may be controlled or regulated. As an example, a
chromosomally integrated Cas9 protein coding sequence may be
operably linked to a regulatable promoter. Further, the amount of
mRNA encoding Cas9 protein introduced into cells may be
regulated.
[0100] With respect to non-coding CRISPR RNA needed to high level
CRISPR activity, at least two formats are possible: (1) separate
crRNA and tracrRNA molecules and (2) Guide RNA (see Table 4).
[0101] The invention thus includes compositions and method for
transient production of CRISPR mediated activities within cells.
Such methods include, for example, the use of a combination of
stable and unstable CRISPR system components. One example is a
system where mRNA encoding wild-type Cas9 protein and a guide RNA
are introduced into a cell in roughly equal amounts. In this
example, the presence of Cas9 mRNA will result in the production of
a stable Cas9 protein and the limiting factor on CRISPR mediated
activity will typically be the determined by the amount of guide
RNA present and guide RNA degradation.
[0102] The production and/or intracellular introduction of various
components of CRISPR mediated systems in a number of ways. For
example, a cell designed for convenient CRISPR system
reconstitution could be produced. One example of such a cell would
be a mammalian cell line (e.g., CHO, 293, etc.) that contains
nucleic acid encoding Cas9 protein and tracrRNA integrated into the
genome. CRISPR mediated activities can then be directed to a
specific target sequence by the introduction into the cell line
(e.g., via transfection) of crRNA. In such an exemplary cell line,
Cas9 and/or tracrRNA coding sequences may be constitutively
expressed or regulatably expressed (e.g., operably linked to an
inducible or a repressible promoter).
[0103] The invention thus includes cell lines (e.g., eukaryotic
cells lines) that contain one or more component of a CRISPR system,
as well as methods for directing one or more CRISPR mediated
activity to specific target loci within such cells. In many
instances, this will result from the addition to or production of
at least one additional component that results in target locus
CRISPR mediated activities within the cell.
[0104] Hybridization Region 1 (HR1)
[0105] HR1 (also referred to as Target Complementary crRNA) is
believed to determine the target nucleic acid sequence to which the
CRISPR complex associates with. HR1 may vary in length, nucleotide
composition (e.g., AT/CG ratio), and level of sequence
complementarity with the target sequence (e.g., 100%).
[0106] As noted above, the length of HR1 may vary. The length of
HR1 is determined by the number of nucleotides of sequence
complementarity to target nucleic acid, not including internal
mismatches. For example, if the crRNA or guide RNA has a twenty-two
nucleotide region where the ten 5' most terminal nucleotide and the
ten 3' most terminal nucleotides are 100% complementary to the
sequence of a target nucleic acid, then the HR1 region is
twenty-two nucleotides in length with two internal mis-matches. In
such an instance, HR1 would share about 91% sequence
complementarity with the sequence of the target nucleic acid.
[0107] HR1 used in compositions and methods of the invention may
vary from about 12 nucleotides to about 35 nucleotides (e.g., from
about 13 nucleotides to about 33 nucleotides, from about 15
nucleotides to about 33 nucleotides, from about 17 nucleotides to
about 33 nucleotides, from about 18 nucleotides to about 33
nucleotides, from about 19 nucleotides to about 33 nucleotides,
from about 20 nucleotides to about 33 nucleotides, from about 21
nucleotides to about 33 nucleotides, from about 13 nucleotides to
about 30 nucleotides, from about 15 nucleotides to about 30
nucleotides, from about 18 nucleotides to about 30 nucleotides,
from about 20 nucleotides to about 30 nucleotides, from about 13
nucleotides to about 27 nucleotides, from about 15 nucleotides to
about 27 nucleotides, from about 18 nucleotides to about 27
nucleotides, from about 20 nucleotides to about 27 nucleotides,
from about 13 nucleotides to about 25 nucleotides, from about 15
nucleotides to about 25 nucleotides, from about 17 nucleotides to
about 25 nucleotides, from about 18 nucleotides to about 25
nucleotides, from about 20 nucleotides to about 25 nucleotides,
from about 13 nucleotides to about 23 nucleotides, from about 15
nucleotides to about 23 nucleotides, from about 18 nucleotides to
about 23 nucleotides, from about 20 nucleotides to about 23
nucleotides, etc.).
[0108] HR1 may be designed with sequence complementarity to target
nucleic acid with particular ratios AT/CG. AT/CG may be altered to
adjust hybridization "affinity" between HR1 and the specific target
nucleic acid. A-T pairs hybridize less tightly than C-G pairs.
Thus, hybridization strength can be varied by altering the AT/CG
ratio of HR1. In some instance, higher binding affinity and in some
instances lower binding affinity may be desired.
[0109] Further, crRNA and guide RNA molecules may be designed with
AT/CG contents for the reduction of off target effects. The human
genome, for example, has an average CG content of around 41 to 42%.
Thus, nucleic acids containing an HR1 with a CG content of greater
or less than 41 to 42% are less likely to share significant
sequence complementarity with nucleic acid other than intended the
target nucleic acid. Also, fewer off target effects would be
expected the further the AT/CG ratio of HR1 and the target nucleic
acid are from the average AT/CG ratio of the genome or other
nucleic acid molecule being altered.
TABLE-US-00005 TABLE 5 Genomic CG Content of Select Eukaryotes
Genome Avg. CG Content Homo sapiens 41 to 42% Arabidopsis thaliana
~36% Saccharomyces cerevisiae ~38% Plasmodium falciparum ~20%
[0110] HR1 used in compositions and methods of the invention thus
may have AT/CG ratios in the range of from about 1:5 to about 5:1
(e.g., from about 1:4 to about 5:1, from about 1:3 to about 5:1,
from about 1:2 to about 5:1, from about 1:1 to about 5:1, from
about 1:5 to about 4:1, from about 1:4 to about 4:1, from about 1:3
to about 4:1, from about 1:2 to about 4:1, from about 1:1 to about
4:1, from about 1:5 to about 3:1, from about 1:4 to about 3:1, from
about 1:3 to about 3:1, from about 1:2 to about 3:1, from about 1:1
to about 3:1, from about 1:5 to about 2:1, from about 1:4 to about
2:1, from about 1:3 to about 2:1, from about 1:2 to about 2:1, or
from about 1:1 to about 2:1).
[0111] Binding affinity between HR1 and the target nucleic acid can
be varied by a combination of HR1 length, AT/CG content, and
percent sequence complementarity. In most instances, sequence
between HR1 and the target nucleic acid will be 100% but this can
vary between from about 80% to about 100%, from about 90% to about
100%, from about 95% to about 100%, from about 80% to about 95%,
from about 85% to about 95%, or from about 90% to about 95%. HR1
used in compositions and methods of the invention may have sequence
complementarity characteristics referred to above.
[0112] HR1 may also be designed using bioinformatic data to limit
off-target effects. Complete genome sequence data is available for
thousands of genomes. When a CRISPR system is engineered to modify
the genome of a specific organism, the genome of that organism
(assuming the genome sequence is known) may be analyzed the select
a region that is unique and/or has no counter-part region with a
sequence similar enough for substantial levels of CRISPR complex
binding. This may be done through a combination of site selection
and preparation of HR1 to binding to the selected site.
[0113] Hybridization Region 2 (HR2)
[0114] HR2 is a region of sequence complementarity either (1)
between the crRNA and the tracrRNA or (2) within the guide RNA. In
a guide RNA, this region forms a hairpin (Hairpin Region 1 in FIG.
3).
[0115] CRISPR Proteins
[0116] Depending upon the type of CRISPR system, one or more CRISPR
proteins (e.g., Cas9) may be used. These CRISPR proteins are
targeted to a first nucleic acid of defined sequence (a target
locus) by a second nucleic acid and function either alone or in
conjunction with other proteins. Thus, the CRISPR complex is a
nucleic acid guided, nucleic acid recognition system.
[0117] CRISPR proteins or protein complexes will typically have
binding activity for one or more CRISPR oligonucleotides and a
nucleic acid modification activity (e.g., recombinase activity,
methylase activity, etc.). Further, a nuclear localization signal
may be present in CRISPR proteins or protein complexes, especially
when (1) generated in or (2) designed or produced for introduction
into a eukaryotic cell.
[0118] Thus, CRISPR proteins may be fusion proteins comprising, for
example, the CRISPR protein or fragment thereof and an effector
domain. Suitable effector domains include, for example nucleic acid
cleavage domains (e.g., heterologous cleavage domains such as the
cleavage domain of the endonuclease FokI), epigenetic modification
domains, transcriptional activation domains (e.g., a VP16 domain),
and transcriptional repressor domains. Each fusion protein may be
guided to a specific chromosomal locus, for example, by a specific
guide RNA, wherein the effector domain mediates targeted genome
modification or gene regulation.
[0119] In some aspects, the fusion proteins can function as dimers
thereby increasing the length of the target site and increasing the
likelihood of its uniqueness in the genome (thus, reducing off
target effects). For example, endogenous CRISPR systems modify
genomic locations based on DNA binding word lengths of
approximately 13-20 bp (Cong et al., Science, 339:819-823
(2013).
[0120] CRISPR proteins may be synthesized and/or purified by any
number of means. In many instances, CRISPR proteins will be
produced within the cell in which activity is desired. In some
instances, CRISPR proteins may be produced extracellular to the
cell in which activity is desired and then introducing into the
cell. Example of methods for producing such CRISPR proteins is by
in vitro translation, extraction of the proteins from cell that
express these proteins encoded by an expression vector, and
extraction of these proteins from cell that normally express
them.
[0121] CRISPR Oligonucleotides
[0122] CRISPR oligonucleotides may be produced by a number of
methods and may be generated to have varying features. In many
instances, CRISPR oligonucleotides will be one component or two
components. By "one component" is meant that only one
oligonucleotide (e.g., guide RNA) is necessary for CRISPR activity.
By "two components" is meant that only two different
oligonucleotides (e.g., crRNA and tracrRNA) are required for CRISPR
activity. CRISPR systems with more than two components may also be
designed, produced and used. Thus, the invention contemplates
multi-components CRISPR oligonucleotides where functionality
involves three, four, five, etc. oligonucleotides.
[0123] In some instances, two or more oligonucleotides may be
generated separately and then joined to each other to form, for
example, one oligonucleotide that functions as part of a CRISPR
system. The number of components of a system is determined by
interaction with Cas9. As an example, if two oligonucleotides are
produced and then joined prior to introduction into a cell, where
the joined oligonucleotide requires no additional oligonucleotides
to facilitate a CRISPR mediated activity, then this is said to be a
one component system.
[0124] Of course, the nucleotide sequences and other features of
CRISPR oligonucleotides may vary with specific systems and desired
functions. Common features of CRISPR oligonucleotides include
association with one or more CRISPR complex protein (e.g., Cas9)
and nucleic acid "targeting" capability.
[0125] The invention thus includes compositions and methods for the
production of CRISPR oligonucleotides, as well as collections of
oligonucleotides generated, for example, using such compositions
and methods.
[0126] In some embodiments, compositions and methods of the
invention are directed to one of or a combination of molecular
biology synthesis (e.g., PCR) and/or chemical synthesis for the
generation of CRISPR oligonucleotides. Using the schematic
representation shown in FIG. 6 for reference, two chemically
synthesized oligonucleotides encoding components of a guide RNA may
be designed to hybridize with each other and be extended to form a
fully double-stranded nucleic acid molecule (e.g., DNA).
[0127] FIG. 6 shows an exemplary workflow of the invention. The
schematic in FIG. 6 shows oligonucleotides designed to generate a
DNA molecule where the guide RNA coding region is operably linked
to a T7 promoter. In this work flow DNA oligonucleotides either
alone or in conjunction with double-stranded DNA are used to
generate, via PCR, a DNA molecule encoding a guide RNA operably
linked to a promoter suitable for in vitro transcription. The DNA
molecule is then transcribed in vitro to generate guide RNA. The
guide RNA may then be "cleaned up" by, for example, column
purification or bead based methods. The guide RNA is then suitable
for use by, as examples, (1) direct introduction into a cell or (2)
introduction into a cell after being complexed with one or more
CRISPR protein. Nucleic acid operably connected to a T7 promoter
can be transcribed in mammalian cells when these cells contain T7
RNA polymerase (Lieber et al., Nucleic Acids Res., 17: 8485-8493
(1989)). Of course, other promoters functional in eukaryotic cells
(e.g., CMV promoter, U6 promoter, H1 promoter, etc.) could also be
used for the intracellular production of guide RNA. The H1
promoter, for example, is about 300 base pairs in length. One
advantage of the T7 promoter is its small size (20 base pairs). On
specific T7 promoter that may be used in compositions and methods
of the invention include those having the following nucleotide
sequence: GAAATTAATACGACTCACTATAG (SEQ ID NO: 12).
[0128] The T7 promoter may also be used to generate guide RNA in an
in vitro transcription system. In this instance, the
double-stranded nucleic acid molecule would be used to generate
guide RNA extracellularly for introduction into a cell.
[0129] Advantages of the guide RNA generation methods set out in
FIG. 6 are speed and low cost of production. In particular, once a
target sequence has been identified the Forward Oligo may be
generated and combined with the Reverse Oligo in a reaction mixture
designed to extend each of the oligonucleotides to form the
double-stranded nucleic acid molecule (see FIG. 7). The Forward
Oligo encodes the crRNA sequence designed with sequence
complementarity to the target locus. Further, the Reverse Oligo has
a sequence that is common to guide RNAs. The Reverse Oligo may be
generated by any means and stored as a standard component. The
Forward Oligo, however, is target sequence specific so it must be
designed in view of the target locus.
[0130] Two oligonucleotides suitable for the generation of
double-stranded DNA suitable for transcription as set out in FIG. 6
are shown in FIG. 7. In the schematic of FIG. 7, the "Forward
Oligo" is tailored for the target locus because it contains
Hybridization Region 1 of the target specific crRNA. The "Reverse
Oligo" contains regions of the tracrRNA and crRNA that are not
target locus specific. Thus, the "Reverse Oligo" can be a "stock"
component. The invention thus includes compositions and methods for
the formation of guide RNA molecules. Methods of this aspect of the
invention may comprise one or more of the following, [0131] a.
identification of a target locus, [0132] b. the in silico design of
one or more CRISPR RNA molecules with sequence complementarity to
that locus, [0133] c. the production of a first oligonucleotide
with a promoter sequence, a region of sequence complementarity
(e.g., 15 to 25 nucleotides in length) to the target locus, [0134]
d. incubating the first oligonucleotide with (i) a second
oligonucleotide and (ii) a polymerase under conditions suitable for
performing polymerase chain reaction (PCR) to generate a
double-stranded nucleic acid molecule, wherein the first
oligonucleotide and the second oligonucleotide have a region of
sequence complementarity of sufficient length to allow for
hybridization between the two oligonucleotides, and [0135] e.
performing an in vitro transcription reaction on the PCR generated
double-stranded nucleic acid molecule to produce a guide RNA
molecule, and [0136] f. purifying the guide RNA molecule from the
other components of the reaction mixture.
[0137] In the work flow shown in FIG. 8, two oligonucleotides with
the T7 promoter and Hybridization Region 1 nucleic acid and a
Double-Stranded Nucleic Acid Segment are assembled by PCR. In this
workflow, the Double-Stranded Nucleic Acid Segment has a constant
sequence and, thus, can be a stock component.
[0138] The two oligonucleotides form the full length
double-stranded nucleic acid segment via a polymerase mediated
assembly reaction. Once the full length product molecule is
assembled, further PCR reactions amplify the product. The primers
prevent the two oligonucleotides from being PCR "limiting"
components. In other words, once the product nucleic acid molecule
has been generated, the primers allow for amplification to continue
after the first and second oligonucleotides have been consumed.
[0139] FIG. 9 shows a process similar to that represented in FIG. 8
but the assembly reaction links two double-stranded nucleic acid
segments and inserts specific nucleic acid in between them. Thus,
the method represented in FIG. 9 is especially useful for the
insertion of a nucleic acid segment of designed sequence between to
selected nucleic acid molecules.
[0140] With respect to CRISPR RNA coding sequence construction, the
First Oligonucleotide and the Second Oligonucleotide may be
synthesized to hybridize with the First Nucleic Acid Segment and
the Second Nucleic Acid Segment. Each of these oligonucleotides
also encode all or part of Hybridization Region 1. Assembly
reactions may thus be designed to generate, for example, a DNA
molecule that encodes a target locus specific guide RNA operably
linked to a promoter.
[0141] While only one oligonucleotide is required for assembly
reactions of the type shown in FIG. 9, two will generally be used
because crRNA Hybridization Region 1 is typically about 20 bases in
length and about 15 bases of sequence identity is desired for
efficient hybridization to the First Nucleic Acid Segment and the
Second Nucleic Acid Segment. While oligonucleotides of 45 to 55
bases can be chemically synthesized, sequence fidelity often drops
with length. The introduction of crRNA Hybridization Region 1
segment with low sequence results in two issues: (1) An increase in
"off-target" effects can occur due to the Hybridization Region 1
associating with loci other that the desired target locus and (2)
decreased target locus interaction efficiency of the encoded guide
RNAs.
[0142] The second issue above occurs when heterogeneous PCR
assembled nucleic acid (e.g., DNA) are transcribed (e.g., via in
vitro transcription) and then introduced into cells. In general,
the lower the level of sequence fidelity in the original assembly
oligonucleotide population, the greater the variation in
Hybridization Region 1 of the expressed guide RNA population. One
way to address this problem is to use oligonucleotides generated
with high sequence fidelity.
[0143] FIG. 9 represents a design for synthetic guide RNA
expression cassette assembly. In this design, target specific
variable crRNA region is encoded by the 35 to 40 base pair DNA
oligo (represented here has first and second oligo). All the
remaining DNA oligos and double stranded DNA segments may be
constant components. These constant components include 1) a first
double stranded nucleic acid segment encoding, for example, an RNA
polymerase III promoter that can be leveraged for expressing the
non-coding guide RNA component in vivo 2) a second double stranded
nucleic acid segment encoding the tracrRNA component, and 3) 5' and
3' primers for amplification and enrichment of full length guide
RNA expression templates containing the RNA polymerase III
promoter. Full length guide RNA expression cassette containing
relevant RNA polymerase III promoter is generated by assembly PCR
using the double stranded nucleic acid segments, target specific
overlapping oligos and flanking PCR primers. Assembly PCR is
performed using a Taq DNA polymerase (e.g., PHUSION.RTM. Taq DNA
polymerase), with the resulting product being column purified prior
to delivery into host cell line of interest. Methods such as this
can also be used to generate guide RNA expression cassettes
containing any user defined promoter.
[0144] The invention further includes compositions and methods for
the assembly of CRISPR RNA molecules (e.g., guide RNA molecules).
CRISPR RNA molecules may be assembled by the connection of two or
more (e.g., two, three, four, five, etc.) RNA segments with each
other. In particular, the invention includes methods for producing
nucleic acid molecules, these methods comprising contacting two or
more linear RNA segments with each other under conditions that
allow for the 5' terminus of a first RNA segment to be covalently
linked with the 3' terminus of a second RNA segment.
[0145] This form of assembly has the advantage that it allows for
rapid and efficient assembly of CRISPR RNA molecules. Using the
schematic shown in FIG. 10 for purposes of illustration, guide RNA
molecules with specificity for different target sites can be
generated using a single tracrRNA molecule/segment connected to a
target site specific crRNA molecule/segment. FIG. 10 shows four
tubes with different crRNA molecules with crRNA molecule 3 being
connected to a tracrRNA molecule to form a guide RNA molecule.
Thus, FIG. 10 shows the connection of two RNA segments to for a
product RNA molecule. Thus, the invention includes compositions and
methods for the connection (e.g., covalent connection) of crRNA
molecules and tracrRNA molecules.
[0146] The invention also includes compositions and methods for the
production of guide RNA molecules with specificity for a target
site, the method comprising: (1) identification of the target site,
(2) production of a crRNA segment, and (3) connection of the crRNA
segment with a tracrRNA segment. In such methods, the tracrRNA
segment may be produced prior to connection with the crRNA and
stored as a "stock" component or the tracrRNA segment may be
generated from a DNA molecule that encodes the tracrRNA.
[0147] RNA molecules/segments connected to each other in the
practice of the invention may be produced by any number of means,
including chemical synthesis and transcription of DNA molecules. In
some instances, RNA segments connected to each other may be
produced by different methods. For example, a crRNA molecule
produced by chemical synthesis may be connected to a tracrRNA
molecule produced by in vitro transcription of DNA or RNA encoding
the tracrRNA.
[0148] RNA segments may also be connected to each other by covalent
coupling. RNA ligase, such as T4 RNA ligase, may be used to connect
two or more RNA segments to each other. When a reagent such as an
RNA ligase is used, a 5' terminus is typically linked to a 3'
terminus. If two segments are connected, then there are two
possible linear constructs that can be formed (i.e., (1) 5'-Segment
1-Segment 2-3' and (2) 5'-Segment 2-Segment 1-3'). Further,
intramolecular circularization can also occur. Both of these issues
can be addressed by blocking one 5' terminus or one 3' terminus so
that RNA ligase cannot ligate the terminus to another terminus.
Thus, if a construct of 5'-Segment 1-Segment 2-3' is desired, then
placing a blocking group on either the 5' end of Segment 1 or the
3' end of Segment 2 will result in the formation of only the
correct linear ligation product and will prevent intramolecular
circularization. The invention thus includes compositions and
methods for the covalent connection of two nucleic acid (e.g., RNA)
segments. Methods of the invention include the use of an RNA ligase
to directionally ligate two single-stranded RNA segments to each
other.
[0149] One example of an end blocker that may be used in
conjunction with, for example, T4 RNA ligase is a dideoxy
terminator.
[0150] T4 RNA ligase catalyzes the ATP-dependent ligation of
phosphodiester bonds between 5'-phosphate and 3'-hydroxyl termini.
Thus, when one uses T4 RNA ligase, suitable termini must be present
on the termini being ligated. One means for blocking T4 RNA ligase
on a terminus is by failing to have the correct terminus format. In
other words, termini of RNA segments with a 5-hydroxyl or a
3'-phosphate will not act as substrates for T4 RNA ligase.
[0151] Another method that may be used to connect RNA segments is
by "click chemistry" (see, e.g., U.S. Pat. Nos. 7,375,234 and
7,070,941, and US Patent Publication No. 2013/0046084, the entire
disclosures of which are incorporated herein by reference). For
example, one click chemistry reaction is between an alkyne group
and an azide group (see FIG. 11). Any click reaction can be used to
link RNA segments (e.g., Cu-azide-alkyne,
strain-promoted-azide-alkyne, staudinger ligation, tetrazine
ligation, photo-induced tetrazole-alkene, thiol-ene, NHS esters,
epoxides, isocyanates, and aldehyde-aminooxy). Ligation of RNA
molecules using a click chemistry reaction is advantageous because
click chemistry reactions are fast, modular, efficient, often do
not produce toxic waste products, can be done with water as a
solvent, and can be set up to be stereospecific.
[0152] In one embodiment the present invention uses the
"Azide-Alkyne Huisgen Cycloaddition" reaction, which is a
1,3-dipolar cycloaddition between an azide and a terminal or
internal alkyne to give a 1,2,3-triazole for the ligation of RNA
segments. One advantage of this ligation method is that this
reaction can initiated by the addition of required Cu(I) ions.
[0153] Other mechanism by which RNA segments may be connected
include the use of halogens (F--, Br--, I--)/alkynes addition
reactions, carbonyls/sulfhydryls/maleimide, and carboxyl/amine
linkages.
[0154] For example, one RNA molecule may be modified with thiol at
3' (using disulfide amidite and universal support or disulfide
modified support), and the other RNA molecule may be modified with
acrydite at 5' (using acrylic phosphoramidite), then the two RNA
molecules can be connected by Michael addition reaction. This
strategy can also be applied to connecting multiple RAN molecules
stepwise.
[0155] The invention also includes methods for linking more than
two (e.g., three, four, five, six, etc.) RNA molecules to each
other. One reason this may be done is when an RNA molecule longer
than about 40 nucleotides is desired, as noted elsewhere herein,
chemical synthesis efficiency degrades.
[0156] By way of example, a tracrRNA is typically around 80
nucleotides. Such RNA molecules may be produced by processes such
as in vitro transcription or chemical synthesis. When chemical
synthesis is used to produce such RNA molecules, they may be
produced as a single synthesis product or by linking two or more
synthesized RNA segments to each other. Further, when three or more
RNA segments are connected to each other, different methods may be
used to link the individual segments together. Also, the RNA
segments may be connected to each other in one "pot", all at the
same time, or in one "pot" at different times or in different
"pots" at different times.
[0157] For purposes of illustration, assume one wishes to assemble
RNA Segments 1, 2 and 3 in numerical order. RNA Segments 1 and 2
may be connected, 5' to 3', to each other. The reaction product may
then be purified for reaction mixture components (e.g., by
chromatography), then placed in a second vessel, "pot", for
connection of the 3' terminus with the 5' terminus of RNA Segment
3. The final reaction product may then be connected to the 5'
terminus of RNA Segment 3.
[0158] A second, more specific illustration of one embodiment of
the invention is as follows. RNA Segment 1 (about 30 nucleotides)
is the target locus recognition sequence of a crRNA and a portion
of Hairpin Region 1. RNA Segment 2 (about 35 nucleotides) contains
the remainder of Hairpin Region 1 and some of the linear tracrRNA
between Hairpin Region 1 and Hairpin Region 2. RNA Segment 3 (about
35 nucleotides) contains the remainder of the linear tracrRNA
between Hairpin Region 1 and Hairpin Region 2 and all of Hairpin
Region 2. In this illustration, RNA Segments 2 and 3 are linked, 5'
to 3', using click chemistry. Further, the 5' and 3' end termini of
the reaction product are both phosphorylated. The reaction product
is then contacted with RNA Segment 1, having a 3' terminal hydroxyl
group, and T4 RNA ligase to produce a guide RNA molecule.
[0159] A number of additional linking chemistries may be used to
connect RNA segments according to method of the invention. Some of
these chemistries are set out in Table 6.
TABLE-US-00006 TABLE 6 Exemplary RNA Ligation Reactions Reaction
Type Reaction Summary Thiol-yne ##STR00001## NHS esters
##STR00002## Thiol-ene ##STR00003## Isocyanates ##STR00004## Epoxy
or aziridine ##STR00005## Aldehyde- aminoxy ##STR00006## Cu-
catalyzed- azid-alkyne ##STR00007## Strain- Cyclooctyne
cycloaddition (with azide or nitrile oxide or nitrone) promoted-
azid- alkyne ##STR00008## ##STR00009## Norbornene cycloaddition
(with azide or nitrile oxide or nitrone) ##STR00010## ##STR00011##
Oxanorbornadiene cycloaddition ##STR00012## ##STR00013## Staudinger
ligation ##STR00014## Tetrazine ligation ##STR00015## Photo-
induced tetrazole- alken ##STR00016## [4 + 1] cyclo- addition
##STR00017## Quadri- cyclane ligation ##STR00018##
[0160] One issue with methods for linking RNA segments is that
often they do not result in complete conversion of the segments to
connected RNA molecules. For example, some chemical linkage
reactions only result in 50% of the reactants forming the desired
end product. In such instances, it will often be desirable to
remove reagents and unreacted RNA segments. This may be done by any
number of means such as dialysis, chromatography (e.g., HPLC),
precipitation, electrophoresis, etc. Thus, the invention includes
compositions and method for linking RNA segments, where the
reaction products RNA molecules are separated from other reaction
mixture components.
[0161] As noted above, CRISPR system components may be "generic"
with respect to target loci (e.g., Cas9 protein) or may be specific
for a particular target locus (e.g., crRNA). This allows for the
production of "generic" components that may be used in conjunction
with target sequence specific components. Thus, when a target locus
of interest is identified, one need only produce a component or
components specific for that target locus. In the instance where
one seeks to make two closely associated "nicks" at the target
sequence, then, for example, two crRNA molecules will typically
need to be produced. These crRNA molecules may be produced when the
target sequence of interest is identified or they may be produced
in advance and stored until needed.
[0162] The invention further includes collections of crRNA
molecules with specificity for individual target sites. For
example, the invention includes collections of rRNA molecules with
specificity for target sites within particular types of cell (e.g.,
human cells). The members of such collection of cells may be
generated based upon sequence information for these particular
types of cells. As an example, one such collection could be
generated using the complete genome sequence of a particular type
of cell. The genome sequence data can be used to generate a library
of crRNA molecules with specificity for the coding region of each
gene within the human genome. Parameters that could be used to
generate such a library may include the location of protospacer
adjacent motif (PAM) sites, off target effects (e.g., sequences
unique to the target region), and, when gene "knockouts" are
desired, locations within coding regions likely to render the gene
expression product fully or partially non-functional (e.g., active
site coding regions, intron/exon junctions, etc.).
[0163] Collections or libraries of crRNA molecules or the invention
may include a wide variety of individual molecules such as from
about five to about 100,000 (e.g., from about 50 to about 100,000,
from about 200 to about 100,000, from about 500 to about 100,000,
from about 800 to about 100,000, from about 1,000 to about 100,000,
from about 2,000 to about 100,000, from about 4,000 to about
100,000, from about 5,000 to about 100,000, from about 50 to about
50,000, from about 100 to about 50,000, from about 500 to about
50,000, from about 1,000 to about 50,000, from about 2,000 to about
50,000, from about 4,000 to about 50,000, from about 50 to about
10,000, from about 100 to about 10,000, from about 200 to about
10,000, from about 500 to about 10,000, from about 1,000 to about
10,000, from about 2,000 to about 10,000, from about 4,000 to about
10,000, from about 50 to about 5,000, from about 100 to about
5,000, from about 500 to about 5,000, from about 1,000 to about
5,000, from about 50 to about 2,000, from about 100 to about 2,000,
from about 500 to about 2,000, etc.).
[0164] RNA molecules generated by and used in the practice of the
invention may be stored in a number of ways. RNA molecules are
generally not as stable as DNA molecules and, thus, to enhance
stability, RNA molecules may be stored at low temperature (e.g.,
-70.degree. C.) and/or in the presence of one or more RNase
inhibitor (e.g., RNASEOUT.TM., RNASECURE.TM. Reagent, both
available from Thermo Fisher Scientific).
[0165] Further, RNA molecules may be chemically modified to be
resistant to RNases by, for example, being generated using
RNase-resistant ribonucleoside triphosphates. Examples of
RNase-resistant modified ribonucleosides include, but are not
limited to, 2-fluoro ribonucleosides, 2-amino ribonucleosides, and
2-methoxy ribonucleosides. Additional examples of RNase-resistant
modified ribonucleosides are disclosed in U.S. Patent Publ.
2014/0235505 A1, the entire disclosure of which is incorporated
herein by reference. 2'-O-allyl-ribonucleotides may also be
incorporated into RNA molecules of the invention.
[0166] Chemical modification used in the practice of the invention
will often be selected based upon a series of criteria, such as
effectiveness for the purpose that the chemical modification is
used (e.g., RNase resistance), level of toxicity to cells (low
generally being better than high), ease of incorporation into the
nucleic acid molecules, and minimal interference with the
biological activities of the nucleic acid molecule (e.g., the
activities of a guide RNA molecule).
[0167] Further, RNA molecules of and used in the practice of the
invention may be stored in a number of different formats. For
example, RNA molecules may be stored in tubes (e.g., 1.5 ml
microcentrifuge tubes) or in the wells of plates (e.g., 96 well,
384 well, or 1536 well plates).
[0168] The invention thus includes compositions and methods for the
production of libraries and/or collections of CRISPR system
components, as well as the libraries and/or collections of CRISPR
system components themselves.
[0169] The invention also includes compositions and methods for the
isolation of gRNA molecules. Such methods will often be based upon
hybridization of a gRNA region to another nucleic acid molecule,
followed by separation of the hybridized complex from other
molecules (e.g., nucleic acid molecules) present in a mixture.
[0170] As an example, beads containing a nucleic acid molecule with
sequence homology to a gRNA molecule may be used to purify the gRNA
from a solution. In some instances, the bead will be a magnetic
bead. Further, the nucleic acid molecule designed to hybridize to
the gRNA molecule may be designed with homology to a sequence
present in gRNA molecules or gRNA molecules may be designed to
contain a sequence that is used for hybridization. The invention
thus includes gRNA molecules that are designed to contain what is
effectively a hybridization "tag".
[0171] Such "tags" are particularly useful in high throughput
applications. As an example, a 96 well plate may contain different
gRNA molecules in each well, wherein each gRNA molecules contains
the same tag. A magnetic bead may be placed in one or more well of
the plate and then removed after a specified period of time to
allow for gRNA/bead bound hybridization to take place. These beads
may then be individually placed in wells of another plate
containing cells and donor DNA under conditions that allow for
release of gRNA molecules from the beads (e.g., competition with an
oligonucleotide of identical or similar sequence to the tag).
[0172] As noted above, hybridization tags may be naturally resident
with gRNA molecules or may be introduced into or added to gRNA
molecules. Such tags may be added by the alteration of a region
present in a gRNA molecule or may be added to the gRNA either
internally or at a terminus. Further, tags may be generated during
synthesis of gRNA molecules or added after gRNA molecules are
produced (e.g., via "click chemistry").
[0173] Hybridization tags will typically be less than 25 (e.g.,
from about 10 to about 25, from about 15 to about 25, from about 16
to about 25, from about 10 to about 20, from about 15 to about 25,
from about 15 to about 20, etc.) bases in length. Such tags will
typically be able to hybridize to homologous sequences with
sufficient affinity for association but will not associate so
strongly that they do not efficiently release when desired.
Further, shorter tags will often have a higher GC content. In many
instances, tags will have a GC content of at least 45% (e.g., from
about 45% to about 75%, from about 50% to about 75%, from about 55%
to about 75%, from about 60% to about 75%, from about 65% to about
75%, etc.).
[0174] Also, tagged gRNA molecules may contain a label. This label
may be used to quantify the amount of gRNA present. Labels may also
be useful when seeking to determine the amount of gRNA transferred
by hybridization based means. Such labels may also be used to
measure cellular uptake as set out elsewhere herein.
[0175] CRISPR Activities
[0176] CRISPR complexes of the invention can have any number of
activities. For example, CRISPR proteins may be fusion proteins
comprising one or more heterologous protein domains (e.g., one,
two, three, four, five, etc.). A CRISPR fusion protein may comprise
any additional protein sequence, and optionally a linker sequence
between any two domains. Examples of protein domains that may be
fused to a CRISPR protein include, without limitation, epitope
tags, reporter gene sequences, and protein domains having one or
more of the following activities: methylase activity, demethylase
activity, transcription activation activity, transcription
repression activity, transcription release factor activity, histone
modification activity, RNA cleavage activity, and nucleic acid
binding activity.
[0177] Non-limiting examples of epitope tags include histidine
(His) tags, V5 tags, FLAG tags, influenza hemagglutinin (HA) tags,
Myc tags, VSV-G tags, and thioredoxin (Trx) tags. Examples of
reporter genes include, but are not limited to,
glutathione-S-transferase (GST), horseradish peroxidase (HRP),
chloramphenicol acetyltransferase (CAT) beta-galactosidase,
beta-glucuronidase, luciferase, green fluorescent protein (GFP),
HcRed, DsRed, cyan fluorescent protein (CFP), yellow fluorescent
protein (YFP), and autofluorescent proteins including blue
fluorescent protein (BFP).
[0178] A CRISPR protein may be fused to a gene sequence encoding a
protein or a fragment of a protein that bind DNA molecules or bind
other cellular molecules, including but not limited to maltose
binding protein (MBP), S-tag, Lex A DNA binding domain (DBD)
fusions, GALA DNA binding domain fusions, and herpes simplex virus
(HSV) BP16 protein fusions. Additional domains that may form part
of a fusion protein comprising a CRISPR protein are described in US
2011/0059502, incorporated herein by reference.
[0179] In particular, provided herein, in part, are CRISPR protein
endonucleases, which comprise at least one nuclear localization
signal, at least one nuclease domain, and at least one domain that
interacts with a guide RNA to target the endonuclease to a specific
nucleotide sequence for cleavage. Also provided are nucleic acids
encoding CRISPR protein endonucleases, as well as methods of using
CRISPR protein endonucleases to modify chromosomal sequences of
eukaryotic cells or embryos. CRISPR protein endonucleases interacts
with specific guide RNAs, each of which directs the endonuclease to
a specific targeted site, at which site the CRISPR protein
endonucleases introduces a double-stranded break that can be
repaired by a DNA repair process such that the chromosomal sequence
is modified. Since the specificity is provided by the guide RNA (or
the crRNA), the CRISPR protein endonucleases are universal and can
be used with different guide RNAs to target different genomic
sequences. Methods disclosed herein can be used to target and
modify specific chromosomal sequences and/or introduce exogenous
sequences at targeted locations in the genome of cells or
embryos.
[0180] CRISPR complexes may also be employed to activate or repress
transcription. For example, a dCas9-transcriptional activator
fusion protein (e.g., dCas9-VP64) may be used in conjunction with a
guide RNA to activate transcription of nucleic acid associated with
a target locus. Similarly, dCas9-repressor fusions (e.g.,
dCas9-KRAB transcriptional repressor) may be used to repress
transcription of nucleic acid associated with a target locus.
Transcriptional activation and repression such as the referred to
above are discussed in, for example, Kearns et al., Cas9
effector-mediated regulation of transcription and differentiation
in human pluripotent stem cells, Development, 141:219-223
(2014).
[0181] The invention thus includes compositions and methods for the
production and use of CRISPR system components for the activation
and repression of transcription.
[0182] CRISPR Systems
[0183] CRISPR systems that may be used in the practice of the
invention vary greatly. These systems will generally have the
functional activities of a being able to form complex comprising a
protein and a first nucleic acid where the complex recognizes a
second nucleic acid. CRISPR systems can be a type I, a type II, or
a type III system (see Table 2). Non-limiting examples of suitable
CRISPR proteins include Cas3, Cas4, Cas5, Cas5e (or CasD), Cas6,
Cas6e, Cas6f, Cas7, Cas8a1, Cas8a2, Cas8b, Cas8c, Cas9, Cas10, Casl
Od, CasF, CasG, CasH, Csy1, Csy2, Csy3, Cse1 (or CasA), Cse2 (or
CasB), Cse3 (or CasE), Cse4 (or CasC), Csc1, Csc2, Csa5, Csn2,
Csm2, Csm3, Csm4, Csm5, Csm6, Cmr1, Cmr3, Cmr4, Cmr5, Cmr6, Csb1,
Csb2, Csb3, Csx17, Csx14, Csx10, Csx16, CsaX, Csx3, Csz1, Csx15,
Csf1, Csf2, Csf3, Csf4, and Cu1966.
[0184] In some embodiments, the CRISPR protein (e.g., Cas9) is
derived from a type II CRISPR system. In specific embodiments, the
CRISPR system is designed to acts as an oligonucleotide (e.g., DNA
or RNA)-guided endonuclease derived from a Cas9 protein. The Cas9
protein for this and other functions set out herein can be from
Streptococcus pyogenes, Streptococcus thermophilus, Streptococcus
sp., Nocardiopsis dassonvillei, Streptomyces pristinaespiralis,
Streptomyces viridochromogenes, Streptomyces viridochromogenes,
Streptosporangium roseum, Streptosporangium roseum,
Alicyclobacillus acidocaldarius, Bacillus pseudomycoides, Bacillus
selenitireducens, Exiguobacterium sibiricum, Lactobacillus
delbrueckii, Lactobacillus salivarius, Microscilla marina,
Burkholderiales bacterium, Polaromonas naphthalenivorans,
Polaromonas sp., Crocosphaera watsonii, Cyanothece sp., Microcystis
aeruginosa, Synechococcus sp., Acetohalobium arabaticum, Ammonifex
degensii, Caldicelulosiruptor becscii, Candidatus Desulforudis,
Clostridium botulinum, Clostridium difficile, Finegoldia magna,
Natranaerobius thermophilus, Pelotomaculum thermopropionicum,
Acidithiobacillus caldus, Acidithiobacillus ferrooxidans,
Allochromatium vinosum, Marinobacter sp., Nitrosococcus halophilus,
Nitrosococcus watsoni, Pseudoalteromonas haloplanktis,
Ktedonobacter racemifer, Methanohalobium evestigatum, Anabaena
variabilis, Nodularia spumigena, Nostoc sp., Arthrospira maxima,
Arthrospira platensis, Arthrospira sp., Lyngbya sp., Microcoleus
chthonoplastes, Oscillatoria sp., Petrotoga mobilis, Thermosipho
africanus, or Acaryochloris marina.
[0185] FIG. 12A-12F shows an alignment of Cas9 amino acid
sequences. In many instances, the compositions and methods of the
invention will be directed to Type II CRISPR systems. In such
instances, a number of different Cas9 proteins may be employed.
Cas9 proteins may be defined, to some extent, by their regions of
sequence homology. Proteins suitable for use in compositions and
methods of the invention will typically include those that have
seven or more (e.g., from about seven to about fifteen, from about
seven to about eleven, from about seven to about ten, from about
seven to about eight, etc.) amino acids identical to the S.
pyogenes Cas9 amino acid sequence shown in FIG. 12A-12F. Additional
features of CRISPR proteins that fall within the scope of the
invention are set out elsewhere herein.
[0186] Vector Components and Cells:
[0187] A number of functional nucleic acid components (e.g.,
promoters, polyA signal, origins of replication, selectable
markers, etc.) may be used in the practice of the invention. The
choice of functional nucleic acid components used in the practice
of the invention, when employed, will vary greatly with the nature
of the use and the specifics of the system (e.g., intracellular,
extracellular, in vitro transcription, coupled in vitro
transcription/translation, etc.).
[0188] Promoter choice depends upon a number of factors such as the
expression products and the type of cell or system that is used.
For example, non-mRNA molecules are often production using RNA
polymerase I or III promoters. mRNA is generally transcribed using
RNA polymerase II promoters. There are exceptions, however. One is
microRNA expression systems where a microRNA can be transcribed
from DNA using an RNA polymerase II promoter (e.g., the CMV
promoter). While RNA polymerase II promoters do not have "sharp"
stop and stop points, microRNAs tend to be processed by removal of
5' and 3' termini. Thus, "extra" RNA segments at the termini are
removed. mRNA (e.g., cas9 mRNA) is normally produced via RNA
polymerase II promoters.
[0189] The choice of a specific promoter varies with the particular
application. For example, the T7, T3 and SP6 promoters are often
used for in vitro transcription and in vitro
transcription/translations systems. When intracellular expression
in desired, the promoter or promoters used will generally be
designed to function efficiently within the cells employed. The CMV
promoter, for example, is a strong promoter for use within
mammalian cells. The hybrid Hsp70A-Rbc S2 promoter is a
constitutive promoter that functions well in eukaryotic algae such
as Chlamydornonas reinhardtii. (see the product manual
"GeneArt.RTM. Chlamydornonas Protein Expression Kit", cat. no.
A24244, version B.0, from Life Technologies Corp., Carlsbad,
Calif.). Additional promoters that may be used in the practice of
the invention include AOX1, GAP, cauliflower mosaic virus 35S,
pGC1, EF1.alpha., and Hsp70 promoters.
[0190] The DNA segment in the expression vector is operatively
linked to an appropriate expression control sequence(s) (promoter)
to direct RNA synthesis. Suitable eukaryotic promoters include the
CMV immediate early promoter, the HSV thymidine kinase promoter,
the early and late SV40 promoters, the promoters of retroviral
LTRs, such as those of the Rous Sarcoma Virus (RSV), and
metallothionein promoters, such as the mouse metallothionein-I
promoter. Exemplary promoters suitable for use with the invention
are from the type III class of RNA polymerase III promoters.
Additionally, the promoters may be selected from the group
consisting of the U6 and H1 promoters. The U6 and H1 promoters are
both members of the type III class of RNA polymerase III
promoters.
[0191] RNA polymerase III promoters are suitable for in vivo
transcription of nucleic acid molecules produced by methods of the
invention. For example, linear DNA molecules produced as set out in
FIG. 9 may be introduced into cells and transcribed by, for
example, naturally resident intracellular transcriptional
processes.
[0192] Promoters in compositions and methods of the invention may
also be inducible, in that expression may be turned "on" or "off."
For example, a tetracycline-regulatable system employing the U6
promoter may be used to control the production of siRNA. Expression
vectors may or may not contain a ribosome binding site for
translation initiation and a transcription terminator. Vectors may
also include appropriate sequences for amplifying expression.
[0193] A great variety of cloning/expression systems can be used to
express proteins and nucleic acid molecules in the practice of the
invention. Such vectors include, among others, chromosomal-,
episomal- and viral-derived vectors, for example, vectors derived
from plasmids, from bacteriophage, from transposons, from yeast
episomes, from insertion elements, from yeast chromosomal elements,
from viruses such as baculoviruses, papova viruses, such as SV40,
vaccinia viruses, adenoviruses, adeno-associated viruses, avipox
(e.g., fowl pox) viruses, suipox viruses, capripox viruses,
pseudorabies viruses, picornaviruses and retroviruses, and vectors
derived from combinations thereof, such as those derived from
plasmid and bacteriophage genetic elements, such as cosmids and
phagemids. The expression system constructs can contain control
regions that regulate as well as engender expression. Generally,
any system or vector suitable to maintain, propagate or express
polynucleotides or to express a polypeptide in a host can be used
for expression in this regard. The appropriate DNA sequence can be
inserted into the expression system by any of a variety of
well-known and routine techniques, such as, for example, those set
forth in Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL,
2nd Ed., Cold Spring Harbour Laboratory Press, Cold Spring Harbour.
N.Y. (1989).
[0194] Cells suitable for use with the present invention include a
wide variety of prokaryotic and eukaryotic cells. In many
instances, the cells one or more CRISPR system component will not
be naturally associated with the cell (i.e., will be exogenous to
the cell).
[0195] Representative cells that may be used in the practice of the
invention include, but are not limited to, bacterial cells, yeast
cells, plant cells and animal cells. Exemplary bacterial cells
include Escherichia spp. cells (particularly E. coli cells and most
particularly E. coli strains DH10B, Stb12, DH5.quadrature., DB3,
DB3.1), Bacillus spp. cells (particularly B. subtilis and B.
megaterium cells), Streptomyces spp. cells, Erwinia spp. cells,
Klebsiella spp. cells, Serratia spp. cells (particularly S.
marcessans cells), Pseudomonas spp. cells (particularly P.
aeruginosa cells), and Salmonella spp. cells (particularly S.
typhimurium and S. typhi cells). Exemplary animal cells include
insect cells (most particularly Drosophila melanogaster cells,
Spodoptera frugiperda Sf9 and Sf21 cells and Trichoplusa High-Five
cells), nematode cells (particularly C. elegans cells), avian
cells, amphibian cells (particularly Xenopus laevis cells),
reptilian cells, and mammalian cells (more particularly NIH3T3,
CHO, COS, VERO, BHK CHO-K1, BHK-21, HeLa, COS-7, HEK 293, HEK 293T,
HT1080, PC12, MDCK, C2C12, Jurkat, NIH3T3, K-562, TF-1, P19 and
human embryonic stem cells like clone H9 (Wicell, Madison, Wis.,
USA)). Exemplary yeast cells include Saccharomyces cerevisiae cells
and Pichia pastoris cells. These and other cells are available
commercially, for example, from Thermo-Fisher Scientific (Waltham,
Mass.), the American Type Culture Collection, and Agricultural
Research Culture Collection (NRRL; Peoria, Ill.). Exemplary plant
cells include cells such as those derived from barley, wheat, rice,
soybean, potato, Arabidopsis and tobacco (e.g., Nicotiana tabacum
SR1).
[0196] Introduction of Crispr System Components into Cells:
[0197] The invention also includes compositions and methods for
introduction of CRISPR system components into cells. Introduction
of a molecules into cells may be done in a number of ways including
by methods described in many standard laboratory manuals, such as
Davis et al., BASIC METHODS IN MOLECULAR BIOLOGY, (1986) and
Sambrook et al., MOLECULAR CLONING: A LABORATORY MANUAL, 2nd Ed.,
Cold Spring Harbour Laboratory Press, Cold Spring Harbour. N.Y.
(1989), such as, calcium phosphate transfection, DEAE-dextran
mediated transfection, transfection, microinjection, cationic
lipid-mediated transfection, electroporation, transduction, scrape
loading, ballistic introduction, nucleoporation, hydrodynamic
shock, and infection.
[0198] The invention includes methods in which different CRISPR
system components are introduced into cells by different means, as
well as compositions of matter for performing such methods. For
example, a lentiviral vector may be used to introduce Cas9 coding
nucleic acid operably linked to an suitable and guide RNA may be
introduced by transfection.
[0199] CRISPR system components may be the functional CRISPR system
molecules or they may be molecules encoding the functional
molecules (e.g., DNA, RNA encoding Cas9, etc.) transfection of
CRISPR system components into cells. Methods of the invention
relate to the introduction into cells one or more of the following:
[0200] a. Guide RNA, [0201] b. crRNA, [0202] c. tracrRNA, [0203] d.
DNA encoding Cas9 or dCas9 (as well as fusion proteins of each),
and [0204] e. mRNA encoding Cas9 or dCas9 (as well as fusion
proteins of each).
[0205] In most instances, CRISPR system components will be
introduced into a cell in a manner that results in the generation
of CRISPR activities within the cell. Thus, in instances where a
cell expresses Cas9 protein (e.g., from chromosomally integrated
CRISPR encoding nucleic acid operably linked to a promoter), crRNA
and tracrRNA or guide may be introduced into the cell by
transfection.
[0206] Transfection agents suitable for use with the invention
include transfection agents that facilitate the introduction of
RNA, DNA and proteins into cells. Exemplary transfection reagents
include TurboFect Transfection Reagent (Thermo Fisher Scientific),
Pro-Ject Reagent (Thermo Fisher Scientific), TRANSPASS.TM. P
Protein Transfection Reagent (New England Biolabs), CHARIOT.TM.
Protein Delivery Reagent (Active Motif), PROTEOJUICE.TM. Protein
Transfection Reagent (EMD Millipore), 293fectin, LIPOFECTAMINE.TM.
2000, LIPOFECTAMINE.TM. 3000 (Thermo Fisher Scientific),
LIPOFECTAMINE.TM. (Thermo Fisher Scientific), LIPOFECTIN.TM.
(Thermo Fisher Scientific), DMRIE-C, CELLFECTIN.TM. (Thermo Fisher
Scientific), OLIGOFECTAMINE.TM. (Thermo Fisher Scientific),
LIPOFECTACE.TM., FUGENE.TM. (Roche, Basel, Switzerland), FUGENE.TM.
HD (Roche), TRANSFECTAM.TM. (Transfectam, Promega, Madison, Wis.),
TFX-10.TM. (Promega), TFX-20.TM. (Promega), TFX-50.TM. (Promega),
TRANSFECTIN.TM. (BioRad, Hercules, Calif.), SILENTFECT.TM.
(Bio-Rad), Effectene.TM. (Qiagen, Valencia, Calif.), DC-chol
(Avanti Polar Lipids), GENEPORTER.TM. (Gene Therapy Systems, San
Diego, Calif.), DHARMAF.sup.ECT 1.TM. (Dharmacon, Lafayette,
Colo.), DHARMAFECT 2.TM. (Dharmacon), DHARMAFECT 3.TM. (Dharmacon),
DHARMAFECT 4.TM. (Dharmacon), ESCORT.TM. III (Sigma, St. Louis,
Mo.), and ESCORT.TM. IV (Sigma Chemical Co.).
[0207] The invention further includes methods in which one molecule
is introduced into a cell, followed by the introduction of another
molecule into the cell. Thus, more than one CRISPR system
components molecule may be introduced into a cell at the same time
or at different times. As an example, the invention includes
methods in which Cas9 is introduced into a cell while the cell is
in contact with a transfection reagent designed to facilitate the
introduction of proteins in to cells (e.g., TurboFect Transfection
Reagent), followed by washing of the cells and then introduction of
guide RNA while the cell is in contact with LIPOFECTAMINE.TM.
2000.
[0208] Conditions will normally be adjusted on, for example, a per
cell type basis for a desired level of CRISPR system component
introduction into the cells. While enhanced conditions will vary,
enhancement can be measure by detection of intracellular CRISPR
system activity. Thus, the invention includes compositions and
methods for measurement of the intracellular introduction of CRISPR
system components in cells.
[0209] The invention also includes compositions and methods related
to the formation and introduction of CRISPR complexes into cells.
One exemplary method of the invention comprises: [0210] a. forming
a complex comprising at least one CRISPR system protein with at
least one CRISPR RNA, [0211] b. contacting the complexed CRISPR
system protein and RNA with a cell, [0212] c. incubating or
culturing the resulting cell for a period of time (e.g., from about
2 minutes to about 8 hours, from about 10 minutes to about 8 hours,
from about 20 minutes to about 8 hours, from about 30 minutes to
about 8 hours, from about 60 minutes to about 8 hours, from about
20 minutes to about 6 hours, from about 20 minutes to about 3
hours, from about 20 minutes to about 2 hours, from about 45
minutes to about 3 hours, etc.), and [0213] d. measuring CRISPR
system activity within the cell.
[0214] In some instances, during the practice of methods of the
invention, molecules introduced into cells may be labeled. One
schematic example of this is set out in FIG. 24 where donor DNA
labeled with ALEXA FLUOR.RTM. 647 dye (Thermo Fisher Scientific)
and GFP-Cas9 RNP complexes are sequentially introduced into HEK293
cells, followed by cell sorting to obtain cells that contain both
labels (lower right of FIG. 24). This is advantageous because cells
containing specific amounts of both labels may be separated from
other cells to obtain a population of cells having enhanced
probabilities of undergoing genetic modification (e.g., homologous
recombination). A similar workflow is set out in FIG. 25.
[0215] Labels may be attached to one or more CRISPR system
component and/or other molecules (e.g., a donor nucleic acid
molecule) for introduction in the cells. In many instances, labels
will be detectable either visually or by cell sorting instruments.
Exemplary labels include cyan florescent protein (CFP), green
florescent protein (GFP), orange florescent protein (OFP), red
florescent protein (RFP), and yellow florescent protein (YFP).
Additional labels include AMCA-6-dUTP, DEAC-dUTP, dUTP-ATTO-425,
dUTP-XX-ATTO-488, Fluorescein-12-dUTP, Rhodamine-12-dUTP,
dUTP-XX-ATTO-532, dUTP-Cy3, dUTP-ATTO-550, dUTP-Texas Red,
dUTP-J647, dUTP-Cy5, dUTP-ATTO-647N, dUTP-ATTO-655,
Fluorescein-12-dCTP, Rhodamine-12-dCTP, dCTP-Cy3dCTP-ATTO-550,
dCTP-Texas Red, dCTP-J647, dCTP-Cy5 and dCTP-ATTO-647N available
from multiple sources including Jena Bioscience.
[0216] Labels may be located in nucleic acid molecules and proteins
at one or both termini and/or interior portions of the particular
molecules.
[0217] When cells are sorted, a number of separation parameters may
be employed. In most instances, sorting may be designed to obtain
cells having enhanced probability of undergoing genetic
modification. For example, cells may be labeled as shown in FIG. 24
with different components required for genetic modification
followed by cell sorting to obtain cells a specific amount of
signal of each component. Using the schematic of FIG. 24 for
purposes of illustration, cells may be selected based upon the
number of donor DNA molecules and the number of GFP-Cas9 RNP
complexes present within the cells. This may be done by choosing a
minimum signal level for each the two labels, resulting in those
cells being sorted as "positive" cells. Another sorting option is
to score as "positive" cells that are in the top 3%, 5%, 8%, 10%,
15%, 20%, 25%, etc. for both signals as compared to all of the
cells in a mixture. Assuming that two labels are equivalently and
independently taken up, then scoring for the top 25% of cells for
both labels would be expected to yield 6.25% of the original
population being sorted. These would likely be the cells in the
mixture that have the highest probabilities of undergoing genetic
modification.
[0218] The invention thus includes methods, as well as compositions
for performing such methods, for obtaining cell populations wherein
the cells therein have an enhanced probabilities of undergoing
genetic modification. In some instances, such methods will involve
one or both of the following: (1) selection of cell (e.g., via cell
sorting) of cells that have taken up one or more component
necessary for genetic modification (e.g., one or more CRISPR system
component and one or more donor DNA molecule) and (2) introduction
of one or more one or more component necessary for genetic
modification into cells by processes designed to result in high
cellular uptake (e.g., sequence component introduction, as set out
herein).
[0219] As noted elsewhere herein, in some instances, sequential
addition of components may be employed. As shown from the data set
out in FIG. 26, sequential delivery of CRISPR system components and
donor DNA generally results in higher efficiency levels of genetic
modification than co-delivery. While not wishing to be bound by
theory, this is possibly low uptake efficiency of combinations of
CRISPR system components and non-CRISPR complex bound nucleic acid
molecules when co-delivered.
[0220] When sequential delivery is employed, various components may
be introduced into cells in a number of orders. For example, Cas9
protein, gRNA, or Cas9 RNP may be introduced into cells first
followed by the introduction of donor DNA. Of course, the reverse
order may be used too. Further, Cas9 protein may be expressed
within cells and gRNA and donor DNA may be co-delivered or
sequentially delivered to the cells in any order. Additionally,
gRNA may be expressed within cells and Cas9 protein and donor DNA
may be co-delivered or sequentially delivered to the cells in any
order. In some instances, gRNA may be introduced into cells first,
followed by Cas9 protein, then followed by donor DNA. Of course,
other delivery orders may be used too, so long as all of the
components required for genetic modification are not delivered
simultaneously.
[0221] In some instances, methods of the invention include the
contacting a cell with a linear DNA segment that has sequence
homology at both termini to the target locus (e.g., a donor DNA
molecule) under conditions that allow for uptake of the linear DNA
segment by the cell (e.g., in conjunction with electroporation,
contacting with a transfection reagent, etc.), followed by
contacting the cell with one or more CRISPR system components
(e.g., Cas9 mRNA, guide RNA, Cas9 mRNA and guide RNA, a Cas9
protein/guide RNA complex, etc.) under conditions that allow for
uptake of the one or more CRISPR system components by the cell.
[0222] In specific aspects, the invention includes methods
comprising steps (a), (b) and (c) below. Furthers, step (c) and
step (a) may be swapped in order.
[0223] Step (a) involves contacting a cell with a linear DNA
segment that has sequence homology at both termini to the target
locus (e.g., a donor DNA molecule) under conditions that allow for
uptake of the linear DNA segment by the cell. This may be done in
any number of means. As examples, cell may be subjected to
electroporation in the presence of the linear DNA segment or a
transfection reagent may be used.
[0224] Step (b) involves waiting a period of time. This time period
may be determined in a number of ways.
[0225] Step (c) involves contacting a cell with a Cas9 RNP complex
under conditions that allow for uptake of the linear DNA segment by
the cell.
[0226] As shown in FIGS. 27 and 28, the amount and characteristics
of nucleic acid molecules introduced into cells in conjunction with
CRISPR system components may be adjusted to enhance genetic
modification.
[0227] Data in FIG. 27 shows that, under the particular conditions
used, efficient homologous recombination occurs with 0.2 and 0.5
.mu.g of donor DNA per 10 .mu.l reaction volume. The number of
cells was between 50,000 to 200,000. Further, homologous
recombination decreases with donor DNA levels lower and higher than
those amounts. The invention this includes compositions and methods
and where donor DNA concentrations are in the range of 0.01
.mu.g/10 .mu.l to 500 .mu.g/10 .mu.l (e.g., from about 0.01 to
about 400, from about 0.01 to about 200, from about 0.01 to about
100, from about 0.01 to about 50, from about 0.01 to about 30, from
about 0.01 to about 20, from about 0.01 to about 15, from about
0.01 to about 10, from about 0.1 to about 50, from about 0.1 to
about 25, from about 0.1 to about 15, from about 0.1 to about 10,
from about 0.1 to about 50, from about 0.1 to about 5, from about
0.1 to about 1, from about 0.1 to about 0.8, etc. .mu.g/10
.mu.l.
[0228] Data in FIG. 27 shows that, under the particular conditions
used, the efficient homologous recombination varies with the
length, amount and presence or absence of certain chemical
modifications. The length variation may be partially due to the
sizes of regions of homology to the locus being modified. For
example, about single-stranded donor nucleic acid molecules of
about 80 bases in length appear to be sufficient for efficient
homologous recombination. In many instances, such donor nucleic
molecules will typically have terminal regions of homology to the
target locus being modified with a central region containing
nucleic acid for insertion at or substitution of nucleic acid at
the target locus. In many instances, terminal homologous regions
with be between 30 and 50 bases (e.g., from about 30 to about 45,
from about 35 to about 45, from about 40 to about 45, from about 40
to about 48, etc.) in length with an intervening region of between
1 and 20 bases (e.g., one, two, three, four five, six, seven,
etc.). Further, donor nucleic acid molecules may be used that
contain regions of homology designed to hybridize the spatially
separated regions of a target locus. In many instances, this
spatial separation will be less than about 20 nucleotides.
Homologous recombination using such donor nucleic acid molecules
would be expected to result in deletion of nucleic acid at the
target locus.
[0229] The invention further includes compositions and methods for
the insertion and correction of single-nucleotide polymorphisms
(SNPs). In some instances, such methods involve the use of
single-stranded donor nucleic acid with terminal regions having
homology to a target site in conjunction with CRISPR system
components. Of course, double-stranded donor nucleic acid may also
be used for SNP insertion or correction.
[0230] Data in FIG. 27 shows that, under the employed conditions
used, efficiency of homologous recombination varies with the
presence or absence of terminal chemical modifications to the donor
nucleic acid. Phosphorothioate modifications were used at both
termini of the modified donor molecules used to generate the data
in FIG. 27. While not wishing to be bound by theory, one
possibility is that the terminal chemical modifications used
protect the donor nucleic acid from nuclease digestion.
[0231] The invention thus includes compositions containing and
methods employing donor nucleic acid molecules having chemical
modifications. In many instances, these chemical modifications will
render nucleic acid molecules containing them resistant to one or
more nuclease (e.g., exonuclease and/or endonuclease). Chemical
modifications that may be used in the practice of the invention
include the following: Phosphorothioate groups, 5' blocking groups
(e.g., 5' diguanosine caps), 3' blocking groups, 2'-fluoro
nucleosides, 2'-O-methyl-3' phosphorothioate, or 2'-O-methyl-3'
thioPACE, inverted dT, inverted ddT, and biotin. Further, a
phosphoramidite C3 Spacer can be incorporated internally, or at
either end of an oligo to introduce a long hydrophilic spacer arm
for the attachment of fluorophores or other groups and can also be
used to inhibit degradation by 3' exonucleases.
[0232] In some instances, the terminal base at one or each end of a
donor DNA molecule will be chemically modified. In other instances,
terminal two or three bases at one or each end will be chemically
modified. In still other instances, internal bases will be
chemically modified. In some instances, from about 1% to about 50%
(e.g., from about 1% to about 45%, from about 1% to about 40%, from
about 1% to about 35%, from about 1% to about 25%, from about 1% to
about 15%, from about 5% to about 50%, from about 10% to about 50%,
from about 15% to about 50%, from about 15% to about 35%, etc.) of
the total number of bases present in donor nucleic acid molecules
will be chemically modified.
[0233] FIG. 29 shows data generated using a series of
electroporation conditions. It has been found that Cas9 RNP uptake
is robust in some cell types (data not shown) but donor DNA uptake
conditions often need to be adjusted with particular cell types in
order to achieve efficient uptake. Further, it is believed that
once efficient uptake conditions are identified for a particular
cell type, those condition show low levels of variation when
different donor DNA molecules are used. Thus, when electroporation
is employed, one of the main factors for adjust of conditions for
achieving efficient genetic modification is the selection of
efficient condition of introduction of donor DNA into the
particular cell being used. This is especially the case when large
donor DNA molecules are used.
[0234] A number of compositions and methods may be used to form
CRISPR complexes. For example, Cas9 mRNA and a guide RNA may be
encapsulated in INVIVOFECTAMINE.TM. for, for example, later in vivo
and in vitro delivery as follows. Cas9 mRNA is mixed (e.g., at a
concentration of at 0.6 mg/ml) with guide RNA. The resulting
mRNA/gRNA solution may be used as is or after addition of a
diluents and then mixed with an equal volume of INVIVOFECTAMINE.TM.
and incubated at 50.degree. C. for 30 min. The mixture is then
dialyzed using a 50 kDa molecular weight curt off for 2 hours in
1.times.PBS, pH7.4. The resulting dialyzed sample containing the
formulated mRNA/gRNA is diluted to the desire concentration and
applied directly on cells in vitro or inject tail vein or
intraperitoneal for in vivo delivery. The formulated mRNA/gRNA is
stable and can be stored at 4.degree. C.
[0235] For Cas9 mRNA transfection with cell culture such as 293
cells, 0.5 .mu.g mRNA was added to 25 .mu.l of Opti-MEM, followed
by addition of 50-100 ng gRNA. Meanwhile, two .mu.l of
LIPOFECTAMINE.TM. 3000 or RNAiMax was diluted into 25 .mu.l of
Opti-MEM and then mixed with mRNA/gRNA sample. The mixture was
incubated for 15 minutes prior to addition to the cells.
[0236] A CRISPR system activity may comprise expression of a
reporter (e.g., green fluorescent protein, .beta.-lactamase,
luciferase, etc.) or nucleic acid cleavage activity. Using nucleic
acid cleavage activity for purposes of illustration, total nucleic
acid can be isolated from cells to be tested for CRISPR system
activity and then analyzed for the amount of nucleic acid that has
been cut at the target locus. If the cell is diploid and both
alleles contain target loci, then the data will often reflect two
cut sites per cell. CRISPR systems can be designed to cut multiple
target sites (e.g., two, three four, five, etc.) in a haploid
target cell genome. Such methods can be used to, in effect,
"amplify" the data for enhancement of CRISPR system component
introduction into cells (e.g., specific cell types). Conditions may
be enhanced such that greater than 50% of the total target loci in
cells exposed to CRISPR system components (e.g., one or more of the
following: Cas9 protein, Cas9 mRNA, crRNA, tracrRNA, guide RNA,
complexed Cas9/guide RNA, etc.) are cleaved. In many instances,
conditions may be adjusted so that greater than 60% (e.g., greater
than 70%, greater than 80%, greater than 85%, greater than 90%,
greater than 95%, from about 50% to about 99%, from about 60% to
about 99%, from about 65% to about 99%, from about 70% to about
99%, from about 75% to about 99%, from about 80% to about 99%, from
about 85% to about 99%, from about 90% to about 99%, from about 95%
to about 99%, etc.) of the total target loci are cleaved.
[0237] Any number of conditions may be altered to enhance the
introduction of CRISPR system components into cells. Exemplary
incubation conditions are pH, ionic strength, cell type, energy
charge of the cells, the specific CRISPR system components present,
the ratio of CRISPR system components (when more than one CRISPR
system component is present), the CRISPR system component/cell
ratio, concentration of cells and CRISPR system components,
incubation times, etc.
[0238] One factor that may be varied, especially when CRISPR
complexes are formed, is ionic strength. Ionic strength is the
total ion concentration in solution. CRISPR complexes are formed
from the association of CRISPR protein with CRISPR RNA and this
association is partially dependent upon the ionic strength of the
surrounding environment. One method for calculating the ionic
strength of a solution is by the Debye and Huckel formula. In many
instances, the ionic strength of solutions used in the practice of
the invention will be from about 0.001 to about 3 (e.g., from about
0.001 to about 2, from about 0.001 to about 1.5, from about 0.001
to about 1, from about 0.001 to about 0.7, from about 0.001 to
about 0.5, from about 0.001 to about 0.25, from about 0.001 to
about 0.1, from about 0.01 to about 1, from about 0.01 to about
0.5, from about 0.01 to about 0.2, from about 0.01 to about 0.1,
etc.).
[0239] pH is another factor that may affect transfection
efficiency. Typically, complexation and/or transfection will occur
at near physiological pH (e.g., pHs from about 6.5 to about 7.5,
pHs from about 6.8 to about 7.5, pHs from about 6.9 to about 7.5,
pHs from about 6.5 to about 7.3, pHs from about 6.5 to about 7.1,
pHs from about 6.8 to about 7.2, etc.). In some instances,
transfection efficiency is known to be sensitive to small
variations in pH (e.g., =/-0.2 pH units).
[0240] The ratio of CRISPR system components to each other and to
other mixture components (e.g., cells) also affects the efficiency
of CRISPR system component cellular update. Using Cas9 protein and
guide RNA for purposes of illustration, Cas9 protein may be
complexed with guide RNA before contact with a cell or
simultaneously with cellular contact. In many instances, CRISPR
protein and CRISPR RNA components will be present in set ratios
(e.g., 1:1, 1.5:1, 2:1, 2.5:1, 3:1, 1:1.5, 1:2, 1:2.5, 1:3, from
about 0.2:1 to about 4:1, from about 0.2:1 to about 3:1, from about
0.2:1 to about 2:1, from about 0.5:1 to about 6:1, from about 0.5:1
to about 4:1, etc.). One useful ratio for Cas9 protein to guide RNA
is 1:1, where each Cas9 protein has available to it one guide RNA
molecular partner for complex formation.
[0241] The uptake of CRISPR complexes by cells is partially
determined by the concentration of the CRISPR complexes and the
cell density and the ratio of the CRISPR complexes to the cells.
Typically, high CRISPR complex concentrations will result in higher
amounts of uptake by available cells. Exemplary CRISPR complex/cell
density conditions include 10.sup.7 CRISPR complexes per cell.
Additionally, CRISPR complexes per cell may be in the range of
10.sup.2 to 10.sup.12 complexes per cell (e.g., from about 10.sup.2
to about 10.sup.11, from about 10.sup.2 to about 10.sup.10, from
about 10.sup.2 to about 10.sup.9, from about 10.sup.2 to about
10.sup.8, from about 10.sup.2 to about 10.sup.7, from about
10.sup.2 to about 10.sup.6, from about 10.sup.3 to about 10.sup.12,
from about 10.sup.4 to about 10.sup.12, from about 10.sup.5 to
about 10.sup.12, from about 10.sup.6 to about 10.sup.12, from about
10.sup.7 to about 10.sup.12, from about 10.sup.8 to about
10.sup.12, from about 10.sup.3 to about 10.sup.10, from about
10.sup.4 to about 10.sup.10, from about 10.sup.5 to about
10.sup.11, etc.). Also, the cell density will typically be about
10.sup.5 cells per ml. Typically, cell density will be in the range
of 10.sup.2 to 10.sup.8 cells per ml (e.g., from about 10.sup.2 to
about 10.sup.7, from about 10.sup.2 to about 10.sup.6, from about
10.sup.2 to about 10.sup.5, from about 10.sup.2 to about 10.sup.4,
from about 10.sup.3 to about 10.sup.8, from about 10.sup.3 to about
10.sup.7, from about 10.sup.4 to about 10.sup.7, etc.).
[0242] The invention includes methods in which one or both of the
CRISPR complex/cell density and/or the total cell density are
adjusted such that, when double-stranded target locus cutting is
assayed, the percentage of target loci cut are between 80 and 99.9%
(e.g., from about 80% to about 99%, from about 85% to about 99%,
from about 90% to about 99%, from about 95% to about 99%, from
about 96% to about 99%, from about 80% to about 95%, from about 90%
to about 97%, etc.).
[0243] One exemplary set of conditions that may be use is where
.about.5.sup.5 cells are contacted with 500 ng of Cas9
(.about.2.sup.12 molecules) complexed with target locus specific
guide RNA.
[0244] The invention also includes compositions and methods for
storing reagent for intracellular genetic modification. FIGS. 30,
31, and 32 show the result of three month stability testing of
CRISPR complexes stored at 4.degree. C. and frozen. Data set out in
FIG. 30 was generated using gRNA and Cas9 protein alone. Data set
out in FIG. 31 was generated using gRNA, Cas9 protein and
OPTI-MEM.RTM. culture medium. Data set out in FIG. 32 was generated
using Cas9 protein and LIPOFECTAMINE.RTM. RNAiMax transfection
reagent. In all cases, high levels of functional activity were
retained for three months with freezing. Similar results were
observed with Cas9 protein and OPTI-MEM.RTM. culture medium. Cas9
protein and LIPOFECTAMINE.RTM. RNAiMax transfection reagent data
shows that functional activity appears to drop off relatively
quickly at 4.degree. C.
[0245] Data shown in FIGS. 30, 31, and 32 each show that CRISPR
system component reagents are stable for a minimum of six months.
This is particularly useful for high-throughput applications. The
invention thus includes high-throughput reagents containing CRISPR
system components. In some embodiments, such components comprise
one or more of the following: one or more gRNA, one or more Cas9
protein, one or more cell culture medium (e.g., one or more
mammalian cell culture medium), one or more transfection reagent,
and one or more donor nucleic acid molecule.
[0246] For purposes of illustration, the invention includes
multi-well plates, as well as high throughput methods employing
such plates, in which different wells contain Cas9 protein and a
transfection reagent. Further, different wells contain different
gRNA molecules. Such plates may be used in high throughput methods
for altering multiple genetic sites within cells. Each well may
further contain, for example, donor DNA with termini homologous to
the gRNA directed cleavage site for alteration of different loci
within cells.
[0247] The invention also includes CRISPR system reagents that
remain stable when stored for specified periods of time. For
purposes of illustration, the invention provides CRISPR system
reagents that retain at least 75% (e.g., from about 75% to about
100%, from about 80% to about 100%, from about 85% to about 100%,
from about 90% to about 100%, from about 95% to about 100%, from
about 75% to about 90%, from about 80% to about 90%, etc.) of their
original CRISPR related activity after 3 months of storage at
-20.degree. C. Of course, CRISPR system reagents may be stored at
different temperatures (e.g., 4.degree. C., -20.degree. C.,
-70.degree. C., from about 4.degree. C. to about -70.degree. C.,
from about -20.degree. C. to about -70.degree. C., etc.). Further,
the invention also includes CRISPR system reagents and method for
storing such reagents where at least 75% of their original CRISPR
related activity after up to 1 year (e.g., from about 1 month to
about 12 months, from about 2 months to about 12 months, from about
3 months to about 12 months, from about 4 months to about 12
months, from about 5 months to about 12 months, from about 1 months
to about 9 months, from about 3 months to about 9 months, from
about 2 months to about 6 months, etc.).
[0248] In some instances, CRISPR complexes may not be stable during
storage, especially under certain conditions. For example, under
some conditions Cas9, gRNA and transfection reagents may be stable
under one set of conditions but not under another set of
conditions. It has been determined that under some conditions
(e.g., in certain buffer formulations), Cas9, gRNA and transfection
reagent mixtures are not stable upon freezing but are stable upon
storage at 4.degree. C. The invention this includes compositions
that are stable under on set of storage conditions but not another
set of storage conditions.
[0249] The data set out in FIGS. 30, 31, and 32 were generated
using specific conditions. RNA was prepared in water but EDTA
(e.g., 0.1 mM) and/or sodium acetate buffer may be used. Cas9
protein was prepared in 15 mM Tris HCl, 250 mM NaCl, 0.6 mM TCEP,
50% glycerol, pH 8.
[0250] Storage data was generated using reagent mixtures contained
in wells of multiwall plates. Cas9 was present in wells in an
amount of 500 ng/well (0.5 .mu.l of a 0.5 .mu.g/.mu.l stock
solution) and gRNA was present in an amount of 200 ng/well (0.7
.mu.l of a 300 ng/.mu.l stock solution). All reagents were stored
as 4.times. solutions. Cas9/gRNA samples were placed under storage
conditions as 1.2 .mu.l aliquots in each well.
Cas9/gRNA/OPTI-MEM.RTM. samples were placed under storage
conditions as 20 .mu.l aliquots in each well with 18.8 .mu.l of
OPTI-MEM.RTM. being present in each well. Cas9/OPTI-MEM.RTM.
samples were placed under storage conditions as 10 .mu.l aliquots
in each well with 9.5 .mu.l of OPTI-MEM.RTM. being present in each
well. Cas9/RNAiMax samples were placed under storage conditions as
6.5 .mu.l aliquots in each well with 6 .mu.l of RNAiMax
transfection reagent being present in each well.
[0251] The above reagents were then used after storage in cleavage
assay after being combined with additional reagents and cells. The
data set out in FIG. 30 was generated by combining the 1.2 .mu.l of
Cas9 protein and gRNA with 18.8 .mu.l OPTI-MEM.RTM. which was
incubated at room temperature for 5 minutes. 6 .mu.l of
LIPOFECTAMINE.RTM. RNAiMax was also mixed with 14 .mu.l of
OPTI-MEM.RTM. which was incubated at room temperature for 5
minutes. These two mixtures were then combined and incubated at
room temperature for 5 minutes then contacted with cells.
Cas9/gRNA/OPTI-MEM.RTM. samples (FIG. 31) were combined with 6
.mu.l LIPOFECTAMINE.RTM. RNAiMax and 14 .mu.l OPTI-MEM.RTM. that
had been incubated at room temperature for 5 minutes. These two
mixtures were then combined and incubated at room temperature for 5
minutes then contacted with cells. Cas9/OPTI-MEM.RTM. samples were
mixed with both 0.7 .mu.l or gRNA and 9.3 .mu.l of OPTI-MEM.RTM.
(incubated for 5 minutes at room temperature) and 6 .mu.l
LIPOFECTAMINE.RTM. RNAiMax and 14 .mu.l OPTI-MEM.RTM. incubated for
5 minutes at room temperature), then contacted with cells after
incubation for 5 minutes at room temperature.
Cas9/LIPOFECTAMINE.RTM. RNAiMax samples (FIG. 32) were mixed with
0.7 .mu.l gRNA and 32.8 .mu.l OPTI-MEM.RTM. (incubated at room
temperature for 5 minutes), then contacted with cells.
[0252] For transfection, 293FT cells were seeded one day prior to
transfection at 20,000 cells per well in a 96 well plate format to
get around 50% to 60% cell confluency on the day of transfection.
Each well at the time of seeding has 100 .mu.l of cell culture
media (DMEM, 10% FBS, and 5% each of sodium pyruvate, non-essential
amino acids and GlutaMAX.TM.). At the time of transfection 10 .mu.l
of final transfection mix (containing Cas9, gRNA,
LIPOFECTAMINE.RTM. RNAiMAX and OPTIMEM.RTM.) was added to each well
in 96 well format. Following incubation at 37.degree. C. for 72
hours the cells were harvested for measuring % cleavage efficiency
at the respective target loci (in this case HPRT gene target) using
GENEART.TM. cleavage detection assay.
[0253] In one aspect, the invention relates to compositions and
methods related to ready to use reagents. A ready to use reagent
may be in any number of forms. For example, a ready to use reagent
may contain one or more Cas9 protein, one or more gRNA, one or more
transfection reagent, and one or more cell culture medium. As
specific example is a reagent that contains a Cas9 protein, two
gRNAs, and LIPOFECTAMINE.RTM. RNAiMax all in 2.times. concentration
and OPTI-MEM.RTM. culture medium in a 1.times. concentration. A
ready to use reagent of this type may be mixed 1:1 with cells
contained in OPTI-MEM.RTM. culture medium to yield a transfection
reaction mixture for the introduction of two gRNAs into the cells,
where the gRNAs share sequence homology with two locations in the
genome of the cells. If appropriate, the cells may simultaneously
or subsequently be contacted with one or more nucleic acid
molecules for insertion into the genomic cut sites.
[0254] Another example of a ready to use reagent includes a
combination of one or more Cas9 protein, one or more gRNA, and one
or more cell culture medium. As specific example is a reagent that
contains a Cas9 protein and two gRNAs in 2.times. concentration and
OPTI-MEM.RTM. culture medium in a 1.times. concentration. A ready
to use reagent of this type may be mixed first with
LIPOFECTAMINE.RTM. RNAiMax and then 1:1 with cells contained in
OPTI-MEM.RTM. culture medium to yield a transfection reaction
mixture for the introduction of two gRNAs into the cells.
[0255] Ready to use reagents such as those set out above may be
stored at 4.degree. C. for a period of time prior to use. As noted
elsewhere herein, under some conditions, Cas9, gRNA and
transfection reagent mixtures are not stable upon freezing but are
stable upon storage at 4.degree. C.
[0256] Ready to use reagents may be labeled with preferred storage
conditions and expiration dates that are designed to reflect a
specified decrease in activity (e.g., less than 80% of activity).
For example, expiration dates may range from about two weeks to
about one year (e.g., from about two weeks to about ten months,
from about two weeks to about eight months, from about two weeks to
about six months, from about two weeks to about four months, from
about one month to about one year, from about one month to about
ten months, from about one month to about six months, from about
one month to about four months, from about three months to about
one year, from about three months to about eight months, etc.).
[0257] It has also been found that, in some instances, higher
concentrations of CRISPR system components result in higher
stability upon storage. Thus, in some aspects, the invention
includes reagents that contain greater than 50 ng/.mu.l (e.g., from
about 50 ng/.mu.l to about 500 ng/.mu.l, from about 100 ng/.mu.l to
about 500 ng/.mu.l, from about 150 ng/.mu.l to about 500 ng/.mu.l,
from about 200 ng/.mu.l to about 500 ng/.mu.l, from about 250
ng/.mu.l to about 500 ng/.mu.l, from about 300 ng/.mu.l to about
500 ng/.mu.l, from about 400 ng/.mu.l to about 500 ng/.mu.l, etc.)
of gRNA. In many instances, the molar amount of Cas9 protein, when
present, to gRNA will be in the range of from about 5:1 to about
1:5 (e.g., from about 5:1 to about 1:4, from about 5:1 to about
1:3, from about 5:1 to about 1:2, from about 5:1 to about 1:1, from
about 5:1 to about 1:1, from about 4:1 to about 1:5, from about 5:1
to about 1:5, from about 2:1 to about 1:5, from about 1:2 to about
1:5, from about 4:1 to about 1:4, from about 3:1 to about 1:3, from
about 2:1 to about 1:2, etc.).
[0258] Kits:
[0259] The invention also provides kits for, in part, the assembly
and/or storage of nucleic acid molecules and for the editing of
cellular genomes. As part of these kits, materials and instruction
are provided for both the assembly of nucleic acid molecules and
the preparation of reaction mixtures for storage and use of kit
components.
[0260] Kits of the invention will often contain one or more of the
following components:
[0261] 1. One or more nucleic acid molecule (e.g., one or more
primer, one or more DNA molecule encoding Cas9, dCas9, guide RNA,
etc., one or more mRNA encoding a CRISPR system component, such as
Cas9, dCas9, etc.),
[0262] 2. One or more polymerase,
[0263] 3. One or more protein (e.g., one or more CRISPR protein
such as Cas9, dCas9, etc.),
[0264] 4. One or more partial vector (e.g., one or more nucleic
acid segment containing an origin of replication and/or a
selectable marker) or complete vector, and
[0265] 5. Instructions for how to use kits components.
[0266] In particular, some kits of the invention may include one or
more of the following: (a) a double-stranded nucleic acid molecule
encoding the 3' end of a guide RNA molecule (see FIG. 8), wherein
this double-stranded nucleic acid molecule does not encode all or
part of Hybridization Region 1, (b) a polymerase, and (c) at least
one buffer.
[0267] In some embodiments, kits may comprise one or more reagents
for use in a process utilizing one or more of the CRISPR system
components discussed herein or for producing one or more CRISPR
system component discussed herein.
[0268] Kit reagents may be provided in any suitable container. A
kit may provide, for example, one or more reaction or storage
buffers. Reagents may be provided in a form that is usable in a
particular reaction, or in a form that requires addition of one or
more other components before use (e.g., in concentrate or
lyophilized form). A buffer can be any buffer, including but not
limited to a sodium carbonate buffer, a sodium bicarbonate buffer,
a borate buffer, a Tris buffer, a MOPS buffer, a HEPES buffer, and
combinations thereof. In some embodiments, the buffer is alkaline.
In some embodiments, the buffer has a pH from about 7 to about
10.
EXAMPLES
Example 1: One Step Synthesis of gRNA Template and High Efficiency
Cell Engineering Workflow
[0269] Abstract
[0270] CRISPR-Cas9 systems provide innovative applications in
genome engineering. To edit the genome, expression of Cas9, mature
crRNA and tracrRNA or a single guide RNA (gRNA) is required.
Elements of the mature crRNA and tracrRNA or a gRNA are often built
into a Cas9 expression plasmid or constructed in a standard plasmid
driven by a U6 promoter for mammalian expression. A novel method
for the rapid synthesis of gRNA template is described in this
example, which combines gene synthesis and DNA fragment assembly
technologies with an accuracy of assembly of >96%. In other
words, over 96% of the assembled nucleic acid molecules are the
desired assembly products. The method allows rapid synthesis of
guide RNA (gRNA) via in vitro transcription using short DNA
oligonucleotides. In conjunction with Cas9 protein delivery,
Cas9/gRNA complexes can be transfected into the cells through
processes such as lipid-mediated methods, electroporation, and cell
penetrating peptide mediated delivery. Overall, cell engineering
workflows can be reduced to at least four days and, in some
instances, two days. Methods described herein are applicable for
high throughput gRNA synthesis and genome-wide editing.
[0271] Introduction
[0272] CRISPR-Cas9 mediated genome engineering enables researchers
to modify genomic DNA in vivo directly and efficiently. Three
components (Cas9, mature crRNA and tracrRNA) are essential for
efficient cell engineering. Although the mature crRNA and tracrRNA
can be synthesized chemically, the quality of the synthetic RNA is
often not sufficient for in vivo cell engineering due, for example,
to the presence of truncated by-products. Thus, mature crRNA and
tracrRNA or a combined single gRNA are often transcribed from a
Cas9 expression plasmid or built into a separate plasmid driven by
a U6 promoter. The resulting plasmids are then transfected or
co-transfected into the cells. Because the constructs are
relatively large, the delivery of plasmid DNA often becomes the
limiting step, especially for suspension cells. Recently Cas9 mRNA
has employed to increase the rate of DNA cleavage. To make gRNA, a
pre-cloned all-in-one plasmid based upon, for example, a vector
shown in FIG. 17 or FIG. 18 may serve as template to prepare a gRNA
PCR fragment containing a T7 promoter, followed by gel extraction.
Alternatively a synthetic DNA string may be used as a template.
[0273] Overall, it is time-consuming to prepare the gRNA template
for in vitro transcription. A gRNA template can be assembled via
PCR in about one hour. Further, gRNA can be generated in vitro
transcription in about 3 hours. DNA oligonucleotides can be
converted to into gRNA in about 4 hours. A workflow with the above
timing elements was tested and. Furthermore, in combination with
Cas9 protein transfection technology, cell engineering cycle was
accomplished as described herein in four days.
[0274] Materials and Methods
[0275] Materials
[0276] 293FT cells, DMEM medium, Fetal Bovine Serum (FBS),
OPTI-MEM.RTM. Medium, LIPOFECTAMINE.RTM. 3000, RNAIMAX.TM.,
MESSENGERMAX.TM., GENEART.RTM. CRISPR Nuclease Vector with OFP
Reporter, 2% E-GEL.RTM. EX Agarose Gels, PURELINK.RTM. PCR Micro
Kit, TranscriptAid T7 High Yield Transcription Kit,
MEGASHORTSCRIPT.TM. T7 Transcription Kit, MEGACLEAR.TM.
Transcription Clean-Up Kit, ZERO BLUNT.RTM. TOPO.RTM. PCR Cloning
Kit, PURELINK.RTM. Pro Quick96 Plasmid Purification Kit, Qubit.RTM.
RNA BR Assay Kit, QUBIT.RTM. Protein Assay Kit, Pierce LAL
Chromogenic Endotoxin Quantitation Kit, GENEART.RTM. Genomic
Cleavage Detection Kit, and POROS.RTM. Heparin column were from
Thermo Fisher Scientific. PHUSION.RTM. High-Fidelity DNA Polymerase
was purchased from New England Biolabs. HIPREP.TM. 16/60 Sephacryl
S-300 HR gel filtration column was purchased from GE Healthcare.
All the DNA oligonucleotides used for gRNA synthesis were from
Thermo Fisher Scientific.
[0277] Methods
[0278] One Step Synthesis of gRNA Template
[0279] The design of oligonucleotides for the synthesis of gRNA
template is depicted in FIG. 13. The forward primer:
[0280] 5'-GTT TTA GAG CTA GAA ATA GCA AG-3' (SEQ ID NO: 13) and
reverse primer:
[0281] 5'-AAA AGC ACC GAC TCG GTG CCA C-3' (SEQ ID NO: 14) were
used to amplify the 80 bp constant region of tracrRNA from a
GENEART.RTM. CRISPR Nuclease Vector, followed by purification using
agarose gel extraction. The concentration of PCR product was
measured by Nanodrop (Thermo Fisher Scientific) and the molarity
was calculated based on the molecular weight of 24.8 kd. To prepare
a pool of oligonucleotides, an aliquot of the 80 bp PCR product was
mixed with two end primers 5'-taatacgactcactatagg-3' (SEQ ID NO:
15) and 5'-AAA AGC ACC GAC TCG GTG CCA C-3' (SEQ ID NO: 14) with a
final concentration of 0.3 .mu.M for the 80 bp PCR product and 10
.mu.M for each of the end primers. For a specific target, a 34 bp
forward primer consisting of the 19 bp T7 promoter sequence
taatacgactcactatagg (SEQ ID NO: 15) and 15 bp of the 5' end target
sequence, and a 34 bp reverse primer consisting of 20 bp target
sequence and 14 bp of the 5' end tracrRNA sequence gttttagagctaga
(SEQ ID NO: 16) were chemically synthesized with 15 bp overlap. A
working solution containing the two 34 bp oligonucleotides was
prepared at a final concentration of 0.3 .mu.M. Alternatively, a
pair of 39 bp forward and reverse primers with 20 bp overlap was
synthesized and tested. To set up the one step synthesis of gRNA
template, 1.5 .mu.l of pool oligonucleotides and 1.5 .mu.l of the
working solution were added to a PCR tube containing 10 .mu.l of
5.times. Phusion HF buffer, 1 .mu.l of 10 mM dNTP, 35.5 .mu.l H2O,
and 0.5 .mu.l PHUSION.RTM. High-Fidelity DNA polymerase. The PCR
program was set at 98.degree. C. for 30 sec and then 30 cycles of
98.degree. C. for 5 sec and 55.degree. C. for sec, followed by
incubation at 72.degree. C. for 30 sec and 4.degree. C. forever.
The PCR product was analyzed by a 2% E-GEL.RTM. EX Agarose Gel,
followed by purification using Purelink PCR micro column. The DNA
concentration was determined by Nanodrop instrument.
[0282] To determine the error rate, the PCR product was cloned into
ZERO BLUNT.RTM. TOPO.RTM. vector, followed by plasmid DNA isolation
and sequencing.
[0283] In Vitro Transcription
[0284] The in vitro transcription of gRNA template was carried out
using TRANSCRIPTAID.TM. T7 High Yield Transcription Kit. Briefly, 6
.mu.l of gRNA template (250-500 ng) was added to a reaction mixture
containing 8 .mu.l of NTP, 4 .mu.l of 5.times. reaction buffer and
2 .mu.l of T7 enzyme mix. The reaction was carried out at
37.degree. C. for 2 hrs, followed by incubation with DNase I (2
units per 120 ng DNA template) for 15 minutes. The gRNA product was
purified using MEGACLEAR.TM. Transcription Clean-Up kit as
described in the manual. The concentration of RNA was determined
using QUBIT.RTM. RNA BR Assay Kit.
[0285] Expression and Purification of Cas9 Protein
[0286] A glycerol stock BL21(DE3) star E. coli strain expressing
NLS Cas9 protein was inoculated in 20 ml BRM medium and grown
overnight at 37.degree. C. in a shaking incubator. The overnight
culture was then added to 1 liter of BRM medium and grown cells to
an OD.sub.600 nm of 0.6-0.8 at 37.degree. C. in a shaking incubator
(.about.4-5 hours). An aliquot of un-induced sample was taken for
monitoring protein induction with IPTG. 0.5 ml of 1 M IPTG was
added to the culture and incubated overnight at room temperature in
a shaking incubator. An aliquot of induced sample along with
un-induced sample were analyzed by SDS-PAGE. Upon validation of
protein induction, the culture medium was centrifuged at 5000 rpm
for 15 minutes to harvest the cell pellets (.about.24 grams of wet
weight). 100 ml of buffer A containing 20 mM Tris (pH7.5), 100 mM
NaCl, 10% Glycerol, and 1 mM PMSF was used to resuspend the cell
pellet. The cell suspension was sonicated on ice for 30 minutes
with power level of medium tip set at 8, 10 sec "on", and 20 sec
"off". The cell lysate was clarified by centrifugation at 16500 rpm
for 30 minutes. The supernatant was filtered through a 0.2 .mu.m
filter device prior to loading to a 16 ml heparin column previously
equilibrated with buffer A at a flow rate of 2 ml/min. The column
was first washed with five column volume of buffer A and then
gradually increased to 40% of buffer B containing 20 mM Tris
(pH7.5), 1.2 M NaCl and 10% glycerol. The Cas9 protein was eluted
with a 5 CV gradient from 40% to 100% buffer B. The fractions were
analyzed by SDS-PAGE. Fractions containing Cas9 protein were
combined and concentrated using two 15 ml Amicon Centrifugal filter
units (EMD Millipore, Cat. No. UFC905024). The concentrated protein
was filtered through a 0.2 .mu.m filter device and loaded twice
onto a 120 ml of HIPREP.TM. 16/60 Sephacryl S-300 HR column
previously equilibrated with buffer C containing 20 mM Tris (pH 8),
250 mM KCl and 10% Glycerol. The fractions containing Cas9 protein
were pooled and concentrated. The protein concentration was
determined by QUBIT.RTM. Protein Assay Kit. The endotoxin level in
the purified protein was measured by Endotoxin Quantitation Kit.
The concentrated protein was adjusted to 50% glycerol and stored at
-20.degree. C.
[0287] Cell Culture
[0288] 293FT cells were maintained in DMEM medium supplemented with
10% FBS in a 5% CO.sub.2 incubator. One day prior to transfection,
the cells were seeded in a 24-well plate at a cell density of
2.5.times.10.sup.5 cells/0.5 ml medium. For transfection, 500 ng of
purified Cas9 was added to 25 .mu.l of OPTI-MEM.RTM. medium,
followed by addition of 120 ng gRNA. The sample was mixed by gently
tapping the tubes a few times and then incubated at room
temperature for 10 minutes. To a separate test tube, 3 .mu.l of
RNAIMAX.TM. was added to 25 .mu.l of OPTI-MEM.RTM. medium. The
diluted transfection reagent was transferred to the tube containing
Cas9 protein/gRNA complexes, followed by incubation at room
temperature for 15 minutes. The entire solution was then added to
the cells in a 24-well and mixed by gently swirling the plate a few
times. The plate was incubated at 37.degree. C. for 48 hours in a
5% CO.sub.2 incubator. The percentage of genome editing was
measured by GENEART.RTM. Genomic Cleavage Detection Kit.
[0289] Results and Discussion
[0290] One Step Synthesis of gRNA Template
[0291] Since gRNA synthesis is one of the limiting steps in genome
engineering, an attempt was made to reduce the time for gRNA
synthesis. As an example, HPRT-T1 target catttctcagtcctaaaca (SEQ
ID NO: 17) was chosen, but these methods were also found to work
for GFP and VEGFA-T3 targets (data not shown). Initially, a gene
synthesis approach was utilized to assemble a gRNA template using a
set of 6 synthetic DNA oligonucleotides (Set 1 oligonucleotides in
Table 8). Through optimization of oligonucleotide pool
concentration and PCR condition, a clean PCR product was obtained
on an agarose gel (data not shown). An aliquot of the PCR product
served as template to synthesize the gRNA via in vitro
transcription. The quality of synthetic gRNA was analyzed by a
denaturing gel.
[0292] To test the functionality of synthetic gRNA, gRNA was
associated with Cas9 protein. The resulting complexes were then
delivered to the 293FT cells via lipid-based transfection. However,
the evaluation of in vivo genome cleavage assay indicated that gRNA
did not work well (data not shown). To determine the problem, gRNA
templates were cloned into a ZERO BLUNT.RTM. TOPO vector and then
sequenced. As shown in FIG. 15, it was observed that more than 20%
of the gRNA templates harbored mutations, mostly deletions. To
minimize the potential sources of errors, instead of using long
synthetic oligos to create the complete T7 promoter/guide RNA
template, the constant 80 bp tracrRNA region was amplified from a
sequence-validated plasmid template, followed by gel purification
to remove the template. Then to fuse the T7 promoter sequence and
target sequence to the constant tracrRNA, a pair of 34 bp or 39 bp
forward and reverse oligonucleotides that share 15 bp or 20 bp
homology, respectively, across the variable target sequence were
designed, wherein the middle oligo 2 also shared 19 bases of
homology with the tracrRNA region (FIG. 13).
[0293] As described in Materials and Methods, the gRNA template was
assembled in a single PCR reaction using a pool of DNA
oligonucleotides and tracrRNA fragment (FIG. 13). Upon PCR micro
column purification, the gRNA template was used to prepare gRNA via
in vitro transcription. The quality of gRNA was examined using a
TBE-urea denaturing gel. gRNA prepared via PCR amplification from
an all-in-one plasmid was used as positive control. An "all-in-one
plasmid" is a plasmid that contains all of the components of a
CRISPR system, such as guide RNA and Cas9 coding sequences. Vector
maps of two similar all-in-one plasmids used in the experiments
here are shown in FIG. 17 and FIG. 18.
[0294] To examine in vivo functionality of synthesized gRNA, the
Cas9 protein from E. coli was expressed and purified. The Cas9
protein was pre-incubated with synthetic gRNA to form the complexes
prior to cell transfection. The gRNA prepared from an all-in-one
plasmid served as a positive control. The genome modification was
examined by Genome Cleavage and Detection assay. As depicted in Gel
Image B of FIG. 14, the percentage of Indel for the newly
synthesized gRNAs was similar to the positive control. To determine
the error rate in the gRNA template, sequencing analysis was also
performed. As depicted in FIG. 15, approximately 7% of gRNA
template harbored mutation with most deletion occurred at 3' end
and 5' end. One mutation was detected within the target region when
longer 39 bp oligonucleotides were used. The use of PAGE-purified
end primers (.about.20 bp each) further decreased the error rate to
3.6% with no mutation detected in the target region, which was
similar to the control gRNA prepared from an all-in-one plasmid
with a 2% error rate. These results indicated that the quality of
gRNA were good enough for most of our applications.
[0295] Because the 80 bp tracrRNA contains a polyT at the 3' end,
there was a possibility that the Poly T had no effect on genome
editing. To test this, serial deletions of PolyT at the 3' end of
gRNA (set 3 oligos in Table 8) were made. Based on in vivo genome
cleavage assay, removal of the PolyT at 3' end of gRNA appeared to
have no effect on the performance of gRNA. The addition of three
extra Ts at the 3' end also did not affect the functionality of
gRNA either (data not shown).
[0296] The standard T7 promoter sequence "taatacgactcactataggg"
(SEQ ID NO: 18) contains GGG at the 3' end, which is thought to be
essential for maximal production of gRNA via in vitro
transcription. However, because the transcription starts from the
first G, three extra G will be added to the gRNA sequence assuming
the target does not have a G at the 5' end, which might affect the
functionality of gRNA. To examine this, the AAVS target
ccagtagccagccccgtcc (SEQ ID NO: 19) and the IP3R2 target
tcgtgtccctgtacgcgga (SEQ ID NO: 20) were chosen and G deletions at
the 3' end of T7 promoter were made (see FIG. 16 and Table 7). The
addition of Gs, especially 3G in a row, significantly decreased the
activity of gRNA. The addition of 1 G exhibited slightly better
cleavage efficiency than that of 2 G, even although both produced
similar amount of gRNA in in vitro transcription reaction. However,
without any G, the yield of in vitro transcription reaction was
dramatically reduced.
TABLE-US-00007 TABLE 7 Effect of G on gRNA synthesis Construct PCR
yield (ng/.mu.l) RNA yield (ng/.mu.l) AAVS-0G 124 220 AAVS-1G 82
394 AAVS-2G 70 294 AAVS-3G 53 290 IP3R2-0G 100 65 IP3R2-1G 54 272
IP3R2-2G 46 300 IP3R2-3G 122 289 EMX1-0G 75 156 EMX1-1G 119 490
EMX1-2G 101 680 EMX1-3G 98 750
[0297] In conclusion, compositions and methods provided herein
related to gRNA synthesis and associated workflows allow for four
day cell engineering. On Day 1, the biologists (1) design and (2)
synthesize or order short DNA oligonucleotides and seed the cells
of interest. On Day 2, the biologists prepare the gRNA template by
one pot PCR, followed by in vitro transcription for making gRNA.
Upon association of gRNA with purified Cas9 protein, the Cas9
protein/gRNA complexes are transfected into the cells via
lipid-mediated method or electroporation. On Day 4, the biologists
harvest the cells to analyze genome modification. Thus, the
invention provides compositions and methods related to improve
workflows for genome engineering. In some aspects, these workflows
allow for the genome modification experiments to occur in four days
from concept to completion.
TABLE-US-00008 TABLE 8 Oligonucleotides for gRNA synthesis SEQ ID
NO Set 1 oligos gF1 Taatacgactcactataggg 21 gcatttctcagtcctaaaca
gR1 GCT ATT TCT AGC TCT 22 AAA ACT GTT TAG GAC TGA GAA ATG C
Gttttagagctagaaatag 23 Caagttaaaataaggctag Tccgttatcaacttgaaaa agt
AAA AGC ACC GAC TCG 24 GTG CCA CTT TTT CAA GTT GAT AAC gR2 GGA CTA
GCC TTA TTT TAA CTT gEnd-F taatacgactcactataggg 18 gEnd-R AAA AGC
ACC GAC TCG 14 GTG CCA C Set 2 oligos Con-F GTT TTA GAG CTA GAA 13
ATA GCA AG gEnd-R AAA AGC ACC GAC TCG 14 GTG CCA C gR1-20 bp GCT
ATT TCT AGC TCT 25 AAA ACT GTT TAG GAC TGA GAA ATG gR1-15 bp TTC
TAG CTC TAA AAC 26 TGT TTA GGA CTG AGA AAT G gF1-20 bp
Taatacgactcactataggc 27 atttctcagtcctaaacag gF1-15 bp
Taatacgactcactataggc 28 atttctcagtccta gEnd-F-2G
taatacgactcactatagg 15 Set 3 oligos gEnd-R4T AAA AGC ACC GAC 14 TCG
GTG CCA C gEnd-R3T AA AGC ACC GAC 29 TCG GTG CCA C gEnd-R2T A AGC
ACC GAC 30 TCG GTG CCA C gEnd-R1T AGC ACC GAC TCG 31 GTG CCA C
gEnd-R0T GC ACC GAC TCG 32 GTG CCA C Set 4 oligos AAVS3G
Taatacgactcactata 33 gggCCACTAGCCAGCCCC AAVS2G Taatacgactcactatag
34 gCCAGTAGCCAGCCCC AAVS1G Taatacgactcactatag 35
CCAGTAGCCAGCCCC
TABLE-US-00009 TABLE 9 Nucleotide sequence of the vector shown in
FIG. 17. (SEQ ID NO: 36) GTTAGGCGTTTTGCGCTGCTTCGCGATGTACGGGCC
AGATATACGCGTTGACATTGATTATTGACTAGTTA
TTAATAGTAATCAATTACGGGGTCATTAGTTCATA
GCCCATATATGGAGTTCCGCGTTACATAACTTACG
GTAAATGGCCCGCCTGGCTGACCGCCCAACGACCC
CCGCCCATTGACGTCAATAATGACGTATGTTCCCA
TAGTAACGCCAATAGGGACTTTCCATTGACGTCAA
TGGGTGGAGTATTTACGGTAAACTGCCCACTTGGC
AGTACATCAAGTGTATCATATGCCAAGTACGCCCC
CTATTGACGTCAATGACGGTAAATGGCCCGCCTGG
CATTATGCCCAGTACATGACCTTATGGGACTTTCC
TACTTGGCAGTACATCTACGTATTAGTCATCGCTA
TTACCATGGTGATGCGGTTTTGGCAGTACATCAAT
GGGCGTGGATAGCGGTTTGACTCACGGGGATTTCC
AAGTCTCCACCCCATTGACGTCAATGGGAGTTTGT
TTTGGCACCAAAATCAACGGGACTTTCCAAAATGT
CGTAACAACTCCGCCCCATTGACGCAAATGGGCGG
TAGGCGTGTACGGTGGGAGGTCTATATAAGCAGAG
CTCGTTTAGTGAACCGTCAGATCGCCTGGAGACGC
CATCCACGCTGTTTTGACCTCCATAGAAGACACCG
GGACCGATCCAGCCTCCGGAGCGGCCGCCACCATG
GGCAAGCCCATCCCTAACCCCCTGTTGGGGCTGGA
CAGCACCGCTCCCAAAAAGAAAAGGAAGGTGGGCA
TTCACGGCGTGCCTGCGGCCGACAAAAAGTACAGC
ATCGGCCTTGATATCGGCACCAATAGCGTGGGCTG
GGCCGTTATCACAGACGAATACAAGGTACCCAGCA
AGAAGTTCAAGGTGCTGGGGAATACAGACAGGCAC
TCTATCAAGAAAAACCTTATCGGGGCTCTGCTGTT
TGACTCAGGCGAGACCGCCGAGGCCACCAGGTTGA
AGAGGACCGCAAGGCGAAGGTACACCCGGAGGAAG
AACAGGATCTGCTATCTGCAGGAGATCTTCAGCAA
CGAGATGGCCAAGGTGGACGACAGCTTCTTCCACA
GGCTGGAGGAGAGCTTCCTTGTCGAGGAGGATAAG
AAGCACGAACGACACCCCATCTTCGGCAACATAGT
CGACGAGGTCGCTTATCACGAGAAGTACCCCACCA
TCTACCACCTGCGAAAGAAATTGGTGGATAGCACC
GATAAAGCCGACTTGCGACTTATCTACTTGGCTCT
GGCGCACATGATTAAGTTCAGGGGCCACTTCCTGA
TCGAGGGCGACCTTAACCCCGACAACAGTGACGTA
GACAAATTGTTCATCCAGCTTGTACAGACCTATAA
CCAGCTGTTCGAGGAAAACCCTATTAACGCCAGCG
GGGTGGATGCGAAGGCCATACTTAGCGCCAGGCTG
AGCAAAAGCAGGCGCTTGGAGAACCTGATAGCCCA
GCTGCCCGGTGAAAAGAAGAACGGCCTCTTCGGTA
ATCTGATTGCCCTGAGCCTGGGCCTGACCCCCAAC
TTCAAGAGCAACTTCGACCTGGCAGAAGATGCCAA
GCTGCAGTTGAGTAAGGACACCTATGACGACGACT
TGGACAATCTGCTCGCCCAAATCGGCGACCAGTAC
GCTGACCTGTTCCTCGCCGCCAAGAACCTTTCTGA
CGCAATCCTGCTTAGCGATATCCTTAGGGTGAACA
CAGAGATCACCAAGGCCCCCCTGAGCGCCAGCATG
ATCAAGAGGTACGACGAGCACCATCAGGACCTGAC
CCTTCTGAAGGCCCTGGTGAGGCAGCAACTGCCCG
AGAAGTACAAGGAGATCTTTTTCGACCAGAGCAAG
AACGGCTACGCCGGCTACATCGACGGCGGAGCCAG
CCAAGAGGAGTTCTACAAGTTCATCAAGCCCATCC
TGGAGAAGATGGATGGCACCGAGGAGCTGCTGGTG
AAGCTGAACAGGGAAGATTTGCTCCGGAAGCAGAG
GACCTTTGACAACGGTAGCATCCCCCACCAGATCC
ACCTGGGCGAGCTGCACGCAATACTGAGGCGACAG
GAGGATTTCTACCCCTTCCTCAAGGACAATAGGGA
GAAAATCGAAAAGATTCTGACCTTCAGGATCCCCT
ACTACGTGGGCCCTCTTGCCAGGGGCAACAGCCGA
TTCGCTTGGATGACAAGAAAGAGCGAGGAGACCAT
CACCCCCTGGAACTTCGAGGAAGTGGTGGACAAAG
GAGCAAGCGCGCAGTCTTTCATCGAACGGATGACC
AATTTCGACAAAAACCTGCCTAACGAGAAGGTGCT
GCCCAAGCACAGCCTGCTTTACGAGTACTTCACCG
TGTACAACGAGCTCACCAAGGTGAAATATGTGACC
GAGGGCATGCGAAAACCCGCTTTCCTGAGCGGCGA
GCAGAAGAAGGCCATCGTGGACCTGCTGTTCAAGA
CCAACAGGAAGGTGACCGTGAAGCAGCTGAAGGAG
GACTACTTCAAGAAGATCGAGTGCTTTGATAGCGT
GGAAATAAGCGGCGTGGAGGACAGGTTCAACGCCA
GCCTGGGCACCTACCACGACTTGTTGAAGATAATC
AAAGACAAGGATTTCCTGGATAATGAGGAGAACGA
GGATATACTCGAGGACATCGTGCTGACTTTGACCC
TGTTTGAGGACCGAGAGATGATTGAAGAAAGGCTC
AAAACCTACGCCCACCTGTTCGACGACAAAGTGAT
GAAACAACTGAAGAGACGAAGATACACCGGCTGGG
GCAGACTGTCCAGGAAGCTCATCAACGGCATTAGG
GACAAGCAGAGCGGCAAGACCATCCTGGATTTCCT
GAAGTCCGACGGCTTCGCCAACCGAAACTTCATGC
AGCTGATTCACGATGACAGCTTGACCTTCAAGGAG
GACATCCAGAAGGCCCAGGTTAGCGGCCAGGGCGA
CTCCCTGCACGAACATATTGCAAACCTGGCAGGCT
CCCCTGCGATCAAGAAGGGCATACTGCAGACCGTT
AAGGTTGTGGACGAATTGGTCAAGGTCATGGGCAG
GCACAAGCCCGAAAACATAGTTATAGAGATGGCCA
GAGAGAACCAGACCACCCAAAAGGGCCAGAAGAAC
AGCCGGGAGCGCATGAAAAGGATCGAGGAGGGTAT
CAAGGAACTCGGAAGCCAGATCCTCAAAGAGCACC
CCGTGGAGAATACCCAGCTCCAGAACGAGAAGCTG
TACCTGTACTACCTGCAGAACGGCAGGGACATGTA
CGTTGACCAGGAGTTGGACATCAACAGGCTTTCAG
ACTATGACGTGGATCACATAGTGCCCCAGAGCTTT
CTTAAAGACGATAGCATCGACAACAAGGTCCTGAC
CCGCTCCGACAAAAACAGGGGCAAAAGCGACAACG
TGCCAAGCGAAGAGGTGGTTAAAAAGATGAAGAAC
TACTGGAGGCAACTGCTCAACGCGAAATTGATCAC
CCAGAGAAAGTTCGATAACCTGACCAAGGCCGAGA
GGGGCGGACTCTCCGAACTTGACAAAGCGGGCTTC
ATAAAGAGGCAGCTGGTCGAGACCCGACAGATCAC
GAAGCACGTGGCCCAAATCCTCGACAGCAGAATGA
ATACCAAGTACGATGAGAATGACAAACTCATCAGG
GAAGTGAAAGTGATTACCCTGAAGAGCAAGTTGGT
GTCCGACTTTCGCAAAGATTTCCAGTTCTACAAGG
TGAGGGAGATCAACAACTACCACCATGCCCACGAC
GCATACCTGAACGCCGTGGTCGGCACCGCCCTGAT
TAAGAAGTATCCAAAGCTGGAGTCCGAATTTGTCT
ACGGCGACTACAAAGTTTACGATGTGAGGAAGATG
ATCGCTAAGAGCGAACAGGAGATCGGCAAGGCCAC
CGCTAAGTATTTCTTCTACAGCAACATCATGAACT
TTTTCAAGACCGAGATCACACTTGCCAACGGCGAA
ATCAGGAAGAGGCCGCTTATCGAGACCAACGGTGA
GACCGGCGAGATCGTGTGGGACAAGGGCAGGGACT
TCGCCACCGTGAGGAAAGTCCTGAGCATGCCCCAG
GTGAATATTGTGAAAAAAACTGAGGTGCAGACAGG
CGGCTTTAGCAAGGAATCCATCCTGCCCAAGAGGA
ACAGCGACAAGCTGATCGCCCGGAAGAAGGACTGG
GACCCTAAGAAGTATGGAGGCTTCGACAGCCCCAC
CGTAGCCTACAGCGTGCTGGTGGTCGCGAAGGTAG
AGAAGGGGAAGAGCAAGAAACTGAAGAGCGTGAAG
GAGCTGCTCGGCATAACCATCATGGAGAGGTCCAG
CTTTGAGAAGAACCCCATTGACTTTTTGGAAGCCA
AGGGCTACAAAGAGGTCAAAAAGGACCTGATCATC
AAACTCCCCAAGTACTCCCTGTTTGAATTGGAGAA
CGGCAGAAAGAGGATGCTGGCGAGCGCTGGGGAAC
TGCAAAAGGGCAACGAACTGGCGCTGCCCAGCAAG
TACGTGAATTTTCTGTACCTGGCGTCCCACTACGA
AAAGCTGAAAGGCAGCCCCGAGGACAACGAGCAGA
AGCAGCTGTTCGTGGAGCAGCACAAGCATTACCTG
GACGAGATAATCGAGCAAATCAGCGAGTTCAGCAA
GAGGGTGATTCTGGCCGACGCGAACCTGGATAAGG
TCCTCAGCGCCTACAACAAGCACCGAGACAAACCC
ATCAGGGAGCAGGCCGAGAATATCATACACCTGTT
CACCCTGACAAATCTGGGCGCACCTGCGGCATTCA
AATACTTCGATACCACCATCGACAGGAAAAGGTAC
ACTAGCACTAAGGAGGTGCTGGATGCCACCTTGAT
CCACCAGTCCATTACCGGCCTGTATGAGACCAGGA
TCGACCTGAGCCAGCTTGGAGGCGACTCTAGGGCG
GACCCAAAAAAGAAAAGGAAGGTGGAATTCTCTAG
AGGCAGTGGAGAGGGCAGAGGAAGTCTGCTAACAT
GCGGTGACGTCGAGGAGAATCCTGGCCCAATGAAC
CGGGGAGTCCCTTTTAGGCACTTGCTTCTGGTGCT
GCAACTGGCGCTCCTCCCAGCAGCCACTCAGGGAA
AGAAAGTGGTGCTGGGCAAAAAAGGGGATACAGTG
GAACTGACCTGTACAGCTTCCCAGAAGAAGAGCAT
ACAATTCCACTGGAAAAACTCCAACCAGATAAAGA
TTCTGGGAAATCAGGGCTCCTTCTTAACTAAAGGT
CCATCCAAGCTGAATGATCGCGCTGACTCAAGAAG
AAGCCTTTGGGACCAAGGAAACTTCCCCCTGATCA
TCAAGAATCTTAAGATAGAAGACTCAGATACTTAC
ATCTGTGAAGTGGAGGACCAGAAGGAGGAGGTGCA
ATTGCTAGTGTTCGGATTGACTGCCAACTCTGACA
CCCACCTGCTTCAGGGGCAGAGCCTGACCCTGACC
TTGGAGAGCCCCCCTGGTAGTAGCCCCTCAGTGCA
ATGTAGGAGTCCAAGGGGTAAAAACATACAGGGGG
GGAAGACCCTCTCCGTGTCTCAGCTGGAGCTCCAG
GATAGTGGCACCTGGACATGCACTGTCTTGCAGAA
CCAGAAGAAGGTGGAGTTCAAAATAGACATCGTGG
TGCTAGCTTTCCAGAAGGCCTCCAGCATAGTCTAT
AAGAAAGAGGGGGAACAGGTGGAGTTCTCCTTCCC
ACTCGCCTTTACAGTTGAAAAGCTGACGGGCAGTG
GCGAGCTGTGGTGGCAGGCGGAGAGGGCTTCCTCC
TCCAAGTCTTGGATCACCTTTGACCTGAAGAACAA
GGAAGTGTCTGTAAAACGGGTTACCCAGGACCCTA
AGCTCCAGATGGGCAAGAAGCTCCCGCTCCACCTC
ACCCTGCCCCAGGCCTTGCCTCAGTATGCTGGCTC
TGGAAACCTCACCCTGGCCCTTGAAGCGAAAACAG
GAAAGTTGCATCAGGAAGTGAACCTGGTGGTGATG
AGAGCCACTCAGCTCCAGAAAAATTTGACCTGTGA
GGTGTGGGGACCCACCTCCCCTAAGCTGATGCTGA
GCTTGAAACTGGAGAACAAGGAGGCAAAGGTCTCG
AAGCGGGAGAAGGCGGTGTGGGTGCTGAACCCTGA
GGCGGGGATGTGGCAGTGTCTGCTGAGTGACTCGG
GACAGGTCCTGCTGGAATCCAACATCAAGGTTCTG
CCCACATGGTCGACCCCGGTGCAGCCAATGGCCCT
GATTGTGCTGGGGGGCGTCGCCGGCCTCCTGCTTT
TCATTGGGCTAGGCATCTTCTTCTGTGTCAGGTGC
CGGCACACCGGTTAGTAATGAGTTTAAACGGGGGA
GGCTAACTGAAACACGGAAGGAGACAATACCGGAA
GGAACCCGCGCTATGACGGCAATAAAAAGACAGAA
TAAAACGCACGGGTGTTGGGTCGTTTGTTCATAAA
CGCGGGGTTCGGTCCCAGGGCTGGCACTCTGTCGA
TACCCCACCGAGACCCCATTGGGGCCAATACGCCC
GCGTTTCTTCCTTTTCCCCACCCCACCCCCCAAGT
TCGGGTGAAGGCCCAGGGCTCGCAGCCAACGTCGG
GGCGGCAGGCCCTGCCATAGCAGATCTGCGCAGCT
GGGGCTCTAGGGGGTATCCCCACGCGCCCTGTAGC
GGCGCATTAAGCGCGGCGGGTGTGGTGGTTACGCG
CAGCGTGACCGCTACACTTGCCAGCGCCCTAGCGC
CCGCTCCTTTCGCTTTCTTCCCTTCCTTTCTCGCC
ACGTTCGCCGGCTTTCCCCGTCAAGCTCTAAATCG
GGGGCTCCCTTTAGGGTTCCGATTTAGTGCTTTAC
GGCACCTCGACCCCAAAAAACTTGATTAGGGTGAT
GGTTCACGTAGTGGGCCATCGCCCTGATAGACGGT
TTTTCGCCCTTTGACGTTGGAGTCCACGTTCTTTA
ATAGTGGACTCTTGTTCCAAACTGGAACAACACTC
AACCCTATCTCGGTCTATTCTTTTGATTTATAAGG
GATTTTGCCGATTTCGGCCTATTGGTTAAAAAATG
AGCTGATTTAACAAAAATTTAACGCGAATTAATTA
AGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATT
CCTTCATATTTGCATATACGATACAAGGCTGTTAG
AGAGATAATTAGAATTAATTTGACTGTAAACACAA
AGATATTAGTACAAAATACGTGACGTAGAAAGTAA
TAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATG
TTTTAAAATGGACTATCATATGCTTACCGTAACTT
GAAAGTATTTCGATTTCTTGGCTTTATATATCTTG
TGGAAAGGACGAAACACCGNNNNNNNNNNNNNNNN
NNNNGTTTTAGAGCTAGAAATAGCAAGTTAAAATA
AGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACC
GAGTCGGTGCTTTTTTCTAGTATACCGTCGACCTC
TAGCTAGAGCTTGGCGTAATCATGGTCATAGCTGT
TTCCTGTGTGAAATTGTTATCCGCTCACAATTCCA
CACAACATACGAGCCGGAAGCATAAAGTGTAAAGC
CTGGGGTGCCTAATGAGTGAGCTAACTCACATTAA
TTGCGTTGCGCTCACTGCCCGCTTTCCAGTCGGGA
AACCTGTCGTGCCAGCTGCATTAATGAATCGGCCA
ACGCGCGGGGAGAGGCGGTTTGCGTATTGGGCGCT
CTTCCGCTTCCTCGCTCACTGACTCGCTGCGCTCG
GTCGTTCGGCTGCGGCGAGCGGTATCAGCTCACTC
AAAGGCGGTAATACGGTTATCCACAGAATCAGGGG
ATAACGCAGGAAAGAACATGTGAGCAAAAGGCCAG
CAAAAGGCCAGGAACCGTAAAAAGGCCGCGTTGCT
GGCGTTTTTCCATAGGCTCCGCCCCCCTGACGAGC
ATCACAAAAATCGACGCTCAAGTCAGAGGTGGCGA
AACCCGACAGGACTATAAAGATACCAGGCGTTTCC
CCCTGGAAGCTCCCTCGTGCGCTCTCCTGTTCCGA
CCCTGCCGCTTACCGGATACCTGTCCGCCTTTCTC
CCTTCGGGAAGCGTGGCGCTTTCTCATAGCTCACG
CTGTAGGTATCTCAGTTCGGTGTAGGTCGTTCGCT
CCAAGCTGGGCTGTGTGCACGAACCCCCCGTTCAG
CCCGACCGCTGCGCCTTATCCGGTAACTATCGTCT
TGAGTCCAACCCGGTAAGACACGACTTATCGCCAC
TGGCAGCAGCCACTGGTAACAGGATTAGCAGAGCG
AGGTATGTAGGCGGTGCTACAGAGTTCTTGAAGTG
GTGGCCTAACTACGGCTACACTAGAAGAACAGTAT
TTGGTATCTGCGCTCTGCTGAAGCCAGTTACCTTC
GGAAAAAGAGTTGGTAGCTCTTGATCCGGCAAACA
AACCACCGCTGGTAGCGGTGGTTTTTTTGTTTGCA
AGCAGCAGATTACGCGCAGAAAAAAAGGATCTCAA
GAAGATCCTTTGATCTTTTCTACGGGGTCTGACGC
TCAGTGGAACGAAAACTCACGTTAAGGGATTTTGG
TCATGAGATTATCAAAAAGGATCTTCACCTAGATC
CTTTTAAATTAAAAATGAAGTTTTAAATCAATCTA
AAGTATATATGAGTAAACTTGGTCTGACAGTTACC
AATGCTTAATCAGTGAGGCACCTATCTCAGCGATC
TGTCTATTTCGTTCATCCATAGTTGCCTGACTCCC
CGTCGTGTAGATAACTACGATACGGGAGGGCTTAC
CATCTGGCCCCAGTGCTGCAATGATACCGCGAGAC
CCACGCTCACCGGCTCCAGATTTATCAGCAATAAA
CCAGCCAGCCGGAAGGGCCGAGCGCAGAAGTGGTC
CTGCAACTTTATCCGCCTCCATCCAGTCTATTAAT
TGTTGCCGGGAAGCTAGAGTAAGTAGTTCGCCAGT
TAATAGTTTGCGCAACGTTGTTGCCATTGCTACAG
GCATCGTGGTGTCACGCTCGTCGTTTGGTATGGCT
TCATTCAGCTCCGGTTCCCAACGATCAAGGCGAGT
TACATGATCCCCCATGTTGTGCAAAAAAGCGGTTA
GCTCCTTCGGTCCTCCGATCGTTGTCAGAAGTAAG
TTGGCCGCAGTGTTATCACTCATGGTTATGGCAGC
ACTGCATAATTCTCTTACTGTCATGCCATCCGTAA
GATGCTTTTCTGTGACTGGTGAGTACTCAACCAAG
TCATTCTGAGAATAGTGTATGCGGCGACCGAGTTG
CTCTTGCCCGGCGTCAATACGGGATAATACCGCGC
CACATAGCAGAACTTTAAAAGTGCTCATCATTGGA
AAACGTTCTTCGGGGCGAAAACTCTCAAGGATCTT
ACCGCTGTTGAGATCCAGTTCGATGTAACCCACTC
GTGCACCCAACTGATCTTCAGCATCTTTTACTTTC
ACCAGCGTTTCTGGGTGAGCAAAAACAGGAAGGCA
AAATGCCGCAAAAAAGGGAATAAGGGCGACACGGA
AATGTTGAATACTCATACTCTTCCTTTTTCAATAT
TATTGAAGCATTTATCAGGGTTATTGTCTCATGAG
CGGATACATATTTGAATGTATTTAGAAAAATAAAC
AAATAGGGGTTCCGCGCACATTTCCCCGAAAAGTG
CCACCTGACGTCGACGGATCGGGAGATCTCCCGAT
CCCCTATGGTGCACTCTCAGTACAATCTGCTCTGA
TGCCGCATAGTTAAGCCAGTATCTGCTCCCTGCTT
GTGTGTTGGAGGTCGCTGAGTAGTGCGCGAGCAAA
ATTTAAGCTACAACAAGGCAAGGCTTGACCGACAA TTGCATGAAGAATCTGCTTAGG
TABLE-US-00010 TABLE 10 Nucleotide sequence of the vector shown in
FIG. 18. (SEQ ID NO: 37) GTTAGGCGTTTTGCGCTGCTTCGCGATGTACGGGCC
AGATATACGCGTTGACATTGATTATTGACTAGTTA
TTAATAGTAATCAATTACGGGGTCATTAGTTCATA
GCCCATATATGGAGTTCCGCGTTACATAACTTACG
GTAAATGGCCCGCCTGGCTGACCGCCCAACGACCC
CCGCCCATTGACGTCAATAATGACGTATGTTCCCA
TAGTAACGCCAATAGGGACTTTCCATTGACGTCAA
TGGGTGGAGTATTTACGGTAAACTGCCCACTTGGC
AGTACATCAAGTGTATCATATGCCAAGTACGCCCC
CTATTGACGTCAATGACGGTAAATGGCCCGCCTGG
CATTATGCCCAGTACATGACCTTATGGGACTTTCC
TACTTGGCAGTACATCTACGTATTAGTCATCGCTA
TTACCATGGTGATGCGGTTTTGGCAGTACATCAAT
GGGCGTGGATAGCGGTTTGACTCACGGGGATTTCC
AAGTCTCCACCCCATTGACGTCAATGGGAGTTTGT
TTTGGCACCAAAATCAACGGGACTTTCCAAAATGT
CGTAACAACTCCGCCCCATTGACGCAAATGGGCGG
TAGGCGTGTACGGTGGGAGGTCTATATAAGCAGAG
CTCGTTTAGTGAACCGTCAGATCGCCTGGAGACGC
CATCCACGCTGTTTTGACCTCCATAGAAGACACCG
GGACCGATCCAGCCTCCGGAGCGGCCGCCACCATG
GGCAAGCCCATCCCTAACCCCCTGTTGGGGCTGGA
CAGCACCGCTCCCAAAAAGAAAAGGAAGGTGGGCA
TTCACGGCGTGCCTGCGGCCGACAAAAAGTACAGC
ATCGGCCTTGATATCGGCACCAATAGCGTGGGCTG
GGCCGTTATCACAGACGAATACAAGGTACCCAGCA
AGAAGTTCAAGGTGCTGGGGAATACAGACAGGCAC
TCTATCAAGAAAAACCTTATCGGGGCTCTGCTGTT
TGACTCAGGCGAGACCGCCGAGGCCACCAGGTTGA
AGAGGACCGCAAGGCGAAGGTACACCCGGAGGAAG
AACAGGATCTGCTATCTGCAGGAGATCTTCAGCAA
CGAGATGGCCAAGGTGGACGACAGCTTCTTCCACA
GGCTGGAGGAGAGCTTCCTTGTCGAGGAGGATAAG
AAGCACGAACGACACCCCATCTTCGGCAACATAGT
CGACGAGGTCGCTTATCACGAGAAGTACCCCACCA
TCTACCACCTGCGAAAGAAATTGGTGGATAGCACC
GATAAAGCCGACTTGCGACTTATCTACTTGGCTCT
GGCGCACATGATTAAGTTCAGGGGCCACTTCCTGA
TCGAGGGCGACCTTAACCCCGACAACAGTGACGTA
GACAAATTGTTCATCCAGCTTGTACAGACCTATAA
CCAGCTGTTCGAGGAAAACCCTATTAACGCCAGCG
GGGTGGATGCGAAGGCCATACTTAGCGCCAGGCTG
AGCAAAAGCAGGCGCTTGGAGAACCTGATAGCCCA
GCTGCCCGGTGAAAAGAAGAACGGCCTCTTCGGTA
ATCTGATTGCCCTGAGCCTGGGCCTGACCCCCAAC
TTCAAGAGCAACTTCGACCTGGCAGAAGATGCCAA
GCTGCAGTTGAGTAAGGACACCTATGACGACGACT
TGGACAATCTGCTCGCCCAAATCGGCGACCAGTAC
GCTGACCTGTTCCTCGCCGCCAAGAACCTTTCTGA
CGCAATCCTGCTTAGCGATATCCTTAGGGTGAACA
CAGAGATCACCAAGGCCCCCCTGAGCGCCAGCATG
ATCAAGAGGTACGACGAGCACCATCAGGACCTGAC
CCTTCTGAAGGCCCTGGTGAGGCAGCAACTGCCCG
AGAAGTACAAGGAGATCTTTTTCGACCAGAGCAAG
AACGGCTACGCCGGCTACATCGACGGCGGAGCCAG
CCAAGAGGAGTTCTACAAGTTCATCAAGCCCATCC
TGGAGAAGATGGATGGCACCGAGGAGCTGCTGGTG
AAGCTGAACAGGGAAGATTTGCTCCGGAAGCAGAG
GACCTTTGACAACGGTAGCATCCCCCACCAGATCC
ACCTGGGCGAGCTGCACGCAATACTGAGGCGACAG
GAGGATTTCTACCCCTTCCTCAAGGACAATAGGGA
GAAAATCGAAAAGATTCTGACCTTCAGGATCCCCT
ACTACGTGGGCCCTCTTGCCAGGGGCAACAGCCGA
TTCGCTTGGATGACAAGAAAGAGCGAGGAGACCAT
CACCCCCTGGAACTTCGAGGAAGTGGTGGACAAAG
GAGCAAGCGCGCAGTCTTTCATCGAACGGATGACC
AATTTCGACAAAAACCTGCCTAACGAGAAGGTGCT
GCCCAAGCACAGCCTGCTTTACGAGTACTTCACCG
TGTACAACGAGCTCACCAAGGTGAAATATGTGACC
GAGGGCATGCGAAAACCCGCTTTCCTGAGCGGCGA
GCAGAAGAAGGCCATCGTGGACCTGCTGTTCAAGA
CCAACAGGAAGGTGACCGTGAAGCAGCTGAAGGAG
GACTACTTCAAGAAGATCGAGTGCTTTGATAGCGT
GGAAATAAGCGGCGTGGAGGACAGGTTCAACGCCA
GCCTGGGCACCTACCACGACTTGTTGAAGATAATC
AAAGACAAGGATTTCCTGGATAATGAGGAGAACGA
GGATATACTCGAGGACATCGTGCTGACTTTGACCC
TGTTTGAGGACCGAGAGATGATTGAAGAAAGGCTC
AAAACCTACGCCCACCTGTTCGACGACAAAGTGAT
GAAACAACTGAAGAGACGAAGATACACCGGCTGGG
GCAGACTGTCCAGGAAGCTCATCAACGGCATTAGG
GACAAGCAGAGCGGCAAGACCATCCTGGATTTCCT
GAAGTCCGACGGCTTCGCCAACCGAAACTTCATGC
AGCTGATTCACGATGACAGCTTGACCTTCAAGGAG
GACATCCAGAAGGCCCAGGTTAGCGGCCAGGGCGA
CTCCCTGCACGAACATATTGCAAACCTGGCAGGCT
CCCCTGCGATCAAGAAGGGCATACTGCAGACCGTT
AAGGTTGTGGACGAATTGGTCAAGGTCATGGGCAG
GCACAAGCCCGAAAACATAGTTATAGAGATGGCCA
GAGAGAACCAGACCACCCAAAAGGGCCAGAAGAAC
AGCCGGGAGCGCATGAAAAGGATCGAGGAGGGTAT
CAAGGAACTCGGAAGCCAGATCCTCAAAGAGCACC
CCGTGGAGAATACCCAGCTCCAGAACGAGAAGCTG
TACCTGTACTACCTGCAGAACGGCAGGGACATGTA
CGTTGACCAGGAGTTGGACATCAACAGGCTTTCAG
ACTATGACGTGGATCACATAGTGCCCCAGAGCTTT
CTTAAAGACGATAGCATCGACAACAAGGTCCTGAC
CCGCTCCGACAAAAACAGGGGCAAAAGCGACAACG
TGCCAAGCGAAGAGGTGGTTAAAAAGATGAAGAAC
TACTGGAGGCAACTGCTCAACGCGAAATTGATCAC
CCAGAGAAAGTTCGATAACCTGACCAAGGCCGAGA
GGGGCGGACTCTCCGAACTTGACAAAGCGGGCTTC
ATAAAGAGGCAGCTGGTCGAGACCCGACAGATCAC
GAAGCACGTGGCCCAAATCCTCGACAGCAGAATGA
ATACCAAGTACGATGAGAATGACAAACTCATCAGG
GAAGTGAAAGTGATTACCCTGAAGAGCAAGTTGGT
GTCCGACTTTCGCAAAGATTTCCAGTTCTACAAGG
TGAGGGAGATCAACAACTACCACCATGCCCACGAC
GCATACCTGAACGCCGTGGTCGGCACCGCCCTGAT
TAAGAAGTATCCAAAGCTGGAGTCCGAATTTGTCT
ACGGCGACTACAAAGTTTACGATGTGAGGAAGATG
ATCGCTAAGAGCGAACAGGAGATCGGCAAGGCCAC
CGCTAAGTATTTCTTCTACAGCAACATCATGAACT
TTTTCAAGACCGAGATCACACTTGCCAACGGCGAA
ATCAGGAAGAGGCCGCTTATCGAGACCAACGGTGA
GACCGGCGAGATCGTGTGGGACAAGGGCAGGGACT
TCGCCACCGTGAGGAAAGTCCTGAGCATGCCCCAG
GTGAATATTGTGAAAAAAACTGAGGTGCAGACAGG
CGGCTTTAGCAAGGAATCCATCCTGCCCAAGAGGA
ACAGCGACAAGCTGATCGCCCGGAAGAAGGACTGG
GACCCTAAGAAGTATGGAGGCTTCGACAGCCCCAC
CGTAGCCTACAGCGTGCTGGTGGTCGCGAAGGTAG
AGAAGGGGAAGAGCAAGAAACTGAAGAGCGTGAAG
GAGCTGCTCGGCATAACCATCATGGAGAGGTCCAG
CTTTGAGAAGAACCCCATTGACTTTTTGGAAGCCA
AGGGCTACAAAGAGGTCAAAAAGGACCTGATCATC
AAACTCCCCAAGTACTCCCTGTTTGAATTGGAGAA
CGGCAGAAAGAGGATGCTGGCGAGCGCTGGGGAAC
TGCAAAAGGGCAACGAACTGGCGCTGCCCAGCAAG
TACGTGAATTTTCTGTACCTGGCGTCCCACTACGA
AAAGCTGAAAGGCAGCCCCGAGGACAACGAGCAGA
AGCAGCTGTTCGTGGAGCAGCACAAGCATTACCTG
GACGAGATAATCGAGCAAATCAGCGAGTTCAGCAA
GAGGGTGATTCTGGCCGACGCGAACCTGGATAAGG
TCCTCAGCGCCTACAACAAGCACCGAGACAAACCC
ATCAGGGAGCAGGCCGAGAATATCATACACCTGTT
CACCCTGACAAATCTGGGCGCACCTGCGGCATTCA
AATACTTCGATACCACCATCGACAGGAAAAGGTAC
ACTAGCACTAAGGAGGTGCTGGATGCCACCTTGAT
CCACCAGTCCATTACCGGCCTGTATGAGACCAGGA
TCGACCTGAGCCAGCTTGGAGGCGACTCTAGGGCG
GACCCAAAAAAGAAAAGGAAGGTGGAATTCTCTAG
AGGCAGTGGAGAGGGCAGAGGAAGTCTGCTAACAT
GCGGTGACGTCGAGGAGAATCCTGGCCCAATGAAC
CTGAGCAAAAACGTGAGCGTGAGCGTGTATATGAA
GGGGAACGTCAACAATCATGAGTTTGAGTACGACG
GGGAAGGTGGTGGTGATCCTTATACAGGTAAATAT
TCCATGAAGATGACGCTACGTGGTCAAAATTCCCT
ACCCTTTTCCTATGATATCATTACCACGGCATTTC
AGTATGGTTTCCGCGTATTTACAAAATACCCTGAG
GGAATTGTTGACTATTTTAAGGACTCGCTTCCCGA
CGCATTCCAGTGGAACAGACGAATTGTGTTTGAAG
ATGGTGGAGTACTAAACATGAGCAGTGATATCACA
TATAAAGATAATGTTCTGCATGGTGACGTCAAGGC
TGAGGGAGTGAACTTCCCGCCGAATGGGCCAGTGA
TGAAGAATGAAATTGTGATGGAGGAACCGACTGAA
GAAACATTTACTCCAAAAAACGGGGTTCTTGTTGG
CTTTTGTCCCAAAGCGTACTTACTTAAAGACGGTT
CCTATTACTATGGAAATATGACAACATTTTACAGA
TCCAAGAAATCTGGCCAGGCACCTCCTGGGTATCA
CTTTGTTAAGCATCGTCTCGTCAAGACCAATGTGG
GACATGGATTTAAGACGGTTGAGCAGACTGAATAT
GCCACTGCTCATGTCAGTGATCTTCCCAAGTTCGA
AGCTTGATAATGAGTTTAAACGGGGGAGGCTAACT
GAAACACGGAAGGAGACAATACCGGAAGGAACCCG
CGCTATGACGGCAATAAAAAGACAGAATAAAACGC
ACGGGTGTTGGGTCGTTTGTTCATAAACGCGGGGT
TCGGTCCCAGGGCTGGCACTCTGTCGATACCCCAC
CGAGACCCCATTGGGGCCAATACGCCCGCGTTTCT
TCCTTTTCCCCACCCCACCCCCCAAGTTCGGGTGA
AGGCCCAGGGCTCGCAGCCAACGTCGGGGCGGCAG
GCCCTGCCATAGCAGATCTGCGCAGCTGGGGCTCT
AGGGGGTATCCCCACGCGCCCTGTAGCGGCGCATT
AAGCGCGGCGGGTGTGGTGGTTACGCGCAGCGTGA
CCGCTACACTTGCCAGCGCCCTAGCGCCCGCTCCT
TTCGCTTTCTTCCCTTCCTTTCTCGCCACGTTCGC
CGGCTTTCCCCGTCAAGCTCTAAATCGGGGGCTCC
CTTTAGGGTTCCGATTTAGTGCTTTACGGCACCTC
GACCCCAAAAAACTTGATTAGGGTGATGGTTCACG
TAGTGGGCCATCGCCCTGATAGACGGTTTTTCGCC
CTTTGACGTTGGAGTCCACGTTCTTTAATAGTGGA
CTCTTGTTCCAAACTGGAACAACACTCAACCCTAT
CTCGGTCTATTCTTTTGATTTATAAGGGATTTTGC
CGATTTCGGCCTATTGGTTAAAAAATGAGCTGATT
TAACAAAAATTTAACGCGAATTAATTAAGGTCGGG
CAGGAAGAGGGCCTATTTCCCATGATTCCTTCATA
TTTGCATATACGATACAAGGCTGTTAGAGAGATAA
TTAGAATTAATTTGACTGTAAACACAAAGATATTA
GTACAAAATACGTGACGTAGAAAGTAATAATTTCT
TGGGTAGTTTGCAGTTTTAAAATTATGTTTTAAAA
TGGACTATCATATGCTTACCGTAACTTGAAAGTAT
TTCGATTTCTTGGCTTTATATATCTTGTGGAAAGG
ACGAAACACCGNNNNNNNNNNNNNNNNNNNNGTTT
TAGAGCTAGAAATAGCAAGTTAAAATAAGGCTAGT
CCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGT
GCTTTTTTCTAGTATACCGTCGACCTCTAGCTAGA
GCTTGGCGTAATCATGGTCATAGCTGTTTCCTGTG
TGAAATTGTTATCCGCTCACAATTCCACACAACAT
ACGAGCCGGAAGCATAAAGTGTAAAGCCTGGGGTG
CCTAATGAGTGAGCTAACTCACATTAATTGCGTTG
CGCTCACTGCCCGCTTTCCAGTCGGGAAACCTGTC
GTGCCAGCTGCATTAATGAATCGGCCAACGCGCGG
GGAGAGGCGGTTTGCGTATTGGGCGCTCTTCCGCT
TCCTCGCTCACTGACTCGCTGCGCTCGGTCGTTCG
GCTGCGGCGAGCGGTATCAGCTCACTCAAAGGCGG
TAATACGGTTATCCACAGAATCAGGGGATAACGCA
GGAAAGAACATGTGAGCAAAAGGCCAGCAAAAGGC
CAGGAACCGTAAAAAGGCCGCGTTGCTGGCGTTTT
TCCATAGGCTCCGCCCCCCTGACGAGCATCACAAA
AATCGACGCTCAAGTCAGAGGTGGCGAAACCCGAC
AGGACTATAAAGATACCAGGCGTTTCCCCCTGGAA
GCTCCCTCGTGCGCTCTCCTGTTCCGACCCTGCCG
CTTACCGGATACCTGTCCGCCTTTCTCCCTTCGGG
AAGCGTGGCGCTTTCTCATAGCTCACGCTGTAGGT
ATCTCAGTTCGGTGTAGGTCGTTCGCTCCAAGCTG
GGCTGTGTGCACGAACCCCCCGTTCAGCCCGACCG
CTGCGCCTTATCCGGTAACTATCGTCTTGAGTCCA
ACCCGGTAAGACACGACTTATCGCCACTGGCAGCA
GCCACTGGTAACAGGATTAGCAGAGCGAGGTATGT
AGGCGGTGCTACAGAGTTCTTGAAGTGGTGGCCTA
ACTACGGCTACACTAGAAGAACAGTATTTGGTATC
TGCGCTCTGCTGAAGCCAGTTACCTTCGGAAAAAG
AGTTGGTAGCTCTTGATCCGGCAAACAAACCACCG
CTGGTAGCGGTGGTTTTTTTGTTTGCAAGCAGCAG
ATTACGCGCAGAAAAAAAGGATCTCAAGAAGATCC
TTTGATCTTTTCTACGGGGTCTGACGCTCAGTGGA
ACGAAAACTCACGTTAAGGGATTTTGGTCATGAGA
TTATCAAAAAGGATCTTCACCTAGATCCTTTTAAA
TTAAAAATGAAGTTTTAAATCAATCTAAAGTATAT
ATGAGTAAACTTGGTCTGACAGTTACCAATGCTTA
ATCAGTGAGGCACCTATCTCAGCGATCTGTCTATT
TCGTTCATCCATAGTTGCCTGACTCCCCGTCGTGT
AGATAACTACGATACGGGAGGGCTTACCATCTGGC
CCCAGTGCTGCAATGATACCGCGAGACCCACGCTC
ACCGGCTCCAGATTTATCAGCAATAAACCAGCCAG
CCGGAAGGGCCGAGCGCAGAAGTGGTCCTGCAACT
TTATCCGCCTCCATCCAGTCTATTAATTGTTGCCG
GGAAGCTAGAGTAAGTAGTTCGCCAGTTAATAGTT
TGCGCAACGTTGTTGCCATTGCTACAGGCATCGTG
GTGTCACGCTCGTCGTTTGGTATGGCTTCATTCAG
CTCCGGTTCCCAACGATCAAGGCGAGTTACATGAT
CCCCCATGTTGTGCAAAAAAGCGGTTAGCTCCTTC
GGTCCTCCGATCGTTGTCAGAAGTAAGTTGGCCGC
AGTGTTATCACTCATGGTTATGGCAGCACTGCATA
ATTCTCTTACTGTCATGCCATCCGTAAGATGCTTT
TCTGTGACTGGTGAGTACTCAACCAAGTCATTCTG
AGAATAGTGTATGCGGCGACCGAGTTGCTCTTGCC
CGGCGTCAATACGGGATAATACCGCGCCACATAGC
AGAACTTTAAAAGTGCTCATCATTGGAAAACGTTC
TTCGGGGCGAAAACTCTCAAGGATCTTACCGCTGT
TGAGATCCAGTTCGATGTAACCCACTCGTGCACCC
AACTGATCTTCAGCATCTTTTACTTTCACCAGCGT
TTCTGGGTGAGCAAAAACAGGAAGGCAAAATGCCG
CAAAAAAGGGAATAAGGGCGACACGGAAATGTTGA
ATACTCATACTCTTCCTTTTTCAATATTATTGAAG
CATTTATCAGGGTTATTGTCTCATGAGCGGATACA
TATTTGAATGTATTTAGAAAAATAAACAAATAGGG
GTTCCGCGCACATTTCCCCGAAAAGTGCCACCTGA
CGTCGACGGATCGGGAGATCTCCCGATCCCCTATG
GTGCACTCTCAGTACAATCTGCTCTGATGCCGCAT
AGTTAAGCCAGTATCTGCTCCCTGCTTGTGTGTTG
GAGGTCGCTGAGTAGTGCGCGAGCAAAATTTAAGC
TACAACAAGGCAAGGCTTGACCGACAATTGCATGA AGAATCTGCTTAGG
Example 2: Rapid and Highly Efficient Mammalian Cell Engineering
Via Cas9 Protein Transfection
[0298] Abstract
[0299] CRISPR-Cas9 systems provide a platform for high efficiency
genome editing that are enabling innovative applications of
mammalian cell engineering. However, the delivery of Cas9 and
synthesis of guide RNA (gRNA) remain as steps that can limit
overall efficiency and general ease of use. Described here are
methods for rapid synthesis of gRNA and for delivery of Cas9
protein/gRNA ribonucleoprotein complexes (Cas9 RNPs) into a variety
of mammalian cells through liposome-mediated transfection or
electroporation. Using these methods, nuclease-mediated indel rates
of up to 94% in Jurkat T cells and 87% in induced pluripotent stem
cells (iPSC) for a single target are reported. When this approach
is used for multigene targeting in Jurkat cells, it was found that
two-locus and three-locus indels were achieved in approximately 93%
and 65% of the resulting isolated cell lines, respectively.
Further, in this study, it was found that the off-target cleavage
rate is significantly reduced using Cas9 protein when compared to
plasmid DNA transfection. Taken together, a streamlined cell
engineering workflow is presented that enables gRNA design to
analysis of edited cells in as little as four days and results in
highly efficient genome modulation in hard-to-transfect cells. The
reagent preparation and delivery to cells requires no plasmid
manipulation, and is thus amenable to high throughput, multiplexed
genome-wide cell engineering.
[0300] Introduction
[0301] CRISPR-Cas9 mediated genome engineering enables researchers
to modify genomic DNA in vivo directly and efficiently (Cho et al.,
"Targeted genome engineering in human cells with the Cas9
RNA-guided endonuclease," Nat. Biotechnol. 31:230-232 (2013); Mali
et al., "RNA-guided human genome engineering via Cas9," Science
339:823-826 (2013); Jiang et al., "RNA-guided editing of bacterial
genomes using CRISPR-Cas systems," Nat. Biotechnol. 31:233-239
(2013); Wang et al., "One-step generation of mice carrying
mutations in multiple genes by CRISPR/Cas-mediated genome
engineering," Cell 153:910-918 (2013)). Three components (Cas9,
mature crRNA and tracrRNA) are essential for functional activity.
Although the mature crRNA and tracrRNA can be synthesized
chemically, the quality of the synthetic RNA is not sufficient for
in vivo cell engineering due to the presence of truncated
by-products (data not shown). Therefore, templates for the mature
crRNA and tracrRNA or a combined single gRNA are often cloned into
a Cas9 expression plasmid or built into separate plasmids driven by
either U6 or H1 promoters for transcription after transfection of
mammalian cells. Because the constructs are relatively large,
delivery rates can be low, which would limit genomic cleavage
efficiency, especially for hard-to-transfect cells. Recently, the
use of Cas9 delivered as mRNA has led to increases in the rate of
genomic cleavage in some cells. For example, a mixture of Cas9 mRNA
and a single species of gRNA were co-injected into mouse embryonic
stem (ES) cells resulting in biallelic mutations in 95% of newborn
mice (Wang et al., "One-step generation of mice carrying mutations
in multiple genes by CRISPR/Cas-mediated genome engineering," Cell
153:910-918 (2013)). To make guide RNA, often precloned plasmid is
used directly or a linear template is created via PCR amplification
of the targeting sequence from a plasmid. If a 5' T7 promoter does
not appear in the plasmid, it is often added at this step and the
resulting PCR product can be used in an in vitro transcription
reaction. Alternatively, a synthetic DNA fragment containing a T7
promoter, crRNA and tracerRNA can be used as a template to prepare
a gRNA by in vitro transcription. Overall, these represent a
labor-intensive and time-consuming workflow, which led us to seek a
simpler method to synthesize high quality gRNA. To that, describe
here is a streamlined modular approach for gRNA production in
vitro. Starting with two short single stranded oligos, the gRNA
template is assembled in a `one pot` PCR reaction. The product is
then used as template in an in vitro transcription (IVT) reaction
which is followed by a rapid purification step, yielding
transfection-ready gRNA in as little as four hours.
[0302] To streamline the cell engineering workflow further, it was
sought to eliminate any remaining cellular transcription or
translation by directly introducing Cas9/gRNA ribonucleoprotein
(RNP) complexes directly to the cells. Microinjection of Cas9
protein and gRNA complexes into C. elegans was first described in
2013 (Cho et al., "Heritable gene knockout in Caenorhabditis
elegans by direct injection of Cas9-sgRNA ribonucleoproteins,"
Genetics 195:1177-1180 (2013)) and was subsequently used to
generate gene-knockout mice and zebrafish with mutation rates of up
to 93% in newborn mice (Sung et al., "Highly efficient gene
knockout in mice and zebrafish with RNA-guided endonucleases,"
Genome Res. 24:125-131 (2014)). Following that report, Cas9
protein/gRNA complexes were delivered into cultured human
fibroblasts and induced pluripotent stem cells (iPSC) via
electroporation with high efficiency and relatively low off-target
effects (Kim et al., "Highly efficient RNA-guided genome editing in
human cells via delivery of purified Cas9 ribonucleoproteins"
Genome Res. 24:1012-1019 (2014)). In that study, a large amount of
Cas9 protein (4.5 to 45 .mu.g) and gRNA (6 to 60 .mu.g) were
necessary for efficient genome modification (up to 79% indel
efficiency). Most recently, delivery of Cas9 protein-associated
gRNA complexes via liposomes was reported, in which RNAiMAX was
used to deliver Cas9:sgRNA nuclease complexes into cultured human
cells and into the mouse inner ear in vivo with up to 80% and 20%
genome modification efficiency respectively (Zuris et al.,
"Cationic lipid-mediated delivery of proteins enables efficient
protein-based genome editing in vitro and in vivo" Nat Biotechnol.
October 30. doi: 10.1038/nbt.3081 (2014)).
[0303] The CRISPR/Cas system has been demonstrated as an efficient
gene-targeting tool for multiplexed genome editing (Wang et al.,
"One-step generation of mice carrying mutations in multiple genes
by CRISPR/Cas-mediated genome engineering," Cell 153:910-918
(2013); Kabadi et al., "Multiplex CRISPR/Cas9-based genome
engineering from a single lentiviral vector" Nucleic Acids Res.
October 29; 42(19):e147. doi: 10.1093/nar/gku749 (2014); Sakuma et
al., "Multiplex genome engineering in human cells using all-in-one
CRISPR/Cas9 vector system," Sci Rep. June 23; 4:5400. doi:
10.1038/srep05400 (2014); Cong et al., "Multiplex genome
engineering using CRISPR/Cas systems. Science. 339: 819-823
(2013)). For example, co-transfections of mouse ES cells with
constructs expressing Cas9 and three sgRNAs targeting Tet1, 2, and
3 resulted in 20% of cells having mutations in all six alleles of
the three genes based on restriction fragment length polymorphism
(RFLP) assay (Wang et al., "One-step generation of mice carrying
mutations in multiple genes by CRISPR/Cas-mediated genome
engineering," Cell 153:910-918 (2013)). Lentiviral delivery of a
single vector expressing Cas9 and four sgRNAs into primary human
dermal fibroblasts resulted in about 30% simultaneous editing of
four genomic loci among ten clonal populations based upon genomic
cleavage detection assays (Kabadi et al., "Multiplex
CRISPR/Cas9-based genome engineering from a single lentiviral
vector" Nucleic Acids Res. October 29; 42(19):e147. doi:
10.1093/nar/gku749 (2014)). In one recent study, `all-in-one`
expression vectors containing seven guide RNA expression cassettes
and a Cas9 nuclease/nickase expression cassette were delivered into
293T cells with genome cleavage efficiency ranging from 4 to 36%
for each individual target (Sakuma et al., "Multiplex genome
engineering in human cells using all-in-one CRISPR/Cas9 vector
system," Sci Rep. June 23; 4:5400. doi: 10.1038/srep05400 (2014)).
In general, the efficiency of editing multiple genes in the human
genome using plasmid-based delivery methods remains relatively low
which subsequently increases the workload for downstream clonal
isolation.
[0304] An in vitro gRNA production system has been developed and
used a systematic approach to optimize the conditions for delivery
of Cas9:gRNA complexes via lipid-mediated transfection or
electroporation. A variety of mammalian cell lines were tested,
including primary cells and other hard-to-transfect cells. Plasmid
DNA, mRNA and Cas9 protein transfections were evaluated side by
side. Using Cas9 protein transfection via electroporation, a
superior genome editing efficiencies even in hard-to-transfect
cells was achieved. In addition, the genome editing of multiple
targets simultaneously using the Cas9 RNPs delivery system were
assessed and are described here. It was found that delivery of Cas9
RNPs not only led to high indel production at single locus, but
supports highly efficient biallelic modulation of at least two
genes in a single transfection.
[0305] Materials and Methods
[0306] Materials: 293FT cells, The Gibco.RTM. Human Episomal iPSC
Line, DMEM medium, RPMI 1640 medium, IMDM, DMEM/F-12, Fetal Bovine
Serum (FBS), Knockout.TM. Serum Replacement, Non-Essential Amino
Acid solution, basic fibroblast growth factor, Collagenase IV,
TrypLE.TM. Express Enzyme, Geltrex, Opti-MEM Medium,
FluoroBrite.TM. DMEM, Lipofectamine 2000, Lipofectamine 3000,
RNAiMAX, Lipofectamine.RTM. MessengerMAX, GeneArt.RTM. CRISPR
Nuclease Vector with OFP Reporter, 2% E-Gel.RTM. EX Agarose Gels,
PureLink.RTM. PCR Micro Kit, TranscriptAid T7 High Yield
Transcription Kit, MEGAclear.TM. Transcription Clean-Up Kit, Zero
Blunt.RTM. TOPO.RTM. PCR Cloning Kit, PureLink.RTM. Pro Quick96
Plasmid Purification Kit, Endotoxin Quantitation Kit, Qubit.RTM.
RNA BR Assay Kit, TRA-1-60 Alexa Fluor.RTM. 488 conjugated
antibodies, SSEA4 Alexa Fluor.RTM.647, and Phusion Flash
High-Fidelity PCR Master Mix were from Thermo Fisher Scientific.
Jurkat T cells and K562 cells were obtained from the American Type
Culture Collection (ATCC). MEF feeder cells and ROCK inhibitor
Y-27632 were purchased from EMD Millipore. Monoclonal Cas9 antibody
was ordered from Diagenode. Recombinant Cas9 protein was purified
as described by Kim et al. (7). All oligonucleotides used for gRNA
synthesis were from Thermo Fisher Scientific (Supplementary Table
1s).
[0307] One Step Synthesis of gRNA Template
[0308] The 80 nt constant region of tracrRNA from a GeneArt.RTM.
CRISPR Nuclease Vector was amplified by PCR and purified via
agarose gel extraction. The concentration of PCR product was
measured by Nanodrop (Thermo Fisher Scientific) and the molarity
was calculated based on the molecular weight of 49.6 kDa. To
prepare a pool of oligonucleotides, an aliquot of the 80 nt PCR
product was mixed with two end primers and target-specific forward
and reverse primers, with a final concentration of 0.15 .mu.M for
the 80 nt PCR product and 10 .mu.M for each of the end primers. For
a specific target, a 34 nt forward primer consisting of the T7
promoter sequence and 5' end target sequence, and a 34 nt reverse
primer consisting of the target sequence and 5' end tracrRNA
sequence were chemically synthesized with a 15 nt overlap. To set
up the synthesis of gRNA template, aliquots of the pooled
oligonucleotides were added to a Phusion Flash High-Fidelity PCR
Master Mix and amplified using manufacturer's recommended reaction
conditions. The PCR product was analyzed by a 2% E-Gel.RTM. EX
Agarose Gel, followed by purification using Purelink PCR micro
column. The gRNA template was eluted with 13 .mu.l water and the
concentration was determined by Nanodrop instrument.
[0309] To determine the error rate, the PCR product was cloned into
Zero Blunt.RTM. TOPO.RTM. vector, followed by plasmid DNA isolation
and sequencing with a 3500xl DNA analyzer (Thermo Fisher
Scientific).
[0310] In Vitro Transcription
[0311] The in vitro transcription of gRNA template was carried out
using TranscriptAid T7 High Yield Transcription Kit using the
manufacturer's recommended conditions. The gRNA product was
purified using MEGAclear.TM. Transcription Clean-Up kit as
described in the manual. The concentration of RNA was determined
using Qubit.RTM. RNA BR Assay Kit.
[0312] Cell Culture
[0313] HEK 293FT cells were maintained in DMEM medium supplemented
with 10% FBS. Jurkat T cells were propagated in RPMI medium
containing 10% FBS, whereas K562 cells were cultured in IMDM medium
supplemented with 10% FBS. Feeder-dependent human episomal iPSC
were cultured on mitotically inactivated MEF feeder cells in human
ESC (hESC) media containing 20% Knockout.TM. Serum Replacement, 10
.mu.M Non-Essential Amino Acid solution, 55 .mu.M
2-Mercaptoethanol, and 4 ng/ml basic fibroblast growth factor in
DMEM/F-12. All cultures were maintained in a 5% CO.sub.2,
37.degree. C. humidified incubator. iPSC cultures were maintained
with daily media changes and were passaged regularly using
Collagenase IV.
[0314] Lipid-Mediated Cell Transfection
[0315] One day prior to transfection, the cells were seeded in a
24-well plate at a cell density of 2.5.times.10.sup.5 cells per
well. For plasmid DNA transfection, 0.5 .mu.g DNA was added to 25
.mu.l of Opti-MEM medium, followed by addition of 25 .mu.l of
Opti-MEM containing 2 .mu.l of Lipofectamine 2000. The mixture was
incubated at room temperature for 15 minutes and then added to the
cells. For Cas9 mRNA transfection, 0.5 .mu.g Cas9 mRNA (Thermo
Fisher Scientific) was added to 25 .mu.l of Opti-MEM, followed by
addition of 50-100 ng gRNA. Meanwhile, 2 .mu.l of Lipofectamine
3000 was diluted into 25 .mu.l of Opti-MEM and then mixed with
mRNA/gRNA sample. The mixture was incubated for 15 minutes prior to
addition to the cells. For Cas9 protein transfection, 500 ng of
purified Cas9 protein (Thermo Fisher Scientific) was added to 25
.mu.l of Opti-MEM medium, followed by addition of 120 ng gRNA. The
molar ratio of gRNA over Cas9 protein was approximately 1:1.2. The
sample was mixed by gently tapping the tubes a few times and then
incubated at room temperature for 10 minutes. To a separate test
tube, 2 .mu.l of RNAiMAX or Lipofectamine 3000 was added to 25
.mu.l of Opti-MEM medium. The diluted transfection reagent was
transferred to the tube containing Cas9 protein/gRNA complexes,
followed by incubation at room temperature for 15 minutes. The
entire solution was then added to the cells in a 24-well plate and
mixed by gently swirling the plate. The plate was incubated at
37.degree. C. for 48 hours in a 5% CO.sub.2 incubator. The
percentage of locus-specific indel formation was measured by
GeneArt.RTM. Genomic Cleavage Detection Kit. The band intensities
were quantitated using built-in software in Alpha Imager
(Bio-Rad).
[0316] Electroporation
[0317] For suspension cells, such as Jurkat T cells or K562 cells,
2.times.10.sup.5 cells were used per electroporation using
Neon.RTM. Transfection System 10 .mu.L Kit (Thermo Fisher
Scientific). To maximize the genome cleavage efficiency, the Neon
24 optimized protocol was applied according to the manufacturer's
instruction. To set up a master mix, 24 .mu.g of purified Cas9
protein was added to 240 .mu.L of Resuspension Buffer R provided in
the kit, followed by addition of 4.8 .mu.g of gRNA. The mixture was
incubated at room temperature for 10 minutes. Meanwhile,
4.8.times.10.sup.6 cells were transferred to a sterile test tube
and centrifuged at 500.times.g for 5 minutes. The supernatant was
aspirated and the cell pellet was resuspended in 1 ml of PBS
without Ca.sup.2+ and Mg.sup.2+. Upon centrifugation, the
supernatant was carefully aspirated so that almost all the PBS
buffer was removed with no or minimum loss of cells. The
Resuspension Buffer R containing the Cas9 protein/gRNA complexes
was then used to resuspend the cell pellets. A 10 .mu.l cell
suspension was used for each of the 24 optimized conditions, which
varied in pulse voltage, pulse width and the number of pulses. The
electroporated cells were transferred immediately to a 24 well
containing 0.5 ml of the corresponding growth medium and then
incubated for 48 hours in a 5% CO.sub.2 incubator. The cells were
harvested by centrifugation and then washed once with PBS, followed
by Genomic Cleavage and Detection assay as described by the manual.
Upon optimization of electroporation condition, a higher amount of
Cas9 protein (1.5 to 2 .mu.g) and gRNA (300 to 400 ng) could be
applied to further increase the genome editing efficiency. For each
target in the multiplexing assays, 1 to 2 .mu.g of Cas9 protein and
200-400 ng of gRNA were pre-incubated separately prior to mixing
with cell pellet for electroporation. For clonal isolation, the
cell number of transfected cells was counted upon 48 hour
incubation, followed by a serial of dilution to 96 well plates with
a cell density of 10-20 cells per plate based on the cell count.
After clonal expansion for three weeks, cells from each individual
well were harvested, followed by PCR amplification of the target
locus. The PCR fragments were then cloned using a TOPO vector and
transformed into TOP10 competent cells. Approximately 8 E. coli
colonies were randomly picked for sequencing for each individual
target locus. The single cell population was determined by the
homogeneity of sequences for each allele. Single cells containing
bi-allelic mutations on all desired targets were considered
homozygotic indels. Downstream sequence analysis to confirm
frame-shift induced stop codon introduction was not done.
[0318] For transfection of feeder free adaptation of iPSC, feeder
dependent iPSC were grown to 80% confluency prior to harvest with
collagenase. Following removal of the cell clusters from the feeder
layer, they were gravity sedimented to prevent MEF contamination.
The cell clusters were then seeded on to tissue culture dishes
coated with Geltrex.RTM. in MEF conditioned media supplemented with
4 ng/mL bFGF. MEF conditioned media was produced using inactivated
feeder cells, which was harvested on 7 continuous days, sterile
filtered and frozen until usage. The cultures were allowed to reach
80-90% confluence. The day prior to transfection, the cultures were
pretreated with 5 .mu.M ROCK inhibitor Y-27632. On the day of
harvest the cultures were inspected for signs of differentiation
and any contamination differentiated cells were removed via
micro-dissection. The cultures were washed once with DPBS and then
harvested using TrypLE.TM. Express Enzyme. Single cells suspensions
were counted using the Countess.RTM. automated cell counter.
Following transfections, the cells were seeded onto multi-well (24
well) tissue culture dish coated with Geltrex.RTM. and incubated
overnight with MEF conditioned media containing 5 .mu.M ROCK. Media
was replaced daily, without ROCK inhibitor, prior to analysis.
[0319] Cell Surface Immunostaining
[0320] To ensure maintenance of pluripotency post transfection and
genome editing, iPSC cells were tested for expression of cell
surface markers of self-renewal. The wells to be probed were washed
with DMEM/F12 basal media. TRA-1-60 Alexa Fluor.RTM. 488 conjugated
antibodies and SSEA4 Alexa Fluor.RTM.647 were multiplexed in basal
DMEM/F-12 media. Both antibodies were added at a concentration of 2
.mu.l of each antibody into 0.5 mL of pre-warmed DMEM/F-12 media
and incubated at 37.degree. C. for 45 minutes. Following the
incubation, the antibody solution was removed and the wells were
washed twice with DMEM/F-12. Prior to observation the media was
exchanged with pre-warmed FluoroBrite.TM. DMEM. Images were taken
using a Zeiss Axiovision microscope using a FITC and Cy5
laser/filter combination.
[0321] Analysis of Pluripotency Markers
[0322] Cultures were detached and dissociated using TrypLE.TM.
Select and trituration. Single cell suspensions were incubated with
TRA-1-60 Alexa Fluor.RTM. 488 conjugated antibodies and SSEA4 Alexa
Fluor.RTM.647 for 1 hour at room temperature with gentle agitation.
Two microliters (50.times.) of each antibody were added to 0.5 mL
of DMEM/F-12. Following the incubation, the cells were centrifuged
and washed once with Dulbecco's Phosphate-Buffered Saline (DPBS).
After the removal of the DPBS wash, the pelleted cells were gently
resuspended in 1 mL of DPBS and stained through a strainer capped
tube. The cells were then measured for the expression of both
markers using the ATTUNE.RTM. Acoustic Focusing Cytometer and the
data was analyzed using FlowJo software.
[0323] Western Blot Analysis
[0324] 293FT cells were transfected with either plasmid DNA, mRNA
or Cas9 protein as described above. Cells were harvested at
indicated times to perform both Genome Cleavage and Detection assay
and Western Blot analysis. The cell lysate was fractionated using a
4-12% Novex Bis-tris gel. The proteins were transferred to a PVDF
membrane using an iBlot following the manufacturer's protocol. Upon
blocking, the membrane was incubated for 2 hours with monoclonal
mouse Cas9 antibody at 1:3000 dilution. After washing, the membrane
was incubated for 1 hour with rabbit anti-mouse antibody-HRP
conjugate at 1:2000 dilution. Upon extensive washing, the membrane
was developed with Pierce ECL reagent, followed by imaging using a
Fuji imager LAS 4000 instrument.
[0325] Results
[0326] Three Day Cell Engineering Workflow
[0327] To streamline the genome engineering workflow, it was sought
to simplify the gRNA synthesis procedure and shorten the time from
experimental design to initial analysis as much as possible.
Presented herein is a process where on day 1, the researcher
designs and orders short DNA oligonucleotides and seeds the cells
of interest for next day transfection (FIG. 19). Upon receiving the
oligonucleotides on day 2, the researcher assembles the gRNA
template in less than 1 hour by `one pot` PCR. The resulting PCR
product is then subjected to in vitro transcription to synthesize
gRNA in approximately 3 hours. Upon association of gRNA with
purified Cas9 protein, the Cas9 protein/gRNA complexes (Cas9 RNPs)
are used to transfect cells via lipid-mediated delivery or
electroporation. As early as day 3 (24 hours post transfection),
the cells can be harvested for analysis of locus-specific genome
modification efficiency.
[0328] To assemble the DNA template for gRNA production, a total of
4 synthetic DNA oligonucleotides and a purified PCR product
representing the constant (non-targeting) crRNA region and tracrRNA
sequence (gRNA lacking target sequence) are used (FIG. 20A). A pair
of 34 nt forward and reverse oligonucleotide primers were designed
by an online web tool (Beta Testing Version, Thermo Fisher
Scientific), and share 15 nt homology with the CRISPR and tracer
RNA regions respectively. The oligonucleotide pool concentrations
as well as the PCR conditions were optimized such that the template
was amplified in less than 40 minutes in a single tube with no
obvious by-products (FIG. 20B). The gRNA template was used directly
to prepare gRNA via in vitro transcription (IVT). The resulting
gRNA was purified yielding high levels of gRNA with no detectable
by-products (FIG. 20C). This approach was validated by synthesis of
more than 96 distinct gRNAs. To determine the error rate in the
synthetic DNA template, the PCR fragments were cloned and sequenced
and it was found that approximately 7% of gRNA templates harbored
mutations, mainly small deletions occurring at the extreme 3' end
and 5' ends of the mature template. The use of HPLC-purified end
primers further decreased the error rate to 3.6% with no mutations
detected in the target region, which was similar to what was
observed with the control template prepared from an `all-in-one`
plasmid with a 2% error rate (FIG. 20D). Taken together, this
optimized process facilitates the conversion of a small set of DNA
oligonucleotides into purified gRNA in approximately 4 hours with
an accuracy of 96% and no errors detected in the targeting or Cas9
complexing (cr/tracrRNA) regions. Given that the process consists
solely of liquid handling PCR, transcription, and RNA isolation
steps, it is well suited for high throughput gRNA production and
screening.
[0329] Liposome-Mediated Cas9 Protein Transfection
[0330] To examine the activity of synthetic gRNA, pre-complexed
purified synthetic IVT gRNA with Cas9 protein were produced. It was
hypothesizing that creating complexes of purified gRNAs with Cas9
protein prior to delivery to the cells might lead to higher genome
editing efficiency due to the protection of the gRNA as it transits
to the nucleus during the transfection process. To examine in vivo
functionality of the system, human embryonic kidney (HEK293) cells
were transfected with pre-complexed Cas9/gRNA ribonucleoproteins
(Cas9 RNPs) using a set of cationic lipid reagents, followed by a
genomic cleavage detection assay. Interestingly, the commonly-used
plasmid DNA or RNA transfection reagents were able to efficiently
deliver Cas9 RNPs. Lipofectamine 3000 and RNAiMAX outperformed
Lipofectamine 2000 in HEK 293 cells (data not shown), which is in
agreement with the recent finding that RNAiMAX performed better
than Lipofectamine 2000 for delivery of Cas9 mRNA (Zuris et al.,
"Cationic lipid-mediated delivery of proteins enables efficient
protein-based genome editing in vitro and in vivo" Nat Biotechnol.
October 30. doi: 10.1038/nbt.3081 (2014)). For protein
transfection, serum-free medium is generally used to avoid serum
protein inference. In this study however, it was observed that the
complete medium containing 10% FBS facilitated protein transfection
and genome modification (FIG. 21A). The efficiencies of genome
editing via plasmid DNA, mRNA and Cas9 RNP transfection were
evaluated using three different target loci, HPRT, AAVS and RelA.
Plasmid DNA and mRNA were delivered into HEK293 cells by
Lipofectamine 3000, whereas Cas9 RNPs were delivered with RNAiMAX.
As shown in FIG. 21A, the efficiencies of genome modification were
similar among three target loci in DNA, mRNA and Cas9
protein-transfected cells.
[0331] Next examined was the kinetics of genome cleavage by
transfecting cells with either plasmid DNA, mRNA or Cas9 RNPs,
followed by genome cleavage assays and Western Blot analysis of
cell lysates. In this study, it was observed similar cleavage
kinetics between Cas9 delivered as plasmid DNA, mRNA and protein
with efficient cleavage seen at 24 hours plateauing at 48 to 72
hours post-transfection in HEK293 cells (FIG. 21B). It was found
that the kinetics of Cas9 RNP and mRNA encoded Cas9 appearance and
turnover inside the transfected cells was quite different from that
seen with Cas9 delivered via plasmid DNA. Measuring by Western Blot
(FIG. 21C), it was found that Cas9 protein accumulated over time as
expected in plasmid DNA-transfected cells, whereas the relatively
low expression of Cas9 in mRNA-transfected cells seemed to peak as
early as four hours post transfection and remained relatively
stable for approximately 44 hours before diminishing. In the Cas9
RNP-transfected cells, the level of Cas9 protein peaked in four
hours or less then rapidly decreased and was barely detectable in
our assay at 48 hours. As a control, the blot membrane was stripped
and re-probed with anti-actin antibody. Similar levels of actin
expression were observed among samples (data not shown).
[0332] Because of the difference in protein appearance and apparent
turnover rates, it was hypothesized that the off-target cleavage
activity for Cas9 RNP transfection would be lower than that of
plasmid DNA transfection. This was tested by targeting a locus in
the VEGFA gene which has been identified as having several high
activity off-target sites (Tsai et al., "GUIDE-seq enables
genome-wide profiling of off-target cleavage by CRISPR-Cas
nucleases," Nat Biotechnol. doi:10.1038/nbt.3117 (2014)) via DNA,
mRNA, and Cas9 RNP protein transfection followed by genome cleavage
and locus sequencing analysis. Among the six potential off-target
sites that have been studied previously (OT3-1, OT3-2, OT3-4,
OT3-9, OT3-17 and OT3-18), only OT3-2 and OT3-18 were detected to
harbor off-target mutation based on genome cleavage analysis.
Further analysis of locus OT3-2 by sequencing indicated that the
ratio of indel mutation of OT3-2 over on target in mRNA and Cas9
RNP transfected cells was 2 fold and 2.5 fold lower than that in
DNA-transfected cells, respectively. The ratio of indel mutation of
OT3-18 over on on-target was 1.6 fold and 28 fold lower in mRNA or
Cas9 RNP-transfected cells respectively than in DNA-transfected
cells (FIG. 21D). The on-target editing efficiency increased with
an increased dose of Cas9 RNP, reaching plateau at around 2 .mu.g
of Cas9 protein, while the off-target modification at the loci
examined remained low and constant (data not shown). Taken
together, these data suggest that Cas9 delivery as mRNA and
pre-complexed protein supports increased genomic cleavage
specificity compared with standard DNA plasmid transfection.
[0333] Electroporation-Mediated Cas9 Protein Transfection
[0334] Many biologically and physiologically relevant cell lines,
such as patient derived iPSC and progenitor cells, are refractory
to efficient transfection by lipid-based reagents. Any improvement
in the efficiency of genome modulation would facilitate isolation
of appropriately engineered cells for experimentation and therapy
so alternate means of delivering Cas9 RNPs and Cas9 mRNA/gRNA
formulations and their effect on indel generation were explored.
Using Jurkat T cells as an initial model, the delivery of Cas9 and
gRNA plasmid DNA, Cas9 mRNA/gRNA formulations and Cas9 RNPs were
compared using microporation (described in Materials and Methods,
data not shown). Our results showed that, compared with plasmid DNA
and mRNA deliveries, superior genome editing efficiency was
achieved via delivery of Cas9 RNPs with approximately 90% HPRT
locus-specific modification under several electroporation
conditions (FIG. 22A). In general, Cas9 RNP delivery was more
robust than DNA or mRNA delivery over most of the electroporation
conditions tested. The cleavage efficiency was dose-dependent,
reaching a maximum at approximately 1.5 .mu.g Cas9 protein and 300
ng gRNA (.about.1:1 molar ratio) per transfection. After sequencing
the cell pools it was found that 94% of target loci harbored
mutations at a cleavage site located at 3 bases upstream of NGG PAM
sequence (Supplementary sequencing data). In agreement with
previous work, the majority of mutations were distinct from each
other with 73% insertion, 18% deletion and 3% base substitution.
Given the high single-locus cleavage efficiency measured with the
Cas9 RNP system, the ability to efficiently lesion multiple genes
in a single transfection was testes. Here the capability of
multiplexing Cas9 RNP transfection at three loci (AAVS1, RelA and
HPRT) were examined. After pooling and delivering multiple species
of Cas9 RNP (differing only by gRNA target), it was found that the
efficiency of simultaneous editing of AAVS1/HPRT or AAVS1/RelA/HPRT
loci was significantly greater at all loci compared with either
plasmid or mRNA delivery of Cas9 (FIGS. 23A and 23C). To gain
insight into the molecular level of multiplexing, one round of
clonal isolation by serial dilution was performed. After clonal
expansion each of the loci was PCR amplified, followed by DNA
cloning and sequencing. In the case of two gene editing, it was
found that all of 16 isolated clonal cell lines harbored bi-allelic
indel mutations on single AAVS1 loci and 93.7% (15 of 16) of clonal
cells harbored one allelic indel mutation at the HPRT locus as the
HPRT target was located on the X chromosome of a male Jurkat T cell
line. Overall, 93.7% of the clonal cell populations carried indel
mutations on both the AAVS1 and HPRT loci (FIG. 23B). For
multiplexing of three genes, three individual cell transfections
and clonal isolation were performed with a total of 53 single cell
lines analyzed. In this experiment, 90% and 65% of the clonal cell
lines analyzed harbored bi-allelic indel mutations at the AAVS1 and
RelA loci respectively, whereas 80% of the clonal cells carried
indel mutations at the HPRT locus. Approximately 65% of the clonal
cells carried bi-allelic indel mutations on both AAVS1 and RelA
loci, whereas 80% and 65% of the clonal cells harbored indel
mutations on AAVS1/HPRT loci and RelA/HPRT loci respectively.
Overall, 65% of the clonal cell lines harbored indel mutations on
all three targets (FIG. 23D). Further, 100% of the Jurkat T cell
clones were edited at least once, suggesting that the transfection
efficiency reached nearly 100%. Taken together, Cas9 RNP delivery
via electroporation under the conditions used here achieved
exceptionally high mutagenesis frequencies. This represents a
substantial improvement in Cas9-mediated genome editing and
significantly reduces the workload needed for clonal isolation by
substantially reducing the number of cells that must be screened in
order to identify and isolate the desired cell line.
[0335] Discussion
[0336] The ability to easily modulate the sequence specificity of
the Cas9 nuclease by simply changing the 20 nucleotide targeting
sequence of the gRNA offers significant versatility in delivery
options over other nucleases that have been utilized for genome
editing, such as zinc finger nucleases and TAL effectors. Now,
researchers are able to choose from cost-effective and rapid design
options by formulating the nuclease as either plasmid DNA, pre-made
mRNA or purified protein. The design versatility is enabled by
rapid production of the guide RNA component. Until recently, the
gRNA was generally produced via cloning of a template sequence into
a plasmid vector or vectors and expressing the Cas9 and gRNA in
vivo. Described here is a streamlined protocol where gRNA design
and template construction is facilitated by synthesis of two short
single stranded oligonucleotides. The oligonucleotides are
incorporated into gRNA templates via a short PCR reaction followed
by conversion to gRNA by in vitro transcription. Target-specific
oligos can be designed, ordered, and converted to purified gRNA in
as little as two days. On the second day, the gRNA is formulated
with either Cas9 mRNA or protein, and immediately used to transfect
cells. The entire process consists completely of liquid handling
and enzymatic reaction steps, which make it amenable to higher
throughput gRNA production and transfection in multi-well
plates.
[0337] The streamlined gRNA workflow was compared across the three
delivery options and found that in general, Cas9/gRNA
ribonucleoprotein complexes (Cas9 RNPs) offered superior indel
production efficiency in most of the cell lines was used as a test
bed. It is currently not clear why Cas9 RNP and total RNA
formulations perform as they do but a factor could be overall size
of the lipid complexes, the ability of Cas9 protein to protect the
gRNA from cellular degradation, and the elimination of DNA-based
cellular toxicity. In relation to plasmid delivery, Cas9 introduced
as a Cas9 RNP or mRNA appears in the cell at low but evidently
functional levels and is cleared rapidly which could also reduce
the opportunity for off-target binding and cleavage. The data
presented above suggests that this could be the case but a
significantly more detailed evaluation is needed for
confirmation.
[0338] Much progress has been made to reduce or eliminate
off-target cleavage in CRISPR systems, such as use of paired Cas9
nickases and dimeric `dead Cas9` FokI fusions, which has been shown
to reduce off-target activity by 50- to 1,500-fold (Tsai et al.,
"GUIDE-seq enables genome-wide profiling of off-target cleavage by
CRISPR-Cas nucleases," Nat Biotechnol. doi:10.1038/nbt.3117 (2014);
Fu et al., "High-frequency off-target mutagenesis induced by
CRISPR-Cas nucleases in human cells," Nat. Biotechnol. 31:822-826
(2013)). Perhaps delivery of these tools via Cas9 RNPs would lead
to even higher specificity while retaining high activity
levels.
[0339] In this work, it was shown that it is possible to multiplex
three Cas9 RNP species targeting separate loci in Jurkat T cells
while achieving high levels indel production at all three loci.
Further, it was observed high rates of biallelic modification at
two diploid alleles (AAVS1 and RelA) in these experiments even when
also modifying a haploid locus (HPRT) at similarly high levels.
Taken together, the high rates of biallelic modification in cell
populations suggest that employing Cas9 RNP delivery would
significantly simplify the workflow by facilitating the selection
of multigene knockout cell lines from a single experiment.
[0340] A survey was performed of eleven commonly used mammalian
cell lines comparing CRISPR delivery via plasmid, Cas9 mRNA/gRNA,
and Cas9 RNP (Table 11) and found that Cas9 mRNA/gRNA or Cas9 RNPs
were superior to plasmid delivery in all cell lines tested.
Delivery of these reagents via microporation offered the highest
target-specific indel production under the conditions tested. In
all but one case (NHEK cells), Cas9 RNP out performed Cas9
mRNA/gRNA and in human CD34+ cord blood cells, Cas9 RNP delivered
via microporation was the only method that yielded a significantly
robust editing solution.
TABLE-US-00011 TABLE 11 Transfection efficiency in variety of cell
lines DNA RNA Protein Cell lines Lipid Elect. Lipid Elect. Lipid
Elect. 293FT 49.4 48.7 70 40.3 51.4 88 U2OS 15.0 50.3 21.4 23.6
.sup.# 18.4 69.5 Mouse ESCs 30 45 45 20 25 70 Human ESCs 0 8 20 50
0 64 (H9) Human iPSCs 0 20 66 31.6 0 87* N2A 65.8 75.7 65.6 80.2
66.3 82.3 Jurkat 0 63 0 42 0 94* K562 0 45 0 27 0 72 A549 15.0 44.3
23.1 28.7 19.7 65.5 Human keratin. 0 30 0 50 0 35 (NHEK) Human Cord
n/a 5 n/a 0 n/a 24 blood cells CD34+ Notes: 1) HPRT for human cell
lines and Rosa 26 for mouse cell lines 2) *confirmed by sequencing
3) .sup.# Cleavage efficiency could be increased to 68% when Lipid
was added into reaction before electroporation.
[0341] Described here is a streamlined approach to the mammalian
genome engineering workflow that takes as few three days to modify
mammalian genomes from CRISPR target design to evaluation of genome
editing. To achieve a high mutagenesis efficiency in
hard-to-transfect cells, a systematic approach was used to optimize
transfection conditions and compare delivery of CRISPR editing
tools via plasmid DNA, Cas9 mRNA/purified guide RNA (gRNA)
formulations, and pre-complexed Cas9 protein and gRNA
ribonucleoproteins (Cas9 RNPs). It was found Cas9 mRNA/gRNA and
Cas9 RNP performance superior to `all-in-one` plasmid DNA
constructs in the variety of cell lines analyzed in this work. Most
likely due to the high efficiency of Cas9 RNP delivery, it was
possible to efficiently modify the genome at multiple loci
simultaneously, thereby reducing the workload for downstream clonal
isolation in schemes where more than one gene knock-out is desired.
Further, it was found that delivery of Cas9 RNPs to cell lines
considered hard to transfect (Jurkat, iPSC, CD4+) via
electroporation yielded high levels of locus specific
modification.
TABLE-US-00012 TABLE 12 Structure of Donor DNA Molecules SEQ Oligo
Sequence ID BT1/ OOCTGGCCCACCCTCGTGACCACCT 38 T8 TCACCTFOG
GEEACCGGGTGGGAGCACTGGTGGA 39 AGTGGATEO 3OT1/
OOCTGGCCCACCCTCGTGACCACCT 40 T8 TCACCTACGGCGZEC
GEECACGGGACCGGGTGGGAGCACT 41 GGTGGAAGTGGATEO 5OT1/
OOCGTGCCCTGGCCCACCCTCGTGA 42 T8 CCACCTTCACCTFOG
GEEACCGGGTGGGAGCACTGGTGGA 43 AGTGGATGCCGCAOE 3O/ OZTCACCTACGGCGZEC
44 T8 CFOTGGTGGAAGTGGATEO 45 5O/ EZGACCACCTTCACCTFOG 46 T8
GFFGTGGATGCCGCAOE 47 BT2/ OFCCGGCAAGCTGCCCGTGCCCTGG 48 T8
CCCACCCTCGTGACCACCTTCACCT FOG GZEGCCGTTCGACGGGCACGGGACC 49
GGGTGGGAGCACTGGTGGAAGTGGA TEO 3OT/ OFCCGGCAAGCTGCCCGTGCCCTGG 50 T8
CCCACCCTCGTGACCACCTTCACCT ACGGCGZEC GFOGTGGTGGCCGTTCGACGGGCAC 51
GGGACCGGGTGGGAGCACTGGTGGA AGTGGATEO 5OT2/ OZGCACCACCGGCAAGCTGCCCGTG
52 T8 CCCTGGCCCACCCTCGTGACCACCT TCACCTFOG GZEGCCGTTCGACGGGCACGGGACC
53 GGGTGGGAGCACTGGTGGAAGTGGA TGCCGCAOE SS
P-OFTCTGCACCACCGGCAAGCTGCC 54 CGTGCCCTGGCCCACCCTCGTGACCA
CCTTCACCTACGGCGTGCAGTGCTT CGCCCGCTACCCCGACCACFZG DS
ATGGTGAGCAAGGGCGAGGAGCTGT 55 DNA TCACCGGGGTGGTGCCCATCCTGGT
CGAGCTGGACGGCGACGTAAAC GGCCACAAGTTCAGCGTGTCCGGCG
AGGGCGAGGGCGATGCCACCTACGG CAAGCTGACCCTGAAGTTCATCTGC
ACCACCGGCAAGCTGCCCGTGCCCT GGCCCACCCTCGTGACCACCTTCAC
CTACGGCGTGCAGTGCTTCGCCCGC TACCCCGACCACATGAAGCAGCACG
ACTTCTTCAAGTCCGCCATGCCCGA AGGCTACGTCCAGGAGCGCACCATC
TTCTTCAAGGACGACGGCAACTACA AGACCCGCGCCGAGGTGAAGTTCGA
GGGCGACACCCTGGTGAACCGCATC GAGCTGAAGGGCATCGACTTCAAGG AGG Legend: F =
Phosphorothioate-A, O = Phosphorothioate-C, E = Phosphorothioate-G,
Z = Phosphorothioate-T Regions of sequence homology are
underlined
[0342] While the foregoing embodiments have been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the embodiments disclosed herein. For
example, all the techniques, apparatuses, systems and methods
described above can be used in various combinations.
Sequence CWU 1
1
6511368PRTStreptococcus pyogenes 1Met Asp Lys Lys Tyr Ser Ile Gly
Leu Asp Ile Gly Thr Asn Ser Val1 5 10 15Gly Trp Ala Val Ile Thr Asp
Glu Tyr Lys Val Pro Ser Lys Lys Phe 20 25 30Lys Val Leu Gly Asn Thr
Asp Arg His Ser Ile Lys Lys Asn Leu Ile 35 40 45Gly Ala Leu Leu Phe
Asp Ser Gly Glu Thr Ala Glu Ala Thr Arg Leu 50 55 60Lys Arg Thr Ala
Arg Arg Arg Tyr Thr Arg Arg Lys Asn Arg Ile Cys65 70 75 80Tyr Leu
Gln Glu Ile Phe Ser Asn Glu Met Ala Lys Val Asp Asp Ser 85 90 95Phe
Phe His Arg Leu Glu Glu Ser Phe Leu Val Glu Glu Asp Lys Lys 100 105
110His Glu Arg His Pro Ile Phe Gly Asn Ile Val Asp Glu Val Ala Tyr
115 120 125His Glu Lys Tyr Pro Thr Ile Tyr His Leu Arg Lys Lys Leu
Val Asp 130 135 140Ser Thr Asp Lys Ala Asp Leu Arg Leu Ile Tyr Leu
Ala Leu Ala His145 150 155 160Met Ile Lys Phe Arg Gly His Phe Leu
Ile Glu Gly Asp Leu Asn Pro 165 170 175Asp Asn Ser Asp Val Asp Lys
Leu Phe Ile Gln Leu Val Gln Thr Tyr 180 185 190Asn Gln Leu Phe Glu
Glu Asn Pro Ile Asn Ala Ser Gly Val Asp Ala 195 200 205Lys Ala Ile
Leu Ser Ala Arg Leu Ser Lys Ser Arg Arg Leu Glu Asn 210 215 220Leu
Ile Ala Gln Leu Pro Gly Glu Lys Lys Asn Gly Leu Phe Gly Asn225 230
235 240Leu Ile Ala Leu Ser Leu Gly Leu Thr Pro Asn Phe Lys Ser Asn
Phe 245 250 255Asp Leu Ala Glu Asp Ala Lys Leu Gln Leu Ser Lys Asp
Thr Tyr Asp 260 265 270Asp Asp Leu Asp Asn Leu Leu Ala Gln Ile Gly
Asp Gln Tyr Ala Asp 275 280 285Leu Phe Leu Ala Ala Lys Asn Leu Ser
Asp Ala Ile Leu Leu Ser Asp 290 295 300Ile Leu Arg Val Asn Thr Glu
Ile Thr Lys Ala Pro Leu Ser Ala Ser305 310 315 320Met Ile Lys Arg
Tyr Asp Glu His His Gln Asp Leu Thr Leu Leu Lys 325 330 335Ala Leu
Val Arg Gln Gln Leu Pro Glu Lys Tyr Lys Glu Ile Phe Phe 340 345
350Asp Gln Ser Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Gly Ala Ser
355 360 365Gln Glu Glu Phe Tyr Lys Phe Ile Lys Pro Ile Leu Glu Lys
Met Asp 370 375 380Gly Thr Glu Glu Leu Leu Val Lys Leu Asn Arg Glu
Asp Leu Leu Arg385 390 395 400Lys Gln Arg Thr Phe Asp Asn Gly Ser
Ile Pro His Gln Ile His Leu 405 410 415Gly Glu Leu His Ala Ile Leu
Arg Arg Gln Glu Asp Phe Tyr Pro Phe 420 425 430Leu Lys Asp Asn Arg
Glu Lys Ile Glu Lys Ile Leu Thr Phe Arg Ile 435 440 445Pro Tyr Tyr
Val Gly Pro Leu Ala Arg Gly Asn Ser Arg Phe Ala Trp 450 455 460Met
Thr Arg Lys Ser Glu Glu Thr Ile Thr Pro Trp Asn Phe Glu Glu465 470
475 480Val Val Asp Lys Gly Ala Ser Ala Gln Ser Phe Ile Glu Arg Met
Thr 485 490 495Asn Phe Asp Lys Asn Leu Pro Asn Glu Lys Val Leu Pro
Lys His Ser 500 505 510Leu Leu Tyr Glu Tyr Phe Thr Val Tyr Asn Glu
Leu Thr Lys Val Lys 515 520 525Tyr Val Thr Glu Gly Met Arg Lys Pro
Ala Phe Leu Ser Gly Glu Gln 530 535 540Lys Lys Ala Ile Val Asp Leu
Leu Phe Lys Thr Asn Arg Lys Val Thr545 550 555 560Val Lys Gln Leu
Lys Glu Asp Tyr Phe Lys Lys Ile Glu Cys Phe Asp 565 570 575Ser Val
Glu Ile Ser Gly Val Glu Asp Arg Phe Asn Ala Ser Leu Gly 580 585
590Thr Tyr His Asp Leu Leu Lys Ile Ile Lys Asp Lys Asp Phe Leu Asp
595 600 605Asn Glu Glu Asn Glu Asp Ile Leu Glu Asp Ile Val Leu Thr
Leu Thr 610 615 620Leu Phe Glu Asp Arg Glu Met Ile Glu Glu Arg Leu
Lys Thr Tyr Ala625 630 635 640His Leu Phe Asp Asp Lys Val Met Lys
Gln Leu Lys Arg Arg Arg Tyr 645 650 655Thr Gly Trp Gly Arg Leu Ser
Arg Lys Leu Ile Asn Gly Ile Arg Asp 660 665 670Lys Gln Ser Gly Lys
Thr Ile Leu Asp Phe Leu Lys Ser Asp Gly Phe 675 680 685Ala Asn Arg
Asn Phe Met Gln Leu Ile His Asp Asp Ser Leu Thr Phe 690 695 700Lys
Glu Asp Ile Gln Lys Ala Gln Val Ser Gly Gln Gly Asp Ser Leu705 710
715 720His Glu His Ile Ala Asn Leu Ala Gly Ser Pro Ala Ile Lys Lys
Gly 725 730 735Ile Leu Gln Thr Val Lys Val Val Asp Glu Leu Val Lys
Val Met Gly 740 745 750Arg His Lys Pro Glu Asn Ile Val Ile Glu Met
Ala Arg Glu Asn Gln 755 760 765Thr Thr Gln Lys Gly Gln Lys Asn Ser
Arg Glu Arg Met Lys Arg Ile 770 775 780Glu Glu Gly Ile Lys Glu Leu
Gly Ser Gln Ile Leu Lys Glu His Pro785 790 795 800Val Glu Asn Thr
Gln Leu Gln Asn Glu Lys Leu Tyr Leu Tyr Tyr Leu 805 810 815Gln Asn
Gly Arg Asp Met Tyr Val Asp Gln Glu Leu Asp Ile Asn Arg 820 825
830Leu Ser Asp Tyr Asp Val Asp His Ile Val Pro Gln Ser Phe Leu Lys
835 840 845Asp Asp Ser Ile Asp Asn Lys Val Leu Thr Arg Ser Asp Lys
Asn Arg 850 855 860Gly Lys Ser Asp Asn Val Pro Ser Glu Glu Val Val
Lys Lys Met Lys865 870 875 880Asn Tyr Trp Arg Gln Leu Leu Asn Ala
Lys Leu Ile Thr Gln Arg Lys 885 890 895Phe Asp Asn Leu Thr Lys Ala
Glu Arg Gly Gly Leu Ser Glu Leu Asp 900 905 910Lys Ala Gly Phe Ile
Lys Arg Gln Leu Val Glu Thr Arg Gln Ile Thr 915 920 925Lys His Val
Ala Gln Ile Leu Asp Ser Arg Met Asn Thr Lys Tyr Asp 930 935 940Glu
Asn Asp Lys Leu Ile Arg Glu Val Lys Val Ile Thr Leu Lys Ser945 950
955 960Lys Leu Val Ser Asp Phe Arg Lys Asp Phe Gln Phe Tyr Lys Val
Arg 965 970 975Glu Ile Asn Asn Tyr His His Ala His Asp Ala Tyr Leu
Asn Ala Val 980 985 990Val Gly Thr Ala Leu Ile Lys Lys Tyr Pro Lys
Leu Glu Ser Glu Phe 995 1000 1005Val Tyr Gly Asp Tyr Lys Val Tyr
Asp Val Arg Lys Met Ile Ala 1010 1015 1020Lys Ser Glu Gln Glu Ile
Gly Lys Ala Thr Ala Lys Tyr Phe Phe 1025 1030 1035Tyr Ser Asn Ile
Met Asn Phe Phe Lys Thr Glu Ile Thr Leu Ala 1040 1045 1050Asn Gly
Glu Ile Arg Lys Arg Pro Leu Ile Glu Thr Asn Gly Glu 1055 1060
1065Thr Gly Glu Ile Val Trp Asp Lys Gly Arg Asp Phe Ala Thr Val
1070 1075 1080Arg Lys Val Leu Ser Met Pro Gln Val Asn Ile Val Lys
Lys Thr 1085 1090 1095Glu Val Gln Thr Gly Gly Phe Ser Lys Glu Ser
Ile Leu Pro Lys 1100 1105 1110Arg Asn Ser Asp Lys Leu Ile Ala Arg
Lys Lys Asp Trp Asp Pro 1115 1120 1125Lys Lys Tyr Gly Gly Phe Asp
Ser Pro Thr Val Ala Tyr Ser Val 1130 1135 1140Leu Val Val Ala Lys
Val Glu Lys Gly Lys Ser Lys Lys Leu Lys 1145 1150 1155Ser Val Lys
Glu Leu Leu Gly Ile Thr Ile Met Glu Arg Ser Ser 1160 1165 1170Phe
Glu Lys Asn Pro Ile Asp Phe Leu Glu Ala Lys Gly Tyr Lys 1175 1180
1185Glu Val Lys Lys Asp Leu Ile Ile Lys Leu Pro Lys Tyr Ser Leu
1190 1195 1200Phe Glu Leu Glu Asn Gly Arg Lys Arg Met Leu Ala Ser
Ala Gly 1205 1210 1215Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro
Ser Lys Tyr Val 1220 1225 1230Asn Phe Leu Tyr Leu Ala Ser His Tyr
Glu Lys Leu Lys Gly Ser 1235 1240 1245Pro Glu Asp Asn Glu Gln Lys
Gln Leu Phe Val Glu Gln His Lys 1250 1255 1260His Tyr Leu Asp Glu
Ile Ile Glu Gln Ile Ser Glu Phe Ser Lys 1265 1270 1275Arg Val Ile
Leu Ala Asp Ala Asn Leu Asp Lys Val Leu Ser Ala 1280 1285 1290Tyr
Asn Lys His Arg Asp Lys Pro Ile Arg Glu Gln Ala Glu Asn 1295 1300
1305Ile Ile His Leu Phe Thr Leu Thr Asn Leu Gly Ala Pro Ala Ala
1310 1315 1320Phe Lys Tyr Phe Asp Thr Thr Ile Asp Arg Lys Arg Tyr
Thr Ser 1325 1330 1335Thr Lys Glu Val Leu Asp Ala Thr Leu Ile His
Gln Ser Ile Thr 1340 1345 1350Gly Leu Tyr Glu Thr Arg Ile Asp Leu
Ser Gln Leu Gly Gly Asp 1355 1360 1365213PRTStreptococcus sp. 2Tyr
Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val Gly1 5
1037PRTStreptococcus sp. 3Pro Thr Ile Tyr His Leu Arg1
547PRTStreptococcus sp. 4Arg Gly His Phe Leu Ile Glu1
559PRTStreptococcus sp. 5Thr Lys Ala Pro Leu Ser Ala Ser Met1
5610PRTStreptococcus sp. 6Leu Arg Lys Gln Arg Thr Phe Asp Asn Gly1
5 10714PRTStreptococcus sp. 7Leu Thr Phe Arg Ile Pro Tyr Tyr Val
Gly Pro Leu Ala Arg1 5 10811PRTStreptococcus sp. 8Thr Leu Thr Leu
Phe Glu Asp Arg Glu Met Ile1 5 10912PRTStreptococcus sp. 9Ala Gly
Ser Pro Ala Ile Lys Lys Gly Ile Leu Gln1 5 101014PRTStreptococcus
sp. 10Arg Gln Leu Val Glu Thr Arg Gln Ile Thr Lys His Val Ala1 5
101111PRTStreptococcus sp. 11Gln Thr Gly Gly Phe Ser Lys Glu Ser
Ile Leu1 5 101223DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 12gaaattaata cgactcacta tag
231323DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 13gttttagagc tagaaatagc aag
231422DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 14aaaagcaccg actcggtgcc ac
221519DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 15taatacgact cactatagg
191614DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 16gttttagagc taga 141719DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 17catttctcag tcctaaaca 191820DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 18taatacgact cactataggg 201919DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 19ccagtagcca gccccgtcc 192019DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 20tcgtgtccct gtacgcgga 192140DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 21taatacgact cactataggg gcatttctca gtcctaaaca
402240DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 22gctatttcta gctctaaaac tgtttaggac
tgagaaatgc 402360DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 23gttttagagc tagaaatagc
aagttaaaat aaggctagtc cgttatcaac ttgaaaaagt 602460DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 24aaaagcaccg actcggtgcc actttttcaa gttgataacg
gactagcctt attttaactt 602539DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 25gctatttcta
gctctaaaac tgtttaggac tgagaaatg 392634DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 26ttctagctct aaaactgttt aggactgaga aatg
342739DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 27taatacgact cactataggc atttctcagt
cctaaacag 392834DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 28taatacgact cactataggc
atttctcagt ccta 342921DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 29aaagcaccga
ctcggtgcca c 213020DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 30aagcaccgac tcggtgccac
203119DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 31agcaccgact cggtgccac
193218DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 32gcaccgactc ggtgccac 183335DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 33taatacgact cactataggg ccagtagcca gcccc
353434DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 34taatacgact cactataggc cagtagccag cccc
343533DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 35taatacgact cactatagcc agtagccagc ccc
33369823DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotidemodified_base(7336)..(7355)a, c, t, g,
unknown or other 36gttaggcgtt ttgcgctgct tcgcgatgta cgggccagat
atacgcgttg acattgatta 60ttgactagtt attaatagta atcaattacg gggtcattag
ttcatagccc atatatggag 120ttccgcgtta cataacttac ggtaaatggc
ccgcctggct gaccgcccaa cgacccccgc 180ccattgacgt caataatgac
gtatgttccc atagtaacgc caatagggac tttccattga 240cgtcaatggg
tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat
300atgccaagta cgccccctat tgacgtcaat gacggtaaat ggcccgcctg
gcattatgcc 360cagtacatga ccttatggga ctttcctact tggcagtaca
tctacgtatt agtcatcgct 420attaccatgg tgatgcggtt ttggcagtac
atcaatgggc gtggatagcg gtttgactca 480cggggatttc caagtctcca
ccccattgac gtcaatggga gtttgttttg gcaccaaaat 540caacgggact
ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg
600cgtgtacggt gggaggtcta tataagcaga gctcgtttag tgaaccgtca
gatcgcctgg 660agacgccatc cacgctgttt tgacctccat agaagacacc
gggaccgatc cagcctccgg 720agcggccgcc accatgggca agcccatccc
taaccccctg ttggggctgg acagcaccgc 780tcccaaaaag aaaaggaagg
tgggcattca cggcgtgcct gcggccgaca aaaagtacag 840catcggcctt
gatatcggca ccaatagcgt gggctgggcc gttatcacag acgaatacaa
900ggtacccagc aagaagttca aggtgctggg gaatacagac aggcactcta
tcaagaaaaa 960ccttatcggg gctctgctgt ttgactcagg cgagaccgcc
gaggccacca ggttgaagag 1020gaccgcaagg cgaaggtaca cccggaggaa
gaacaggatc tgctatctgc aggagatctt 1080cagcaacgag atggccaagg
tggacgacag cttcttccac aggctggagg agagcttcct 1140tgtcgaggag
gataagaagc acgaacgaca ccccatcttc ggcaacatag tcgacgaggt
1200cgcttatcac gagaagtacc ccaccatcta ccacctgcga aagaaattgg
tggatagcac 1260cgataaagcc gacttgcgac ttatctactt ggctctggcg
cacatgatta agttcagggg 1320ccacttcctg atcgagggcg accttaaccc
cgacaacagt gacgtagaca aattgttcat 1380ccagcttgta cagacctata
accagctgtt cgaggaaaac cctattaacg ccagcggggt 1440ggatgcgaag
gccatactta gcgccaggct gagcaaaagc aggcgcttgg agaacctgat
1500agcccagctg cccggtgaaa agaagaacgg cctcttcggt aatctgattg
ccctgagcct 1560gggcctgacc cccaacttca agagcaactt cgacctggca
gaagatgcca agctgcagtt 1620gagtaaggac acctatgacg acgacttgga
caatctgctc gcccaaatcg gcgaccagta 1680cgctgacctg ttcctcgccg
ccaagaacct ttctgacgca atcctgctta gcgatatcct 1740tagggtgaac
acagagatca ccaaggcccc cctgagcgcc agcatgatca agaggtacga
1800cgagcaccat caggacctga cccttctgaa ggccctggtg aggcagcaac
tgcccgagaa 1860gtacaaggag atctttttcg accagagcaa gaacggctac
gccggctaca tcgacggcgg 1920agccagccaa gaggagttct acaagttcat
caagcccatc ctggagaaga tggatggcac 1980cgaggagctg ctggtgaagc
tgaacaggga agatttgctc cggaagcaga ggacctttga 2040caacggtagc
atcccccacc agatccacct gggcgagctg cacgcaatac tgaggcgaca
2100ggaggatttc taccccttcc tcaaggacaa tagggagaaa atcgaaaaga
ttctgacctt 2160caggatcccc tactacgtgg gccctcttgc caggggcaac
agccgattcg cttggatgac 2220aagaaagagc gaggagacca tcaccccctg
gaacttcgag gaagtggtgg acaaaggagc 2280aagcgcgcag tctttcatcg
aacggatgac caatttcgac
aaaaacctgc ctaacgagaa 2340ggtgctgccc aagcacagcc tgctttacga
gtacttcacc gtgtacaacg agctcaccaa 2400ggtgaaatat gtgaccgagg
gcatgcgaaa acccgctttc ctgagcggcg agcagaagaa 2460ggccatcgtg
gacctgctgt tcaagaccaa caggaaggtg accgtgaagc agctgaagga
2520ggactacttc aagaagatcg agtgctttga tagcgtggaa ataagcggcg
tggaggacag 2580gttcaacgcc agcctgggca cctaccacga cttgttgaag
ataatcaaag acaaggattt 2640cctggataat gaggagaacg aggatatact
cgaggacatc gtgctgactt tgaccctgtt 2700tgaggaccga gagatgattg
aagaaaggct caaaacctac gcccacctgt tcgacgacaa 2760agtgatgaaa
caactgaaga gacgaagata caccggctgg ggcagactgt ccaggaagct
2820catcaacggc attagggaca agcagagcgg caagaccatc ctggatttcc
tgaagtccga 2880cggcttcgcc aaccgaaact tcatgcagct gattcacgat
gacagcttga ccttcaagga 2940ggacatccag aaggcccagg ttagcggcca
gggcgactcc ctgcacgaac atattgcaaa 3000cctggcaggc tcccctgcga
tcaagaaggg catactgcag accgttaagg ttgtggacga 3060attggtcaag
gtcatgggca ggcacaagcc cgaaaacata gttatagaga tggccagaga
3120gaaccagacc acccaaaagg gccagaagaa cagccgggag cgcatgaaaa
ggatcgagga 3180gggtatcaag gaactcggaa gccagatcct caaagagcac
cccgtggaga atacccagct 3240ccagaacgag aagctgtacc tgtactacct
gcagaacggc agggacatgt acgttgacca 3300ggagttggac atcaacaggc
tttcagacta tgacgtggat cacatagtgc cccagagctt 3360tcttaaagac
gatagcatcg acaacaaggt cctgacccgc tccgacaaaa acaggggcaa
3420aagcgacaac gtgccaagcg aagaggtggt taaaaagatg aagaactact
ggaggcaact 3480gctcaacgcg aaattgatca cccagagaaa gttcgataac
ctgaccaagg ccgagagggg 3540cggactctcc gaacttgaca aagcgggctt
cataaagagg cagctggtcg agacccgaca 3600gatcacgaag cacgtggccc
aaatcctcga cagcagaatg aataccaagt acgatgagaa 3660tgacaaactc
atcagggaag tgaaagtgat taccctgaag agcaagttgg tgtccgactt
3720tcgcaaagat ttccagttct acaaggtgag ggagatcaac aactaccacc
atgcccacga 3780cgcatacctg aacgccgtgg tcggcaccgc cctgattaag
aagtatccaa agctggagtc 3840cgaatttgtc tacggcgact acaaagttta
cgatgtgagg aagatgatcg ctaagagcga 3900acaggagatc ggcaaggcca
ccgctaagta tttcttctac agcaacatca tgaacttttt 3960caagaccgag
atcacacttg ccaacggcga aatcaggaag aggccgctta tcgagaccaa
4020cggtgagacc ggcgagatcg tgtgggacaa gggcagggac ttcgccaccg
tgaggaaagt 4080cctgagcatg ccccaggtga atattgtgaa aaaaactgag
gtgcagacag gcggctttag 4140caaggaatcc atcctgccca agaggaacag
cgacaagctg atcgcccgga agaaggactg 4200ggaccctaag aagtatggag
gcttcgacag ccccaccgta gcctacagcg tgctggtggt 4260cgcgaaggta
gagaagggga agagcaagaa actgaagagc gtgaaggagc tgctcggcat
4320aaccatcatg gagaggtcca gctttgagaa gaaccccatt gactttttgg
aagccaaggg 4380ctacaaagag gtcaaaaagg acctgatcat caaactcccc
aagtactccc tgtttgaatt 4440ggagaacggc agaaagagga tgctggcgag
cgctggggaa ctgcaaaagg gcaacgaact 4500ggcgctgccc agcaagtacg
tgaattttct gtacctggcg tcccactacg aaaagctgaa 4560aggcagcccc
gaggacaacg agcagaagca gctgttcgtg gagcagcaca agcattacct
4620ggacgagata atcgagcaaa tcagcgagtt cagcaagagg gtgattctgg
ccgacgcgaa 4680cctggataag gtcctcagcg cctacaacaa gcaccgagac
aaacccatca gggagcaggc 4740cgagaatatc atacacctgt tcaccctgac
aaatctgggc gcacctgcgg cattcaaata 4800cttcgatacc accatcgaca
ggaaaaggta cactagcact aaggaggtgc tggatgccac 4860cttgatccac
cagtccatta ccggcctgta tgagaccagg atcgacctga gccagcttgg
4920aggcgactct agggcggacc caaaaaagaa aaggaaggtg gaattctcta
gaggcagtgg 4980agagggcaga ggaagtctgc taacatgcgg tgacgtcgag
gagaatcctg gcccaatgaa 5040ccggggagtc ccttttaggc acttgcttct
ggtgctgcaa ctggcgctcc tcccagcagc 5100cactcaggga aagaaagtgg
tgctgggcaa aaaaggggat acagtggaac tgacctgtac 5160agcttcccag
aagaagagca tacaattcca ctggaaaaac tccaaccaga taaagattct
5220gggaaatcag ggctccttct taactaaagg tccatccaag ctgaatgatc
gcgctgactc 5280aagaagaagc ctttgggacc aaggaaactt ccccctgatc
atcaagaatc ttaagataga 5340agactcagat acttacatct gtgaagtgga
ggaccagaag gaggaggtgc aattgctagt 5400gttcggattg actgccaact
ctgacaccca cctgcttcag gggcagagcc tgaccctgac 5460cttggagagc
ccccctggta gtagcccctc agtgcaatgt aggagtccaa ggggtaaaaa
5520catacagggg gggaagaccc tctccgtgtc tcagctggag ctccaggata
gtggcacctg 5580gacatgcact gtcttgcaga accagaagaa ggtggagttc
aaaatagaca tcgtggtgct 5640agctttccag aaggcctcca gcatagtcta
taagaaagag ggggaacagg tggagttctc 5700cttcccactc gcctttacag
ttgaaaagct gacgggcagt ggcgagctgt ggtggcaggc 5760ggagagggct
tcctcctcca agtcttggat cacctttgac ctgaagaaca aggaagtgtc
5820tgtaaaacgg gttacccagg accctaagct ccagatgggc aagaagctcc
cgctccacct 5880caccctgccc caggccttgc ctcagtatgc tggctctgga
aacctcaccc tggcccttga 5940agcgaaaaca ggaaagttgc atcaggaagt
gaacctggtg gtgatgagag ccactcagct 6000ccagaaaaat ttgacctgtg
aggtgtgggg acccacctcc cctaagctga tgctgagctt 6060gaaactggag
aacaaggagg caaaggtctc gaagcgggag aaggcggtgt gggtgctgaa
6120ccctgaggcg gggatgtggc agtgtctgct gagtgactcg ggacaggtcc
tgctggaatc 6180caacatcaag gttctgccca catggtcgac cccggtgcag
ccaatggccc tgattgtgct 6240ggggggcgtc gccggcctcc tgcttttcat
tgggctaggc atcttcttct gtgtcaggtg 6300ccggcacacc ggttagtaat
gagtttaaac gggggaggct aactgaaaca cggaaggaga 6360caataccgga
aggaacccgc gctatgacgg caataaaaag acagaataaa acgcacgggt
6420gttgggtcgt ttgttcataa acgcggggtt cggtcccagg gctggcactc
tgtcgatacc 6480ccaccgagac cccattgggg ccaatacgcc cgcgtttctt
ccttttcccc accccacccc 6540ccaagttcgg gtgaaggccc agggctcgca
gccaacgtcg gggcggcagg ccctgccata 6600gcagatctgc gcagctgggg
ctctaggggg tatccccacg cgccctgtag cggcgcatta 6660agcgcggcgg
gtgtggtggt tacgcgcagc gtgaccgcta cacttgccag cgccctagcg
6720cccgctcctt tcgctttctt cccttccttt ctcgccacgt tcgccggctt
tccccgtcaa 6780gctctaaatc gggggctccc tttagggttc cgatttagtg
ctttacggca cctcgacccc 6840aaaaaacttg attagggtga tggttcacgt
agtgggccat cgccctgata gacggttttt 6900cgccctttga cgttggagtc
cacgttcttt aatagtggac tcttgttcca aactggaaca 6960acactcaacc
ctatctcggt ctattctttt gatttataag ggattttgcc gatttcggcc
7020tattggttaa aaaatgagct gatttaacaa aaatttaacg cgaattaatt
aaggtcgggc 7080aggaagaggg cctatttccc atgattcctt catatttgca
tatacgatac aaggctgtta 7140gagagataat tagaattaat ttgactgtaa
acacaaagat attagtacaa aatacgtgac 7200gtagaaagta ataatttctt
gggtagtttg cagttttaaa attatgtttt aaaatggact 7260atcatatgct
taccgtaact tgaaagtatt tcgatttctt ggctttatat atcttgtgga
7320aaggacgaaa caccgnnnnn nnnnnnnnnn nnnnngtttt agagctagaa
atagcaagtt 7380aaaataaggc tagtccgtta tcaacttgaa aaagtggcac
cgagtcggtg cttttttcta 7440gtataccgtc gacctctagc tagagcttgg
cgtaatcatg gtcatagctg tttcctgtgt 7500gaaattgtta tccgctcaca
attccacaca acatacgagc cggaagcata aagtgtaaag 7560cctggggtgc
ctaatgagtg agctaactca cattaattgc gttgcgctca ctgcccgctt
7620tccagtcggg aaacctgtcg tgccagctgc attaatgaat cggccaacgc
gcggggagag 7680gcggtttgcg tattgggcgc tcttccgctt cctcgctcac
tgactcgctg cgctcggtcg 7740ttcggctgcg gcgagcggta tcagctcact
caaaggcggt aatacggtta tccacagaat 7800caggggataa cgcaggaaag
aacatgtgag caaaaggcca gcaaaaggcc aggaaccgta 7860aaaaggccgc
gttgctggcg tttttccata ggctccgccc ccctgacgag catcacaaaa
7920atcgacgctc aagtcagagg tggcgaaacc cgacaggact ataaagatac
caggcgtttc 7980cccctggaag ctccctcgtg cgctctcctg ttccgaccct
gccgcttacc ggatacctgt 8040ccgcctttct cccttcggga agcgtggcgc
tttctcatag ctcacgctgt aggtatctca 8100gttcggtgta ggtcgttcgc
tccaagctgg gctgtgtgca cgaacccccc gttcagcccg 8160accgctgcgc
cttatccggt aactatcgtc ttgagtccaa cccggtaaga cacgacttat
8220cgccactggc agcagccact ggtaacagga ttagcagagc gaggtatgta
ggcggtgcta 8280cagagttctt gaagtggtgg cctaactacg gctacactag
aagaacagta tttggtatct 8340gcgctctgct gaagccagtt accttcggaa
aaagagttgg tagctcttga tccggcaaac 8400aaaccaccgc tggtagcggt
ggtttttttg tttgcaagca gcagattacg cgcagaaaaa 8460aaggatctca
agaagatcct ttgatctttt ctacggggtc tgacgctcag tggaacgaaa
8520actcacgtta agggattttg gtcatgagat tatcaaaaag gatcttcacc
tagatccttt 8580taaattaaaa atgaagtttt aaatcaatct aaagtatata
tgagtaaact tggtctgaca 8640gttaccaatg cttaatcagt gaggcaccta
tctcagcgat ctgtctattt cgttcatcca 8700tagttgcctg actccccgtc
gtgtagataa ctacgatacg ggagggctta ccatctggcc 8760ccagtgctgc
aatgataccg cgagacccac gctcaccggc tccagattta tcagcaataa
8820accagccagc cggaagggcc gagcgcagaa gtggtcctgc aactttatcc
gcctccatcc 8880agtctattaa ttgttgccgg gaagctagag taagtagttc
gccagttaat agtttgcgca 8940acgttgttgc cattgctaca ggcatcgtgg
tgtcacgctc gtcgtttggt atggcttcat 9000tcagctccgg ttcccaacga
tcaaggcgag ttacatgatc ccccatgttg tgcaaaaaag 9060cggttagctc
cttcggtcct ccgatcgttg tcagaagtaa gttggccgca gtgttatcac
9120tcatggttat ggcagcactg cataattctc ttactgtcat gccatccgta
agatgctttt 9180ctgtgactgg tgagtactca accaagtcat tctgagaata
gtgtatgcgg cgaccgagtt 9240gctcttgccc ggcgtcaata cgggataata
ccgcgccaca tagcagaact ttaaaagtgc 9300tcatcattgg aaaacgttct
tcggggcgaa aactctcaag gatcttaccg ctgttgagat 9360ccagttcgat
gtaacccact cgtgcaccca actgatcttc agcatctttt actttcacca
9420gcgtttctgg gtgagcaaaa acaggaaggc aaaatgccgc aaaaaaggga
ataagggcga 9480cacggaaatg ttgaatactc atactcttcc tttttcaata
ttattgaagc atttatcagg 9540gttattgtct catgagcgga tacatatttg
aatgtattta gaaaaataaa caaatagggg 9600ttccgcgcac atttccccga
aaagtgccac ctgacgtcga cggatcggga gatctcccga 9660tcccctatgg
tgcactctca gtacaatctg ctctgatgcc gcatagttaa gccagtatct
9720gctccctgct tgtgtgttgg aggtcgctga gtagtgcgcg agcaaaattt
aagctacaac 9780aaggcaaggc ttgaccgaca attgcatgaa gaatctgctt agg
9823379220DNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotidemodified_base(6733)..(6752)a, c, t, g,
unknown or other 37gttaggcgtt ttgcgctgct tcgcgatgta cgggccagat
atacgcgttg acattgatta 60ttgactagtt attaatagta atcaattacg gggtcattag
ttcatagccc atatatggag 120ttccgcgtta cataacttac ggtaaatggc
ccgcctggct gaccgcccaa cgacccccgc 180ccattgacgt caataatgac
gtatgttccc atagtaacgc caatagggac tttccattga 240cgtcaatggg
tggagtattt acggtaaact gcccacttgg cagtacatca agtgtatcat
300atgccaagta cgccccctat tgacgtcaat gacggtaaat ggcccgcctg
gcattatgcc 360cagtacatga ccttatggga ctttcctact tggcagtaca
tctacgtatt agtcatcgct 420attaccatgg tgatgcggtt ttggcagtac
atcaatgggc gtggatagcg gtttgactca 480cggggatttc caagtctcca
ccccattgac gtcaatggga gtttgttttg gcaccaaaat 540caacgggact
ttccaaaatg tcgtaacaac tccgccccat tgacgcaaat gggcggtagg
600cgtgtacggt gggaggtcta tataagcaga gctcgtttag tgaaccgtca
gatcgcctgg 660agacgccatc cacgctgttt tgacctccat agaagacacc
gggaccgatc cagcctccgg 720agcggccgcc accatgggca agcccatccc
taaccccctg ttggggctgg acagcaccgc 780tcccaaaaag aaaaggaagg
tgggcattca cggcgtgcct gcggccgaca aaaagtacag 840catcggcctt
gatatcggca ccaatagcgt gggctgggcc gttatcacag acgaatacaa
900ggtacccagc aagaagttca aggtgctggg gaatacagac aggcactcta
tcaagaaaaa 960ccttatcggg gctctgctgt ttgactcagg cgagaccgcc
gaggccacca ggttgaagag 1020gaccgcaagg cgaaggtaca cccggaggaa
gaacaggatc tgctatctgc aggagatctt 1080cagcaacgag atggccaagg
tggacgacag cttcttccac aggctggagg agagcttcct 1140tgtcgaggag
gataagaagc acgaacgaca ccccatcttc ggcaacatag tcgacgaggt
1200cgcttatcac gagaagtacc ccaccatcta ccacctgcga aagaaattgg
tggatagcac 1260cgataaagcc gacttgcgac ttatctactt ggctctggcg
cacatgatta agttcagggg 1320ccacttcctg atcgagggcg accttaaccc
cgacaacagt gacgtagaca aattgttcat 1380ccagcttgta cagacctata
accagctgtt cgaggaaaac cctattaacg ccagcggggt 1440ggatgcgaag
gccatactta gcgccaggct gagcaaaagc aggcgcttgg agaacctgat
1500agcccagctg cccggtgaaa agaagaacgg cctcttcggt aatctgattg
ccctgagcct 1560gggcctgacc cccaacttca agagcaactt cgacctggca
gaagatgcca agctgcagtt 1620gagtaaggac acctatgacg acgacttgga
caatctgctc gcccaaatcg gcgaccagta 1680cgctgacctg ttcctcgccg
ccaagaacct ttctgacgca atcctgctta gcgatatcct 1740tagggtgaac
acagagatca ccaaggcccc cctgagcgcc agcatgatca agaggtacga
1800cgagcaccat caggacctga cccttctgaa ggccctggtg aggcagcaac
tgcccgagaa 1860gtacaaggag atctttttcg accagagcaa gaacggctac
gccggctaca tcgacggcgg 1920agccagccaa gaggagttct acaagttcat
caagcccatc ctggagaaga tggatggcac 1980cgaggagctg ctggtgaagc
tgaacaggga agatttgctc cggaagcaga ggacctttga 2040caacggtagc
atcccccacc agatccacct gggcgagctg cacgcaatac tgaggcgaca
2100ggaggatttc taccccttcc tcaaggacaa tagggagaaa atcgaaaaga
ttctgacctt 2160caggatcccc tactacgtgg gccctcttgc caggggcaac
agccgattcg cttggatgac 2220aagaaagagc gaggagacca tcaccccctg
gaacttcgag gaagtggtgg acaaaggagc 2280aagcgcgcag tctttcatcg
aacggatgac caatttcgac aaaaacctgc ctaacgagaa 2340ggtgctgccc
aagcacagcc tgctttacga gtacttcacc gtgtacaacg agctcaccaa
2400ggtgaaatat gtgaccgagg gcatgcgaaa acccgctttc ctgagcggcg
agcagaagaa 2460ggccatcgtg gacctgctgt tcaagaccaa caggaaggtg
accgtgaagc agctgaagga 2520ggactacttc aagaagatcg agtgctttga
tagcgtggaa ataagcggcg tggaggacag 2580gttcaacgcc agcctgggca
cctaccacga cttgttgaag ataatcaaag acaaggattt 2640cctggataat
gaggagaacg aggatatact cgaggacatc gtgctgactt tgaccctgtt
2700tgaggaccga gagatgattg aagaaaggct caaaacctac gcccacctgt
tcgacgacaa 2760agtgatgaaa caactgaaga gacgaagata caccggctgg
ggcagactgt ccaggaagct 2820catcaacggc attagggaca agcagagcgg
caagaccatc ctggatttcc tgaagtccga 2880cggcttcgcc aaccgaaact
tcatgcagct gattcacgat gacagcttga ccttcaagga 2940ggacatccag
aaggcccagg ttagcggcca gggcgactcc ctgcacgaac atattgcaaa
3000cctggcaggc tcccctgcga tcaagaaggg catactgcag accgttaagg
ttgtggacga 3060attggtcaag gtcatgggca ggcacaagcc cgaaaacata
gttatagaga tggccagaga 3120gaaccagacc acccaaaagg gccagaagaa
cagccgggag cgcatgaaaa ggatcgagga 3180gggtatcaag gaactcggaa
gccagatcct caaagagcac cccgtggaga atacccagct 3240ccagaacgag
aagctgtacc tgtactacct gcagaacggc agggacatgt acgttgacca
3300ggagttggac atcaacaggc tttcagacta tgacgtggat cacatagtgc
cccagagctt 3360tcttaaagac gatagcatcg acaacaaggt cctgacccgc
tccgacaaaa acaggggcaa 3420aagcgacaac gtgccaagcg aagaggtggt
taaaaagatg aagaactact ggaggcaact 3480gctcaacgcg aaattgatca
cccagagaaa gttcgataac ctgaccaagg ccgagagggg 3540cggactctcc
gaacttgaca aagcgggctt cataaagagg cagctggtcg agacccgaca
3600gatcacgaag cacgtggccc aaatcctcga cagcagaatg aataccaagt
acgatgagaa 3660tgacaaactc atcagggaag tgaaagtgat taccctgaag
agcaagttgg tgtccgactt 3720tcgcaaagat ttccagttct acaaggtgag
ggagatcaac aactaccacc atgcccacga 3780cgcatacctg aacgccgtgg
tcggcaccgc cctgattaag aagtatccaa agctggagtc 3840cgaatttgtc
tacggcgact acaaagttta cgatgtgagg aagatgatcg ctaagagcga
3900acaggagatc ggcaaggcca ccgctaagta tttcttctac agcaacatca
tgaacttttt 3960caagaccgag atcacacttg ccaacggcga aatcaggaag
aggccgctta tcgagaccaa 4020cggtgagacc ggcgagatcg tgtgggacaa
gggcagggac ttcgccaccg tgaggaaagt 4080cctgagcatg ccccaggtga
atattgtgaa aaaaactgag gtgcagacag gcggctttag 4140caaggaatcc
atcctgccca agaggaacag cgacaagctg atcgcccgga agaaggactg
4200ggaccctaag aagtatggag gcttcgacag ccccaccgta gcctacagcg
tgctggtggt 4260cgcgaaggta gagaagggga agagcaagaa actgaagagc
gtgaaggagc tgctcggcat 4320aaccatcatg gagaggtcca gctttgagaa
gaaccccatt gactttttgg aagccaaggg 4380ctacaaagag gtcaaaaagg
acctgatcat caaactcccc aagtactccc tgtttgaatt 4440ggagaacggc
agaaagagga tgctggcgag cgctggggaa ctgcaaaagg gcaacgaact
4500ggcgctgccc agcaagtacg tgaattttct gtacctggcg tcccactacg
aaaagctgaa 4560aggcagcccc gaggacaacg agcagaagca gctgttcgtg
gagcagcaca agcattacct 4620ggacgagata atcgagcaaa tcagcgagtt
cagcaagagg gtgattctgg ccgacgcgaa 4680cctggataag gtcctcagcg
cctacaacaa gcaccgagac aaacccatca gggagcaggc 4740cgagaatatc
atacacctgt tcaccctgac aaatctgggc gcacctgcgg cattcaaata
4800cttcgatacc accatcgaca ggaaaaggta cactagcact aaggaggtgc
tggatgccac 4860cttgatccac cagtccatta ccggcctgta tgagaccagg
atcgacctga gccagcttgg 4920aggcgactct agggcggacc caaaaaagaa
aaggaaggtg gaattctcta gaggcagtgg 4980agagggcaga ggaagtctgc
taacatgcgg tgacgtcgag gagaatcctg gcccaatgaa 5040cctgagcaaa
aacgtgagcg tgagcgtgta tatgaagggg aacgtcaaca atcatgagtt
5100tgagtacgac ggggaaggtg gtggtgatcc ttatacaggt aaatattcca
tgaagatgac 5160gctacgtggt caaaattccc tacccttttc ctatgatatc
attaccacgg catttcagta 5220tggtttccgc gtatttacaa aataccctga
gggaattgtt gactatttta aggactcgct 5280tcccgacgca ttccagtgga
acagacgaat tgtgtttgaa gatggtggag tactaaacat 5340gagcagtgat
atcacatata aagataatgt tctgcatggt gacgtcaagg ctgagggagt
5400gaacttcccg ccgaatgggc cagtgatgaa gaatgaaatt gtgatggagg
aaccgactga 5460agaaacattt actccaaaaa acggggttct tgttggcttt
tgtcccaaag cgtacttact 5520taaagacggt tcctattact atggaaatat
gacaacattt tacagatcca agaaatctgg 5580ccaggcacct cctgggtatc
actttgttaa gcatcgtctc gtcaagacca atgtgggaca 5640tggatttaag
acggttgagc agactgaata tgccactgct catgtcagtg atcttcccaa
5700gttcgaagct tgataatgag tttaaacggg ggaggctaac tgaaacacgg
aaggagacaa 5760taccggaagg aacccgcgct atgacggcaa taaaaagaca
gaataaaacg cacgggtgtt 5820gggtcgtttg ttcataaacg cggggttcgg
tcccagggct ggcactctgt cgatacccca 5880ccgagacccc attggggcca
atacgcccgc gtttcttcct tttccccacc ccacccccca 5940agttcgggtg
aaggcccagg gctcgcagcc aacgtcgggg cggcaggccc tgccatagca
6000gatctgcgca gctggggctc tagggggtat ccccacgcgc cctgtagcgg
cgcattaagc 6060gcggcgggtg tggtggttac gcgcagcgtg accgctacac
ttgccagcgc cctagcgccc 6120gctcctttcg ctttcttccc ttcctttctc
gccacgttcg ccggctttcc ccgtcaagct 6180ctaaatcggg ggctcccttt
agggttccga tttagtgctt tacggcacct cgaccccaaa 6240aaacttgatt
agggtgatgg ttcacgtagt gggccatcgc cctgatagac ggtttttcgc
6300cctttgacgt tggagtccac gttctttaat agtggactct tgttccaaac
tggaacaaca 6360ctcaacccta tctcggtcta ttcttttgat ttataaggga
ttttgccgat ttcggcctat 6420tggttaaaaa atgagctgat ttaacaaaaa
tttaacgcga attaattaag gtcgggcagg 6480aagagggcct atttcccatg
attccttcat atttgcatat acgatacaag gctgttagag 6540agataattag
aattaatttg actgtaaaca caaagatatt agtacaaaat acgtgacgta
6600gaaagtaata atttcttggg tagtttgcag ttttaaaatt atgttttaaa
atggactatc 6660atatgcttac cgtaacttga aagtatttcg atttcttggc
tttatatatc ttgtggaaag 6720gacgaaacac cgnnnnnnnn nnnnnnnnnn
nngttttaga gctagaaata gcaagttaaa 6780ataaggctag tccgttatca
acttgaaaaa gtggcaccga gtcggtgctt ttttctagta 6840taccgtcgac
ctctagctag agcttggcgt aatcatggtc atagctgttt cctgtgtgaa
6900attgttatcc gctcacaatt ccacacaaca tacgagccgg aagcataaag
tgtaaagcct 6960ggggtgccta atgagtgagc taactcacat taattgcgtt
gcgctcactg cccgctttcc 7020agtcgggaaa cctgtcgtgc cagctgcatt
aatgaatcgg ccaacgcgcg gggagaggcg 7080gtttgcgtat tgggcgctct
tccgcttcct cgctcactga ctcgctgcgc tcggtcgttc 7140ggctgcggcg
agcggtatca gctcactcaa aggcggtaat acggttatcc acagaatcag
7200gggataacgc aggaaagaac atgtgagcaa aaggccagca aaaggccagg
aaccgtaaaa 7260aggccgcgtt gctggcgttt ttccataggc tccgcccccc
tgacgagcat cacaaaaatc 7320gacgctcaag tcagaggtgg cgaaacccga
caggactata aagataccag gcgtttcccc
7380ctggaagctc cctcgtgcgc tctcctgttc cgaccctgcc gcttaccgga
tacctgtccg 7440cctttctccc ttcgggaagc gtggcgcttt ctcatagctc
acgctgtagg tatctcagtt 7500cggtgtaggt cgttcgctcc aagctgggct
gtgtgcacga accccccgtt cagcccgacc 7560gctgcgcctt atccggtaac
tatcgtcttg agtccaaccc ggtaagacac gacttatcgc 7620cactggcagc
agccactggt aacaggatta gcagagcgag gtatgtaggc ggtgctacag
7680agttcttgaa gtggtggcct aactacggct acactagaag aacagtattt
ggtatctgcg 7740ctctgctgaa gccagttacc ttcggaaaaa gagttggtag
ctcttgatcc ggcaaacaaa 7800ccaccgctgg tagcggtggt ttttttgttt
gcaagcagca gattacgcgc agaaaaaaag 7860gatctcaaga agatcctttg
atcttttcta cggggtctga cgctcagtgg aacgaaaact 7920cacgttaagg
gattttggtc atgagattat caaaaaggat cttcacctag atccttttaa
7980attaaaaatg aagttttaaa tcaatctaaa gtatatatga gtaaacttgg
tctgacagtt 8040accaatgctt aatcagtgag gcacctatct cagcgatctg
tctatttcgt tcatccatag 8100ttgcctgact ccccgtcgtg tagataacta
cgatacggga gggcttacca tctggcccca 8160gtgctgcaat gataccgcga
gacccacgct caccggctcc agatttatca gcaataaacc 8220agccagccgg
aagggccgag cgcagaagtg gtcctgcaac tttatccgcc tccatccagt
8280ctattaattg ttgccgggaa gctagagtaa gtagttcgcc agttaatagt
ttgcgcaacg 8340ttgttgccat tgctacaggc atcgtggtgt cacgctcgtc
gtttggtatg gcttcattca 8400gctccggttc ccaacgatca aggcgagtta
catgatcccc catgttgtgc aaaaaagcgg 8460ttagctcctt cggtcctccg
atcgttgtca gaagtaagtt ggccgcagtg ttatcactca 8520tggttatggc
agcactgcat aattctctta ctgtcatgcc atccgtaaga tgcttttctg
8580tgactggtga gtactcaacc aagtcattct gagaatagtg tatgcggcga
ccgagttgct 8640cttgcccggc gtcaatacgg gataataccg cgccacatag
cagaacttta aaagtgctca 8700tcattggaaa acgttcttcg gggcgaaaac
tctcaaggat cttaccgctg ttgagatcca 8760gttcgatgta acccactcgt
gcacccaact gatcttcagc atcttttact ttcaccagcg 8820tttctgggtg
agcaaaaaca ggaaggcaaa atgccgcaaa aaagggaata agggcgacac
8880ggaaatgttg aatactcata ctcttccttt ttcaatatta ttgaagcatt
tatcagggtt 8940attgtctcat gagcggatac atatttgaat gtatttagaa
aaataaacaa ataggggttc 9000cgcgcacatt tccccgaaaa gtgccacctg
acgtcgacgg atcgggagat ctcccgatcc 9060cctatggtgc actctcagta
caatctgctc tgatgccgca tagttaagcc agtatctgct 9120ccctgcttgt
gtgttggagg tcgctgagta gtgcgcgagc aaaatttaag ctacaacaag
9180gcaaggcttg accgacaatt gcatgaagaa tctgcttagg
92203834DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 38ccctggccca ccctcgtgac caccttcacc tacg
343934DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 39gggaccgggt gggagcactg gtggaagtgg atgc
344040DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 40ccctggccca ccctcgtgac caccttcacc
tacggcgtgc 404140DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 41gggcacggga ccgggtggga
gcactggtgg aagtggatgc 404240DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 42cccgtgccct
ggcccaccct cgtgaccacc ttcacctacg 404340DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 43gggaccgggt gggagcactg gtggaagtgg atgccgcacg
404417DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 44cttcacctac ggcgtgc 174519DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 45cactggtgga agtggatgc 194619DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 46gtgaccacct tcacctacg 194717DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 47gaagtggatg ccgcacg 174853DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 48caccggcaag ctgcccgtgc cctggcccac cctcgtgacc
accttcacct acg 534953DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 49gtggccgttc
gacgggcacg ggaccgggtg ggagcactgg tggaagtgga tgc 535059DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 50caccggcaag ctgcccgtgc cctggcccac cctcgtgacc
accttcacct acggcgtgc 595159DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 51gacgtggtgg
ccgttcgacg ggcacgggac cgggtgggag cactggtgga agtggatgc
595259DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 52ctgcaccacc ggcaagctgc ccgtgccctg
gcccaccctc gtgaccacct tcacctacg 595359DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 53gtggccgttc gacgggcacg ggaccgggtg ggagcactgg
tggaagtgga tgccgcacg 595497DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 54catctgcacc
accggcaagc tgcccgtgcc ctggcccacc ctcgtgacca ccttcaccta 60cggcgtgcag
tgcttcgccc gctaccccga ccacatg 9755400DNAArtificial
SequenceDescription of Artificial Sequence Synthetic polynucleotide
55atggtgagca agggcgagga gctgttcacc ggggtggtgc ccatcctggt cgagctggac
60ggcgacgtaa acggccacaa gttcagcgtg tccggcgagg gcgagggcga tgccacctac
120ggcaagctga ccctgaagtt catctgcacc accggcaagc tgcccgtgcc
ctggcccacc 180ctcgtgacca ccttcaccta cggcgtgcag tgcttcgccc
gctaccccga ccacatgaag 240cagcacgact tcttcaagtc cgccatgccc
gaaggctacg tccaggagcg caccatcttc 300ttcaaggacg acggcaacta
caagacccgc gccgaggtga agttcgaggg cgacaccctg 360gtgaaccgca
tcgagctgaa gggcatcgac ttcaaggagg 4005641RNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 56ccaguagcca gccccguccg uuuuagagcu augcuguuuu g
415785RNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 57ggaaccauuc aaaacagcau agcaaguuaa
aauaaggcua guccguuauc aacuugaaaa 60agggcaccga gucggugcuu uuuuu
8558104RNAArtificial SequenceDescription of Artificial Sequence
Synthetic polynucleotide 58gcauuucggu augcauauga augaguuuua
gagcuagaaa uagcaaguua aaauaaggcu 60aguccguuau caacuugaaa aaguggcacc
gagucggugc uuuu 1045923DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 59ccatcatatg
cataccgaaa tgc 236023DNAArtificial SequenceDescription of
Artificial Sequence Synthetic
oligonucleotidemodified_base(21)..(21)a, c, t, g, unknown or other
60gcatttcggt atgcatatga ngg 23611370PRTStreptococcus agalactiae
61Met Asn Lys Pro Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val1
5 10 15Gly Trp Ser Ile Ile Thr Asp Asp Tyr Lys Val Pro Ala Lys Lys
Met 20 25 30Arg Val Leu Gly Asn Thr Asp Lys Glu Tyr Ile Lys Lys Asn
Leu Ile 35 40 45Gly Ala Leu Leu Phe Asp Gly Gly Asn Thr Ala Ala Asp
Arg Arg Leu 50 55 60Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Arg
Asn Arg Ile Leu65 70 75 80Tyr Leu Gln Glu Ile Phe Ala Glu Glu Met
Ser Lys Val Asp Asp Ser 85 90 95Phe Phe His Arg Leu Glu Asp Ser Phe
Leu Val Glu Glu Asp Lys Arg 100 105 110Gly Ser Lys Tyr Pro Ile Phe
Ala Thr Met Gln Glu Glu Lys Tyr Tyr 115 120 125His Glu Lys Phe Pro
Thr Ile Tyr His Leu Arg Lys Glu Leu Ala Asp 130 135 140Lys Lys Glu
Lys Ala Asp Leu Arg Leu Ile Tyr Leu Ala Leu Ala His145 150 155
160Ile Ile Lys Phe Arg Gly His Phe Leu Ile Glu Asp Asp Arg Phe Asp
165 170 175Val Arg Asn Thr Asp Ile Gln Lys Gln Tyr Gln Ala Phe Leu
Glu Ile 180 185 190Phe Asp Thr Thr Phe Glu Asn Asn Asp Leu Leu Ser
Gln Asn Val Asp 195 200 205Val Glu Ala Ile Leu Thr Asp Lys Ile Ser
Lys Ser Ala Lys Lys Asp 210 215 220Arg Ile Leu Ala Arg Tyr Pro Asn
Gln Lys Ser Thr Gly Ile Phe Ala225 230 235 240Glu Phe Leu Lys Leu
Ile Val Gly Asn Gln Ala Asp Phe Lys Lys His 245 250 255Phe Asn Leu
Glu Asp Lys Thr Pro Leu Gln Phe Ala Lys Asp Ser Tyr 260 265 270Asp
Glu Asp Leu Glu Asn Leu Leu Gly Gln Ile Gly Asp Glu Phe Ala 275 280
285Asp Leu Phe Ser Ala Ala Lys Lys Leu Tyr Asp Ser Val Leu Leu Ser
290 295 300Gly Ile Leu Thr Val Thr Asp Leu Ser Thr Lys Ala Pro Leu
Ser Ala305 310 315 320Ser Met Ile Gln Arg Tyr Asp Glu His Arg Glu
Asp Leu Lys Gln Leu 325 330 335Lys Gln Phe Val Lys Ala Ser Leu Pro
Glu Lys Tyr Gln Glu Ile Phe 340 345 350Ala Asp Ser Ser Lys Asp Gly
Tyr Ala Gly Tyr Ile Glu Gly Lys Thr 355 360 365Asn Gln Glu Ala Phe
Tyr Lys Tyr Leu Ser Lys Leu Leu Thr Lys Gln 370 375 380Glu Gly Ser
Glu Tyr Leu Leu Glu Lys Ile Lys Asn Glu Asp Phe Leu385 390 395
400Arg Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Val His
405 410 415Leu Thr Glu Leu Arg Ala Ile Ile Arg Arg Gln Ser Glu Tyr
Tyr Pro 420 425 430Phe Leu Lys Glu Asn Leu Asp Arg Ile Glu Lys Ile
Leu Thr Phe Arg 435 440 445Ile Pro Tyr Tyr Val Gly Pro Leu Ala Arg
Glu Lys Ser Asp Phe Ala 450 455 460Trp Met Thr Arg Lys Thr Asp Asp
Ser Ile Arg Pro Trp Asn Phe Glu465 470 475 480Asp Leu Val Asp Lys
Glu Lys Ser Ala Glu Ala Phe Ile His Arg Met 485 490 495Thr Asn Asn
Asp Leu Tyr Leu Pro Glu Glu Lys Val Leu Pro Lys His 500 505 510Ser
Leu Ile Tyr Glu Lys Phe Thr Val Tyr Asn Glu Leu Thr Lys Val 515 520
525Arg Phe Leu Ala Glu Gly Phe Lys Asp Phe Gln Phe Leu Asn Arg Lys
530 535 540Gln Lys Glu Thr Ile Phe Asn Ser Leu Phe Lys Glu Lys Arg
Lys Val545 550 555 560Thr Glu Lys Asp Ile Ile Ser Phe Leu Asn Lys
Val Asp Gly Tyr Glu 565 570 575Gly Ile Ala Ile Lys Gly Ile Glu Lys
Gln Phe Asn Ala Ser Leu Ser 580 585 590Thr Tyr His Asp Leu Lys Lys
Ile Leu Gly Lys Asp Phe Leu Asp Asn 595 600 605Thr Asp Asn Glu Leu
Ile Leu Glu Asp Ile Val Gln Thr Leu Thr Leu 610 615 620Phe Glu Asp
Arg Glu Met Ile Arg Lys Arg Leu Asp Ile Tyr Lys Asp625 630 635
640Phe Phe Thr Glu Ser Gln Leu Lys Lys Leu Tyr Arg Arg His Tyr Thr
645 650 655Gly Trp Glu Arg Leu Ser Ala Lys Leu Ile Asn Gly Ile Arg
Asn Lys 660 665 670Glu Asn Gln Lys Thr Ile Leu Asp Tyr Leu Ile Asp
Asp Gly Ser Ala 675 680 685Asn Arg Asn Phe Met Gln Leu Ile Lys Asp
Ala Gly Leu Ser Phe Lys 690 695 700Pro Ile Ile Asp Lys Ala Arg Thr
Gly Ser His Leu Asp Asn Leu Lys705 710 715 720Glu Val Val Gly Glu
Leu Ala Gly Ser Pro Ala Ile Lys Lys Gly Ile 725 730 735Leu Gln Ser
Leu Lys Ile Val Asp Glu Leu Val Lys Val Met Gly Tyr 740 745 750Glu
Pro Glu Gln Ile Val Val Glu Met Ala Arg Glu Asn Gln Thr Thr 755 760
765Ala Lys Gly Leu Ser Arg Ser Arg Gln Arg Leu Thr Thr Leu Arg Glu
770 775 780Ser Leu Ala Asn Leu Lys Ser Asn Ile Leu Glu Glu Lys Lys
Pro Lys785 790 795 800Tyr Val Lys Asp Gln Val Glu Asn His His Leu
Ser Asp Asp Arg Leu 805 810 815Phe Leu Tyr Tyr Leu Gln Asn Gly Lys
Asp Met Tyr Thr Asp Asp Glu 820 825 830Leu Asp Ile Asp Asn Leu Ser
Gln Tyr Asp Ile Asp His Ile Ile Pro 835 840 845Gln Ala Phe Ile Lys
Asp Asp Ser Ile Asp Asn Arg Val Leu Val Ser 850 855 860Ser Ala Lys
Asn Arg Gly Lys Ser Asp Asp Val Pro Ser Leu Glu Ile865 870 875
880Val Lys Asp Cys Lys Val Phe Trp Lys Lys Leu Leu Asp Ala Lys Leu
885 890 895Met Ser Gln Arg Lys Tyr Asp Asn Leu Thr Lys Ala Glu Arg
Gly Gly 900 905 910Leu Thr Ser Asp Asp Lys Ala Arg Phe Ile Gln Arg
Gln Leu Val Glu 915 920 925Thr Arg Gln Ile Thr Lys His Val Ala Arg
Ile Leu Asp Glu Arg Phe 930 935 940Asn Asn Glu Leu Asp Ser Lys Gly
Arg Arg Ile Arg Lys Val Lys Ile945 950 955 960Val Thr Leu Lys Ser
Asn Leu Val Ser Asn Phe Arg Lys Glu Phe Gly 965 970 975Phe Tyr Lys
Ile Arg Glu Val Asn Asn Tyr His His Ala His Asp Ala 980 985 990Tyr
Leu Asn Ala Val Val Ala Lys Ala Ile Leu Thr Lys Tyr Pro Gln 995
1000 1005Leu Glu Pro Glu Phe Val Tyr Gly Asp Tyr Pro Lys Tyr Asn
Ser 1010 1015 1020Tyr Lys Thr Arg Lys Ser Ala Thr Glu Lys Leu Phe
Phe Tyr Ser 1025 1030 1035Asn Ile Met Asn Phe Phe Lys Thr Lys Val
Thr Leu Ala Asp Gly 1040 1045 1050Thr Val Val Val Lys Asp Asp Ile
Glu Val Asn Asn Asp Thr Gly 1055 1060 1065Glu Ile Val Trp Asp Lys
Lys Lys His Phe Ala Thr Val Arg Lys 1070 1075 1080Val Leu Ser Tyr
Pro Gln Val Asn Ile Val Lys Lys Thr Glu Val 1085 1090 1095Gln Thr
Gly Gly Phe Ser Lys Glu Ser Ile Leu Ala His Gly Asn 1100 1105
1110Ser Asp Lys Leu Ile Pro Arg Lys Thr Lys Asp Ile Tyr Leu Asp
1115 1120 1125Pro Lys Lys Tyr Gly Gly Phe Asp Ser Pro Ile Val Ala
Tyr Ser 1130 1135 1140Val Leu Val Val Ala Asp Ile Lys Lys Gly Lys
Ala Gln Lys Leu 1145 1150 1155Lys Thr Val Thr Glu Leu Leu Gly Ile
Thr Ile Met Glu Arg Ser 1160 1165 1170Arg Phe Glu Lys Asn Pro Ser
Ala Phe Leu Glu Ser Lys Gly Tyr 1175 1180 1185Leu Asn Ile Arg Thr
Asp Lys Leu Ile Ile Leu Pro Lys Tyr Ser 1190 1195 1200Leu Phe Glu
Leu Glu Asn Gly Arg Arg Arg Leu Leu Ala Ser Ala 1205 1210 1215Gly
Glu Leu Gln Lys Gly Asn Glu Leu Ala Leu Pro Thr Gln Tyr 1220 1225
1230Met Lys Phe Leu Tyr Leu Ala Ser Arg Tyr Asn Glu Leu Lys Gly
1235 1240 1245Lys Pro Glu Glu Ile Glu Gln Lys Gln Glu Phe Val Val
Gln His 1250 1255 1260Val Ser Tyr Phe Asp Asp Ile Leu Gln Ile Ile
Asn Asp Phe Ser 1265 1270 1275Asn Arg Val Ile Leu Ala Asp Ala Asn
Leu Glu Lys Ile Asn Lys 1280 1285 1290Leu Tyr Gln Asp Asn Lys Glu
Asn Ile Pro Val Asp Glu Leu Ala 1295 1300 1305Asn Asn Ile Ile Asn
Leu Phe Thr Phe Thr Ser Leu Gly Ala Pro 1310 1315 1320Ala Ala Phe
Lys Phe Phe Asp Lys Ile Val Asp Arg Lys Arg Tyr 1325 1330 1335Thr
Ser Thr Lys Glu Val Leu Asn Ser Thr Leu Ile His Gln Ser 1340 1345
1350Ile Thr Gly Leu Tyr Glu Thr Arg Ile Asp Leu Gly Lys Leu Gly
1355 1360 1365Glu Gly 1370621345PRTStreptococcus mutans 62Met Lys
Lys Pro Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val1 5 10 15Gly
Trp Ala Val Val Thr Asp Asp Tyr Lys Val Pro Ala Lys Lys Met 20 25
30Lys Val Leu Gly Asn Thr Asp Lys Ser His Ile Lys Lys Asn Leu Leu
35 40 45Gly Ala Leu Leu Phe Asp Ser Gly Asn Thr Ala Glu Asp Arg Arg
Leu 50 55 60Lys Arg Thr Ala Arg Arg Arg Tyr Thr Arg Arg Arg Asn Arg
Ile Leu65 70 75 80Tyr Leu Gln Glu Ile Phe Ser Glu Glu Met Gly Lys
Val Asp Asp Ser 85 90 95Phe Phe His Arg Leu Glu Asp Ser Phe Leu Val
Thr Glu Asp Lys Arg 100 105 110Gly Glu Arg His Pro Ile Phe Gly Asn
Leu Glu Glu Glu Val Lys Tyr 115 120 125His Glu Asn Phe Pro Thr Ile
Tyr His Leu Arg Gln Tyr Leu Ala Asp 130 135 140Asn
Pro Glu Lys Val Asp Leu Arg Leu Val Tyr Leu Ala Leu Ala His145 150
155 160Ile Ile Lys Phe Arg Gly His Phe Leu Ile Glu Gly Lys Phe Asp
Thr 165 170 175Arg Asn Asn Asp Val Gln Arg Leu Phe Gln Glu Phe Leu
Ala Val Tyr 180 185 190Asp Asn Thr Phe Glu Asn Ser Ser Leu Gln Glu
Gln Asn Val Gln Val 195 200 205Glu Glu Ile Leu Thr Asp Lys Ile Ser
Lys Ser Ala Lys Lys Asp Arg 210 215 220Val Leu Lys Leu Phe Pro Asn
Glu Lys Ser Asn Gly Arg Phe Ala Glu225 230 235 240Phe Leu Lys Leu
Ile Val Gly Asn Gln Ala Asp Phe Lys Lys His Phe 245 250 255Glu Leu
Glu Glu Lys Ala Pro Leu Gln Phe Ser Lys Asp Thr Tyr Glu 260 265
270Glu Glu Leu Glu Val Leu Leu Ala Gln Ile Gly Asp Asn Tyr Ala Glu
275 280 285Leu Phe Leu Ser Ala Lys Lys Leu Tyr Asp Ser Ile Leu Leu
Ser Gly 290 295 300Ile Leu Thr Val Thr Asp Val Ser Thr Lys Ala Pro
Leu Ser Ala Ser305 310 315 320Met Ile Gln Arg Tyr Asn Glu His Gln
Met Asp Leu Ala Gln Leu Lys 325 330 335Gln Phe Ile Arg Gln Lys Leu
Ser Asp Lys Tyr Asn Glu Val Phe Ser 340 345 350Asp Val Ser Lys Asp
Gly Tyr Ala Gly Tyr Ile Asp Gly Lys Thr Asn 355 360 365Gln Glu Ala
Phe Tyr Lys Tyr Leu Lys Gly Leu Leu Asn Lys Ile Glu 370 375 380Gly
Ser Gly Tyr Phe Leu Asp Lys Ile Glu Arg Glu Asp Phe Leu Arg385 390
395 400Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro His Gln Ile His
Leu 405 410 415Gln Glu Met Arg Ala Ile Ile Arg Arg Gln Ala Glu Phe
Tyr Pro Phe 420 425 430Leu Ala Asp Asn Gln Asp Arg Ile Glu Lys Ile
Leu Thr Phe Arg Ile 435 440 445Pro Tyr Tyr Val Gly Pro Leu Ala Arg
Gly Lys Ser Asp Phe Ala Trp 450 455 460Leu Ser Arg Lys Ser Ala Asp
Lys Ile Thr Pro Trp Asn Phe Asp Glu465 470 475 480Ile Val Asp Lys
Glu Ser Ser Ala Glu Ala Phe Ile Asn Arg Met Thr 485 490 495Asn Tyr
Asp Leu Tyr Leu Pro Asn Gln Lys Val Leu Pro Lys His Ser 500 505
510Leu Leu Tyr Glu Lys Phe Thr Val Tyr Asn Glu Leu Thr Lys Val Lys
515 520 525Tyr Lys Thr Glu Gln Gly Lys Thr Ala Phe Phe Asp Ala Asn
Met Lys 530 535 540Gln Glu Ile Phe Asp Gly Val Phe Lys Val Tyr Arg
Lys Val Thr Lys545 550 555 560Asp Lys Leu Met Asp Phe Leu Glu Lys
Glu Phe Asp Glu Phe Arg Ile 565 570 575Val Asp Leu Thr Gly Leu Asp
Lys Glu Asn Lys Val Phe Asn Ala Ser 580 585 590Tyr Gly Thr Tyr His
Asp Leu Cys Lys Ile Leu Asp Lys Asp Phe Leu 595 600 605Asp Asn Ser
Lys Asn Glu Lys Ile Leu Glu Asp Ile Val Leu Thr Leu 610 615 620Thr
Leu Phe Glu Asp Arg Glu Met Ile Arg Lys Arg Leu Glu Asn Tyr625 630
635 640Ser Asp Leu Leu Thr Lys Glu Gln Val Lys Lys Leu Glu Arg Arg
His 645 650 655Tyr Thr Gly Trp Gly Arg Leu Ser Ala Glu Leu Ile His
Gly Ile Arg 660 665 670Asn Lys Glu Ser Arg Lys Thr Ile Leu Asp Tyr
Leu Ile Asp Asp Gly 675 680 685Asn Ser Asn Arg Asn Phe Met Gln Leu
Ile Asn Asp Asp Ala Leu Ser 690 695 700Phe Lys Glu Glu Ile Ala Lys
Ala Gln Val Ile Gly Glu Thr Asp Asn705 710 715 720Leu Asn Gln Val
Val Ser Asp Ile Ala Gly Ser Pro Ala Ile Lys Lys 725 730 735Gly Ile
Leu Gln Ser Leu Lys Ile Val Asp Glu Leu Val Lys Ile Met 740 745
750Gly His Gln Pro Glu Asn Ile Val Val Glu Met Ala Arg Glu Asn Gln
755 760 765Phe Thr Asn Gln Gly Arg Gln Asn Ser Gln Gln Arg Leu Lys
Gly Leu 770 775 780Thr Asp Ser Ile Lys Glu Phe Gly Ser Gln Ile Leu
Lys Glu His Pro785 790 795 800Val Glu Asn Ser Gln Leu Gln Asn Asp
Arg Leu Phe Leu Tyr Tyr Leu 805 810 815Gln Asn Gly Arg Asp Met Tyr
Thr Gly Glu Glu Leu Asp Ile Asp Tyr 820 825 830Leu Ser Gln Tyr Asp
Ile Asp His Ile Ile Pro Gln Ala Phe Ile Lys 835 840 845Asp Asn Ser
Ile Asp Asn Arg Val Leu Thr Ser Ser Lys Glu Asn Arg 850 855 860Gly
Lys Ser Asp Asp Val Pro Ser Glu Asp Val Val Arg Lys Met Lys865 870
875 880Ser Tyr Trp Ser Lys Leu Leu Ser Ala Lys Leu Ile Thr Gln Arg
Lys 885 890 895Phe Asp Asn Leu Thr Lys Ala Glu Arg Gly Gly Leu Thr
Asp Asp Asp 900 905 910Lys Ala Gly Phe Ile Lys Arg Gln Leu Val Glu
Thr Arg Gln Ile Thr 915 920 925Lys His Val Ala Arg Ile Leu Asp Glu
Arg Phe Tyr Thr Glu Thr Asp 930 935 940Glu Asn Asn Lys Lys Ile Arg
Gln Val Lys Ile Val Thr Leu Lys Ser945 950 955 960Asn Leu Val Ser
Asn Phe Arg Lys Glu Phe Glu Leu Tyr Lys Val Arg 965 970 975Glu Ile
Asn Asp Tyr His His Ala His Asp Ala Tyr Leu Asn Ala Val 980 985
990Ile Gly Lys Ala Leu Leu Gly Val Tyr Pro Gln Leu Glu Pro Glu Phe
995 1000 1005Val Tyr Gly Asp Tyr Pro His Phe His Gly His Lys Glu
Asn Lys 1010 1015 1020Ala Thr Ala Lys Lys Phe Phe Tyr Ser Asn Ile
Met Asn Phe Phe 1025 1030 1035Lys Lys Asp Asp Val Arg Thr Asp Lys
Asn Gly Glu Ile Ile Trp 1040 1045 1050Lys Lys Asp Glu His Ile Ser
Asn Ile Lys Lys Val Leu Ser Tyr 1055 1060 1065Pro Gln Val Asn Ile
Val Lys Lys Val Glu Glu Gln Thr Gly Gly 1070 1075 1080Phe Ser Lys
Glu Ser Ile Leu Pro Lys Gly Asn Ser Asp Lys Leu 1085 1090 1095Ile
Pro Arg Lys Thr Lys Lys Phe Tyr Trp Asp Thr Lys Lys Tyr 1100 1105
1110Gly Gly Phe Asp Ser Pro Ile Val Ala Tyr Ser Ile Leu Val Ile
1115 1120 1125Ala Asp Ile Glu Lys Gly Lys Ser Lys Lys Leu Lys Thr
Val Lys 1130 1135 1140Ala Leu Val Gly Val Thr Ile Met Glu Lys Met
Thr Phe Glu Arg 1145 1150 1155Asp Pro Val Ala Phe Leu Glu Arg Lys
Gly Tyr Arg Asn Val Gln 1160 1165 1170Glu Glu Asn Ile Ile Lys Leu
Pro Lys Tyr Ser Leu Phe Lys Leu 1175 1180 1185Glu Asn Gly Arg Lys
Arg Leu Leu Ala Ser Ala Arg Glu Leu Gln 1190 1195 1200Lys Gly Asn
Glu Ile Val Leu Pro Asn His Leu Gly Thr Leu Leu 1205 1210 1215Tyr
His Ala Lys Asn Ile His Lys Val Asp Glu Pro Lys His Leu 1220 1225
1230Asp Tyr Val Asp Lys His Lys Asp Glu Phe Lys Glu Leu Leu Asp
1235 1240 1245Val Val Ser Asn Phe Ser Lys Lys Tyr Thr Leu Ala Glu
Gly Asn 1250 1255 1260Leu Glu Lys Ile Lys Glu Leu Tyr Ala Gln Asn
Asn Gly Glu Asp 1265 1270 1275Leu Lys Glu Leu Ala Ser Ser Phe Ile
Asn Leu Leu Thr Phe Thr 1280 1285 1290Ala Ile Gly Ala Pro Ala Thr
Phe Lys Phe Phe Asp Lys Asn Ile 1295 1300 1305Asp Arg Lys Arg Tyr
Thr Ser Thr Thr Glu Ile Leu Asn Ala Thr 1310 1315 1320Leu Ile His
Gln Ser Ile Thr Gly Leu Tyr Glu Thr Arg Ile Asp 1325 1330 1335Leu
Ser Lys Leu Gly Gly Asp 1340 1345631347PRTStreptococcus plurextorum
63Met Gln Lys Thr Tyr Ser Ile Gly Leu Asp Ile Gly Thr Asn Ser Val1
5 10 15Gly Phe Ser Val Val Thr Asp Asp Tyr Lys Val Pro Ser Lys Lys
Met 20 25 30Lys Val Asn Gly Asn Thr Asp Lys Lys Tyr Leu Lys Lys Asn
Leu Leu 35 40 45Gly Thr Leu Leu Phe Asp Ser Gly Glu Thr Ala Ala Gly
Thr Arg Met 50 55 60Arg Arg Thr Thr Arg Arg Arg Tyr Val Arg Arg Asn
Asn Arg Leu Arg65 70 75 80Tyr Leu Gln Glu Ile Phe Ala Asp Gln Met
Glu Gln Ile Asp Pro Asn 85 90 95Phe Phe His Arg Leu Lys Glu Ser Phe
Leu Asp Glu Glu Asp Lys Gln 100 105 110Phe Glu Gln His Pro Ile Phe
Gly Thr Leu Ala Glu Glu Val Ala Tyr 115 120 125His Gln Gln Phe Pro
Thr Ile Tyr His Leu Arg Lys His Leu Ala Asp 130 135 140Ser Lys Glu
Gln Val Asp Leu Arg Leu Val Tyr Met Ala Leu Ala His145 150 155
160Ile Ile Lys Tyr Arg Gly His Phe Leu Ile Glu Gly Gly Leu Glu Ser
165 170 175Gln Ala Val Gly Ile Gln Gln Leu Phe Asp Glu Phe Val Gln
Val Tyr 180 185 190Asp Ser Val Phe Glu Gly Ser Asp Leu Val Ser Ile
His Ala Glu Val 195 200 205Glu Pro Ile Leu Val Asp Lys Leu Ser Lys
Ser Val Lys Lys Asp Arg 210 215 220Val Met Gln Leu Phe Pro Thr Glu
Lys Ser Asn Gly Asn Phe Ala Glu225 230 235 240Phe Met Lys Leu Ile
Val Gly Asn Gln Ala Asp Phe Lys Lys Val Phe 245 250 255Ser Leu Asp
Glu Lys Ala Val Leu Gln Leu Ser Lys Asp Thr Tyr Glu 260 265 270Glu
Glu Leu Ala Asp Leu Leu Gly Lys Val Gly Asp Asp Tyr Leu Asp 275 280
285Leu Phe His Ala Ala Lys Arg Leu Tyr Asp Ala Val Leu Leu Ala Gly
290 295 300Ile Ile Thr Ser Gln Asp Ile Ala Thr Lys Ala Pro Leu Ser
Ala Ser305 310 315 320Met Val Gln Arg Tyr Glu Glu His Gln Ser Asp
Leu Lys Ala Leu Lys 325 330 335Lys His Ile Pro Asn Tyr Lys Pro Asp
Glu Arg Lys Leu Tyr Lys Glu 340 345 350Met Phe Asn Asp Ser Thr Lys
Asn Gly Tyr Ala Gly Tyr Ile Glu Gly 355 360 365Gly Val Lys Gln Glu
Glu Phe Tyr Lys Tyr Thr Lys Ala Leu Leu Ser 370 375 380Glu Ile Glu
Asn Ser Gln Tyr Phe Ile Asp Lys Ile Glu Arg Glu Asp385 390 395
400Phe Leu Arg Lys Gln Arg Thr Phe Asp Asn Gly Ala Ile Pro His Gln
405 410 415Ile His Leu Gln Glu Leu Lys Ala Ile Val Arg Arg Gln Gly
Glu His 420 425 430Tyr Pro Phe Leu Lys Glu Glu Gln His Lys Ile Glu
Ala Leu Leu Thr 435 440 445Phe Arg Ile Pro Tyr Tyr Val Gly Pro Leu
Ala Arg Gly Asn Ser Arg 450 455 460Phe Ala Trp Ala Val Arg Lys Ser
Asn Glu Lys Ile Thr Pro Trp Asn465 470 475 480Phe Glu Glu Ile Ile
Asp Lys Glu Glu Ser Ala Arg Lys Phe Ile Glu 485 490 495Arg Met Thr
Asn Val Asp Leu Tyr Leu Pro Asp Glu Lys Val Leu Pro 500 505 510Lys
His Ser Phe Leu Tyr Glu Lys Phe Ala Val Phe Asn Glu Leu Thr 515 520
525Lys Val Lys Tyr Ile Thr Glu Gln Gly Lys Glu Glu Phe Phe Asp Cys
530 535 540His Leu Lys Arg Glu Ile Phe Glu Gln Val Phe Lys Asn Ser
Arg Lys545 550 555 560Val Lys Lys Lys Asp Leu Leu Asn Phe Leu Asp
Lys Glu Phe Glu Glu 565 570 575Phe Arg Ile Val Asp Ile Thr Gly Leu
Asp Ser Glu Lys Gln Glu Phe 580 585 590Asn Ala Ser Leu Gly Thr Tyr
His Asp Leu Lys Lys Ile Leu Asp Lys 595 600 605Asp Phe Leu Asp Asp
Val Ala Asn Glu His Leu Leu Glu Glu Leu Ile 610 615 620Leu Thr Leu
Thr Leu Phe Glu Asp Arg Glu Met Ile Arg Lys Arg Leu625 630 635
640Ser Lys Tyr Ser Glu Ala Leu Thr Lys Glu Gln Leu Lys Lys Leu Glu
645 650 655Arg Arg His Tyr Thr Gly Trp Gly Arg Leu Ser Ala Lys Leu
Leu Asn 660 665 670Gly Ile Arg His Lys Ala Thr Asn Lys Thr Ile Leu
Asp Tyr Leu Met 675 680 685Asp Asp Gly Gln Ile Asn Arg Asn Phe Met
Gln Leu Ile His Asp Asp 690 695 700Gly Leu Asp Phe Lys Thr Ile Ile
Ser Glu Ala Gln Val Ile Gly Glu705 710 715 720Arg Asp Asp Leu Lys
Ala Ile Val Asp Asp Ile Ala Gly Ser Pro Ala 725 730 735Ile Lys Lys
Gly Ile Leu Gln Ser Leu Lys Val Val Glu Glu Leu Val 740 745 750Ser
Ile Met Gly His Asn Pro Glu Ser Ile Ile Ile Glu Met Ala Arg 755 760
765Glu Asn Gln Thr Thr Gln Lys Gly Arg Lys Asn Ser Gln Gln Arg Leu
770 775 780Thr Gly Leu Thr Asn Ser Ile Arg Glu Leu Gly Ser Asp Ile
Leu Lys785 790 795 800Glu Phe Pro Val Asp Asn Ser Gln Leu Gln Asn
Asp Arg Leu Tyr Leu 805 810 815Tyr Tyr Leu Gln Asn Gly Lys Asp Met
Tyr Thr Gly Glu Thr Leu Asn 820 825 830Ile Asp Gln Leu Ser His Tyr
Asp Ile Asp His Ile Ile Pro Gln Ser 835 840 845Phe Ile Lys Asp Asp
Ser Leu Asp Asn Arg Val Leu Thr Ser Ser Lys 850 855 860Ser Asn Arg
Gly Lys Ser Asp Ser Val Pro Ser Gln Glu Ile Val Gln865 870 875
880Lys Met Lys Pro Phe Trp Lys Lys Leu Arg Asp Ala Gln Leu Ile Ser
885 890 895Lys Arg Lys Phe Asp Asn Leu Thr Lys Ser Glu Arg Gly Gly
Leu Ser 900 905 910Gln Glu Asp Lys Ala Gly Phe Ile Lys Arg Gln Leu
Val Glu Thr Arg 915 920 925Gln Ile Thr Lys His Val Ala Arg Ile Leu
Asp Glu Arg Phe Asn Gln 930 935 940Lys Arg Asp Asp Asn Asn Lys Leu
Ile Arg Asp Val Lys Ile Ile Thr945 950 955 960Leu Lys Ser Asn Leu
Val Ser Gln Phe Arg Lys Glu Phe Glu Leu Tyr 965 970 975Lys Ile Arg
Glu Leu Asn Asp Tyr His His Ala His Asp Ala Tyr Leu 980 985 990Asn
Ala Val Val Gly Lys Ala Leu Leu Ala Lys Tyr Pro Gln Leu Glu 995
1000 1005Ala Glu Phe Val Phe Gly Asp Tyr Pro Lys Tyr Asn Ser Tyr
Lys 1010 1015 1020Glu Arg Met Thr Ala Thr Gln Lys Val Leu Phe Tyr
Ser Asn Ile 1025 1030 1035Leu Asn Phe Leu Lys Asp Gly Asn Lys His
Gly Asn Glu Asp Gly 1040 1045 1050Glu Val Ile Trp Asp Pro Asn Tyr
His Leu Pro Met Ile Lys Lys 1055 1060 1065Val Leu Ser Tyr Pro Gln
Val Asn Ile Val Lys Lys Thr Glu Ile 1070 1075 1080Gln Thr Gly Gly
Phe Ser Lys Glu Ser Ile Leu Pro Lys Gly Asp 1085 1090 1095Ser Asp
Lys Leu Ile Arg Arg Lys Asn Asn Trp Asp Pro Lys Lys 1100 1105
1110Tyr Gly Gly Phe Asp Ser Pro Thr Val Ala Tyr Ser Val Leu Val
1115 1120 1125Ile Ala Asp Val Ala Lys Gly Lys Ala Gln Lys Leu Lys
Thr Val 1130 1135 1140Lys Glu Leu Val Gly Ile Thr Ile Met Glu Arg
Ser Ala Phe Glu 1145 1150 1155Lys Asn Pro Ile Val Phe Leu Glu Ser
Lys Gly Tyr Gln Asn Ile 1160 1165 1170Gln Glu Lys Asn Ile Ile Lys
Leu Pro Lys Tyr Ser Leu Phe Glu 1175 1180 1185Leu Glu Glu Gly Arg
Arg Arg Leu Leu Ala Ser Ala Ile Glu Leu 1190 1195 1200Gln Lys Gly
Asn Gln Leu Val Leu Ser Gln Glu Gln Ile Asn Leu 1205 1210 1215Leu
Tyr His Ala Gln Arg Val Lys Asn Leu Glu Gln Pro Glu His 1220 1225
1230Leu Arg Tyr Val Glu Glu His Lys Ala Glu Phe Glu Val Ile Leu
1235 1240 1245Asn Thr Leu Leu Ile Ala Ala Glu Arg Tyr Ile Leu
Lys
Pro Lys 1250 1255 1260Val Ile Glu Met Ile Lys Lys Ala Leu Glu Ser
Asn Gln Leu Asp 1265 1270 1275Ile Thr Gln Tyr Ala Glu Ser Phe Val
Asn Leu Leu Lys Phe Thr 1280 1285 1290Ala Phe Gly Ala Pro Gly Gly
Phe Lys Cys Phe Gly Ile Glu Ile 1295 1300 1305Lys Gln Ala Asn Leu
Arg Tyr Gln Thr Val Thr Glu Cys Leu Asn 1310 1315 1320Ala Thr Leu
Ile His Gln Tyr Val Thr Gly Leu Tyr Glu Thr Arg 1325 1330 1335Ile
Asp Leu Ser Lys Leu Gly Gly Glu 1340 1345641388PRTStreptococcus
thermophilus 64Met Thr Lys Pro Tyr Ser Ile Gly Leu Asp Ile Gly Thr
Asn Ser Val1 5 10 15Gly Trp Ala Val Ile Thr Asp Asn Tyr Lys Val Pro
Ser Lys Lys Met 20 25 30Lys Val Leu Gly Asn Thr Ser Lys Lys Tyr Ile
Lys Lys Asn Leu Leu 35 40 45Gly Val Leu Leu Phe Asp Ser Gly Ile Thr
Ala Glu Gly Arg Arg Leu 50 55 60Lys Arg Thr Ala Arg Arg Arg Tyr Thr
Arg Arg Arg Asn Arg Ile Leu65 70 75 80Tyr Leu Gln Glu Ile Phe Ser
Thr Glu Met Ala Thr Leu Asp Asp Ala 85 90 95Phe Phe Gln Arg Leu Asp
Asp Ser Phe Leu Val Pro Asp Asp Lys Arg 100 105 110Asp Ser Lys Tyr
Pro Ile Phe Gly Asn Leu Val Glu Glu Lys Ala Tyr 115 120 125His Asp
Glu Phe Pro Thr Ile Tyr His Leu Arg Lys Tyr Leu Ala Asp 130 135
140Ser Thr Lys Lys Ala Asp Leu Arg Leu Val Tyr Leu Ala Leu Ala
His145 150 155 160Met Ile Lys Tyr Arg Gly His Phe Leu Ile Glu Gly
Glu Phe Asn Ser 165 170 175Lys Asn Asn Asp Ile Gln Lys Asn Phe Gln
Asp Phe Leu Asp Thr Tyr 180 185 190Asn Ala Ile Phe Glu Ser Asp Leu
Ser Leu Glu Asn Ser Lys Gln Leu 195 200 205Glu Glu Ile Val Lys Asp
Lys Ile Ser Lys Leu Glu Lys Lys Asp Arg 210 215 220Ile Leu Lys Leu
Phe Pro Gly Glu Lys Asn Ser Gly Ile Phe Ser Glu225 230 235 240Phe
Leu Lys Leu Ile Val Gly Asn Gln Ala Asp Phe Arg Lys Cys Phe 245 250
255Asn Leu Asp Glu Lys Ala Ser Leu His Phe Ser Lys Glu Ser Tyr Asp
260 265 270Glu Asp Leu Glu Thr Leu Leu Gly Tyr Ile Gly Asp Asp Tyr
Ser Asp 275 280 285Val Phe Leu Lys Ala Lys Lys Leu Tyr Asp Ala Ile
Leu Leu Ser Gly 290 295 300Phe Leu Thr Val Thr Asp Asn Glu Thr Glu
Ala Pro Leu Ser Ser Ala305 310 315 320Met Ile Lys Arg Tyr Asn Glu
His Lys Glu Asp Leu Ala Leu Leu Lys 325 330 335Glu Tyr Ile Arg Asn
Ile Ser Leu Lys Thr Tyr Asn Glu Val Phe Lys 340 345 350Asp Asp Thr
Lys Asn Gly Tyr Ala Gly Tyr Ile Asp Gly Lys Thr Asn 355 360 365Gln
Glu Asp Phe Tyr Val Tyr Leu Lys Asn Leu Leu Ala Glu Phe Glu 370 375
380Gly Ala Asp Tyr Phe Leu Glu Lys Ile Asp Arg Glu Asp Phe Leu
Arg385 390 395 400Lys Gln Arg Thr Phe Asp Asn Gly Ser Ile Pro Tyr
Gln Ile His Leu 405 410 415Gln Glu Met Arg Ala Ile Leu Asp Lys Gln
Ala Lys Phe Tyr Pro Phe 420 425 430Leu Ala Lys Asn Lys Glu Arg Ile
Glu Lys Ile Leu Thr Phe Arg Ile 435 440 445Pro Tyr Tyr Val Gly Pro
Leu Ala Arg Gly Asn Ser Asp Phe Ala Trp 450 455 460Ser Ile Arg Lys
Arg Asn Glu Lys Ile Thr Pro Trp Asn Phe Glu Asp465 470 475 480Val
Ile Asp Lys Glu Ser Ser Ala Glu Ala Phe Ile Asn Arg Met Thr 485 490
495Ser Phe Asp Leu Tyr Leu Pro Glu Glu Lys Val Leu Pro Lys His Ser
500 505 510Leu Leu Tyr Glu Thr Phe Asn Val Tyr Asn Glu Leu Thr Lys
Val Arg 515 520 525Phe Ile Ala Glu Ser Met Arg Asp Tyr Gln Phe Leu
Asp Ser Lys Gln 530 535 540Lys Lys Asp Ile Val Arg Leu Tyr Phe Lys
Asp Lys Arg Lys Val Thr545 550 555 560Asp Lys Asp Ile Ile Glu Tyr
Leu His Ala Ile Tyr Gly Tyr Asp Gly 565 570 575Ile Glu Leu Lys Gly
Ile Glu Lys Gln Phe Asn Ser Ser Leu Ser Thr 580 585 590Tyr His Asp
Leu Leu Asn Ile Ile Asn Asp Lys Glu Phe Leu Asp Asp 595 600 605Ser
Ser Asn Glu Ala Ile Ile Glu Glu Ile Ile His Thr Leu Thr Ile 610 615
620Phe Glu Asp Arg Glu Met Ile Lys Gln Arg Leu Ser Lys Phe Glu
Asn625 630 635 640Ile Phe Asp Lys Ser Val Leu Lys Lys Leu Ser Arg
Arg His Tyr Thr 645 650 655Gly Trp Gly Lys Leu Ser Ala Lys Leu Ile
Asn Gly Ile Arg Asp Glu 660 665 670Lys Ser Gly Asn Thr Ile Leu Asp
Tyr Leu Ile Asp Asp Gly Ile Ser 675 680 685Asn Arg Asn Phe Met Gln
Leu Ile His Asp Asp Ala Leu Ser Phe Lys 690 695 700Lys Lys Ile Gln
Lys Ala Gln Ile Ile Gly Asp Glu Asp Lys Gly Asn705 710 715 720Ile
Lys Glu Val Val Lys Ser Leu Pro Gly Ser Pro Ala Ile Lys Lys 725 730
735Gly Ile Leu Gln Ser Ile Lys Ile Val Asp Glu Leu Val Lys Val Met
740 745 750Gly Gly Arg Lys Pro Glu Ser Ile Val Val Glu Met Ala Arg
Glu Asn 755 760 765Gln Tyr Thr Asn Gln Gly Lys Ser Asn Ser Gln Gln
Arg Leu Lys Arg 770 775 780Leu Glu Lys Ser Leu Lys Glu Leu Gly Ser
Lys Ile Leu Lys Glu Asn785 790 795 800Ile Pro Ala Lys Leu Ser Lys
Ile Asp Asn Asn Ala Leu Gln Asn Asp 805 810 815Arg Leu Tyr Leu Tyr
Tyr Leu Gln Asn Gly Lys Asp Met Tyr Thr Gly 820 825 830Asp Asp Leu
Asp Ile Asp Arg Leu Ser Asn Tyr Asp Ile Asp His Ile 835 840 845Ile
Pro Gln Ala Phe Leu Lys Asp Asn Ser Ile Asp Asn Lys Val Leu 850 855
860Val Ser Ser Ala Ser Asn Arg Gly Lys Ser Asp Asp Phe Pro Ser
Leu865 870 875 880Glu Val Val Lys Lys Arg Lys Thr Phe Trp Tyr Gln
Leu Leu Lys Ser 885 890 895Lys Leu Ile Ser Gln Arg Lys Phe Asp Asn
Leu Thr Lys Ala Glu Arg 900 905 910Gly Gly Leu Leu Pro Glu Asp Lys
Ala Gly Phe Ile Gln Arg Gln Leu 915 920 925Val Glu Thr Arg Gln Ile
Thr Lys His Val Ala Arg Leu Leu Asp Glu 930 935 940Lys Phe Asn Asn
Lys Lys Asp Glu Asn Asn Arg Ala Val Arg Thr Val945 950 955 960Lys
Ile Ile Thr Leu Lys Ser Thr Leu Val Ser Gln Phe Arg Lys Asp 965 970
975Phe Glu Leu Tyr Lys Val Cys Glu Ile Asn Asp Phe His His Ala His
980 985 990Asp Ala Tyr Leu Asn Ala Val Ile Ala Ser Ala Leu Leu Lys
Lys Tyr 995 1000 1005Pro Lys Leu Glu Pro Glu Phe Val Tyr Gly Asp
Tyr Pro Lys Tyr 1010 1015 1020Asn Ser Phe Arg Glu Arg Lys Ser Ala
Thr Glu Lys Val Tyr Phe 1025 1030 1035Tyr Ser Asn Ile Met Asn Ile
Phe Lys Lys Ser Ile Ser Leu Ala 1040 1045 1050Asp Gly Arg Val Ile
Glu Arg Pro Leu Ile Glu Val Asn Glu Glu 1055 1060 1065Thr Gly Glu
Ser Val Trp Asn Lys Glu Ser Asp Leu Ala Thr Val 1070 1075 1080Arg
Arg Val Leu Ser Tyr Pro Gln Val Asn Val Val Lys Lys Val 1085 1090
1095Glu Glu Gln Asn His Gly Leu Asp Arg Gly Lys Pro Lys Gly Leu
1100 1105 1110Phe Asn Ala Asn Leu Ser Ser Lys Pro Lys Pro Asn Ser
Asn Glu 1115 1120 1125Asn Leu Val Gly Ala Lys Glu Tyr Leu Asp Pro
Lys Lys Tyr Gly 1130 1135 1140Gly Tyr Ala Gly Ile Ser Asn Ser Phe
Ala Val Leu Val Lys Gly 1145 1150 1155Thr Ile Glu Lys Gly Ala Lys
Lys Lys Ile Thr Asn Val Leu Glu 1160 1165 1170Phe Gln Gly Ile Ser
Ile Leu Asp Arg Ile Asn Tyr Arg Lys Asp 1175 1180 1185Lys Leu Asn
Phe Leu Leu Glu Lys Gly Tyr Lys Asp Ile Glu Leu 1190 1195 1200Ile
Ile Glu Leu Pro Lys Tyr Ser Leu Phe Glu Leu Ser Asp Gly 1205 1210
1215Ser Arg Arg Met Leu Ala Ser Ile Leu Ser Thr Asn Asn Lys Arg
1220 1225 1230Gly Glu Ile His Lys Gly Asn Gln Ile Phe Leu Ser Gln
Lys Phe 1235 1240 1245Val Lys Leu Leu Tyr His Ala Lys Arg Ile Ser
Asn Thr Ile Asn 1250 1255 1260Glu Asn His Arg Lys Tyr Val Glu Asn
His Lys Lys Glu Phe Glu 1265 1270 1275Glu Leu Phe Tyr Tyr Ile Leu
Glu Phe Asn Glu Asn Tyr Val Gly 1280 1285 1290Ala Lys Lys Asn Gly
Lys Leu Leu Asn Ser Ala Phe Gln Ser Trp 1295 1300 1305Gln Asn His
Ser Ile Asp Glu Leu Cys Ser Ser Phe Ile Gly Pro 1310 1315 1320Thr
Gly Ser Glu Arg Lys Gly Leu Phe Glu Leu Thr Ser Arg Gly 1325 1330
1335Ser Ala Ala Asp Phe Glu Phe Leu Gly Val Lys Ile Pro Arg Tyr
1340 1345 1350Arg Asp Tyr Thr Pro Ser Ser Leu Leu Lys Asp Ala Thr
Leu Ile 1355 1360 1365His Gln Ser Val Thr Gly Leu Tyr Glu Thr Arg
Ile Asp Leu Ala 1370 1375 1380Lys Leu Gly Glu Gly
13856554DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 65tcgaattcca cttacggatc gttcaacgca
ggctacggtt agctacctag tagg 54
* * * * *