U.S. patent application number 16/736258 was filed with the patent office on 2020-10-15 for high efficiency, small volume nucleic acid synthesis.
The applicant listed for this patent is LIFE TECHNOLOGIES CORPORATION, THERMO FISHER SCIENTIFIC GENEART GMBH. Invention is credited to Federico KATZEN, Xiquan LIANG, Todd PETERSON, Thomas POEHMERER, Axel TREFZER.
Application Number | 20200325514 16/736258 |
Document ID | / |
Family ID | 1000004916696 |
Filed Date | 2020-10-15 |
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United States Patent
Application |
20200325514 |
Kind Code |
A1 |
PETERSON; Todd ; et
al. |
October 15, 2020 |
HIGH EFFICIENCY, SMALL VOLUME NUCLEIC ACID SYNTHESIS
Abstract
The disclosure generally relates to compositions and methods for
the production of nucleic acid molecules. In some aspects, the
invention allows for the microscale generation of nucleic acid
molecules, optionally followed by assembly of these nucleic acid
molecules into larger molecules. In some aspects, the invention
allows for efficient production of nucleic acid molecules (e.g.,
large nucleic acid molecules such as genomes).
Inventors: |
PETERSON; Todd; (Coronado,
CA) ; TREFZER; Axel; (Tegernheim, DE) ;
POEHMERER; Thomas; (Regensburg, DE) ; KATZEN;
Federico; (San Marcos, CA) ; LIANG; Xiquan;
(Escondido, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
LIFE TECHNOLOGIES CORPORATION
THERMO FISHER SCIENTIFIC GENEART GMBH |
Carlsbad
Regensburg |
CA |
US
DE |
|
|
Family ID: |
1000004916696 |
Appl. No.: |
16/736258 |
Filed: |
January 7, 2020 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
14775648 |
Sep 11, 2015 |
10563240 |
|
|
PCT/US14/29500 |
Mar 14, 2014 |
|
|
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16736258 |
|
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61784752 |
Mar 14, 2013 |
|
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
C12P 19/34 20130101;
C12N 15/1093 20130101; C12N 15/1031 20130101 |
International
Class: |
C12P 19/34 20060101
C12P019/34; C12N 15/10 20060101 C12N015/10 |
Claims
1. A method for assembling nucleic acid molecules, the method
comprising: (a) forming a reaction mixture of: (1) one or more
insert nucleic acid molecule, one or more acceptor nucleic acid
molecule, a plurality of oligonucleotides, wherein each
oligonucleotide shares sequence complementarity with (i) one
terminus of the insert nucleic acid molecule and the insertion site
of the acceptor nucleic acid molecule or (ii) one terminus of two
different insert nucleic acid molecules and wherein the number of
oligonucleotides is represented by the formula O=2+2I, where O is
the number of oligonucleotides and I is the number of insert
nucleic acid molecules, (2) a cell extract, and (3) a protein
composition comprising an exonuclease and, optionally, a
single-stranded binding protein, and (b) incubating the reaction
formed in (a) under conditions which allow for the introduction of
the insert nucleic acid molecule into the acceptor nucleic acid
molecule.
2. The method of claim 1, wherein the cell extract is obtained from
a single cellular organism selected from the group consisting of:
(a) Escherichia coli; (b) Bacillus subtilis; (c)
Schizosaccharomyces pombe; and (d) Saccharomyces cerevisiae.
3. The method of claim 2, wherein the Escherichia coli cells do not
express redET genes.
4. The method of claim 3, wherein the Escherichia coli cells are
strain DH10B.
5. The method of claim 1, wherein the exonuclease activity is
provided by a DNA polymerase.
6. The method of claim 1, wherein the single-stranded binding
protein is encoded by T4 gene 32.
7. The method of claim 1, wherein the number of inserts is three
and the number of oligonucleotides is six.
8. A method for the generation of an assembled nucleic acid
molecule, the method comprising: (a) synthesizing a plurality of
nucleic acid molecules, wherein each nucleic acid molecule is
prepared in a well of a plate in an average amount of from about
0.001 nanomoles to about 1,000 nanomoles; (b) combining the nucleic
acid molecules generated in (a) to produce a pool of
single-stranded nucleic acid molecules; (c) generating
double-stranded nucleic acid molecules from nucleic acid molecules
present in the pool of single-stranded nucleic acid molecules
formed in step (b) to generate a pool of double-stranded nucleic
acid molecules; (d) eliminating nucleic acid molecules which
contain sequence errors from the pool of double-stranded nucleic
acid molecules formed in step (c) to produce an error corrected
pool of double-stranded nucleic acid molecules; and (e)
simultaneously assembling the nucleic acid molecules in the error
corrected pool of double-stranded nucleic acid molecules and an
acceptor nucleic acid molecule to form the assembled nucleic acid
molecule.
9. The method of claim 8, wherein synthesis of the nucleic acid
molecules on the separate beads involves deblocking in step (a) by
an acid generated by in a redox reaction mixture in the wells of
the plate.
10. The method of claim 9, wherein the redox reaction mixture in
the wells of the plate contains hydroquinone.
11. The method of claim 8, wherein the joining in step (c) is
mediated by polymerase chain reaction.
12. The method of claim 8, wherein the accept nucleic acid molecule
is a linearized vector.
13. The method of claim 8, wherein the pool of double-stranded
nucleic acid molecules have blunt termini.
14. The method of claim 13, wherein at least two nucleic acid
molecules in the pool of double-stranded nucleic acid molecules
comprise a terminus comprising a region of sequence complementarity
with a terminus of the acceptor nucleic acid molecule.
15. The method of claim 14, wherein the region of sequence
complementarity is from twenty to sixty nucleotides in length.
16. A method for producing a plurality of nucleic acid molecules,
the method comprising: (a) synthesizing the plurality of nucleic
acid molecules on separate beads in wells of a plate, wherein each
well is configured to accommodate a single bead, wherein the volume
of each well is between 0.1 picoliters and 10 nanoliters, wherein
the wells comprise an electrode for the production of
electrochemically generated acid, wherein the nucleic acid
molecules synthesized on each bead are designed to have the same
nucleotide sequence, and wherein less than 1% of the purine bases
in the synthesizing a plurality of nucleic acid molecules are
depurinated; (b) selectively removing a plurality of beads from the
wells, wherein the beads removed from the wells comprise a first
set of individual nucleic acid molecules, wherein beads comprising
nucleic acid molecules that are not part of the first set of
individual nucleic acid molecules are not removed from their
respective wells; and (c) collecting the beads selectively removed
from wells in step (b) in a vessel.
17. The method of claim 16, further comprising: (e) selectively
removing a plurality of beads from the wells, wherein the beads
removed from the wells comprise a second set of individual nucleic
acid molecules, wherein beads comprising nucleic acid molecules
that are not part of the second set of individual nucleic acid
molecules are not removed from their respective wells; and (f)
collecting the beads selectively removed from wells in step (e) in
a vessel.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a division of U.S. application Ser. No.
14/775,648 filed on Sep. 11, 2015, which is a 371 National Phase
Application of International Application No. PCT/US2014/029500
filed Mar. 14, 2014, which claims priority under 35 U.S.C..sctn.
119(e) of U.S. Provisional Application No. 61/784,752 filed Mar.
14, 2013, the entire disclosures of which are incorporated herein
by reference.
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 Nov. 5, 2015, is named LT00586US1_SL.txt and is 11,986 bytes in
size.
FIELD OF THE INVENTION
[0003] The disclosure generally relates to compositions and methods
for the production of nucleic acid molecules. In some aspects, the
invention allows for the microscale generation of nucleic acid
molecules, optionally followed by assembly of these nucleic acid
molecules into larger molecules. In some aspects, the invention
allows for efficient production of nucleic acid molecules (e.g.,
large nucleic acid molecules such as genomes).
BACKGROUND
[0004] Production of nucleic acid molecules can be fairly simple or
complex depending on factors such as the type of nucleic acid
molecules to be produced. For example, historically, short single
stranded nucleic acid molecules such as primers have been typically
generated by chemical synthesis (see, e.g., U.S. Pat. No.
5,837,858, the disclosure of which is incorporated herein by
reference). Further, longer nucleic acid molecules have typically
been generated by polymerase chain reaction (PCR). One disadvantage
of PCR is that generally template nucleic acid is required.
[0005] Many nucleic acid synthesis methods have limited
capabilities for the generation of large de novo nucleic acid
molecules. One aspect of the current disclosure is to address this
limitation.
SUMMARY OF THE INVENTION
[0006] The invention relates, in part, to compositions and methods
for the synthesis of nucleic acid molecules. The invention further
relates to compositions and methods for the assembly of nucleic
acid molecules to form molecules such as plasmids, chromosomes and
genomes.
[0007] In some aspects, the invention relates to multiwell plates
for non-template directed synthesis of nucleic acid molecules. In
some embodiments, the plate comprises a bead (e.g., a magnetic
bead) located in each of a plurality of wells of the plate and an
electrochemically generated acid (EGA) being present in one or more
of the plurality of wells. Instead of or in addition to having EGA
in one or more wells, wells of the plate may contain other reagents
set out elsewhere wherein associated with the synthesis of nucleic
acid molecules.
[0008] Bead sizes used in the practice of the invention may vary
widely but include beads with diameters between 0.01 .mu.m and 100
.mu.m, 0.005 .mu.m and 100 .mu.m, 0.005 .mu.m and 10 .mu.m, 0.01
.mu.m and 100 .mu.m, 0.01 .mu.m and 1,000 .mu.m, between 1.0 .mu.m
and 2.0 .mu.m, between 1.0 .mu.m and 100 .mu.m, between 2.0 .mu.m
and 100 .mu.m, between 3.0 .mu.m and 100 .mu.m, between 0.5 .mu.m
and 50 .mu.m, between 0.5 .mu.m and 20 .mu.m, between 1.0 .mu.m and
10 .mu.m, between 1.0 .mu.m and 20 .mu.m, between 1.0 .mu.m and 30
.mu.m, between 10 .mu.m and 40 .mu.m, between 10 .mu.m and 60
.mu.m, between 10 .mu.m and 80 .mu.m, or between 0.5 .mu.m and 10
.mu.m. As one skilled in the art would recognize, when solid
particle fall below a particular size, they begin to act acquire
attributes of fluids (e.g., form the equivalent of colloidal
suspensions). Thus, in some instances (e.g., with the use of beads
below about 500 nm in diameter), it may be desirable to treat the
bead as a fluid. This may mean removal of a bead from a magnetic
tip, for example, by agitation, washing, or with the use of a
surfactant.
[0009] In specific embodiments of the invention, the bead size may
be chosen depending on the size of the well to allow only one
single bead to occupy a well. In other embodiments, more than one
bead (or nucleic acid synthesis substrates of other shapes) may be
in some of all of the wells. In some instances, the number beads
per well may be between two and twenty, between two and thirty,
between two and ten, between four and twenty, between four and ten,
between four and fifty, etc.
[0010] The number of wells may also vary widely and is limited by
factors such as the amount of nucleic acid to be produced and
technical factors such as manufacturability and mechanic factors
related to use (e.g., the lower size limit of magentic bead
extractors). In any event, the number of wells may be in number,
for example, between 10 and 10,000,000, between 10 and 5,000,000,
between 10 and 2,000,000, between 10 and 1,000,000, between 10 and
800,000, between 10 and 650,000, between 10 and 500,000, between
500 and 500,000, between 10 and 50,000, between 1,000 and 500,000,
between 10,000 and 500,000, between 20,000 and 500,000, or between
1,000 and 50,000. Further, multiwell surfaces have been prepared
with wells numbering in the range of 10 million. Thus, under some
instances, the number of wells may be less than 5 million, 10
million, 20 million, etc.
[0011] The total volume of each well is another item which may vary
and may be, for example, between 1.0.times.10.sup.-9 .mu.l and 50
.mu.l, between 1.0.times.10.sup.-9 .mu.l and 10 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 1.0 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 0.1 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 1.0.times.10.sup.-2 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 1.0.times.10.sup.-3 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 1.0.times.10.sup.-4 .mu.l, between
1.0.times.10.sup.-9 .mu.l and 50 .mu.l, between 1.0.times.10.sup.-5
.mu.l and 1.0.times.10.sup.-6 .mu.l, between 1.0.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-7 .mu.l, between 2.5.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-2 .mu.l, between 2.5.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-3 .mu.l, between 2.5.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-4 .mu.l, between 2.5.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-5 .mu.l, between 2.5.times.10.sup.-9
.mu.l and 1.0.times.10.sup.-6 .mu.l, between 1.0.times.10.sup.-8
.mu.l and 1.0.times.10.sup.-6 .mu.l, between 1.0.times.10.sup.-8
.mu.l and 1.0.times.10.sup.-5 .mu.l, between 1.0.times.10.sup.-7
.mu.l and 1.0.times.10.sup.-5 .mu.l, between 1.0.times.10.sup.-7
.mu.l and 1.0.times.10.sup.-4 .mu.l, between 1.0.times.10.sup.-7
.mu.l and 1.0.times.10.sup.-3 .mu.l, between 1.0.times.10.sup.-7
.mu.l and 1.0.times.10.sup.-2 .mu.l, between 0.1 .mu.l and 50
.mu.l, between 0.01 .mu.l and 50 .mu.l, between 0.01 .mu.l and 25
.mu.l, between 0.01 .mu.l and 15 .mu.l, between 0.01 .mu.l and 10
.mu.l, between 0.001 .mu.l and 50 .mu.l, between 0.001 .mu.l and 5
.mu.l, between 0.001 .mu.l and 1 .mu.l, between 0.001 .mu.l and
0.01 .mu.l, or between 0.001 .mu.l and 1 .mu.l.
[0012] In many instances, multiwell plates of the invention or
multiwell plates suitable for use with the invention will be
operably connected to either one electrode or a set (e.g., one or
several pairs) of electrodes. As discussed elsewhere herein, these
electrodes can be used to generate a microenvironment associated
with catalysis of one or more chemical reactions (e.g., EGA for
nucleotide deprotection).
[0013] In some embodiments, multiwell plates of the invention or
multiwell plates suitable for use with the invention will be
connected to microfluidic channels for the introduction and removal
of reagents. This allows for efficient and automated controlling of
reagents.
[0014] The invention also provides method for the generation of
assembled nucleic acid molecules formed from smaller chemically
synthesized nucleic acid molecules. In some embodiments, such
method may comprise one or more of the following steps:
[0015] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a microquantity
in the well of a plate;
[0016] (b) combining the nucleic acid molecules generated in (a),
or a portion thereof, to produce a pool;
[0017] (c) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules;
[0018] (d) eliminating nucleic acid molecules which contain
sequence errors from the plurality of larger nucleic acid molecules
formed in (c) to produce an error corrected nucleic acid molecule
pool; and
[0019] (e) assembling the nucleic acid molecules in the error
corrected nucleic acid molecule pool to form the assembled nucleic
acid molecule.
[0020] In some embodiments, the joining of nucleic acid molecules
present in the pool will be mediated by polymerase chain reaction
(PCR).
[0021] In some embodiments step (b) may further comprise combining
nucleic acid molecules generated in (a) with nucleic acid molecules
obtained by other means to form a pool, wherein said other means
include PCR, restriction enzyme digest or exonuclease treatment. In
some instances, the assembled nucleic acid molecule generated in
(c) and/or (e) may be assembled and introduced into a vector (e.g.,
a cloning vector, a destination vector, etc.).
[0022] The number of nucleic acid molecules assembled by methods of
the invention can vary and, when appropriate, will correlate with
the number of pooled nucleic acid molecules. In any event, nucleic
acid molecules assembled in methods of the invention may be
composed of at least five other (e.g., smaller) nucleic acid
molecules (e.g., from about five to about five thousand, from about
five to about twenty thousand, from about five to about one hundred
thousand, from about fifty to about five thousand, from about fifty
to about twenty thousand, from about fifty to about one hundred
thousand, from about one hundred to about five thousand, from about
one hundred to about one hundred thousand, from about five hundred
to about five thousand, from about five hundred to about one
hundred thousand, etc. nucleic acid molecules).
[0023] Nucleic acid molecules assembled by methods of the invention
may vary greatly and include molecules of at least 20 kilobases
(e.g., between from about 0.5 kilobase and to about 10 megabases,
between from about 0.5 kilobase and to about 5 megabases, between
from about 0.5 kilobase and to about 1 megabase, between from about
0.5 kilobase and to about 500 kilobases, between from about 0.5
kilobase and to about 100 kilobases, between from about 0.5
kilobase and to about 10 megabases, between from about 0.5 kilobase
and to about 1 kilobase, between from about 1 kilobase and to about
10 megabases, between from about 10 kilobases and to about 5
megabases, between from about 1 kilobase and to about 5 megabases,
between from about 1 kilobase and to about 2 megabases, between
from about 1 kilobase and to about 1 megabase, between from about 1
kilobase and to about 500 kilobases, between from about 10
kilobases and to about 1 megabases, between from about 10 kilobase
and to about 500 kilobases, between from about 10 kilobase and to
about 100 kilobases, etc.).
[0024] Nucleic acid molecule assembled by methods of the invention
may be, for example, single stranded, partly single stranded or
double stranded, closed, circular (e.g., a plasmid); nicked,
circular; or linear (e.g., a plasmid, a chromosome, etc.). Further,
methods of the invention may be performed such that two or more
(e.g., two, three, four, five, six, ten, twenty, etc.) assembled
nucleic acid molecules are simultaneously formed in the same
reaction mixture.
[0025] The invention further provides methods for producing product
nucleic acid molecules. In some instances such the methods
comprise:
[0026] (a) designing a product nucleic acid molecule of between 10
kilobases and 500 kilobases in size (e.g., between 500 bases and
500 kilobases, between 500 bases and 100 kilobases, between 500
bases and 1 kilobase, between 500 bases and 800 bases between 2
kilobases and 100 kilobases, between 2 kilobases and 50 kilobases,
between 2 kilobases and 5 kilobases, between 10 kilobases and 500
kilobases, between 10 kilobases and 300 kilobases, between 10
kilobases and 200 kilobases, between 10 kilobases and 100
kilobases, between 10 kilobases and 50 kilobases, etc.), wherein
the product nucleic acid molecule is defined by nucleotide
sequence;
[0027] (b) synthesizing a plurality of individual nucleic acid
molecules which differ in nucleotide sequence, wherein each
individual nucleic acid molecule is synthesized to prepare a
quantity of between 1,000 and 1.0.times.10.sup.9 copies and wherein
the individual nucleic acid molecules are capable of hybridizing
with one or more of the other individual nucleic acid
molecules;
[0028] (c) combining the individual nucleic acid molecules
synthesized in (b) under conditions which allow for hybridization
of the individual nucleic acid molecules under conditions which
allow for the formation of at least one larger nucleic acid
molecule; and
[0029] (d) combining the at least one larger nucleic acid molecule
formed in (c) with one or more additional nucleic acid molecules to
form the product nucleic acid molecule, wherein the product nucleic
acid molecule contains less than one sequence error per
kilobase.
[0030] In many instances, an error correction process is employed
during generation of product nucleic acid molecules. One place in
the above work flow where an error correction process may be
performed is after step (b). Error correction processes are
described elsewhere herein and will often include the use of one or
more mis-match repair endonuclease.
[0031] The number of individual nucleic acid molecule synthesized
as part of the preparation of product nucleic acid molecules may
vary greatly but include between 1,000 and 1.0.times.10.sup.9
copies, between 1,000 and 1.0.times.10.sup.8 copies, between 1,000
and 1.0.times.10.sup.7 copies, between 1,000 and 1.0.times.10.sup.6
copies, between 1,000 and 1.0.times.10.sup.5 copies, between
2.0.times.10.sup.7 and 1.0.times.10.sup.9 copies, between
5.0.times.10.sup.7 and 1.0.times.10.sup.9 copies, between
7.0.times.10.sup.7 and 1.0.times.10.sup.9 copies, between
2.0.times.10.sup.7 and 8.0.times.10.sup.8 copies, between
2.0.times.10.sup.7 and 5.0.times.10.sup.8 copies, between
5.0.times.10.sup.4 and 1.0.times.10.sup.9 copies, between
1.0.times.10.sup.6 and 1.0.times.10.sup.9 copies, between
1.0.times.10.sup.7 and 1.0.times.10.sup.8 copies; etc.
[0032] In many instances, polymerase chain reactions may be used to
amplify the at least one larger nucleic acid molecule formed in
step (c) in the above product nucleic acid molecule preparation
processes.
[0033] Plate formats for the synthesis of nucleic acid molecules
are described elsewhere herein and they may be used in the above
product nucleic acid molecule preparation processes. Further, when
individual nucleic acid molecules are synthesized on beads, wherein
each bead may be contained in a well. Further, beads used in this
aspect of the invention, as well as other aspects of the invention
may be, for example of sizes such as between 1 .mu.m and 100 .mu.m
in diameter, between 5 .mu.m and 50 .mu.m in diameter, between 3
.mu.m and 100 .mu.m in diameter, between 5 .mu.m and 100 .mu.m in
diameter, between 20 .mu.m and 100 .mu.m in diameter, between 5
.mu.m and 60 .mu.m in diameter, between 10 .mu.m and 100 .mu.m in
diameter, etc. In some embodiments beads may be of a size of about
30 .mu.m in diameter (e.g. between 28 and 32 .mu.m).
[0034] The invention also includes methods for producing nucleic
acid molecule in small amounts and with high sequence fidelity. In
some aspects, the invention includes a method for generating a
nucleic acid molecule, the method comprising synthesizing the
nucleic acid molecule in a total amount of between
3.0.times.10.sup.6 and 4.0.times.10.sup.8 molecules, wherein the
number of sequence errors is between 1 in 100 to 1 in 500.
[0035] The invention thus includes methods for the generation of
collections of nucleic acid molecules, including methods
comprising:
[0036] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a
microquantity;
[0037] (b) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules; and
[0038] (c) assembling the plurality of larger nucleic acid
molecules to form the collection of nucleic acid molecules, wherein
the collection of nucleic acid molecules from bioinformatic
information selected from the group consisting of:
[0039] (1) a copy DNA (cDNA) library containing only DNA
corresponding to messenger RNA (mRNA) molecules;
[0040] (2) a partial cDNA library containing DNA molecules
corresponding to less than the full complement of mRNA molecules
found in the cell type that the bioinformatic information was
derived from; and
[0041] (3) a collection of nucleic acid molecules in which some or
all of the nucleic acid molecules are codon altered variants of
nucleic acid molecules found in the cell type that the
bioinformatic information was derived from.
[0042] The invention also provides method for the generation of
self replicating nucleic acid molecules formed from smaller
chemically synthesized nucleic acid molecules. In some embodiments,
such method may comprise one or more of the following steps:
[0043] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a microquantity
in a plate;
[0044] (b) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules; and
[0045] (c) assembling the plurality of larger nucleic acid
molecules to form the self replicating nucleic acid molecule.
[0046] Self replicating nucleic acid molecules prepared by methods
of the invention include chromosomes, artificial chromosomes (such
as, for example, BACs or YACs), plasmids and genomes (e.g., genomes
such as viral, nuclear, prokaryotic (e.g., bacterial, algal, etc.)
chloroplast, or mitochondrial genomes).
[0047] The invention also includes methods for synthesizing and
assembling nucleic acid molecules which encode more than one
expression product, the methods comprising:
[0048] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a
microquantity;
[0049] (b) joining some or all of the nucleic acid molecules
present in the pool formed in (a) to form a plurality of larger
nucleic acid molecules; and
[0050] (c) assembling the plurality of larger nucleic acid
molecules to form the nucleic acid molecules which encode more than
one expression product.
[0051] In various aspects of the invention, the more than one
expression products may be proteins involved in the same biological
pathway. In more specific aspects, the more than one expression
products may be proteins involved in the same biological pathway
are enzymes that catalyze a series of chemical reactions in the
biological pathway. Further, such chemical reactions in the same
biological pathway may be sequential reactions in the sense that
one chemical reaction follows another either directly (directly
sequential) or after one or more intervening reaction has
occurred.
[0052] Biological pathway referred to herein include those that
results in the production of an end product selected from the group
consisting of (a) biofuel precursors; (b) antibiotics or antibiotic
precursors; (c) food components; (d) a chemical intermediate (e.g.,
1,4-butanediol, 2,3-butanediol, benzene, butadiene, 2-butanol,
3-hydroxypropionic acid, acrylic acid, adipic acid, aminocaproic
acid, caprolactam, acetylene, n-butanol, cyclohexanone, fumarate,
4-hydroy butyrate, GBL/BDO, hexamethylenediamine, isobutanol,
isopropanol, n-propanol, long chain alcohol, methacrylic
acid/methyl methacrylate, methyl ethyl ketone, propylene,
putrescine, muconic acid, p-toluate, terepthalic acid, acetic acid,
glucaric acid); (d) industrial enzymes, and (e) natural products.
Biofuel precursors include alcohols selected from the group
consisting of (a) butanol; (b) pentanol; (c) hexanol; (d) heptanol;
and (e) octanol. Food components include livestock feed components,
including amino acids selected from the group consisting of: (a)
L-lysine; (b) L-threonine; (c) L-methionine; (d) L-leucine; (e)
L-isoleucine: (f) L-valine, and (g) Homoserine.
[0053] Assembled nucleic acid molecules may be introduced into any
number of cells including prokaryotic and eukaryotic cell. Examples
of such cells include members of the genus Corynebacterium (e.g.,
Corynebacterium glutamicum), Pseudomonas sp. (Pseudomonas
aeruginosa), Saccharomyces cerevisiae, Bacillus sp. (Bacillus
lentus, Bacillus coagulans, Bacillus subtilis), Aspergillus sp.
(Aspergillus terreus, A. niger, Aspergillus versicolorr),
Streptomycetes spp. (Streptomyces griseus, Streptomyces Violaceans,
Streptomyceshygroscopicus, Streptomyces octosporus),
Clostridium(clostridia), Clostridium thermocellum, Clostridium
acetobutylicum, Clostridium beijerinckii, Clostridium butyricum,
Clostridium ljungdahlii, Clostridium aceticum, Clostridium
saccharobutylicum, Clostridium saccharoperbutylacetonicum,
Trichoderma reesei (Hypocrea jecorina), Kluyveromyces (lactis),
Neurospora crassa, Yarrowia lipolitica, Humicola (Humicola grisea),
Hansenula polymorpha (Pichia angusta), Acetobacters, Zymomonas,
Chrysosporium, Thermoanaerobacter, Pichia stipitis, Myxobacteria,
Mortierella isabellina, Actinobacillus succinogenes, Anaerobio
Spirillum succiniciproducens, Pichia kudriavzevii/Issatchenkia
orientalis (Yeast) (Candida krusei), Bifidobacterium, Bacillus
coagulans GBI-30, Bifidobacterium animalis subsp. lactis BB-12,
Bifidobacterium longum subsp. infantis 35624, Lactobacillus
acidophilus NCFM, Lactobacillus paracasei, Lactobacillus johnsonii
Lal, Lactobacillus plantarum, Lactobacillus reuteri, Saccharomyces
boulardii, Lactobacillus rhamnosus, Lactobacillus acidophilus NCFM,
Bifidobacterium bifidum BB-12, Lactobacillus casei, Lactobacillus
plantarum, Xanthomonas (X. campestris), Archea (Halobacterium sp.
NRC-1, Sulfolobus tokodaii, Sulfolobus tokodaii Methanocaldococcus
jannaschii, Thermoplasma acidophilum and Thermoplasma volcanium),
Rhodobacter sphaeroides, Ralstonia eutropha, Sporomusa species,
Clostridium ljungdahlii, Clostridium aceticum, Moorella
thermoacetica, Geobacter species, Shewanella sp, Candida glabrata,
Candida sonorensis, Candida tropicalis, Hansenula polymorpha,
Issatchenkia orientalis, Kluyveromyces lactis, Kluyveromyces
marxianus, Kluyveromyces thermotolerans, Pichia stipidis,
Saccharomyces bayanus, Saccharomyces bulderi, Saccharomyces uvarum,
Sachharomyces cerevisiae, Schizosaccharomyces pombe, Yarrowia
Lipolytica, Zygosaccharomyces bailii, Biodegredation (Aromatoleum
aromaticum, Dechloromonas aromatica, Desulfitobacterium hafniense,
Geobacter metallireducens, Alcanivorax borkumensis, Mycobacterium
tuberculosis), Deinococcus radiodurans, Actinoplanes regularis,
Nocardia orientalis, Actinocorrulia regularis, Tolypocladium
inflatum, Monascus ruber, Janibacter limonus, Actinomadura sp.,
Verucosispora sp., Muscodar albus, and Neurospora crassa.
[0054] As one skilled in the art would understand, many aspects of
the invention are well suited for automation. Automated systems are
often driven by software which may perform repetitive tasks,
especially when integrated with hardware designed for
micromanipulation of components and reagent flows. Thus, according
to various embodiments described herein, methods of assembling and
synthesizing nucleic acids may be implemented on a computing
system. Further, according to various embodiments described herein,
processor-executable instructions for assembling and synthesizing
nucleic acids. Thus, in some aspects the invention includes
non-transitory computer-readable storage media encoded with
instructions, executable by a processor, for generating assembled
nucleic acid molecule, the instructions comprising instructions
for:
[0055] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a microquantity
in the well of a plate;
[0056] (b) combining the nucleic acid molecules generated in (a) to
produce a pool;
[0057] (c) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules;
[0058] (d) eliminating nucleic acid molecules which contain
sequence errors from the plurality of larger nucleic acid molecules
formed in (c) to produce an error corrected nucleic acid molecule
pool; and
[0059] (e) assembling the nucleic acid molecules in the error
corrected nucleic acid molecule pool to form the assembled nucleic
acid molecule.
[0060] The invention also includes systems for generating assembled
nucleic acid molecules, the system comprising:
[0061] a processor; and
[0062] a memory encoded with processor-executable instructions
for:
[0063] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a microquantity
in the well of a plate;
[0064] (b) combining the nucleic acid molecules generated in (a) to
produce a pool;
[0065] (c) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules;
[0066] (d) eliminating nucleic acid molecules which contain
sequence errors from the plurality of larger nucleic acid molecules
formed in (c) to produce an error corrected nucleic acid molecule
pool; and
[0067] (e) assembling the nucleic acid molecules in the error
corrected nucleic acid molecule pool to form the assembled nucleic
acid molecule.
[0068] The invention also includes methods (e.g., in vitro methods)
for assembling nucleic acid molecules. One such method comprises:
(a) forming a reaction mixture of (1) one or more insert nucleic
acid molecule, one or more acceptor nucleic acid molecule, a
plurality of oligonucleotides, wherein each oligonucleotide shares
sequence complementarity with (i) one terminus of the insert
nucleic acid molecule and the insertion site of the acceptor
nucleic acid molecule or (ii) one terminus of two different insert
nucleic acid molecules and wherein the number of oligonucleotides
may be represented by the formula O=2+2I, where O is the number of
oligonucleotides and I is the number of insert nucleic acid
molecules, (2) a cell extract, and (3) a protein composition
comprising an exonuclease and, optionally, a single stranded
binding protein, and (b) incubating the reaction formed in (a)
under conditions which allow for the introduction of the insert
nucleic acid molecule into the acceptor nucleic acid molecule.
[0069] Oligonucleotides used in this aspect of the invention may be
set up in pairs, where the members of each pair the oligos are
fully complementary or partially complementary (offset oligos) to
each other.
[0070] Cell extracts used in the practice of the invention may be
obtained from any number of organisms, including single cellular
organisms such as selected bacteria (e.g., Escherichia coli,
Bacillus subtilis, etc.) and fungi (e.g., Schizosaccharomyces
pombe, Saccharomyces cerevisiae, etc.) When cells extracts from
prokaryotic cells (e.g., bacteria cells) are prepared and used in
methods of the invention, the cell may or may not express redET
genes. One exemplary strain that may be used in methods of the
invention includes cells of Escherichia coli strain DH10B.
[0071] Exonuclease activity used in methods of the invention may
also be provided by a DNA polymerase or protein with exonuclease
activity not having DNA polymerase activity.
[0072] The number of inserts that may be used in assembly methods
of the invention varies greatly but may be in the range of from
about 1 to about 30, from about 1 to about 20, from about 1 to
about 100, from about 2 to about 15, from about 2 to about 10, from
about 2 to about 8, from about 3 to about 30, from about 3 to about
15, from about 3 to about 10, from about 3 to about 8, from about 3
to about 6, from about 3 to about 5, from about 3 to about 4, from
about 2 to about 6, etc.
[0073] The number of oligonucleotides employed may be represented
by the formula O=2+2I, where O is the number of oligonucleotides
and I is the number of insert nucleic acid molecules. Thus, when
the following number of inserts (I) are used, the following numbers
of oligonucleotides (O) will often be used I=1, O=4; I=2, O=6; I=3,
O=8; I=4, O=10, I=5, O=12, etc.
BRIEF DESCRIPTION OF THE FIGURES
[0074] FIG. 1 is a general description of aspects of work flows of
the invention. The work flow is broken into four sections, referred
to as "modules" for ease of description. The work flow on the right
side of the figure shows some specific step included in some
aspects of methods of the invention.
[0075] FIGS. 2A-2B are schematic representations of a row of wells
according to an embodiment of the invention. The darker area in
well 1 indicates the presence of a reagent (e.g., EGA) not present
at a given time in the other wells.
[0076] FIG. 3 shows a nucleic acid assembly scheme. The thick ends
on the assembled nucleic acid molecule shown at the bottom of the
figure represent regions added by external primers, also referred
to as terminal primers.
[0077] FIG. 4 shows a second nucleic acid assembly scheme. Dotted
lines with arrows show PCR based synthesis direction and area.
[0078] FIG. 5 shows the assembly of two DNA fragments that do not
share any homology into a vector using stitching nucleic acid
molecules. The 69 base pair double-stranded stitching nucleic acid
molecules, shown in bold in the lower portion of the figure, share
30-bp homology with each adjacent fragment (Fragments 1 and 2).
These stitching nucleic acid molecules are used to insert 9 bp at
the junction of the adjacent fragments. The insertion bases are
shown underlined.
[0079] FIG. 6 is a flow chart of an exemplary process for synthesis
of error-minimized nucleic acid molecules.
[0080] FIG. 7 is a work flow chart of an exemplary process for
synthesis of error-minimized nucleic acid molecules. Different
strands of a double-stranded nucleic acid molecule are represented
by thicker and thinner line. "MME" refers to mis-match
endonuclease. Small circles represent sequence errors.
[0081] FIG. 8 generally illustrates methods for assembly and
cloning of nucleic acid segments in yeast. In some embodiments of
the invention, a number of nucleic acid segments (one of which is a
vector) are co-transforming the fragments into a yeast host cell,
where they are assembled by homologous recombination to form, for
example, a closed, circular nucleic acid molecule.
[0082] FIG. 9 is a drawing of an electrical coil that may be used
in the practice of the invention.
[0083] FIG. 10 is cross-sectional view of one embodiment of a fluid
reagent delivery system suitable for use with the invention.
[0084] FIG. 11 shows a library of linear, nucleic acid molecules
(top) generated by methods of the invention and a vector (bottom)
designed to accept library members. The upper portion of the figure
shows a series of lines representing four members of the library.
The lower open circular line represents a vector. The blocks on
each end of the nucleic acid molecule represent nucleic acid
segments which facilitate joining (e.g., GATEWAY.RTM. sites,
regions of homology, etc.). The numbers and the termini of the
nucleic acid molecules indicate compatible ends.
[0085] FIGS. 12A-12B show a series of variant nucleic acid
molecules that may be prepared by methods of the invention and
their encoded amino acid sequences. FIG. 12A shows variant nucleic
acid molecules that encode different amino acid sequences.
[0086] FIG. 12B shows variant nucleic acid molecules that use
different codons but encode the same amino acid sequence.
[0087] FIG. 13 shows two different fluid removal options for
microwell plate embodiments of synthesis platforms.
[0088] FIGS. 14A-14B show two different views of a nucleic acid
molecules synthesis platform designed to generate identical nucleic
acid molecules in each row 1401. FIG. 14A is a top view and FIG.
14B is a side view. Shown in the figure are fluidic channels 1401,
two electrodes associated with each channel/row of wells 1402 and a
series of wells containing nucleic acid synthesis substrates (e.g.,
individual beads) located in wells 1400. In some embodiments, the
wells will be spaced 300 .mu.m apart and will be cylindrical in
shape with a diameter of 40 .mu.m and a depth of 35 .mu.m.
[0089] FIG. 15 is a block diagram that illustrates a computing
system, upon which embodiments of the present teachings may be
implemented.
[0090] FIG. 16 is a schematic of automated system for performing
methods of the invention.
[0091] FIG. 17 is a top view schematic of a channel "chip".
[0092] FIG. 18 is a schematic representation of a Chain Reaction
Cloning (CRC) process. Initially a reaction mixture is prepared
containing two double-stranded nucleic acid molecules (NA1 and
NA2), a bridging oligonucleotide (BO) and a thermostable ligase.
This reaction mixture is heated to a temperature above the melting
point of the two double-stranded nucleic acid molecules (strands
indicated by + and -), then cooled to allow for annealing. In
instances where the BO connects NA1+ and NA2+, the ligase connects
the termini, with the junction point shown as a solid box. In later
cycles of heating and cooling, ligated NA1+ and NA2+ and NA1- and
NA2- single-stranded nucleic acid molecules (see lower far right of
FIG. 18) hybridize with their complements, that are then ligated to
each other by the ligase.
[0093] FIG. 19 is a schematic representation of a Circular
Polymerase Extension Cloning (CPEC) process. Initially a reaction
mixture is prepared containing (1) two double-stranded nucleic acid
molecules (NA1 and NA2) having overlapping regions of sequence
complementarity at the termini (indicated by the double headed
arrows) with each other and ends of a linearized vector and (2) a
thermostable polymerase. The + and - signs indicate the sequence
"polarity" of the nucleic acid strands.
[0094] FIG. 20 is a schematic representation of an Oligonucleotide
Stitching Assembly (OSA) process. In this process a reaction
mixture containing (1) a donor vector, (2) an acceptor vector, (3)
four oligonucleotides with sequence complementarity (represented by
"X"s) to the insertion locus of the acceptor vector and the insert
of the donor vector, and (4) a protein composition/cell extract
mixture. The insert will often be excised from the Donor Vector by,
for example, the use of a restriction enzyme. The box on the lower
right shows a variation where six oligonucleotides are used to
introduce two inserts into an acceptor vector. The numbers below
the data bars refer to the numbers of overlapping base-pairs in the
stitching oligonucleotides. The double-stranded character of the
non-oligonucleotide nucleic acid molecules is not represented in
this box.
[0095] FIG. 21 shows a series of OSA experiments using a cell
extract from E. coli strain DH10B, one acceptor vector and two
insert nucleic acid molecules. Different forms of oligonucleotides
60 nucleotides in length were tested. These oligonucleotides were
either full complementary or had different sized overhangs and
lengths of sequence complementarity with each other. Abbreviations:
CE=Cloning Efficiency, SD=Standard Deviation, CFU=Colony Forming
Units.
[0096] FIG. 22 shows a solid phase synthesis chamber used for
oligonucleotide synthesis methods of the examples. Polyethylene
(PE) filter material has a diameter 2.7 mm and a pore size 60-70
.mu.m. The solid support was obtained from CPG (Biosearch
Technologies Inc.) and was derivatized with one of four initial
bases depending on the first base of the oligonucleotides to be
synthesized. CPG A: 5'-DMT-dA(Bz)-Suc-CPG 1000 A: Catalog Number:
BG1-1000, loaded 40 mol/g, CPG C: 5'-DMT-dC(Bz)-Suc-CPG 1000 A:
Catalog Number: BG1-1100, loaded 40 mol/g, CPG G:
5'-DMT-dC(iBu)-Suc-CPG 1000 A: Catalog Number: BG1-1200, loaded 40
.mu.mol/g, CPG T: 5'-DMT-T-Suc-CPG 1000 A: Catalog Number:
BG1-1300, loaded 40 .mu.mol/g were used.
[0097] FIG. 23 shows a graphical overview of the gene synthesis
work flow. The first step of this process is an ordered,
sequence-determined self-assembly of the oligonucleotides to build
the desired DNA fragment. The subsequent PCR reaction amplifies and
links the individual oligonucleotides to yield a coherent double
stranded DNA fragment. The resulting DNA fragment is cloned into a
vector using standard cloning methods. Following transformation
into E. coli, typically eight of the grown bacterial colonies are
picked and analyzed for correctness, regarding the sequence of
contained inserts. The sequence results are analyzed manually and
the nature and number of occurring sequence errors is determined.
For a reference regarding standard gene synthesis see NOTKA F.,
WAGNER R. (2012) Reprogramming a GFP Reporter Gene Subjects It to
Complex Lentiviral Gene Regulation. Methods Mol Biol. 2012;
813:85-106. This workflow may also include an error correction
step. Typically, error correction would be performed before, as
part of, or after the first PCR step.
[0098] FIGS. 24A-24B show gel images of results of green
fluorescent protein gene synthesis using standard reactions and the
OPENARRAY.TM. system (Life Technologies Corp.). FIG. 24A shows the
assembled nucleic acid molecules generated using the methods for
the 1.sup.st PCR reaction set out in TABLE 18. PCR reactions in 1
and 2 shared the same formulation (0.03 .mu.M overlapping
oligonucleotides, 0.2 mM dNTPs, 1.times. PHUSION.RTM. HF buffer
(New England Biolabs) and 0.02 U/.mu.l PHUSION.RTM.High-Fidelity
DNA Polymerase (New England Biolabs)). A single mastermix was
employed to load 1280 wells (33 nl each) of a single
QUANTSTUDIO.TM. 12KFlex OPENARRAY.RTM. Plate (Life Technologies,
Corp) using the OPENARRAY.RTM. ACCUFILL.TM. System (Life
Technologies Corp) the remaining 1792 wells were filled with
sterile water. Oil overlay distribution and chip sealing was
performed according to the manufacturer's directions. Cycling
parameters and instrumentation are shown in TABLE 18. Once the
assembly PCR reaction concluded, the contents of the chip were
recovered by loosening the inlet valve and centrifuging the chip in
a 50 ml tube at 2000 rpm for 2 min. Approximately 40 .mu.l of the
aqueous phase was recovered by standard pipetting. Products were
analyzed by agarose electrophoresis. Numbers indicate samples 1 and
2 described in TABLE 18. "M" stands for molecular weight standards
FIG. 24B shows assembled nucleic acid molecules generated using the
methods for the 1.sup.st and 2.sup.nd PCR reactions set out in
TABLE 18. Briefly, products of the 1.sup.st PCR reactions described
in (A) were used as a template for the 2.sup.nd PCR reaction, which
shared the same formulation regardless of the instrument, volume
and conditions used (0.3 .mu.M outermost forward oligonucleotide,
0.3 .mu.M outermost reverse oligonucleotide, 0.2 mM dNTPs, 1.times.
PHUSION.RTM. HF buffer (New England Biolabs) and 0.02 U/.mu.l
PHUSION.RTM. High-Fidelity DNA Polymerase (New England Biolabs)).
Reagent loading and product recovery from the QUANTSTUDIO.TM.
12KFlex OPENARRAY.RTM. Plates (Life Technologies Corp), was
performed as described in (A). Products were analyzed by agarose
electrophoresis using the volumes depicted on the figure. Numbers
indicate samples 1, 2, 3, and 4 described in TABLE 18. "M" stands
for molecular weight standards.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
[0099] Solid Support: As used herein, the term solid support refers
to a porous or non-porous material on which polymers such as
nucleic acid molecules can be synthesized and/or immobilized. As
used herein "porous" means that the material contains pores which
may be of non-uniform or uniform diameters (for example in the nm
range). Porous materials include paper, synthetic filters etc. In
such porous materials, the reaction may take place within the
pores. The solid support can have any one of a number of shapes,
such as pin, strip, plate, disk, rod, fiber, bends, cylindrical
structure, planar surface, concave or convex surface or a capillary
or column The solid support can be a particle, including bead,
microparticles, nanoparticles and the like. The solid support can
be a non-bead type particle (e.g., a filament) of similar size. The
support can have variable widths and sizes. For example, sizes of a
bead (e.g., a magnetic bead) which may be used in the practice of
the invention are described elsewhere herein. The support can be
hydrophilic or capable of being rendered hydrophilic and includes
inorganic powders such as silica, magnesium sulfate, and alumina;
natural polymeric materials, particularly cellulosic materials and
materials derived from cellulose, such as fiber containing papers
such as filter paper, chromatographic paper or the like.
[0100] In some embodiments, solid support may be fragmentable.
Solid supports may be synthetic or modified naturally occurring
polymers, such as nitrocellulose, carbon, cellulose acetate,
polyvinyl chloride, polyacrylamide, cross linked dextran, agarose,
polyacrylate, polyethylene, polypropylene, poly (4-methylbutene),
polystyrene, polymethacrylate, poly(ethylene terephthalate), nylon,
poly(vinyl butyrate), polyvinylidene difluoride (PVDF) membrane,
glass, controlled pore glass, magnetic controlled pore glass,
magnetic beads, ceramics, metals, and the like; either used by
themselves or in conjunction with other materials.
[0101] In some embodiments, the support can be in a chip, array,
microarray or microwell plate format. In many instances, a support
generated by methods of the invention will be one where individual
nucleic acid molecules are synthesized on separate or discrete
areas to generate features (i.e., locations containing individual
nucleic acid molecules) on the support.
[0102] In some embodiments, the size of the defined feature is
chosen to allow formation of a microvolume droplet or reaction
volume on the feature, each droplet or reaction volume being kept
separate from each other. As described herein, features are
typically, but need not be, separated by interfeature spaces to
ensure that droplets or reaction volumes or between two adjacent
features do not merge. Interfeatures will typically not carry any
nucleic acid molecules on their surface and will correspond to
inert space. In some embodiments, features and interfeatures may
differ in their hydrophilicity or hydrophobicity properties. In
some embodiments, features and interfeatures may comprise a
modifier. In one embodiment of the invention the feature is a well
or microwell or a notch.
[0103] Nucleic acid molecules may be covalently or non-covalently
attached to the surface or deposited on the surface.
[0104] In one embodiment of the invention, Module 1 can involve the
use of more than one solid support. In some embodiments, two or
more solid supports may be arranged on a plate. Any arrangement of
the solid supports could be employed such as rows or columns or a
combination thereof. For example, rows can be aligned and/or the
columns can be aligned. In other embodiments, rows and/or columns
are equally spaced and staggered. Spacing between rows and/or
between columns can be variable. The number of the solid supports
comprised in, for example, a plate may be variable. In some
embodiments, a plate may contain up to 1536 (or more) solid
supports.
[0105] Nucleic Acid Molecule: As used herein the term "nucleic acid
molecule" refers to a covalently linked sequence of nucleotides or
bases (e.g., ribonucleotides for RNA and deoxyribonucleotides for
DNA but also include DNA/RNA hydrids where the DNA is in separate
strands or in the same strands) in which the 3' position of the
pentose of one nucleotide is joined by a phosphodiester linkage to
the 5' position of the pentose of the next nucleotide. Nucleic acid
molecule may be single- or double-stranded or partially
double-stranded. Nucleic acid molecule may appear in linear or
circularized form in a supercoiled or relaxed formation with blunt
or sticky ends and may contain "nicks". Nucleic acid molecule may
be composed of completely complementary single strands or of
partially complementary single strands forming at least one
mismatch of bases. Nucleic acid molecule may further comprise two
self-complementary sequences that may form a double-stranded stem
region, optionally separated at one end by a loop sequence. The two
regions of nucleic acid molecule which comprise the double-stranded
stem region are substantially complementary to each other,
resulting in self-hybridization. However, the stem can include one
or more mismatches, insertions or deletions.
[0106] Nucleic acid molecules may comprise chemically,
enzymatically, or metabolically modified forms of nucleic acid
molecules or combinations thereof. Chemically synthesized nucleic
acid molecules may refer to nucleic acids typically less than or
equal to 150 nucleotides long (e.g., between 5 and 150, between 10
and 100, between 15 and 50 nucleotides in length) whereas
enzymatically synthesized nucleic acid molecules may encompass
smaller as well as larger nucleic acid molecules as described
elsewhere in the application. Enzymatic synthesis of nucleic acid
molecules may include stepwise processes using enzymes such as
polymerases, ligases, exonucleases, endonucleases or the like or a
combination thereof. Thus, the invention provides, in part,
compositions and combined methods relating to the enzymatic
assembly of chemically synthesized nucleic acid molecules.
[0107] Nucleic acid molecule also refers to short nucleic acid
molecules, often referred to as, for example, primers or probes.
Primers are often referred to as single-stranded starter nucleic
acid molecules for enzymatic assembly reactions whereas probes may
be typically used to detect at least partially complementary
nucleic acid molecules. A nucleic acid molecule has a "5'-terminus"
and a "3'-terminus" because nucleic acid molecule phosphodiester
linkages occur between the 5' carbon and 3' carbon of the pentose
ring of the substituent mononucleotides. The end of a nucleic acid
molecule at which a new linkage would be to a 5' carbon is its 5'
terminal nucleotide. The end of a nucleic acid molecule at which a
new linkage would be to a 3' carbon is its 3' terminal nucleotide.
A terminal nucleotide or base, as used herein, is the nucleotide at
the end position of the 3'- or 5'-terminus. A nucleic acid molecule
sequence, even if internal to a larger nucleic acid molecule (e.g.,
a sequence region within a nucleic acid molecule), also can be said
to have 5'- and 3'-ends.
[0108] Overview:
[0109] The invention relates, in part, to compositions and methods
for the preparation of nucleic acid molecules. While the invention
has numerous aspects and variations associated with it, some of
these aspects and variations are set out in FIG. 1 in outline
form.
[0110] One advantage of the invention is that for, many
applications, small amounts of synthesized nucleic acid are
suitable for achieving an intended purpose (e.g., preparation of
microarrays, construction of a plasmid which contains a selectable
marker, etc.). In some instances, small amounts of nucleic acid are
suitable for working with due to factors such as enzymatic (e.g.,
PCR) and intracellular amplification.
[0111] The left side of FIG. 1 shows four general "modules"
representing different portions of some embodiments of the
invention. Thus, in some aspects, the invention involves one or
more of the following: (1) nucleic acid molecule synthesis, (2)
pooling of nucleic acid molecules, (3) assembly of a plurality of
nucleic acid molecules, and/or (4) transfer of assembled nucleic
acids (e.g., transfer to a cell).
[0112] In relation to more specific embodiments of the invention,
the right side of FIG. 1 shows some additional details related to
the modules shown on the left side of the figure. Above a number of
the text blocks are bolded terms such as "ENZYMATIC" and
"CELLULAR". These terms indicate exemplary general means by which
the process referred to can be performed. As one skilled in the art
would understand, some processes can be performed, for example,
either chemically, enzymatically, or in a cell.
[0113] Module 1, as shown in FIG. 1 refers to a single process
termed "Microscale Parallel Nucleic Acid Molecule Synthesis". As
set out elsewhere herein, this process will typically involve
several steps which will vary with how the process is performed. In
many embodiments, the general function of Module 1 will be the
generation of a plurality of nucleic acid molecules. These nucleic
acid molecules may be designed as a group to be joined to form one
or more larger nucleic acid molecule or when contacted with
additional nucleic acid molecules (e.g., "stitching" nucleic acid
molecules).
[0114] Module 2, as shown in FIG. 1 refers to processes termed
"Pooling of Solid Supports", "Nucleic Acid Molecule Cleavage", and
"Deprotection". The general function of Module 2 will be the
preparation of nucleic acid molecules for participation in one or
more process referred to in Module 3. This will often mean
combining nucleic acid molecules which differ in sequence and the
removal of any chemical groups which are either not necessary or
not desirable for the performance of one or more processes referred
to in Module 3.
[0115] Using Module 2 as an example, as one skilled in the art
would recognize, FIG. 1 shows general embodiments of the invention.
More specifically, Module 2 refers to the pooling of solid
supports. These supports will typically contain nucleic acid
molecules. In some embodiments, nucleic acid molecules may be
obtained in a form free of solid supports, then pooled.
[0116] Module 3, as shown in FIG. 1 refers to the processes termed
"Fragment Amplification and Assembly", "Error Correction", and
"Final Assembly". The general function of Module 3 processes is the
generation of assembled nucleic acid molecules with high sequence
fidelity, with comparison to the sequence of nucleic acid molecules
which were sought to be produced.
[0117] Module 4, as shown in FIG. 1 refers to the processes of
termed "Recipient Cell Insertion". As one skilled in the art would
understand, introduction of nucleic acid molecules generated by
methods of the invention into cells is only one application. In
most instances, a nucleic acid molecule assembled according to
methods of the invention will be designed for a specific
application. Applications vary widely and include biofuel
production, bioremediation, and chemical precursor production.
[0118] In some embodiments, amino group containing support matrix
having a polyvinyl backbone may be used as solid support. For
example, monodispersed particles obtained by methods as described
in U.S. Pat. No. 6,335,438 the disclosure of which is incorporated
herein by reference, may be used in the practice of the
invention.
[0119] Module 1
[0120] In the invention, the nucleic acid molecules may be attached
to solid supports, such as particles or beads (e.g., controlled
pore glass beads). In one embodiment, magnetic microbeads are used
as solid supports. In many instances, single-activated porous 1
.mu.m size microbeads with large surface to volume ratios may be
used in the current invention. The uniform nature of such
monodispersed particles generally provides for uniform reaction
rates particularly suited to synthesis in automated chemical
synthesizers (e.g., nucleic acid molecule synthesizers). Beads may
initially be provided with a reactive group. For example, in some
embodiments of the invention, DYNABEADS.RTM. M-280 (Dynal Biotech
ASA, Oslo, Norway) may be used. DYNABEADS.RTM. M-280 are 2.8 .mu.m
beads which come in a number of forms. M-280 beads tend are fairly
uniform, superparamagnetic, polystyrene beads coated with a
polyurethane layer. These beads may be obtained with various
chemical activation groups suitable for use for different
applications.
[0121] Magnetic bead technology is described in U.S. Pat. No.
5,512,439, which is incorporated herein by reference.
[0122] Synthesis substrates other than those composed of CPG or
magnetic materials may also be used with the invention and include
those composed of polystyrene (e.g., polystyrene-1% divinylbenzene,
macroporous polystyrene, and poly(ethylene glycol)-polystyrene
(PEG-PS)), polyamide (e.g., polyamide bonded silica gel), silica
gel, and cellulose. Some of these substrates are available in resin
form. In many instances, substrates that are resins may be placed
in wells, instead of or in conjunction with beads, and may be used
for nucleic acid synthesis.
[0123] Other nucleic acid ligation methods, and arrays which employ
them, are know in the art. For example, methods are known which use
an amine or a peroxide (which opens to an ether bridge) activated
surface. As noted elsewhere herein, for EGA methods in the art, a
hydroxyl group has been described and used to link nucleic acid to
a silica magnetic bead surface. The invention includes such linking
methods and compositions which contain them.
[0124] In some instances, it may also be desired to use a
semi-solid support that may have a gel-like or viscous consistence
or matrix instead of a solid support. The invention contemplates
this and in suitable instances here where a solid support is
referred to a non-solid support may be used.
[0125] Factors which determine the amount of nucleic acid which can
be synthesized include surface area and size of particles upon
which synthesis occurs. Thus, to some extent, support (e.g., bead)
parameters can be adjusted to alter the amount of nucleic acid
synthesized. Beads which may be used in the practice of the
invention may vary widely in terms of size, including the following
size ranges: from about 0.01 .mu.m to about 1,000 .mu.m, from about
0.1 .mu.m to about 1,000 .mu.m, from about 1.0 .mu.m to about 1,000
.mu.m, from about 0.01 .mu.m to about 400 .mu.m, from about 0.01
.mu.m to about 200 .mu.m, from about 0.01 .mu.m to about 100 .mu.m,
from about 0.1 .mu.m to about 100 .mu.m, from about 0.1 .mu.m to
about 50 .mu.m, from about 1.0 .mu.m to about 600 .mu.m, from about
1.0 .mu.m to about 400 .mu.m, from about 1.0 .mu.m to about 200
.mu.m, from about 1.0 .mu.m to about 100 .mu.m, from about 2.0
.mu.m to about 400 .mu.m, from about 2.0 .mu.m to about 200 .mu.m,
from about 5.0 .mu.m to about 500 .mu.m, etc. in average
diameter.
[0126] Further, beads may be used which allow for an average amount
of nucleic acid to be produced in the following amounts: from about
0.001 nanomoles to about 1,000 nanomoles, from about 0.1 nanomoles
to about 1,000 nanomoles, from about 1.0 nanomole to about 1,000
nanomoles, from about 5.0 nanomoles to about 1,000 nanomoles, from
about 10 nanomoles to about 1,000 nanomoles, from about 30
nanomoles to about 1,000 nanomoles, from about 50 nanomoles to
about 1,000 nanomoles, from about 200 nanomoles to about 1,000
nanomoles, from about 1.0 nanomole to about 500 nanomoles, from
about 1.0 nanomole to about 250 nanomoles, from about 10 nanomoles
to about 500 nanomoles, etc.
TABLE-US-00001 TABLE 1 Number of Nucleic Acid Molecules Nucleic
Acid (Nanomoles) 1.26 .times. 10.sup.5 2.09 .times. 10.sup.-10 3.14
.times. 10.sup.6 5.22 .times. 10.sup.-09 1.26 .times. 10.sup.7 2.09
.times. 10.sup.-08 1.13 .times. 10.sup.8 1.88 .times. 10.sup.-07
3.14 .times. 10.sup.8 5.22 .times. 10.sup.-07 1.26 .times. 10.sup.9
2.09 .times. 10.sup.-06
[0127] In many instances, the yield of nucleic acid molecules
chemically synthesized decreases once a certain size has been
reached. In many embodiments of the invention, chemically
synthesized nucleic acid molecules will be in the range of from
about 8 to about 100 nucleotides, from about 8 to about 35
nucleotides, from about 8 to about 40 nucleotides, from about 8 to
about 50 nucleotides, from about 8 to about 100 nucleotides, from
about 15 to about 100 nucleotides, from about 15 to about 75
nucleotides, from about 15 to about 50 nucleotides, from about 20
to about 60 nucleotides, from about 40 to about 400 nucleotides,
from about 40 to about 300 nucleotides, from about 40 to about 200
nucleotides, from about 40 to about 100 nucleotides, from about 40
to about 90 nucleotides, from about 50 to about 400 nucleotides,
from about 50 to about 300 nucleotides, from about 50 to about 200
nucleotides, from about 50 to about 100 nucleotides, from about 50
to about 90 nucleotides, from about 50 to about 80 nucleotides,
from about 75 to about 400 nucleotides, from about 75 to about 300
nucleotides, or from about 75 to about 200 nucleotides.
[0128] As one skilled in the art would recognize, the amount of
nucleic acid required to be produced will vary with, for examples,
the application and the efficiency of assembly methods used. When a
replicable molecule (e.g., via PCR, insertion into a cell, etc.) is
generated, theoretically only one assembled nucleic acid molecule
need be generated. If the number of nucleic acid molecules
generated are reduced to the point where theoretically only one
fully assembled nucleic acid molecule is generated, then half the
time no fully assembled nucleic acid molecule will generated. Thus,
one lower limit for the amount of nucleic acid to be produced using
methods of the invention is based upon the number of fully
assembled nucleic acid molecules which may be generated. This
number will often vary with the number of synthetic nucleic acid
molecules that must be combined to form the final construct.
Methods of the invention will typically be designed to generate
from about 1 to about 500,000, from about 10 to about 500,000, from
about 100 to about 500,000, from about 500 to about 500,000, from
about 1 to about 1,000, from about 1 to about 500, from about 10 to
about 1,000, from about 10 to about 500, from about 100 to about
1,000, from about 100 to about 500, from about 100 to about 5,000,
from about 100 to about 50,000, from about 100 to about 250,000,
from about 1,000 to about 50,000, etc. assembled nucleic acid
molecules.
[0129] As one skilled in the art would understand, nucleic acid
synthesis substrate area directly reflects the number of nucleic
acid molecules which may be synthesized on that substrate. TABLE 2
below shows bead size, surface area calculations and an estimated
number of nucleic acid molecules that may be generated on the
specified beads.
TABLE-US-00002 TABLE 2 Bead Diam. (.mu.m) Surface Area
(.mu.m.sup.2) No. of Molecules 1 314.2 1.26 .times. 10.sup.5 5
7,855 3.14 .times. 10.sup.6 10 31,416 1.26 .times. 10.sup.7 30
282,743 1.13 .times. 10.sup.8 50 785,398 3.14 .times. 10.sup.8 100
3,141,593 1.26 .times. 10.sup.9 Note: The effective surface area
for the beads used to generate the above data is estimated to be
100 times higher than the spherical surface are.
[0130] In some embodiments, oligonucleotide synthesis will be
performed using 2.8 .mu.m beads in a plate with one bead per well.
Further, the wells may be designed as cylindrical holes or chambers
that are 4 .mu.m and 3 .mu.m deep. When well spacing of 100 .mu.m
is used, a 10 mm.sup.2 chip can accommodate 10,000 wells. In many
instances when plates are made by etching, the wells will be of a
non-cylindrical shapes and may be pyramid, cone or quadratic
shaped. In some instances, the wells may be in the shape of a
reverse, truncated cone.
[0131] The number of individual nucleic acid molecules generated
will also vary with the application. While costs savings can be
achieved by reagent usage reductions, it will generally be
desirable to generate enough nucleic acid molecules need for, for
example, efficient assembly. Further, the number of nucleic acid
molecules having a particular nucleotide sequence produced with
generally reflects the "carrying capacity" of the synthesis
substrate. For example, a 30 micron bead typically can be used to
generate about 1,000,000 nucleic acid molecules. For example, in
many instances, as bead size, decreases, so will the number of
nucleic acid molecules that may be produced on each bead.
[0132] Methods of the invention may be used to generate from about
100 to about 20,000,000, from about 1,000 to about 20,000,000, from
about 10,000 to about 20,000,000, from about 100 to about
5,000,000, from about 1,000 to about 5,000,000, from about 10,000
to about 5,000,000, from about 100 to about 1,000,000, from about
1,000 to about 1,000,000, from about 10,000 to about 10,000,000,
from about 100 to about 500,000, from about 1,000 to about 500,000,
from about 10,000 to about 500,000, etc. nucleic acid molecules
designed to have the same nucleotide sequence.
[0133] The number of nucleic acid molecule synthesis sites (e.g.,
wells) can vary greatly and will be determined by a number of
factors including (1) the limitations of engineering and nucleic
acid molecule synthesis hardware and (2) the amount of nucleic acid
which is desired (see elsewhere herein for a discussion of this
factor). As examples, the number of nucleic acid molecule synthesis
sites (e.g., wells) in synthesis platforms used in the practice of
the invention may vary in total number between 9 and 200,000,
between 9 and 100,000, between 9 and 20,000, between 9 and 1,000,
between 9 and 500, between 1,000 and 200,000, between 1,000 and
400,000, between 1,000 and 500,000, between 1,000 and 1,00,000,
between 1,000 and 10,000,000, between 20,000 and 1,000,000, between
50,000 and 10,000,000, between 10,000 and 5,000,000, between 1,000
and 100,000, between 2,000 and 100,000, between 5,000 and 100,000,
between 10,000 and 100,000, between 20,000 and 100,000, between
30,000 and 100,000, between 1,000 and 80,000, between 1,000 and
70,000, between 1,000 and 50,000, between 1,000 and 40,000, between
1,000 and 30,000, between 1,000 and 20,000, between 1,000 and
10,000, between 1,000 and 8,000, between 1,000 and 5,000, between
5,000 and 50,000, between 10,000 and 50,000, between 5,000 and
35,000, etc. In addition, the number of nucleic acid molecule
synthesis sites (e.g., wells) may vary between 1,000 and 5,000,
between 1,000 and 10,000, between 1,000 and 20,000, between 1,000
and 30,000, between 2,000 and 5,000, between 2,000 and 10,000,
between 4,000 and 15,000, between 100 and 1,000, between 100 and
3,000, between 100 and 5,000, between 250 and 5,000, etc. per
mm.sup.2.
[0134] The amount of reagent space per nucleic acid molecule
synthesis site (e.g., well) will vary with the size and shape of
the well and, in particular, the area of the space capable of
accepting reagents. This will vary with factors such as whether the
nucleic acid molecule synthesis site is a flat surface (e.g.,
relying on surface tension to keep reagents localized over the
synthesis site or a cavity (e.g., a well). Also, the amount of
reagent applied may be determined by the amount of reagent
necessary to cover the synthesis site, deliver the necessary amount
of reactant(s), and/or dilute, remove, or wash away reagents
present at the synthesis site. The amount of reagent applied (when
the reagent is a liquid) and the amount of reagent space at the
synthesis site may vary greatly including between
0.001.times.10.sup.-15 l (femtoliter) and 100 .mu.l, between
0.01.times.10.sup.-15 l (femtoliter) and 100 .mu.l, between
0.1.times.10.sup.-15 l (femtoliter) and 100 .mu.l, between
1.0.times.10.sup.-15 l (femtoliter) and 100 .mu.l, between
0.1.times.10.sup.-15 l (femtoliter) and 1 .mu.l, between
0.1.times.10.sup.-15 l (femtoliter) and 500 nl, between
0.1.times.10.sup.-15 l (femtoliter) and 100 nl, between
0.1.times.10.sup.-15 l (femtoliter) and 1 nl, between
0.1.times.10.sup.-15 l (femtoliter) and 500 pl (picoliter), between
0.1.times.10.sup.-15 l (femtoliter) and 100 .mu.l, between
0.1.times.10.sup.-15 l (femtoliter) and 10 .mu.l, between
0.1.times.10.sup.-15 l (femtoliter) and 1 .mu.l, between
0.001.times.10.sup.-15 l (femtoliter) and 1 .mu.l, between
0.001.times.10.sup.-15 l (femtoliter) and 1.0.times.10.sup.-15 l
(femtoliter), between 0.001.times.10.sup.-15 l (femtoliter) and
100.times.10.sup.-15 l (femtoliter), between 1.0.times.10.sup.-15 l
(femtoliter) and 500.times.10.sup.-15 l (femtoliter), etc.
[0135] To make the solid support material suitable for nucleic acid
molecule synthesis, non-nucleosidic linkers or nucleoside
succinates may be covalently attached to reactive amino groups. If
necessary, however, other surface functions such as carboxyl could
be used to attach a linker carrying a hydroxyl group or
alternatively a 3'-attached nucleotide.
[0136] The linker, when present, may be a chemical entity that
attaches the 3'-0 of the nucleic acid molecule to the solid support
(e.g., a functional group on a solid support). In most cases, the
linker will be stable to all the reagents used during nucleic acid
molecule synthesis, but cleavable under specific conditions at the
end of the synthesis process. One linker commonly used in nucleic
acid molecule synthesis is the succinyl linker. Different linkers
with different properties are known to those skilled in the art and
can be selected by the skilled person depending on the downstream
process requirements.
[0137] Nucleosidic solid supports (e.g., support prederivatized
with base) are widely used in nucleic acid molecule synthesis. One
example of such a support is one where the 3'-hydroxy group of the
3'-terminal nucleoside residue is attached to the solid support via
a 3'-O-succinyl arm. The use of nucleosidic solid supports requires
usage of different types of beads (one for each base). However, the
fact that a nucleosidic solid support has to be selected in a
sequence-specific manner (according to the first base required for
each nucleic acid molecule) reduces the throughput of the entire
synthesis process due to laborious pre-selection and distribution
of beads attached to a specific starter base to individual
microwells.
[0138] A more convenient method for synthesis starts with a
universal support where a non-nucleosidic linker is attached to the
solid support material. An advantage of this approach is that the
same solid support may be used irrespectively of the sequence of
the nucleic acid molecule to be synthesized. One example of a
universal support that can be used in the current invention is
described in U.S. Pat. No. 7,202,264, the disclosure of which is
incorporated herein by reference. However, other universal linkers
known by the skilled in the art may be equally appropriate to carry
out the invention. For the complete removal of the linker and the
3'-terminal phosphate from the assembled nucleic acid molecule,
some of the universal solid supports known in the art require
gaseous ammonia, aqueous ammonium hydroxide, aqueous methylamine or
a mixture thereof.
[0139] A number of methods for synthesizing nucleic acid are known.
Many of these methods follow a series of basic steps, such as, for
example, the following, with appropriate washing steps using, for
example, acetonitrile, ethylacetate or other washing reagents
suitable for practicing the invention:
[0140] a) the first nucleotide, which has been protected at the 5'
position, is derivatized to a solid support, usually controlled
pore glass (CPG), or is obtained prederivatized;
[0141] b) the sugar group of the first nucleotide is deprotected
(e.g., via detritlyation) (a process often referred to as
"Deprotection"), using, for example, tricholoracetic acid in
methylene chloride, which results in a colored product which may be
monitored for reaction progress;
[0142] c) the second nucleotide, which has the phosphorus, sugar
and base groups protected, is added to the growing chain, usually
in the presence of a catalyst, such as, for example, tetrazole or
4,5-dicyanoimidazole (a process often referred to as
"Coupling");
[0143] d) unreacted first nucleotide is capped to avoid
accumulation of deletions, using, for example, acetic anhydride and
N-methylimidazole (a process often referred to as "Capping");
[0144] e) the phosphite triester is oxidized to form the more
stable phosphate triester, usually using, for example, iodine
reagents (a process often referred to "Oxidizing");
[0145] f) the process is repeated as needed depending on the
desired length of the nucleic acid molecule; and
[0146] g) cleavage from the solid support is done, usually using
aqueous or gaseous ammonia at elevated temperatures. The skilled in
the art will recognize that in certain embodiments of the invention
the order of steps may vary or some of the steps including the
washing steps may be repeated as appropriate according to the used
protocol.
[0147] In the current invention, the state of the art
phosphoramidite synthesis chemistry is further improved by
modification of specific steps of the above protocol. In one
embodiment organocatalysts can be used to improve, for example, the
efficiency of the coupling step. Organocatalysts and some uses of
such catalysts are set out in Avenier and Hollfelder, Combining
Medium Effects and Cofactor Catalysis: Metal-Coordinated Synzymes
Accelerate Phosphate Transfer by 10.sup.8 Chem. Eur. J. 15:12371
12380 (2009) and Jordan et al., Asymmetric phosphorylation through
catalytic P(III) phosphoramidite transfer: Enantioselective
synthesis of D-myo-inositol-6-phosphate, Proc. Nat. Acad. Sci. USA,
107: 20620-20624 (2010).
[0148] In some embodiments, the invention makes use of localized
chemical reactions through the production of electrochemically
generated acid (EGA). As an example, addressable electrical signals
may be used for the production of acid at sufficient concentration
to allow deprotection of the dimethoxytrityl (DMT) protecting group
from surface. (Maurer et al., "Electrochemically Generated Acid and
Its Containment to 100 Micron Reaction Areas for the Production of
DNA Microarrays" PLoS, Issue 1, e34 (December 2006).)
[0149] One issue with the production of EGA as part of a nucleic
acid molecule synthesis protocol on a surface (e.g., a
microsurface) is "splash over" to adjoining regions. "Splash over",
which includes diffusion, can result in reactions occurring in
unintended location (e.g., caused by diffusion of EGA). While such
effects may be fairly minor when one reaction occurs, when multiple
reactions occur in succession splash over effects multiple reaction
cycles may result in numerous misincorporated bases. This issue can
be addressed in several ways. One way is to overlay the reaction
areas with a buffer (e.g., a buffer containing an organic base)
which sufficiently neutralizes the acid if it moves from the local
environment. Another way is through physical containment or
compartmentalization. For example, if the EGA is generated in a
well and catalyzes a reaction in that well, the well may be of
sufficient size to prevent the acid from exiting. Containment
within the well is thus a factor of the size of the well and the
amount of acid generated. In some reaction formats, some acid will
invariably exit the well. This should pose no problems unless a
quantity sufficient to catalyze a reaction reaches another well in
which that reaction is not supposed to occur. As noted above, the
use of an overlaying buffer can be used to minimize such
reactions.
[0150] Another issue with EGA is depurination of oligonucleotides.
It has been found that the contacting of oligonucleotides with EGA
at lower pHs (e.g., a pH of 1.5 vs. a pH of 2.2) results in
significant oligonucleotide depurination (data not shown). The
invention includes methods in which the amount of EGA used results
in a pH sufficient to deprotect oligonucleotides while minimizing
depurination. In particular, deprotection may occur at pHs from
about 1.6 to about 2.8, from about 1.8 to about 2.8, from about 2.0
to about 2.8, from about 1.8 to about 2.6, from about 1.8 to about
2.4, from about 1.9 to about 2.5, from about 2.0 to about 2.4,
etc.
[0151] The concentration of the EGA and other incubation conditions
(e.g., time, temperature, etc.) may be adjusted such that a desired
level of deprotection occurs, while minimizing depurination. Thus,
from a "functional" perspective, EGA mediated oligonucleotide
deprotection conditions may be adjusted such that the ratio of
deprotection and depurination is within a desirable range. In some
instances, the EGA mediated deprotection conditions may be adjusted
such that at least 95% (e.g., from about 95.1% to about 100%, from
about 95.5% to about 100%, from about 96% to about 100%, from about
97% to about 100%, from about 98% to about 100%, from about 99% to
about 100%, from about 99.5% to about 100%, from about 95.1% to
about 99.8%, from about 95.5% to about 99.8%, from about 97% to
about 99.8%, from about 98% to about 99.8%, from about 98.5% to
about 99.8%, from about 99% to about 99.8%, from about 99.5% to
about 99.8%, from about 97% to about 99.5%, from about 98% to about
99.5%, etc.) of oligonucleotides contacted are deprotected. In some
instances, the EGA mediated deprotection conditions may be adjusted
such that less than 10% (e.g., less than about 9%, less than about
8%, less than about 7%, less than about 6%, less than about 5%,
less than about 4%, less than about 3%, less than about 2%, less
than about 1.5%, less than about 1%, less than about 0.7%, less
than about 0.5%, less than about 0.4%, less than about 0.3%, less
than about 0.2%, less than about 0.1%, less than about 0.07%, less
than about 0.05%, less than about 0.03%, less than about 0.02%,
less than about 0.01%, etc.) of purines (adenosine and guanosine)
present in oligonucleotides are depurinated. In some instances, the
ratio of deprotection and depurination may be from about 99.9% to
about 0.01%, from about 99.5% to about 0.05%, from about 99.5% to
about 0.1%, from about 99.9% to about 0.05%, from about 99% to
about 0.1%, from about 98% to about 0.5%, from about 97% to about
0.01%, from about 97% to about 0.5%, from about 97% to about 1%,
from about 99% to about 1%, from about 98% to about 0.01%, from
about 98% to about 0.1%, etc.
[0152] As discussed elsewhere herein, both failure to deprotect and
depurination of oligonucleotides during synthesis can result in
nucleic acid synthesis errors. While many errors can be corrected,
the goal of achieving low error rates in final product nucleic acid
molecules is often best achieved by low error introduction, in
combination with high efficiency error correction.
[0153] Exemplary error types include mis-incorporation, skipped
base/"deletion" (e.g., due to failure to deprotect), additional
base/"insertion" (e.g., due to an omitted or inappropriately
removed protecting group), and post-base additional alterations
(e.g., depurination). It will generally be desirable to adjust
oligonucleotide synthesis conditions such that each of these error
types is kept as low as technically possible.
[0154] Plates which may be used in the practice of the present
invention include modified forms of plates described in U.S. Patent
Publication No. 2010/0137143 A1, the disclosure of which is
incorporated herein by reference, shows such a representative plate
format.
[0155] FIGS. 2A-2B are schematic representations of a row of wells
200 according to an embodiment of the invention. The embodiment of
FIGS. 2A-2B illustrate five wells each containing a magnetic bead
201 at the bottom. Beneath each well is an electrode 202 which can
deliver current to the well that it is associated with. Each
electrode is communicates with a current controller 203 which
regulates current to the electrode. The magnetic bead may contain a
linker associated with an initial building block. As an example,
the bead may contain first nucleotide (with an A, T, C, G or U
base, or a modified base, depending on the first base desired in
the nucleic acid molecule to be synthesized). The first base may be
added as part of the synthesis process (e.g., with the bead having
a protected hydroxyl group) or may be prederivatized prior to
insertion into the well. In either event, in most cases, a
protective group will be present (e.g., at the 5' position) which
must be removed before another base may be covalently connected as
part of a nucleic acid molecule chain.
[0156] Microfluidic channels (not shown in FIG. 2A) may be included
for efficiently addition and removal of reagents from the wells.
Thus, the invention includes, in part, a microfluidic plate
designed to interface with a microfluidic system for adding and
removing fluids from wells of the plate. Microfluidic channels used
in similar plates are described in U.S. Patent Publication No.
2010/0137143 A1, the disclosure of which is incorporated herein by
reference for background information.
[0157] The cover of the plate 204 shown in FIG. 2A contains aligned
electrodes which are connected to the current controller. A larger
electrode (e.g., an electrode which extends over the tops of all of
the wells) may be included in the cover to "close the circuit".
Thus, the cover may contain one electrode aligned with each well
for which an electrochemical reaction is sought to be, one
electrode in operable connection with all wells of the plate, or
multiple electrodes some or all of which are in operable connection
with two or more wells. In an alternative embodiment, the cover
electrode for each well is replaced with one or more electrodes
embedded or positioned along one or more sidewall of each well.
Thus, it is not critical that electrodes be positioned in the
cover. In fact, in many instances, it will be desirable (e.g., ease
of manufacturing) to place the electrodes in a place other than the
cover.
[0158] Reference electrodes (RE) 205 may also be included to
provide a stable and pre-defined electric potential. To apply a
specific potential on a working electrode (WE), the potential of
the WE against the potential of the RE may be measured. Next the
potential between counter electrode (CE) and WE may be adjusted
until the potential between RE and CE has the correct value.
[0159] One method for deprotection may employ the oxidization of
hydroquinone to benzoquinone (redox system) on the WE in order to
produce protons. To set a specific pH in a well, a constant current
may be applied for a specified period of time. In instances of a
less active WE, a strong increase of the WE potential will occur.
This can lead to unintended reactions (e.g., oxidation of the
solvent or damage of WE material at high potential). To avoid this
effect, the potential of the WE may be controlled.
[0160] The current controller (interchangeably, controller) may be
a microprocessor or processor, such as shown in FIG. 15, for
example The controller (not shown) may comprise a conventional
current control system, including, for example, a microprocessor
circuit in communication with a memory circuit. The memory circuit
may include instructions for directing the microprocessor circuit
to energize one or more of the electrodes (e.g., energize
electrodes associated with well 1 or a plurality of wells).
Optionally, the memory circuit may include instructions for
activating one of a pair of electrodes (e.g., activate the bottom
electrode associated with well 1). In still another embodiment, the
memory circuit may include instructions for gradually
increasing/decreasing bias to the electrodes so as to reduce
possibility of a sudden surge at the well.
[0161] In another embodiment, the current controller communicates
with external processor circuit(s) such as a potentiostat circuit,
input/output ("I/O") devices and displays. The circuit or circuit
board enables the control of the device and may also be used to
communicate with other devices (such as PC, iPad, etc.).
[0162] In a variation of the embodiment of FIG. 2A, both electrodes
(the anode and the cathode) may be placed at the bottom of the
well. This allows for electrical current to be generated near the
bottom of the well, thereby generating a localized EGA in the area
closely adjacent the bead. Depending on the method by which
reagents are added to and/or removed from the wells and other
factors, such configuration can be used to limit cross-talk between
the wells, interference or unintended EGA contamination.
[0163] A related embodiment is shown in FIG. 2B. Here the cover
contains aligned electrodes 205 which extend into the reagent
portion of the well. Drainage tubes 206 are positioned at the
bottom of each well. These drainage tubes serve several functions.
One function is removing reagents at the completion of a chemical
reaction step (e.g., base addition, washing, deprotection, etc.).
Another function is lowering the fluid level for the deprotection
step. In other words, fluid may be added to all of the wells, then
the fluid level may be lowered through drainage tubes before
biasing the wells. Lowering the well's fluid level reduces
cross-spillage between wells and increases synthesis fidelity. The
lowered fluid level also decreases potential cross-talk and
contamination between adjacent wells. The same is true of general
fluid removal through the bottle of the well. This is so because
cross-well contamination with EGA can result in incorrect base
incorporation. Even EGA generated base mis-incorporation occurs in
0.5% of nucleic acid molecules being synthesized in adjoining
wells, the net result could be roughly a doubling of base
mis-incorporation. Thus, drawing down the fluid level in the wells
and bottom of the well drainage results in increase synthesis
fidelity.
[0164] One means for removing fluid from wells from the top of the
wells. This can be done by any number of means including the use of
pipette tips or the introduction of an absorbent material. In
either instance, the goal would be to remove enough fluid from each
well to minimize "splash over". In some instance, the only wells
that fluid levels will be reduced in will be ones which undergo a
reaction (e.g., the generation of EGA, resulting in deprotection).
In other words, fluid level reduction can be performed only in
wells where one or more reactants are generated.
[0165] The construction of the wells can be accomplished by
conventional manufacturing methods, including, for example, CMOS
and VLSI techniques. The wells can be formed in semiconductor or
polymeric substrates. In an exemplary embodiment, the wells are
configured in a semiconductor substrate using conventional etching
and boring techniques. The insider surface of the wells may be
coated with insulating material to reduce cross talk between
adjacent wells. In corollary embodiment, well surfaces may be
coated to increase conductivity thereby generating EGA more
uniformly. Well surfaces may be coated with different layers to
reduce cross-talk while increasing electro- or thermal-conductivity
inside the well. Thus, the walls may comprise a composite of
different material which while reducing cross-talk between the
wells, would increase conductivity within each well for rapid EGA
generation.
[0166] The top surface of the wells (the span between adjacent
wells) may also be coated to provide reagent repellent surfaces. By
way of example, the top surfaces may be coated with hydrophobic
compositions to repel cross-contamination. Methods for reducing
well to well cross-contamination are set out in U.S. Pat. No.
6,444,111, the disclosure of which is incorporated herein by
reference.
[0167] Finally, the shape of the wells may be configured to reduce
cross-contamination while increasing reaction speed. For example,
the wells may be configured to have cylindrical, barrel or conical
shapes.
[0168] In many methods using, for example, the plate configuration
of FIGS. 2A-2B, the sugar group of the first nucleotide is
deprotected by activating (energizing) a chemical reaction
initiated by an electrical signal (or a pulse). As noted elsewhere
herein, one method for doing this is through the generation of an
electrochemically generated acid (EGA). In many cases, it will be
desirable to control the amount of chemical reactant made (e.g.,
EGA) so as to efficiently catalyze the deprotection reaction while
limiting the possibility of reactant from cross-contamination.
[0169] FIG. 17 shows a top view of a channel chip design having
three electrodes. Counter electrode elements 1700 and 1702 are
located at the top of the two side channels and across the bottom
of the flow channel 1701. Reference electrodes 1703 surround the
two wells with working electrodes 1704 are also present.
[0170] In order to limit the flow of protons a series of steps may
be taken, including (1) the use of buffers which prevent
significant pH shifts in the presence of small amounts of protons,
(2) the use of a quinone redox system, and (3) designing the
dimensions of wells and channels to maintain substantial distances
between them (e.g., using well volume 150 times smaller than
according channel volume).
[0171] For example, using the schematic shown in FIG. 17 for
purposes of illustration, the distances between the working
electrode 1704 and counter electrode elements 1700 and 1702 may be
about 200 .mu.m. Further, interception of protons by base molecules
may be used to decrease the number of protons that reach other
wells. Also, reference electrode strips 1703 between wells having
the same potential as the counter electrode elements 1700 and 1702
can be used to generate base molecules and further could prevent
proton "cross-talk". Methods and components such as these, in
addition to other methods set out herein, provide for high fidelity
nucleic acid molecule synthesis.
[0172] For purposes of illustration, a prederivatized bead (e.g., a
magnetic bead) may be placed in wells 1 through 5 of FIGS. 2A-2B
with an "A" bead in wells 1 and 5, a "C" bead in well 2, a "U bead
in well 3, and a "G" bead in well 4. All five wells may then be
filled with an EGA reagent (e.g., a reagent containing methanol,
acetonitrile, hydroquinone, anthraquinone, tetraethylamonium
p-toluene sulfonate, and 2,6-lutidine). The next base to be added
to chain is G and the only nucleic acid molecule of the molecules
to be generated which contains a G at position 2 is in Well 1.
Thus, current is applied only to Well 1. This current creates an
acidic microenvironment which results in deprotection of the 5'
position of the nucleotide only in Well 1. After a fixed (or
variable) reaction time, all five wells are washed. A nucleotide,
which has the phosphorus, sugar and a base (a T in this instance),
is added to all of the wells in the presence of a catalyst (e.g., a
tetrazole catalyst). After a predefined reaction time, all five
wells are washed and unreacted first nucleotide may be capped to
avoid accumulation of deletions, using, for example, acetic
anhydride and N-methylimidazole. Again, after a predetermined
reaction time, all five wells are washed and phosphite triesters
formed by chemical reaction may be oxidized to form the more stable
phosphate triester, using, for example, iodine containing reagents.
This process is then repeated until the final base of the nucleic
acid molecule has been added. Later, the synthesized nucleic acid
molecules may be cleaved from the solid support. This may be done,
for example, using aqueous or gaseous ammonia with heating. The
cleavage method may vary, however, with factors such as the linker
used.
[0173] The amount of current applied to each well and its duration
will vary with parameters such as the amount of reagent to be
generated and the size of the well. The applied current may be a
pulse of varying shape and/magnitude. The pulse may define a series
of varying amplitude pulses (frequency) or a gradual
increase/decrease amplitude. The amplitude and duration of the
pulse can be adjusted for the optimum generation of reagent. As an
example, the current applied to a well may be adjusted for a
specified period of time to generate a specified quantity of EGA.
The amount of EGA intended for generation will typically be at
least enough sufficient to fully catalyze deprotection of the
nucleic acid molecules present.
[0174] In some aspects of the invention, "electrowetting" may be
employed. Two aspect of the invention where electrowetting may be
particularly useful is for the mixing of reagents for (1) nucleic
acid synthesis and pooling (Modules 1 and 2) and (2) assembly
(Module 3).
[0175] In brief, electrowetting involves modifying the surface
tension of liquids on a solid surface using a voltage. Application
of an electric field (e.g., alternating or direct), the contact
angle between the fluid and surfaces can be modified. For example,
by applying a voltage, the wetting properties of a hydrophobic
surface can become increasingly hydrophilic and therefore wettable.
Electrowetting principle is based on manipulating droplets on a
surface comprising an array of electrodes and using voltage to
change the interfacial tension. In some embodiments, the array of
electrode is not in direct contact with the fluid. In additional
embodiments, the array of electrode may be configured such as the
support has a hydrophilic side and a hydrophobic side. The droplets
subjected to the voltage will move towards the hydrophilic side. In
some embodiments, the array or pattern of electrodes may be a high
density pattern. When used in conjunction with the phosphoramidite
chemistry (as well as other reagents), the array of electrodes
should be able to move droplets volumes ranging from 1 pL (and
less) to 10 pL. Accordingly, aspects of the invention relate to
high voltage complementary semi-conductor microfluidic controller.
In some embodiments, the high voltage complementary semi-conductor
device (HV-CMOS) has an integrated circuit with high density
electrode pattern and high voltage electronics. In some
embodiments, the voltage applied is between 15V and 30V.
Electrowetting methods are set out in U.S. Patent Publication No.
2012/0220497 A1, the disclosure of which is incorporated herein by
reference.
[0176] Electrowetting works by using an electric voltage to alter
the shape of a liquid drop. In some instances, electrowetting
involves a sessile drop positioned on a dielectric-coated
electrode. When current is applied, the drop flattens and flows out
to the sides, thereby wetting additional surface. When current is
removed, the drop returns to its original shape and retracts from
the areas covered upon current application.
[0177] In some embodiments of the invention, nucleic acid synthesis
site may have adjacent to is a series of reagents that flow into
and recede from the synthesis site when current is applied to the
correct reagent location. Thus, the invention includes methods for
the synthesis of nucleic acid molecules by the addition and removal
of reagents from a synthesis site induced by the addition and
removal of current from adjacent reagents. In some instances, the
number of reagents adjacent to a nucleic acid synthesis site may be
from about 2 to about 10, from about 3 to about 10, from about 4 to
about 10, from about 5 to about 10, from about 6 to about 10,
etc.
[0178] Electrowetting methods may also be used for fragment
assembly and error correction (Module 3). Thus, the invention
includes methods for mixing reagents using electrowetting for the
assembly and error correction of nucleic acid molecules. Reagents
that may be contacted with nucleic acid molecules in these aspects
of the invention include exonucleases, mist-match repair
endonucleases (MMEs), ligases, buffers, EDTA solutions, etc.
[0179] One problem with electrowetting methods is "splash over"
which may occur between mixing areas and also because, in many
instances, planar or semi-planar surfaces are used. Thus, unless
microfluidic drainage channels, or the like, are employed, there is
a possibility of splash over contamination of mixing areas during
reagent changes.
[0180] Two means for minimizing this mixing is through the use of
microfluidic channels and barriers. Barrier may be placed (e.g.,
physical barriers such as raised areas) to prevent reagents from
moving from one mixing area to another. After a desired reaction is
finished, the barrier may be removed. Different reactions may be
performed sequentially at different and/or overlapping subsets of
mixing areas.
[0181] Polymer based physical barriers may be used in the practice
of the invention. For example, these may be applied at the tops of
wells and other areas where there is the potential for EGA cross
contamination of "splash over". Typically, such polymers will not
efficiently conduct electrical current. Exemplary polymer materials
include natural and synthetic rubber.
[0182] As mentioned above, the methods of nucleic acid synthesis
may be implemented and controlled in a system according to various
embodiments described herein by a processor or computing system,
such as the exemplary computing system depicted in FIG. 15. For
example, applying current (pulse or continuous wave) to selected
wells to generate a specific quantity of EGA to fully catalyze
deprotection may be controlled by a computing system executing
processor executable instructions according to various embodiments
of the present teachings.
[0183] Deblocking may also occur through the use of redox systems.
Examples of such system systems include hydroquinone/anthraquinone;
pH buffer such as 2,6-lutidine to reduce proton cross talk between
active wells and inactive neighboring wells.
[0184] Efficient production of nucleic acid molecules may require
that nucleic acid synthesis steps be tailored to the molecules
being constructed. Consider the example of the construction of
nucleic acid molecules designed for construction of viral genome
with a CG/AT ratio of 60/40. Nucleic acid molecule building blocks
of such a genome will invariable have more Cs and Gs than As and
Ts. In such an instance, it may be desirable to have more reactions
which add Cs and Gs than As and Ts. As an example, the sequence of
base addition may be a repetition of A T C G C A T G C G (SEQ ID
NO: 1). Thus, the invention further includes chemical synthesis
processes which are tailored for efficient production of specified
nucleic acid molecules. In one aspect, this entails adding bases to
nucleic acid molecules during chemical synthesis in manner which
reflects or closely approximates the prevalence of the bases in
those molecules.
[0185] The invention includes, for example, methods which result in
high fidelity, microscale production of nucleic acid molecules.
Thus, the invention includes methods by which nucleic acid
molecules are produced with the following parameters: between
1.times.10.sup.5 and 1.5.times.10.sup.9 copies of a nucleic acid
molecule are generated with an average number of base
mis-incorporations of between 1 base in 100 and 1 base in 500. The
invention includes similar methods with the parameters set out in
Table 3.
TABLE-US-00003 TABLE 3 Nucleic Acid Molecule Copies No. of Base
Mis-Incorporations (Avg.) 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 150 to 1 in 500 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 150 to 1 in 400 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 100 to 1 in 300 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 200 to 1 in 400 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 300 to 1 in 1,000 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 300 to 1 in 2,000 1 .times. 10.sup.6 and 1.5 .times.
10.sup.9 1 in 500 to 1 in 4,000 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 150 to 1 in 500 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 150 to 1 in 400 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 100 to 1 in 300 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 200 to 1 in 400 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 300 to 1 in 1,000 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 300 to 1 in 2,000 1 .times. 10.sup.7 and 1.5 .times.
10.sup.9 1 in 500 to 1 in 4,000 1 .times. 10.sup.7 and 1.5 .times.
10.sup.10 1 in 150 to 1 in 400 1 .times. 10.sup.7 and 1.5 .times.
10.sup.10 1 in 100 to 1 in 300 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 150 to 1 in 400 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 100 to 1 in 300 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 200 to 1 in 400 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 300 to 1 in 1,000 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 300 to 1 in 2,000 1 .times. 10.sup.8 and 1.5 .times.
10.sup.10 1 in 500 to 1 in 4,000
[0186] Nucleic acid molecules prepared and used in accordance with
the invention may contain modified nucleic acid molecules including
locked nucleic acids (LNA), peptide nucleic acids (PNA), and the
like. A PNA is a polyamide type of DNA analog, and the monomeric
units for A, G, T, U, and C are available commercially.
Furthermore, nucleic acid molecules of the invention may comprise
one or more modified bases selected from the group including, but
not limited to, 5-fluorouracil, 5-bromouracil, 5-chlorouracil,
5-iodouracil, hypoxanthine, xanthine, 4-acetylcytosine,
5-(carboxyhydroxylmethyl)uracil,
5-carboxymethylaminomethyl-2-thiouridine,
5-carboxymethylaminomethyluracil, dihydrouracil,
beta-D-galactosylqueosine, inosine, N6-isopentenyladenine,
1-methylguanine, 1-methylinosine, 2,2-dimethylguanine,
2-methyladenine, 2-methylguanine, 3-methylcytosine,
5-methylcytosine, N6-adenine, 7-methylguanine, 8-azaguanine,
5-methylaminomethyluracil, 5-methoxyaminomethyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarboxymethyluracil,
5-methoxyuracil, 2-methylthio-N6-isopentenyladenine,
uracil-5-oxyacetic acid, wybutoxosine, pseudouracil, queosine,
inosine, 2-thiocytosine, 5-methyl-2-thiouracil, 2-thiouracil,
4-thiouracil, 5-methyluracil, uracil-5-oxyacetic acid methylester,
5-methyl-2-thiouracil, 3-(3-amino-3-N-2-carboxypropyl)uracil, and
2,6-diaminopurine. The latter modified base can form three hydrogen
bonds when base-paired with dT and can increase the T.sup.m of
short nucleic acid molecules by as much as 1-2.degree. C. per
insertion. This effect, however, is complex and is dependent on
sequence context.
[0187] 2-Aminopurine can substitute for dA in a nucleic acid
molecule. It is a naturally fluorescent base that is sensitive to
the local environment making it a useful probe for monitoring the
structure and dynamics of DNA hairpins and for detecting the base
stacking state of a duplex. 2-aminopurine can be destabilizing and
slightly lower the T.sup.m. 5-Bromo-deoxyuridine is a photoreactive
halogenated base that can be incorporated into nucleic acid
molecules to crosslink them to DNA, RNA or proteins with exposure
to UV light. Other modified bases such as inverted dT may be
incorporated at the 3'-end of a nucleic acid molecule, leading to a
3'-3' linkage which inhibits both degradation by 3' exonucleases
and extension by DNA polymerases. In another embodiment of the
invention an inverted dideoxy-T may be placed at the 5' end of a
nucleic acid molecule to prevent unwanted 5' ligations. A
dideoxy-C(ddC) 3' chain terminator may be used to prevent 3'
extension by DNA polymerases. 5-Methyl deoxy-C when substituted for
dC will increase the T.sup.m by as much as 0.5.degree. C. per
insertion. In one embodiment the naturally occurring base
deoxy-Inosine may be used which is less destabilizing than
mismatches involving the four standard bases. Thus, the invention
provides, in part, compositions and methods relating to the
synthesis of modified nucleic acid molecules with novel properties
and/or functions.
[0188] One modification of the plate format shown in FIG. 2 is to
use a "liquid cover" to the wells. One way this could be performed
is for the wells to contain a bilayer. For example, the bottom
portion of the well containing the solid support could contain an
EGA. Above this could be a lower density, optionally non-miscible,
fluid. The lower density fluid layer will prevent or retard the
diffusion of acid out of the desired well and over to an undesired
well. Further, the lower density fluid can be positioned to make
conductive contact with an upper electrode. One example of a
commercially available "liquid coverslip" is sold by Ventana
Medical Systems, Inc (cat. no. 650-010). This product is a solution
used as a barrier between the aqueous reagents and the air, which
prevents evaporation, and is designed to provide a stable aqueous
environment for applications such as immunohistochemistry and in
situ hybridization reactions.
[0189] One exemplary protocol for practicing methods of the
invention is as follows. Porous silane-coated magnetic beads (MyOne
Beads, Dynal) with a uniform diameter of 1 micron are added to the
chip surface by controlled or pulsed flow to ensure uniform
distribution of the beads across the microwells (about 1.3 .mu.m
diameter) on the chip and to ensure that a maximum number of wells
are loaded with one bead. Wells not containing a bead are
identified by a pre-synthesis current check that delineate the
resistance difference among empty wells and well that contain a
conductive magnetic bead.
[0190] A variety of chemistries are possible in the preparation of
the bead surface. For example, a number of layers of silane can be
produced to impart greater functional surface area to the beads.
The silane coating(s) is/are prepared so that there is stable
attachment of the hydroxyl functional group; typically through a
trimethoxy or triethoxy silane linker, of the silane core to the
naked silica bead surface to expose a primary hydroxyl group
through with the initial amidite synthetic step is coupled. The
fundamental chemistry, developed for a planar array surface
electrode, for initiation and coupling in DNA synthesis can be
found in Maurer et al., Electrochemically Generated Acid and Its
Containment to 100 Micron Reaction Areas for the Production of DNA
Microarrays, PLoS ONE 1(1): e34. doi: 10.1371/journal.pone.0000034
(2006).
[0191] Fabrication of the chip: Electrode materials such, as
iridium metal up to 50 nm thick are produced on oxidized
high-resistivity silicon selected for high conductivity and
chemical stability under synthesis, reagent addition and deblocking
conditions. Electrodes are connected by ultrasonic bonding to a
printed circuit board to provide digitally controlled analogue
integrated switch circuits activating electrodes chosen for
deblocking a given well. Printed circuit boards are carefully
aligned and bonded to the regular microwell structure to generate
the synthesis chip. A cover plate providing and sealing the
interior volume for reagents and a general complementary circuit
electrode is bonded at the perimeter and over the upper surface of
the microwell structure to complete the closed synthesis chip.
[0192] Conventional semiconductor or polymer material may be used
for forming wells 200. For example, CMOS technology can be used to
form wells of desired shape or size in the semiconductor material
such as SiO or SiO.sub.2. Depending on the desired application,
electrodes 202 can be fabricates with wells 200 or separately.
[0193] Administration of nucleic acid synthesis (e.g., DNA
synthesis) reagents to the chip can be performed by any number of
means. For example, once the beads are loaded into the chip, a
computing system controls a series of reagent additions and
washings may be carried out to affect phosphoramidite DNA synthesis
on the surface of the beads residing in the microwells of the chip.
Processor-executable instructions may be employed which determine,
for any given population of DNA sequences, the optimal order of DNA
synthesis reagent additions and sequence of reagent additions and
washing steps relative to volume/cost of reagents and time of a
synthesis run. Furthermore, as mentioned above, controller or
processor-controlled current to specific wells on the chip
determine in which wells electrochemically generated acid may be
produced and deprotection to activate the growing nucleic acid
molecule on the bead in the well may be chemically prepared to
couple the next amidite base added into the reaction vessel. A
number of specific configurations of apparatus and components for
administration of synthesis reagents and to ensure precise and
controlled fluid administration are possible through an optimized
development process. Phosphoramidite DNA synthesis steps,
conditions and reagents using EGA to affect deprotection can be
found in, for examples, Maurer et al., Electrochemically Generated
Acid and Its Containment to 100 Micron Reaction Areas for the
Production of DNA Microarrays, PLoS ONE 1(1): e34.
doi:10.1371/journal.pone.0000034 (2006) and Egeland and Southern,
Electrochemically directed synthesis of oligonucleotides for DNA
microarray fabrication, Nucleic Acids Research, 33(14):e125
(2005).
[0194] Composition and concentration of EGA components: The exact
composition and concentration of EGA reagent is influenced by the
precise conductive, structural and geometric properties of the
electrodes and microwells and the parameters associated with the
application (current, voltage and time) of current to convert the
EGA to its acid forms. Generally, the smaller the volume for EGA
production to affect deprotection, the smaller the required current
strength and/or time of current application. Since the amount of
nucleic acid molecule produced in such microscale systems falls
below a threshold that can be directly and accurately measured,
surrogate assays, such as hybridization or product enrichment
following target amplification, for nucleic acid molecule synthesis
and coupling efficiency are typically required. EGA reagents,
including hydroxquinone and benzoquinone, with tetrabutylammonium
hexafluorophosphate in anhydrous acetonitrile are used to generate
electrochemical acid via anodic oxidation to affect deprotection.
EGA reagents above in concentration up to 25 mM are prepared and
administered to the chip prior to the application of current to
affect deprotection. In determination of the optimal parameters, it
will generally be desirable to avoid base damage caused by
depurination from over-exposure of DNA to acid.
[0195] Application of current to affect EGA-based DMT deprotection:
Current may be applied constantly up to 2 .rho.A and voltage up to
2 V is applied to an electrode in the controlled circuit for a time
period of up to 30 seconds. Current may also be applied in pulse
durations from 10 to 2000 ms during a time of 1 to 60 seconds.
Current may also be applied as in various pulses (e.g., from about
two to about 10,000, from about ten to about 10,000, from about
fifty to about 10,000, from about 100 to about 10,000, from about
1,000 to about 10,000, from about ten to about 500, etc. pulses) up
to 2 .rho.A (e.g., from about 0.02 nA to about 20,000 nA, from
about 0.2 nA to about 20,000 nA, from about 0.2 nA to about 5,000
nA, from about 0.2 nA to about 2,000 nA, from about 0.2 nA to about
1,000 nA, from about 0.2 nA to about 5000 nA, from about 2.0 nA to
about 20,000 nA, from about 2.0 nA to about 10,000 nA, from about
2.0 nA to about 5,000 nA, from about 2.0 nA to about 2,000 nA, from
about 5.0 nA to about 20,000 nA, from about 5.0 nA to about 8,000
nA, from about 10 nA to about 20,000 nA, from about 10 nA to about
8,000 nA, from about 10 nA to about 5,000 nA, from about 20 nA to
about 20,000 nA, from about 20 nA to about 8,000 nA, from about 50
nA to about 20,000 nA, from about 50 nA to about 10,000 nA, from
about 50 nA to about 5,000 nA, from about 100 nA to about 10,000
nA, from about 500 nA to about 20,000 nA, from about 500 nA to
about 10,000 nA, from about 500 nA to about 5,000 nA, from about
1,000 nA to about 20,000 nA, from about 1,000 nA to about 10,000
nA, etc.). In some instances, current will be pulsed for anywhere
from about 1 second to about 30 seconds, from about 2 second to
about 30 seconds, from about 4 second to about 30 seconds, from
about 5 second to about 30 seconds, from about 5 second to about 20
seconds, from about 5 second to about 15 seconds, from about 5
second to about 10 seconds, etc. Of course, efficient deprotection
and nucleic acid molecule synthesis must be determined as the exact
composition and concentration of EGA reagent is influenced by the
precise conductive, structural and geometric properties of the
electrodes and microwells and the parameters associated with the
application (current, voltage and time) of current.
[0196] In certain embodiments of the invention the nucleic acid
molecule or a portion thereof may be subject to a sequence
optimization process prior to synthesis. Different computational
approaches for sequence modification are known in the art and may
be employed to optimize a given nucleotide sequence in terms of 1)
efficient assembly and/or 2) improved performance in a given host.
To design a nucleotide sequence for optimal assembly, a full-length
sequence may be broken down into a defined number of smaller
fragments with optimal hybridization properties by means of an
algorithm taking into account parameters such as melting
temperature, overlap regions, self-hybridization, absence or
presence of cloning sites and the like. In certain aspects of the
invention, at least part of the desired nucleic acid sequence may
encode a polypeptide or protein. In such cases, it may be desirable
to optimize the open reading frame for improved performance in a
given homologous or heterologous host, such as expression yield or
solubility. An increase in gene expression may be achieved, for
example, by replacing non-preferred or less preferred codons by
preferred codons or by increasing the number of CpG dinucleotides
in the open reading frame as described, for example, in U.S. Pat.
Nos. 5,786,464 and 6,114,148 and U.S. Patent Publication No.
2009/0324546 AA, the disclosures of which are incorporated herein
by reference.
[0197] In one specific embodiment, an optimized open reading frame
may be combined with an algorithm to encrypt a secret message into
the open reading frame as described in U.S. Patent Publication No.
2011/0119778 AA. Such message may allow the identification or
tracking of certain synthetic nucleic acid molecules. In certain
aspects of the invention, it may be desired to use an optimization
strategy that takes into account multiple different parameters
simultaneously including assembly--as well as expression-related
sequence properties. One example of a comprehensive multiparameter
approach that may be used in the current invention for optimized
sequence design is the GENEOPTIMIZER.RTM. technology described in
U.S. Patent Publication No. 2007/0141557 AA, the disclosure of
which is incorporated herein by reference. Thus, the invention
provides in part aspects of optimal sequence design for downstream
applications including assembly and expression strategies.
[0198] Module 2
[0199] After completion of a synthesis run on Module 1,
support-associated (e.g., bead-associated) nucleic acid molecules
may be subject to post-processing in Module 2. Processes performed
in Module 2 may be performed manually or by computer directed
automation controlling such steps as picking and pooling of a bead
(e.g., a magnetic bead) from the synthesis microwell array and
vapor-phase cleavage and deprotection to prepare the nucleic acid
molecules for subsequent assembly steps, as appropriate.
[0200] To expose a microwell array of bead-attached nucleic acid
molecules, the cover of the synthesis well, when present, may be
removed. In one embodiment, the cover is removed by automatic means
in a computer-controlled manner.
[0201] A bead picking instrument comprising, for example, a
precision-controlled electro-micromagnet can be programmed and
controlled to extract and pool individual beads harboring
synthesized nucleic acid molecules. Depending on the application
and the number of nucleic acid molecules to be assembled, all of
the beads of the microwell array may be pooled or only a subset of
the beads. When only a subset of the beads are pooled or when the
total number of beads is limited, the number of beads pooled may
vary widely and include from about 10 to about 50, from about 50 to
about 100, from about 100 to about 1000, from about 50 to about
10,000, from about 100 to about 10,000, or from about 500 to about
10,000 individual beads. These beads may be deposited in any
suitable container. One example of a container is the well of a
microwell plate (e.g., a well of a 1536 microwell plate).
[0202] Automation suitable use with the invention includes a
precision-controlled electromicromagnet picks up the first bead and
deposits it into a pooling well (i.e., a well which contains
multiple beads for collection of nucleic acid molecules sought to
be used in combination). Alternatively, a precision-controlled
electromicromagnet can be used which picks up the first bead and
then moves in the X-Y direction to the next position, lowers down
in the Z direction to pick up the second bead, back up in the Z
direction to get out of the magnetic field range, moves to the
third well in the X-Y direction, etc. Thus, the magnet is left "on"
and the set of beads (e.g., from about two to about fifty, from
about ten to about fifty, from about two to about one hundred, from
about ten to about one hundred, from about twenty to about eighty,
etc.) is picked up and carried as a string of beads. As a set of
beads is collected, this set is then deposited in simultaneously
deposited into a pooling well. Of course, multiple sets of beads
may be collected and deposited in a single pooling well.
[0203] In some instances, beads may be extracted and pooled using
systems as described, for example, in U.S. Patent Publication Nos.
2008/0281466 AA or 2008/0113361 AA or in U.S. Pat. Nos. 6,887,431;
7,347,975 or 7,384,606, the disclosures of which are incorporated
herein by reference. In other embodiments of the invention a bead
picking instrument with at least one integrated
precision-controlled electro-micromagnet may be used. Such a
picking instrument may be controlled by a control unit which can be
programmed to control the movement of the micromagnet to align with
specific microwells. In a further embodiment, the control unit may
provide means to control the adjustment of the distance between the
micromagnet and the microwell. In a specific embodiment, the
micromagnet may be controlled and activated by electric means to
allow extraction of single magnetic beads carrying a specific
nucleic acid sequence.
[0204] Electro-micromagnets used in the current invention may be
hollow magnets or needle shaped and will often be of a size and
dimension to focus the magnetic field at its tip to allow for
specific targeting of individual beads. In a specific embodiment,
the micromagnet may be composed of an electro-magnet and a
permanent magnet wherein the activity of the permanent magnet can
be controlled by the electro-magnet. Electro-micromagnet used in
conjunction with the invention may be in any number or format and
may, for example, comprise a single magnet or be arranged together
with other micromagnets in a row.
[0205] In certain embodiments of the invention, an
electro-micromagnet may be used to extract and pool all magnetic
beads contained in the microwells of a single arrays. For this
purpose, the electro-micromagnet may be allocated to each microwell
to extract the bead-attached nucleic acid molecules in a step-wise
manner in a pre-defined or random order. In one embodiment, all
nucleic acid molecules required for the assembly of a full-length
construct may be synthesized on a single array. According to the
amount of nucleic acid molecules required to build a full-length
construct, arrays of different sizes and dimensions can be
used.
[0206] In another embodiment, the electro-micromagnet may be
programmed to target only a portion of the microwells of a specific
array to extract and pool a predefined selection of bead-attached
nucleic acid molecules. The electro-micromagnet can be programmed
to extract and pool beads from the microwells of two or more
different plates. The picking may combine full extraction of all
beads of a first plate with selective extraction of a portion of
beads obtained from a second plate. The first and the second plate
may vary in size and dimension.
[0207] Each magnetic bead extracted by the micromagnet may then be
transferred to a pooling station by moveable means of the picking
instrument. In one embodiment the pooling station may contain a
chamber with a microwell plate. In one embodiment the microwell
plate may be a 1536 microwell plate. However, microwell plates of
other sizes and dimensions (e.g., standard 96 well plates) are
known in the art and can be used in the current invention. Defined
fractions of nucleic acid molecules can be pooled in individual
wells of a microwell plate wherein one pooled fraction contains all
nucleic acid molecules required to assemble at least a defined
fragment of a full-length construct. In one embodiment, an
individual nucleic acid molecule pool may contain all nucleic acid
molecules required to assemble a full-length construct. Different
nucleic acid molecule pools allocated to each well can be further
identified using a machine readable identifier disposed on the
microwell plates.
[0208] Electrostatic forces may also be used to remove beads and
other substrates from synthesis platforms. Using FIGS. 2A-2B for
purposes of illustration, oligonucleotide synthesis substrates
(beads in this instance) may have an electrostatic charged and
separated from association with a surface or well using an opposite
charge. For example, if one or more beads shown in FIGS. 2A-2B have
a positive charge then the lower electrode may be used to generate
a positive charge to repel the bead and force it from the well.
Magnetic charges can also be used to achieve the same purpose.
Residual magnetism may also be employed. In essence, residual
magnetism is magnetism that remains in a material after being
exposed to magnetic force. In many instances, magnetic substrates
will be of small size. Thus, attraction of such substrates will
typically not requires strong magnetic fields. Residual magnetism
may be present in the substrate a selection probe used to bind to
the substrate or both. Further, charges may be used to selectively
remove a subset of synthesis substrates from a synthesis
platform.
[0209] Electrostatic forces for required for the removal of beads
and other substrates from synthesis platforms can be readily
calculated. TABLE 4 below assumes a relative homogeneous electrical
field is present and that each bead acts as a single charge point.
Nucleic acid molecules carry with them a charge which should be
taken into consideration when charge is used to extrude a bead from
a well. Further, charge need only be applied to wells that contain
substrates with desired nucleic acid molecules (e.g., nucleic acid
molecules for assembly into larger nucleic acid molecules.
TABLE-US-00004 TABLE 4 Charge per Strand Electrode Number of
Strands (As) Voltage (V) Electrode Distance (m) 1,000,000 1.6
.times. 10.sup.-19 2 1.00 .times. 10.sup.-5 Electrode Distance
(.mu.m) 10 Electric Field Point Charge (As) Strength (V/m) Force N
1.6 .times. 10.sup.-13 200000 0.000000032 Electric Field Strength
(V/mm) Force .mu.N 200 0.032
[0210] In another embodiment, a synthesis platform may contain a
series of regions that separate from other regions of the synthesis
platform. For example, a synthesis platform may contain 100 rows of
synthesis areas in a square 10.times.10 arrangement. Further, the
synthesis platform may be designed so that it is separatable into
ten rows of ten synthesis areas. For purposes of illustration,
assume that one seeks to produce eight different assembled nucleic
acid molecules and these assembled nucleic acid molecules are
designed to be formed from the assembly of the following number or
oligonucleotides:
TABLE-US-00005 TABLE 5 Assembled No. of Row Assembled No. of Row
Nucleic No. Oligos No. Molecule No. Oligos No. 1 7 1 5 9 5 2 8 2 6
10 6 3 8 3 7 13 7-8 4 9 4 8 15 9-10
[0211] Table 5 indicates the numerical designation of the various
assembled nucleic acid molecules, the number of oligonucleotides
that will be used to assemble the assembled nucleic acid molecules,
and the rows in which the oligonucleotides are synthesized in. In
this embodiment, rows 1-5 will each have at least one synthesis
area in which no oligonucleotides will be produced.
[0212] After synthesis is completed, the separatable rows may be
separated and the synthesized nucleic acid molecules,
collected/processed and assembled, for example, as described
elsewhere herein.
[0213] Other methods may also be used to collect nucleic acid
synthesis substrates, including (1) "grabbing", for example by the
use of tweezers like devices which operate based upon mechanical
(e.g., actual grabbing), optical, sonic, magnetic principles, (2)
"destroying" structures surrounding nucleic acid synthesis
substrates by methods such as chemical dissolution or through the
use of lasers, (3) moving nucleic acid synthesis substrates by, for
example, the use of thermal, electrostatic, magnetic, fluidic
energy, (4) hybrid gripper which combine, for examples, (a)
magnetic and fluidic flushing, (b) magnetic and piezoelectric
methods, and (c) electrostatic lifting and fluidic flushing, (5)
magnetic fixing/collecting using, for example, modulated permanent
magnets, external coils, planar coils on synthesis substrates,
etc., (6) electrostatic lifting & collecting, and (7) flux
direction (e.g., the addition of fluid to the bottom of a well to
lift substrates).
[0214] Pooling stations used in the practice of the invention may
further contain a microwell handling device which comprises
controllable moveable means for moving the microwell plate from a
first to at least a second position in X and/or Y and/or Z
direction and can be programmed to perform liquid handling steps.
Such pooling stations may further be equipped with a pipetting
device and a suction apparatus allowing for controlled addition and
removal of reagents. Alternatively the removal of liquid can be
performed by vacuum means. The pipetting device may further be
connected to reagent reservoirs and mixing means to mix and add
defined amounts of reagents required for purification and
subsequent processing and assembly steps. Integrated liquid
handling devices combining the respective functions are known by
those skilled in the art.
[0215] In a specific embodiment, the pooling station integrates
means to allow for further combining of one or more nucleic acid
molecule pools from first and second wells into a third well to
yield a larger nucleic acid molecule pool. Such step-wise pooling
may be required in cases where variants or libraries of full-length
constructs are assembled from identical and variable sequence
elements.
[0216] Pooling stations used in the practice of the invention may
further contain a magnet located beneath the microwell plate. In a
specific embodiment such a plate magnet may serve as counterpart to
the micromagnet in order to trigger release of the extracted beads
into the recipient microwell. Alternatively the electro-micromagnet
may be a hollow magnet connected to a capillary that can be flushed
with liquid to blow out the bound bead into the recipient well.
Other means of bead release may also be employed.
[0217] With respect to pooling of nucleic acid molecules, this may
be done any number of ways. For example, synthesis substrates may
be collected and placed in a single contained. Alternatively,
nucleic acid molecules may be released from synthesis substrates
and then contacted with each other. Further, nucleic acid molecules
may be assembled by hybridization. This means that more than one
assembly may occur in the same container. In other words, the
invention includes methods by which assembly of more than one
(e.g., two, three, four, five, six, etc.) nucleic acid molecule
occurs from smaller, chemically synthesized nucleic acid molecules.
One application where the assembly of more than one larger nucleic
acid molecule (e.g., replicable nucleic acid molecules) may be
useful is where the assembled nucleic acid molecules are intended
for insertion into the same cell. Thus, one of the assembled
nucleic acid molecules could be a chromosome and another could be a
plasmid.
[0218] Once desired pools of nucleic acid molecules have been
generated, bead-attached nucleic acid molecules will often be
further processed, for example, to obtain functional nucleic acid
molecules for downstream reactions. After chain synthesis the
5'-terminal 5'-hydroxy group is usually protected, for example,
with a dimethoxytrityl (DMT) group; the internucleosidic phosphate
or phosphorothioate moieties may also be protected, for example,
with 2-cyanoethyl groups; and the exocyclic amino groups in all
nucleic bases (except for T and U) may be protected, for example,
with acyl protecting groups. Usually, the 5'-terminal DMT group is
cleaved after the last synthesis cycle on the support before the
bead-attached nucleic acid molecules are pooled. However, all
protection groups have to be removed in a deprotection step before
the nucleic acid molecules can be effectively used in subsequent
processes.
[0219] In one embodiment of the invention, deprotection is
performed, for example, without releasing the nucleic acid molecule
form the bead. This can be carried out by choosing a base-stable,
non-cleavable linker. Respective linkers are known by the skilled
person.
[0220] In one embodiment, nucleic acid molecules are released from
the beads prior to downstream assembly. If cleavage of nucleic acid
molecule is required, cleavage and deprotection may be performed in
a single step. Release of the nucleic acid molecules may be
achieved by cleaving the linker attaching the 3'-end of the nucleic
acid molecule to the bead (e.g., a magnetic bead) with a suitable
reagent. Suitable reagents and conditions for cleavage depend on
the nature of the linkage as described elsewhere herein and are
known by those skilled in the art.
[0221] In one embodiment of the invention, nucleic acid molecules
are attached to the magnetic beads via succinyl groups. The
succinyl linker may be cleaved by the use of, for example,
concentrated aqueous ammonium hydroxide. The reaction is usually
carried out at temperatures between 50.degree. C. and 80.degree. C.
for at least one to about eight hours. Of course, cleavage
conditions may vary depending on the protocol and the protecting
groups used. The ammonia solution may then removed by evaporation,
leaving the nucleic acid molecules ready for purification.
[0222] In one embodiment, cleavage may be carried out by
vapor-phase processing. In vapor-phase processing, nucleic acid
molecules may be cleaved in a closed chamber in a gaseous
environment comprising gaseous cleavage/deprotection reagent, such
as gaseous ammonia or ammonium hydroxide vapors. Respective methods
are set out, for example, in U.S. Pat. No. 5,514,789 or 5,738,829,
the disclosures of which are incorporated herein by reference.
[0223] The above reaction will typically also triggers cleavage of
other protecting groups including the cyanoethyl group, the group
protecting the heterocyclic primary amine and the DMT group on the
very last base. Thus, a single cleavage reaction may be used, when
appropriate, to remove all protecting groups present.
[0224] Linkers used in the practice of the invention may be cleaved
using at least two approaches: (a) simultaneously under the same
conditions as the deprotection step or (b) subsequently utilizing a
different condition or reagent for linker cleavage after the
completion of the deprotection step. Various methods to remove
universal linkers from a nucleic acid molecule are described in the
art such as, for example, U.S. Patent Publication No. 2002/0143166
A1, the disclosure of which is incorporated herein by
reference.
[0225] For downstream applications, it may be required to purify
the pooled and deprotected nucleic acid molecules to remove the
cleaved groups, for example, by precipitation. It may further be
required to separate the nucleic acid molecule mixture from the
magnetic particles or other support. In one embodiment, a plate
magnet located beneath the microwell plate can be used to
immobilize the beads in the wells while the nucleic acid molecules
can be eluted, for example, by suction. Alternatively, in the
absence of a plate magnet, the beads may be automatically removed
from the wells by magnetic means while the nucleic acid molecules
would be retained in the well to obtain femtomoles of individual
pools of high quality nucleic acid molecules at picomole
concentration ready for further processing or use.
[0226] In some instances, nucleic acid molecules may be separated
from solid support while the solid supports remain localized in the
same or similar location as to where the nucleic acid molecules
were synthesized. In such instances, typically after synthesis
completion, oligonucleotide synthesis reagents may be removed from
contact with synthesis supports, followed by the addition of one or
more reagents for release of the constructed oligonucleotide, also
referred to as cleavage reagents. These releasing reagents may be
in forms such as liquid or gaseous. Gaseous reagents are referred
to above.
[0227] In many instances, the cleavage reagent agent will be
volatile (e.g., it can be removed via freeze drying) and non-ionic.
The cleaved oligonucleotides may then be recovered by either
removal from wells, when present, or by rinsing the synthesis
substrate. When microwells are employed for synthesis, cleavage
reagents in liquid form may be used. The synthesis substrate may be
coated with such liquid reagents followed by either group removal
of synthesized oligonucleotides or removal of individual
oligonucleotides (less than all of oligonucleotides present).
Removal of individual oligonucleotides may be achieved, for
example, by limiting agitation of the substrate and site specific
removal (e.g., with a pipette tip) of fluid containing individual
oligonucleotides after cleavage has occurred. Such methods will be
particularly useful when the substrate contains wells or
cavities.
[0228] Optionally, synthesized nucleic acid molecules may be
concentrated step after pooling, cleavage and/or deprotection but
to entering into Module 3 processes. One concentration method of
such concentration would be by an additional second binding,
washing, and elution series of sets to reduce the final volume.
This increased concentration will increase the concentration of
synthesized nucleic acid molecules, resulting in accelerated
hybridization of overlapping segments in sub-fragment generation as
may be desired. Concentration to an increased concentration may
also be used to "normalize" the concentration of multiple pools to
a more constant range so that a limited set of, for example,
assembly conditions need be employed in Module 3 processes (e.g.,
all Module 3 processes). FIG. 13 shows two methods by which
synthesized oligonucleotides may be separated from supports. In
this figure, oligonucleotides have been synthesized on beads 1300
and released into the surrounding well of a microwell titer plate
1301. In each instance, wells containing oligonucleotides for
collection are covered with fluid 1302 and pipette tips 1303 are
used to collect that fluid. On the left side of the figure are two
wells where the fluid is contained within the wells. Further to the
right side of FIG. 13, a barrier 1304 extends above the wells to
allow fluid to collect at a higher level. In both instances, the
fluid may be there before the pipette tips are brought into close
proximity or the fluid may be delivered by the pipette tips. Also,
fluid surrounding the beads 1300 may be circulated to distribute
released oligonucleotides by flow delivered by the pipette tips
1303.
[0229] Module 3
[0230] Once the chemical synthesis phase has been completed, the
resulting nucleic acid molecules may be assembled, if desired, into
larger nucleic acid molecules. Depending on the end purpose for
which the final nucleic acid molecules are to be used, the
"quality" (e.g., from a sequence fidelity perspective) of the
chemically synthesized nucleic acid molecules may be too low for
the intended application. As an example, if the chemically
synthesized nucleic acid molecules are to be used as long probes,
then they may be of sufficient quality for that purpose without
further processing. However, consider the situation where one
hundred nucleic acid segments are to be assembled, each nucleic
acid segment is one hundred base pairs in length and there is one
error per fifty base pairs. The net result is that there will be,
on average, 200 sequence errors in each 10,000 base pair assembled
nucleic acid molecule. If one intends, for example, to express one
or more proteins from the assembled nucleic acid molecule, then the
number of sequence errors would likely be considered to be too
high. Also, while sequencing of individual nucleic acid molecules
may be performed, this is time consuming and involves additional
cost. Thus, in many instances, an error removal step may be
performed. Typically, this will be performed after a first round of
assembly. Thus, in one aspect, methods of the invention involve the
following (in this order or different orders):
[0231] 1. Fragment Amplification and Assembly (e.g., PCR/in vitro
assembly).
[0232] 2. Error Correction.
[0233] 3. Final Assembly (e.g., in vivo assembly).
[0234] In various embodiments of the present disclosure, error
removal steps may also be implemented by executing
processor-executable instructions. The invention thus includes
software based instructions for performing mechanical functions
associated with error removal processes, as well as other aspects
of the invention.
[0235] Any number of methods may be used for fragment amplification
and assembly. One exemplary method is described in Yang et al.,
Nucleic Acids Research, 21:1889-1893 (1993) and U.S. Pat. No.
5,580,759, the disclosure of which is incorporated herein by
reference.
[0236] In the process described in the Yang et al. paper, a linear
vector is mixed with double stranded nucleic acid molecules which
share sequence homology at the termini. An enzyme with exonuclease
activity (i.e., T4 DNA polymerase, T5 exonuclease, T7 exonuclease,
etc.) is added which peels back one strand of all termini present
in the mixture. The "peeled back" nucleic acid molecules are then
annealed incubated with a DNA polymerase and deoxynucleotide
triphosphates under condition which allow for the filling in of
single-stranded gaps. Nicks in the resulting nucleic acid molecules
may be repaired by introduction of the molecule into a cell or by
the addition of ligase. Of course, depending on the application and
work flow, the vector may be omitted. Further, the resulting
nucleic acid molecules, or sub-portions thereof, may be amplified
by polymerase chain reaction.
[0237] Other methods of nucleic acid assembly include those
described in U.S. Patent Publication Nos. 2010/0062495 A1;
2007/0292954 A1; 2003/0152984 AA; and 2006/0115850 AA and in U.S.
Pat. Nos. 6,083,726; 6,110,668; 5,624,827; 6,521,427; 5,869,644;
and 6,495,318, the disclosures of which are incorporated herein by
reference.
[0238] A method for the isothermal assembly of nucleic acid
molecules is set out in U.S. Patent Publication No. 2012/0053087,
the disclosure of which is incorporated herein by reference. In one
aspect of this method, nucleic acid molecules for assembly are
contacted with a thermolabile protein with exonuclease activity
(e.g., T5 polymerase) a thermostable polymerase, and a thermostable
ligase under conditions where the exonuclease activity decreases
with time (e.g., 50.degree. C.). The exonuclease "chews back" one
strand of the nucleic acid molecules and, if there is sequence
complementarity, nucleic acid molecule will anneal with each other.
The thermostable polymerase fills in gaps and the thermostable
ligase seals nicks. Methods like this may be used in conjunction
with equipment of FIG. 16. Further, more than one nucleic acid
molecule may be stored with other suitable reagents in the
individual storage units of 1609 and these storage units may be set
to a temperature of, for example, of 50.degree. C. for assembling
the stored molecules.
[0239] One commercially available kit which may be used to assemble
nucleic acid molecules of the invention, as well as for the
insertion of such nucleic acid molecules into vectors is the
GENEART.RTM. Seamless Cloning and Assembly Kit (cat. no. A13288),
available from Life Technologies Corp., Carlsbad, Calif.
[0240] Single-stranded binding proteins such as T4 gene 32 protein
and RecA, as well as other nucleic acid binding or recombination
proteins known in the art, may be included, for example, to
facilitate nucleic acid molecules annealing.
[0241] In some instances, nucleic acid molecules may be amplified
on solid supports. Thus, the invention includes methods where
nucleic acid molecules are synthesized but are not cleaved from
solid supports they are synthesized on. In such instances, the
amplified nucleic acid molecules may be used directed (e.g., as
probes) or assembled as described elsewhere herein.
[0242] One method for assembling nucleic acid molecules (FIG. 3)
involves starting with overlapping nucleic acid molecules which are
"stitched" together using PCR. In many instances, the stitched
nucleic acid molecules will be chemically synthesized and will be
less than 100 nucleotides in length (e.g., from about 40 to 100,
from about 50 to 100, from about 60 to 100, from about 40 to 90,
from about 40 to 80, from about 40 to 75, from about 50 to 85, etc.
nucleotides). A process similar to that shown in FIG. 3 is set out
in U.S. Pat. No. 6,472,184, the disclosure of which is incorporated
herein by reference. Primers may also be used which contain
restriction sites for instances where insertion into a cloning
vector is desired. One suitable cloning system is referred to as
Golden Gate which is set out in various forms in U.S Patent
Publication No. 2010/0291633 A1 and PCT Publication WO 2010/040531,
the disclosures of which are incorporated herein by reference.
Thus, where desirable, assembled nucleic acid molecules may be
directly inserted into vectors and host cells. This may be
appropriate when the desired construct is fairly small (e.g., less
than 5 kilobases). Type IIs restriction site mediated assembly may
be used to assemble multiple fragments (e.g., two, three, five,
eight, ten, etc.) when larger constructs are desired (e.g., 5 to
100 kilobases).
[0243] An alternative method for PCR-based assembly of nucleic acid
molecules (e.g., chemically synthesized nucleic acid molecules) is
based on the direct ligation of overlapping pairs of
5'-phosphorylated nucleic acid molecules ("ligation-based
assembly"). In this process, single-stranded nucleic acid molecules
are synthesized, phosphorylated and annealed to form
double-stranded molecules with complementary overhangs (e.g.,
overhangs of four nucleotides). The individual double stranded
molecules are then ligated to each other to form larger constructs.
In certain embodiments this method may be desirable over PCR
methods in particular where highly repetitive sequences, such as GC
stretches are to be assembled. This method may be used to assemble
from about two to about forty nucleic acid molecules (e.g., from
about two to about forty, from about three to about forty, from
about five to about forty, from about eight to about forty, from
about two to about thirty, from about two to about twenty, from
about two to about ten, etc. nucleic acid molecules). A related
method is described in U.S. Pat. No. 4,652,639, the disclosure of
which is incorporated herein by reference.
[0244] In many instances when ligation-based assembly is employed
using chemically synthesized nucleic acid molecules, the molecules
will be less than 100 base pairs in length. Also, the complementary
overlaps may be used for joining the nucleic acid molecules will
generally be between two and ten (e.g., from about two to about
ten, from about four to about ten, from about five to about ten,
from about two to about eight, from about three to about seven,
etc. nucleotides in length) (FIG. 4).
[0245] One process that may be used to assemble nucleic acid
molecules is Red/ET recombination. This process employs E. coli
based homologous recombination mediated by phage protein pairs,
such as RecE/RecT or Red.alpha./Red.beta.. This process is not
limited by nucleic acid size and is independent of restriction
sites. Essentially any DNA molecule in E. coli of almost any size
can be engineered at any site using Red/ET recombination. In
essence, Red/ET recombination involves three steps/conditions. The
first step or condition is the presence of homology arms (e.g.,
arms of 50 base pairs in length) in linear DNA. The second step or
condition is the insertion or presence of the linear DNA in an E.
coli cell. The third step or condition is the expression or
presence of any appropriate phage pair (e.g., RecE/RecT or
Red.alpha./Red.beta.) in the E. coli cell. Red/ET recombination is
set out in U.S. Pat. Nos. 6,355,412 and 6,509,156, the disclosures
of which are incorporated herein by reference.
[0246] Further, as shown in FIG. 4, multiple rounds of polymerase
chain reactions may be used to generate successively larger nucleic
acid molecules.
[0247] In some embodiments, nucleic acid molecules are assembled
after amplification and/or are assembled by processes involving
amplification. Further, after partial or final assembly, assembled
nucleic acid molecules may be used directly or introduced into
cells where cellular based amplification may occur.
[0248] Some exemplary nucleic acid assembly methods that may be
used in the practice of the invention or employed as standalone
processes include (1) Chain Reaction Cloning (CRC), (2) Circular
Polymerase Extension Cloning (CPEC), and (3) Oligonucleotide
Stitching Assembly (OSA), as well as combinations of these
methods.
[0249] Chain Reaction Cloning (CRC) involves the use if a bridging
oligonucleotide to join the termini of two other nucleic acid
molecules. While variations of the CRC method may be used, one
exemplary method involves preparing a reaction mixture comprising
(1) two double-stranded nucleic acid molecules having termini
having no sequence complementarity with each other, (2) a
single-stranded oligonucleotide that shares sequence
complementarity with one terminus of each of the two
double-stranded nucleic acid molecules, and (3) a thermostable
ligase. This reaction mixture is then cycled to temperatures above
and below the melting point of the two double-stranded nucleic acid
molecules, as represented in FIG. 18.
[0250] CRC may involve more than two (e.g., three, four, five, six,
seven, etc.) double-stranded nucleic acid molecules and more than
one (e.g., three, four, five, six, seven, etc.) bridging
oligonucleotide. Further, CRC may be performed in phases where, for
example, a several nucleic acid molecules (e.g., three) are
connected to each other, then additional nucleic acid molecules are
added and additional cycles are performed.
[0251] The number of cycles performed will vary with factors such
as the amount of two double-stranded nucleic acid molecules
originally present in the reaction mixture and the amount of
ligated nucleic acid that is desired.
[0252] The CRC process shown in FIG. 18 results, after the first
couple of cycles, in the logarithmic ligation of nucleic acid
molecules present in the reaction mixture. Also, one advantage of
this assembly process is that a polymerase is not employed. Thus,
nucleic acid polymerase mediated errors are not introduced into the
assembled nucleic acid molecules.
[0253] In a variation of the process shown in FIG. 18, the
double-stranded nucleic acid molecules in the original reaction
mixture can be single-stranded. In such instances, the reaction
mixture will often contain a fairly high concentration of the
bridging oligonucleotide. This is so because if only the + strands
of the nucleic acid molecules being assembled are present, then
essentially all of the assembled nucleic acid molecules will be
brought together by the BO. Thus, the assembled nucleic acid
molecules will not act as hybridization partners because their
complementary strands would not be present.
[0254] The CRC process is set out in Pachuk et al., Gene 243:19-25
(2000) and U.S. Pat. No. 6,143,527, the entire disclosure of which
is incorporated herein by reference. One disadvantage of this
approach is that ligation of DNA fragments with non-compatible ends
(e.g., 3' protruding end of fragment 1 and 5' protruding end of
fragment 2) may not lead to the exact desired junction. Thus, the
assembly is not always seamless and does not allow for junction
editing.
[0255] FIG. 19 shows a schematic representation of one embodiment
of the CPEC process. In this embodiment, a double stranded, linear
vector and two double-stranded nucleic acid molecules are combined
with a thermostable polymerase and nucleoside triphosphates (e.g.,
deoxynucleoside triphosphates) to form a reaction mixture. This
reaction mixture is then heated to separate the strands of the
vector and nucleic acid molecules and then cooled, allowing for
hybridization of complementary sequences, followed by extension to
generate double-stranded end products. The CPEC process is set out
in Quan and Tian, PloS One 4:e6441 (2009) and Quan and Tian, Nature
Protocols 6:242-251 (2011).
[0256] As one skilled in the art would understand, CPEC may be
employed to connect more than two (e.g., three, four, five, six,
seven, etc.) nucleic acid molecules. Further, assembled nucleic
acid molecules need not be introduced into a vector. Thus, CPEC may
be used assemble multiple nucleic acid molecules to form a linear
or circular assembly, wherein the final assembly may or may not
have the ability to replicate when introduced into a cell. Further,
PCR, especially repeated PCR reactions, may introduce errors into
the assembled nucleic acid molecules.
[0257] FIG. 20 shows an embodiment of Oligonucleotide Stitching
Assembly (OSA). In this embodiment, an insert present in a donor
vector is introduced into an acceptor vector. This is mediated by
(1) oligonucleotides which share sequence complementarity with both
the insert and the insertion locus of the acceptor vector and (2) a
mixture of enzymes and a cell extract. Typically, the insert will
be excised for the donor vector prior to or as part of the reaction
process. In many instances, this will be accomplished by digestion
with a restriction enzyme.
[0258] OSA may be used to assemble nucleic acid molecules produced
by methods of the invention, as well as other nucleic acid
molecules. Thus, the invention includes OSA methods. Such methods
include: (a) forming a reaction mixture of (1) an insert nucleic
acid molecule, an acceptor nucleic acid molecule, oligonucleotides,
wherein each oligonucleotide shares sequence complementarity with
(i) one terminus of the insert nucleic acid molecule and the
insertion site of the acceptor nucleic acid molecule or (ii) one
terminus of two different insert nucleic acid molecules, (2) a cell
extract, (3) a protein composition comprising an exonuclease and,
optionally, a single-stranded binding protein (e.g., T4 gene 32
protein); and (b) incubating the reaction formed in (a) under
conditions which allow for the introduction of the insert nucleic
acid molecule into the acceptor nucleic acid molecule. The
invention also includes reagents and components used in such
methods, as well as kit for performing such methods.
[0259] The process described above is directed to the introduction
of a single insert into a single acceptor nucleic acid molecule. As
one skilled in the art would understand, one or more (e.g., one,
two three, four, five, six, seven, eight, nine, ten, etc.) insert
nucleic acid molecule may be introduced into one or more (e.g.,
one, two three, four, five, six, seven, eight, nine, ten, etc.)
acceptor nucleic acid molecule. In some instances, more than one
insert nucleic acid molecule may be introduced into one acceptor
nucleic acid molecule. One example of this is shown in the box on
the lower right of FIG. 20. In this exemplary embodiment, two
double-stranded insert nucleic acid molecules (the double-stranded
nature of the nucleic acid molecules not being shown in the boxed
representations) are introduced into a double-stranded acceptor
vector. As shown in FIG. 20, six oligonucleotides are used in this
process, with two pairs of oligonucleotides having sequence
complementarity with the junction regions between the two inserts
(one pair for each insert/acceptor vector junction) and each
terminus of the insertion locus of the acceptor vector.
[0260] The number of oligonucleotides present will generally vary
with the number of inserts to be introduced into the acceptor
nucleic acid molecule (e.g., a vector). For one insert, four
oligonucleotides will generally be present; for two inserts, six
oligonucleotides will generally be present; for three inserts,
eight oligonucleotides will generally be present. Thus, two
oligonucleotides will generally be present for each joining point,
with the number of oligonucleotides present being represented by
the following formula: O=2+2I, where O is the number of
oligonucleotides and I is the number of insert nucleic acid
molecules.
[0261] The invention thus includes OSA methods (e.g., in vitro
methods) comprising: (a) forming a reaction mixture of (1) one or
more insert nucleic acid molecule, one or more acceptor nucleic
acid molecule, a plurality of oligonucleotides, wherein each
oligonucleotide shares sequence complementarity with one terminus
of the insert nucleic acid molecule and the insertion site of the
acceptor nucleic acid molecule and wherein the number of
oligonucleotides is represented by the formula O=2+2I, where O is
the number of oligonucleotides and I is the number of insert
nucleic acid molecules, (2) a cell extract, (3) a protein
composition comprising an exonuclease and, optionally, a
single-stranded binding protein (e.g., T4 gene 32 protein); and (b)
incubating the reaction formed in (a) under conditions which allow
for the introduction of the insert nucleic acid molecule into the
acceptor nucleic acid molecule.
[0262] The lengths of the oligonucleotides may vary but they will
typically be between from about 20 and about 100 (e.g., from about
20 to about 80, from about 30 to about 80, from about 40 to about
80, from about 20 to about 60, from about 20 to about 50, from
about 20 to about 40, from about 30 to about 80, from about 30 to
about 60, etc.) nucleotides in length. Further, the regions of
sequence complementarity of oligonucleotides to each component of
an insertion junction (i.e., the acceptor nucleic acid molecule and
the insertion nucleic acid molecule) will typically be between from
about 20 and to about 60 (e.g., from about 20 and to about 50, from
about 40 and to about 60, from about 25 and to about 60, from about
25 and to about 50, from about 25 and to about 40, from about 25
and to about 35, etc.) nucleotides.
[0263] As shown by the data in FIG. 21, offset oligonucleotides
yield higher cloning efficiencies than full complementary
oligonucleotides. Also, the data shown in FIG. 21 was generated
using a cell extract obtained from E. coli DH10B cells. Similar
cloning efficiencies were obtained using extracts of E. coli cells
expressing redET genes, demonstrating that redET gene products are
not necessary for OSA. Thus, the invention includes methods
involving the use of cell extracts derived from cells that do not
express redET genes. Further, the redET gene expression products
are believed to not interfere with the OSA process so their
presence is optional.
[0264] The invention thus includes in vitro OSA methods involving
the use of cell extracts and protein compositions. Extracts may be
prepared from any number of cell types, including prokaryotic
(e.g., bacterial cells) and eukaryotic cells (e.g., yeast cells).
Exemplary prokaryotic cells include those of bacteria of bacterial
groups, families, such as bacteria in the phylum Actinobacteria,
such as organsims of the class Actinobacteridae, such as organsims
of the order Actinomycetales, such as organsims of the families
Actinomycineae: Actinomycetaceae (Actinomyces, Mobiluncus),
Corynebacterineae: Mycobacteriaceae (Mycobacterium), Nocardiaceae,
Corynebacteriaceae, Frankineae: Frankiaceae, Micrococcineae:
Brevibacteriaceae and Propionibacteriaceae (Propionibacterium) and
of the order Bifidobacteriales, such as organsims of the families
Bifidobacteriaceae (Bifidobacterium, Falcivibrio, Gardnerella) and
other subclasses: Acidimicrobidae, Coriobacteridae,
Rubrobacteridae, Sphaerobacteridae; and of the phylum Firmicutes,
such as organsims of the class Bacilli, such as organsims of the
order Bacillales, such as organsims of the families: Bacillaceae
(Bacillus), Listeriaceae (Listeria), Staphylococcaceae
(Staphylococcus, Gemella, Jeotgalicoccus) and of the order
Lactobacillales, such as organsims of the families: Enterococcaceae
(Enterococcus), Lactobacillaceae (Lactobacillus, Pediococcus),
Leuconostocaceae (Leuconostoc), Streptococcaceae (Lactococcus,
Streptococcus) and of the class Clostridia, such as organsims of
the order: Clostridiales (Clostridium, Peptostreptococcus,
Selenomonas), Halanaerobiales and Thermoanaerobacterales, and of
the class Tenericutes/Mollicutes, such as organsims of the order:
Mycoplasmatales (Mycoplasma, Ureaplasma), Entomoplasmatales
(Spiroplasma), Anaeroplasmatales (Erysipelothrix),
Acholeplasmatales (Acholeplasma), Haloplasmatales (Haloplasma).
Specific bacterial cells that may be used to produce cell extracts
for use in the invention include Staphylococcus aureus,
Enterococcus faecalis, Streptococcus spp., Escherichia coli,
Klebsiella pneumoniae, Proteus mirabilis, and Pseudomonas
aeruginsa.
[0265] Exemplary eukaryotic organisms that may be used to produce
cell extracts for use in the invention include yeasts such as
Saccharomyces cerevisiae, Saccharomyces carsvergensis,
Saccharomyces logos, Saccharomyces fragilis, Saccharomyces sake,
Schizosaccharomyces pombe, Saccharomyces paradoxus,
Zygosaccharomyces japonicas, Pichia polymorpha, Pichia farinose,
Pichia haplophila, Pichia saitoi Hansenula saturnus, Kuraishia
capsulate, Wickerhamomyces silvicola, Kuraishia capsulate, Ogataea
glucozyma, Ogataea minuta, Debaryomyces hansenii, Debaryomyces
hansenii, Naumovia castellii, Hanseniaspora valbyensis,
Sporidiobolus salmonicolor, Yarrowia lipolytica, Candida solani,
and Candida albicans.
[0266] Acceptor nucleic acid molecules (e.g., acceptor vectors) may
be of any number forms or lengths. In many instances, acceptor
nucleic acid molecules will be vectors but in some instances such
molecules may lack an origin of replication and may be designed to
integrate into the genome or other nucleic acid molecule in a cell.
Further, the insertion site may be one which results in negative
selection phenotype (e.g., encode ccdB, or other toxic compounds
such that introduction of the insert results in disruption of the
coding region and a resulting loss of the negative selection
phenotype.
[0267] Protein compositions for use in OSA methods will typically
contain at least an exonuclease activity and may optionally contain
a single-stranded binding protein. Exemplary proteins with
exonuclease activity that may be used in the practice of the
invention include proteins polymerases and other proteins with
exonuclease activity. This activity may be 5'.fwdarw.3' or
3'.fwdarw.5' activity. Specific proteins with exonuclease activity
that may be used in the practice of the invention include
Exonuclease I, Exonuclease III, Exonuclease V, Exonuclease VII, T7
exonuclease, Taq DNA polymerase, phage T7 gene 6 product, RedA of
lambda phage, and RecE of Rac prophage. Single-stranded binding
proteins that may be used in the practice of the invention include
recA, E. coli single-stranded binding protein (SSB), Xanthomonas
SSB, Lactococcus lactis siphophage p2 SSB, Rim1 SSB, T7 SSB (T7
gene 2.5 product), and T4 gene 32 protein.
[0268] Kits of the invention may contain one or more of the
following components: (1) one or more oligonucleotide, (2) one or
more protein with exonuclease activity, (3) one or more cell
extract, (4) one of more cell type and, optionally, instructions
for the preparation of one or more cell extracts, (5) one or more
vector nucleic acid molecule, (6) one of more reagent, such as
buffers and salts. These reagents may be in dry form or in
solution. In many instances, the applications of those using kits
of the invention will be different enough that oligonucleotides
will not be included. Comment components that may be included are
items (2), (3), (4), and (6) above.
[0269] The invention further includes reactions mixtures and
combinations of intermediates and end products. Using FIG. 20 for
purposes of illustration, the invention includes compositions of
matter comprising one or more Donor Vector, one or more Acceptor
Vector, a plurality (e.g., two, three, four, five, six, seven,
eight, nine, ten, etc.) of oligonucleotides, at least one protein
with exonuclease activity, at least one cell extract, one or more
Acceptor Vector at various states of introduction of one or more
Insert, and one or more Product Vectors.
[0270] From a functional perspective, the invention includes
compositions of matter comprising one or more nucleic acid insert,
one or more acceptor nucleic acid molecules, a plurality (e.g.,
two, three, four, five, six, seven, eight, nine, ten, etc.) of
oligonucleotides, at least one protein with exonuclease activity,
at least one cell extract, wherein the composition is capable of
facilitating the introduction of the insert into the acceptor
nucleic acid molecule.
[0271] In most instances, regardless of the method by which a
larger nucleic acid molecule is generated from chemically
synthesized nucleic acid molecules, errors from the chemical
synthesis process will be present. Thus, in many instances, error
correction will be desirable. Error correction can be achieved by
any number of means. One method is by individually sequencing
chemically synthesized nucleic acid molecules.
[0272] Another method of error correction is set out in FIG. 6.
FIG. 6 is a flow chart of an exemplary process for synthesis of
error-minimized nucleic acid molecules. In the first step, nucleic
acid molecules of a length smaller than that of the full-length
desired nucleotide sequence (i.e., "nucleic acid molecule
fragments" of the full-length desired nucleotide sequence) are
obtained. Each nucleic acid molecule is intended to have a desired
nucleotide sequence that comprises a part of the full length
desired nucleotide sequence. Each nucleic acid molecule may also be
intended to have a desired nucleotide sequence that comprises an
adapter primer for PCR amplification of the nucleic acid molecule,
a tethering sequence for attachment of the nucleic acid molecule to
a DNA microchip, or any other nucleotide sequence determined by any
experimental purpose or other intention. The nucleic acid molecules
may be obtained in any of one or more ways, for example, through
synthesis, purchase, etc.
[0273] In the optional second step, the nucleic acid molecules are
amplified to obtain more of each nucleic acid molecule. The
amplification may be accomplished by any method, for example, by
PCR. Introduction of additional errors into the nucleotide
sequences of any of the nucleic acid molecules may occur during
amplification.
[0274] In the third step, the amplified nucleic acid molecules are
assembled into a first set of molecules intended to have a desired
length, which may be the intended full length of the desired
nucleotide sequence. Assembly of amplified nucleic acid molecules
into full-length molecules may be accomplished in any way, for
example, by using a PCR-based method.
[0275] In the fourth step, the first set of full-length molecules
is denatured. Denaturation renders single-stranded molecules from
double-stranded molecules. Denaturation may be accomplished by any
means. In some embodiments, denaturation is accomplished by heating
the molecules.
[0276] In the fifth step, the denatured molecules are annealed.
Annealing renders a second set of full-length, double-stranded
molecules from single-stranded molecules. Annealing may be
accomplished by any means. In some embodiments, annealing is
accomplished by cooling the molecules.
[0277] In the sixth step, the second set of full-length molecules
are reacted with one or more endonucleases to yield a third set of
molecules intended to have lengths less than the length of the
complete desired gene sequence. The endonucleases cut one or more
of the molecules in the second set into shorter molecules. The cuts
may be accomplished by any means. Cuts at the sites of any
nucleotide sequence errors are particularly desirable, in that
assembly of pieces of one or more molecules that have been cut at
error sites offers the possibility of removal of the cut errors in
the final step of the process. In an exemplary embodiment, the
molecules are cut with T7 endonuclease I, E. coli endonuclease V,
and Mung Bean endonuclease in the presence of manganese. In this
embodiment, the endonucleases are intended to introduce blunt cuts
in the molecules at the sites of any sequence errors, as well as at
random sites where there is no sequence error.
[0278] In the last step, the third set of molecules is assembled
into a fourth set of molecules, whose length is intended to be the
full length of the desired nucleotide sequence. Because of the
late-stage error correction enabled by the provided method, the set
of molecules is expected to have many fewer nucleotide sequence
errors than can be provided by methods in the prior art.
[0279] The process set out above and in FIG. 6 is also set out in
U.S. Pat. No. 7,704,690, the disclosure of which is incorporated
herein by reference. Furthermore, the process described above may
be encoded onto a computer-readable medium as processor-executable
instructions.
[0280] Another process for effectuating error correction in
chemically synthesized nucleic acid molecules is by a commercial
process referred to as ERRASE.TM. (Novici Biotech). Error
correction methods and reagent suitable for use in error correction
processes are set out in U.S. Pat. Nos. 7,838,210 and 7,833,759,
U.S. Patent Publication No. 2008/0145913 A1 (mismatch
endonucleases), and PCT Publication WO 2011/102802 A1, the
disclosures of which are incorporated herein by reference.
[0281] Exemplary mismatch endonucleases include endonuclease VII
(encoded by the T4 gene 49), RES I endonuclease, CEL I
endonuclease, and SP endonuclease or methyl-directed endonucleases
such as MutH, MutS or MutL. The skilled person will recognize that
other methods of error correction may be practiced in certain
embodiments of the invention such as those described, for example,
in U.S. Patent Publication Nos. 2006/0127920 AA, 2007/0231805 AA,
2010/0216648 A1, 2011/0124049 A1 or U.S. Pat. No. 7,820,412, the
disclosures of which are incorporated herein by reference.
[0282] Another schematic of an error correction method is shown in
FIG. 7.
[0283] Synthetically generate nucleic acid molecules typically have
error rate of about 1 base in 300-500 bases). Further, in many
instances, greater than 80% of errors are single base frameshift
deletions and insertions. Also, less than 2% of errors result from
the action of polymerases when high fidelity PCR amplification is
employed. In many instances, mismatch endonuclease (MME) correction
will be performed using fixed protein:DNA ratio.
[0284] One error correction methods involves the following steps.
The first step is to denature DNA contained in a reaction buffer
(e.g., 200 mM Tris-HCl (pH 8.3), 250 mM KCl, 100 mM MgCl.sub.2, 5
mM NAD, and 0.1% TRITON.RTM. X-100) at 98.degree. C. for 2 minutes,
followed by cooling to 4.degree. C. for 5 minutes, then warming the
solution to 37.degree. C. for 5 minutes, followed by storage at
4.degree. C. At a later time, T7endonuclease I and DNA ligase are
added the solution 37.degree. C. for 1 hour. The reaction is
stopped by the addition EDTA. A similar process is set out in Huang
et al., Electrophoresis 33:788-796 (2012).
[0285] Another method for removal of error from chemically
synthesized nucleic acid molecules is by selection of nucleic acid
molecules having correct nucleotide sequences. This may be done by
the selection of a single nucleic acid molecule for amplification,
then sequencing of the amplification products to determine if any
errors are present. Thus, the invention also includes selection
methods for the reduction of sequence errors. Methods for
amplifying and sequence verifying nucleic acid molecules are set
out in U.S. Pat. No. 8,173,368, the disclosure of which is
incorporated herein by reference. Similar methods are set out in
Matzas et al., Nature Biotechnology, 28:1291-1294 (2010).
[0286] Methods according to this aspect of the invention may
include the following steps: (a) providing a mixture of nucleic
acid molecules synthesized to have the same nucleotide sequence,
(b) separating nucleic acid molecules in the mixture such that
amplification results in progeny nucleic acid molecules being
derived from a single starting nucleic acid molecule, (c)
sequencing more than one amplified nucleic acid molecule generated
in step (b), and (d) identifying at least one individual nucleic
acid with the desired sequence from the nucleic acid molecules
sequenced in step (c). The nucleic acid molecule identified in step
(d) may then be used as one nucleic acid molecule in an assembly
process, as described elsewhere herein.
[0287] According to various embodiments described herein, a
computer-readable medium may be encoded with processor-executable
instructions for: (a) providing a mixture of nucleic acid molecules
synthesized to have the same nucleotide sequence, (b) separating
nucleic acid molecules in the mixture such that amplification
results in progeny nucleic acid molecules being derived from a
single starting nucleic acid molecule, (c) sequencing more than one
amplified nucleic acid molecule generated in step (b), and (d)
identifying at least one individual nucleic acid with the desired
sequence from the nucleic acid molecules sequenced in step (c). The
nucleic acid molecule identified in step (d) may then be used as
one nucleic acid molecule in an assembly process, as described
elsewhere herein. In various embodiments, the computer-readable
medium may be included in a system configured to reduce error from
chemically synthesized nucleic acid molecules by selection of
nucleic acid molecules having correct nucleotide sequences.
[0288] Large nucleic acid molecules are relatively fragile and,
thus, shear, readily. One method for stabilizing such molecules is
by maintaining them intracellularly. Thus, in some aspects, the
invention involves the assembly and/or maintenance of large nucleic
acid molecules in host cells.
[0289] One group of organisms known to perform homologous
recombination fairly efficient is yeasts. Thus, host cells used in
the practice of the invention may be yeast cells (e.g.,
Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pichia,
pastoris, etc.).
[0290] Yeast hosts are particularly suitable for manipulation of
donor genomic material because of their unique set of genetic
manipulation tools. The natural capacities of yeast cells, and
decades of research have created a rich set of tools for
manipulating DNA in yeast. These advantages are well known in the
art. For example, yeast, with their rich genetic systems, can
assemble and re-assemble nucleotide sequences by homologous
recombination, a capability not shared by many readily available
organisms. Yeast cells can be used to clone larger pieces of DNA,
for example, entire cellular, organelle, and viral genomes that are
not able to be cloned in other organisms. Thus, in some
embodiments, the invention employs the enormous capacity of yeast
genetics generate large nucleic acid molecules (e.g., synthetic
genomics) by using yeast as host cells for assembly and
maintenance.
[0291] Exemplary of the yeast host cells are yeast strain VL6-48N,
developed for high transformation efficiency parent strain: VL6-48
(ATCC Number MYA-3666TM)), the W303a strain, the MaV203 strain
(Life Technologies Inc., cat. no. 11281-011), and
recombination-deficient yeast strains, such as the RAD54
gene-deficient strain, VL6-48-.DELTA.54G (MATahis3-.DELTA.200
trp1-.DELTA.1 ura3-52 lys2 ade2-101 met14 rad54-.DELTA.1::kanMX),
which can decrease the occurrence of a variety of recombination
events in yeast artificial chromosomes (YACs).
[0292] There is a large set of selectable markers (e.g., URA3,
HIS3, etc.) for selection and counter-selection of yeast mutants,
making it possible to carry out multiple rounds of seamless nucleic
acid alterations within yeast host cells. Thus, yeast can be used
to introduce a number of different genetic modifications, including
single nucleotide changes (e.g., insertions, deletions, mutations),
modification of target nucleic acid portions and regions, and
construction of entirely new chromosomes. Serial modifications to a
cloned copy of an otherwise intractable genome or other large
nucleic acid can be performed in yeast in rapid succession. The
mating capacity of yeast is favorable for modifying genomes and
other large nucleic acids. Yeast recombination machinery, when
activated during yeast mating, can be used to generate libraries,
e.g., combinatorial libraries containing variants of cloned genomes
or nucleic acids.
[0293] For example, Yeast Artificial Chromosome (YAC) libraries
have been constructed for several different bacteria (Azevedo et
al., PNAS USA 90, 6047 (1993); Heuer et al., Electrophoresis 19,
486 (1998); Kuspa et al., PNAS USA 86, 8917 (1989). Large
prokaryotic DNA segments can be cloned in yeast using the universal
genetic code. Toxic gene expression typically is not a barrier to
cloning nucleic acids in yeast. Studies with bacterial and archeal
genomes, for example, indicate that because eukaryotes use
different protein expression machinery than these bacteria, there
is little risk of harm to yeast hosts by proteins expressed from
the cloned genomes. Thus, the invention further includes methods
for the generation of nucleic acid molecules (e.g., synthetic
genomes) which confer a toxic phenotype when introduced into
non-yeast cell (e.g., bacterial cells).
[0294] The transcription (Kozak, Gene 234, 187 (1999)) and
translation (Kornberg, Trends. Cell. Biol. 9, M46 (1999) signals in
yeast are different from those in bacteria. In fact, most
prokaryotic genes likely are not expressed in yeast. There is no
restriction barrier in yeast (Belfort and Roberts, Nucleic Acids
Res 25, 3379 (1997). If there is a barrier, it may be a replication
barrier, rather than a gene expression barrier (Stinchcomb et al.,
PNAS USA 77, 4559 (1980)). Gene toxicity is minimized because
regulation of gene expression in a eukaryote such as yeast is
different from that in prokaryotes. Also, Mycoplasmas, for example,
use the codon UGA for tryptophan rather than as a translation stop
signal. Thus, most Mycoplasma genes, if expressed, would produce
truncated proteins in yeast. This largely avoids the possibility of
toxic gene products.
[0295] Nucleic acid molecules may be assembled from natural or
synthetic fragments together with yeast vectors prior to
transformation into yeast cells or simultaneously co-transformed
into yeast cells. New organisms may created by transferring these
genomes or other nucleic acid molecules, which have been optionally
manipulated as desired, into compatible recipient cells. Thus, one
embodiment provides suitable techniques for transferring genomes
and other nucleic acid molecules to yeast host cells, modifying the
genomes within host cells while maintaining their stability and
integrity, and transplanting the cloned and manipulated genomes
from yeast host cells back into recipient cells that more closely
resemble original donors (e.g., organisms from which the
nucleotides sequences were obtained), thus creating.
[0296] A commercially available product for the assembly of nucleic
acid molecules in yeast cells is the GENEART.RTM. High-Order
Genetic Assembly Systems (Life Technology, Cat. No. A13286). This
is a kit for the simultaneous and seamless assembly of up to 10 DNA
fragments, totaling up to 110 kilobases in length, into vectors.
The system uses the ability of yeast to take up and recombine DNA
fragments with high efficiency. This greatly reduces the in vitro
handling of DNA and eliminates the need for enzymatic treatments,
such as restriction and ligation, while allowing for precise
fusions of DNA sequences. The kit contains materials for the
transformation and purification from yeast, including yeast
selective media, and competent E. coli for plasmid amplification of
correct clones.
[0297] Organisms other than yeast may be used for in vivo assembly.
For example, it has been shown that exogenous DNA is integrated
into homologous sequences in the genome of Neurospora crassa at a
frequency of 100% in mutant strains deficient in non-homologous end
joining. (Ninomiya et al., Highly efficient gene replacements in
Neurospora strains deficient for nonhomologous end-joining, PNAS,
100:12248-12253 2004.) Thus, the invention further includes methods
involving organisms other than yeast (e.g., fungi such as N.
crassa) and methods which involve the suppression and/or
elimination of non-homologous end joining to increase the
efficiency of homologous recombination. In essence, any cell which
undergoes homologous recombination may be used to assemble nucleic
acid molecules. However, cell most suitable for this aspect of the
invention will be ones which naturally are efficient at performing
homologous recombination (e.g., yeasts) or can be altered (e.g.,
through mutagenesis) to increase the frequency of which they
homologous recombination.
[0298] Assembly and maintenance of nucleic acid molecules in will
often involve either the generation of or the insertion into cells
nucleic acid molecule which contain elements such as one or more
origin of replication (e.g., two origins of replication which are
functional in different cell types) and one or selection marker
(e.g., one or more positive selection marker and/or one of more
negative selection marker).
[0299] Nucleic acid molecules introduced into cells for assembly
will normally have certain features which allow them to be
assembled in a particular order. One feature is terminal sequence
homology between nucleic acid molecules being assembled.
[0300] Assembled nucleic acid molecules may be introduced into
other nucleic acid molecules located within a cell (e.g., a viral
genome, a nuclear genome, an organelle genome, a bacterial
chromosome, etc.). In such instances, functional elements such as
origins of replication, centromeres, etc. will generally be present
in the other nucleic acid molecules located within the cell. Thus,
the invention provides, in part, compositions and methods relating
to the assembly of nucleic acid molecules and the insertion of the
resulting assembly into other nucleic acid molecules.
[0301] In some instances, standard ligase based joining of
partially and fully assembled nucleic acid molecules may be
employed. For example, fully assembled nucleic acid molecule may be
generated with restriction enzyme sites near their termini These
nucleic acid molecules may then be treated with one of more
suitably restrictions enzymes to generate, for example, either one
or two "sticky ends". These sticky end molecules may then be
introduced into a vector by standard restriction enzyme-ligase
methods. In instances where the inert nucleic acid molecules have
only one sticky end, ligases may be used for blunt end ligation of
the "non-sticky" terminus.
[0302] Assembled nucleic acid molecules may also include functional
elements which confer desirable properties (e.g., origins of
replication, selectable markers, etc.). In many instances, the
assembled nucleic acid molecules will be assembled from multiple
individual nucleic acid segments with one of the segments being a
vector (e.g., a linear vector).
[0303] Using the schematic of FIG. 8 for purposes of illustration,
this approach may be carried out by co-transforming into the host
cell, along with the host vector, a plurality (e.g., two, three,
five, eight, ten, fifteen, twenty, thirty, etc.) of "overlapping"
nucleic acid fragments for which assembly is desired. In this
instance, each of the fragments contains are two regions of
homology to regions of other nucleic acid segments introduced into
the host cell. The nucleic acid segments after transformation into
the host cell, for example by homologous recombination through
regions of homology. In the instance shown in FIG. 8, the result is
an assembled, closed circular nucleic acid molecule.
[0304] In one variation of the illustrative example shown in FIG.
8, overlapping fragments of a circular bacterial genome are
co-transformed into a yeast host cell along with a linear yeast
vector. Again, the yeast vector contains regions of homology at its
termini to portions of the bacterial genome. Upon introduction of
the genome fragments and yeast host vector into the host cell, the
fragments and vector recombine, thereby joining the genome
fragments and host vector.
[0305] The process shown in FIG. 8 relies, in part, on selection
for the assembly of a closed, circular, replicable nucleic acid
molecule. As similar selection mechanisms is set out in U.S. Patent
Publication No. 2004/0219516 A1 (see, e.g., FIG. 20 of this
application), the disclosure of which is incorporated herein by
reference. Of course, nucleic acid molecules assembled by methods
of the invention need not always generate a closed circular nucleic
acid molecules. Other nucleic acid molecules which may be generated
by methods of the invention include linear plasmids (e.g., plasmids
which can replicate in linear form) and chromosomes.
[0306] In vivo assembly systems of the type shown in FIG. 8 may be
composed of two core components: (1) Nucleic acid segments for
assembly and (2) a suitable host cell. In certain embodiments where
desired functional elements (e.g., origins of replication,
selectable markers, etc.) are not represented in the nucleic acid
segments for assembly, a vector may be included as an additional
nucleic acid segment.
[0307] Fragments to be assembled will generally contain sequences
that are overlapping at their termini In one embodiment, the
overlaps are approximately 10 bp; in other embodiments, the
overlaps may be 15, 25, 50, 60, 70, 80 or 100 base pairs, etc.
(e.g., from about 10 to about 120, from about 15 to about 120, from
about 20 to about 120, from about 25 to about 120, from about 30 to
about 120, from about 40 to about 120, from about 10 to about 40,
from about 15 to about 50, from about 20 to about 50, etc. base
pairs). In order to avoid misassembly, individual overlaps that
should not be duplicated or closely match amongst the fragments.
Since homologous recombination does not require 100% sequence
identity between the participating nucleic acid molecules or
regions, each terminus should be sufficiently different to prevent
misassembly. Further, termini intended to undergo homologous
recombination with each other should share at least 90%, 93%, 95%,
or 98% sequence identity.
[0308] In in vivo assembly methods, a mixture of all of the
fragments to be assembled is used to transfect the host
recombination and assembly cell using standard transfection
techniques. The ratio of the number of molecules of fragments in
the mixture to the number of cells in the culture to be transfected
should be high enough to permit at least some of the cells to take
up more molecules of fragments than there are different fragments
in the mixture. Thus, in most instances, the higher the efficiency
of transfection, the larger number of cells will be present which
contain all of the nucleic acid segments required to form the final
desired assembled nucleic acid molecule. Technical parameters along
these lines are set out in U.S. Patent Publication No. 2009/0275086
A1, the disclosure of which is incorporated herein by
reference.
[0309] One example of an assembly method which for joining
double-stranded nucleic acid molecules which do not share terminal
sequence homology is shown in FIG. 5. In this embodiment, two
double-stranded fragments are introduced into a linear vector using
singe-stranded "stitching nucleic acid molecules". In a sense, this
is an assembling of five nucleic acid segments, wherein one of the
segments is the vector, two of the segments are the two stitching
nucleic acid molecules, and final two segments are the segments are
labeled Fragment 1 and Fragment 2. In addition to facilitating the
joining of other nucleic acid molecules, the stitching nucleic acid
molecules introduced short insertion (e.g., nine base pairs) into
the assembled nucleic acid molecule. A commercially available
product which contains these features is the GENEART.RTM.
High-Order Genetic Assembly Systems (Life Technology, Cat. No.
A13286).
[0310] Nucleic acid molecules may also be assembled or otherwise
designed with site specific recombination sites (e.g., GATEWAY.RTM.
sites) and/or topoisomerase sites. Site specific recombinases are
recombinase which typically have at least the following four
activities (or combinations thereof): (1) recognition of one or two
specific nucleic acid sequences; (2) cleavage of said sequence or
sequences; (3) topoisomerase activity involved in strand exchange;
and (4) ligase activity to reseal the cleaved strands of nucleic
acid. (See Sauer, B., Current Opinions in Biotechnology 5:521-527
(1994)). Conservative site-specific recombination is distinguished
from homologous recombination and transposition by a high degree of
specificity for both partners. The strand exchange mechanism
involves the cleavage and rejoining of specific nucleic acid
sequences in the absence of DNA synthesis (Landy, A., Ann. Rev.
Biochem. 58:913-949 (1989)).
[0311] One means by which nucleic acid molecules may be assembled
is by the use of recombinational cloning. Thus, the invention
includes compositions and methods related to recombination cloning
and recombination sites, as well as recombination cloning
components.
[0312] A number of recombinational cloning systems are known.
Examples of recombination sites which may be sued in such systems
include, but are not limited to, loxP sites; loxP site mutants,
variants or derivatives such as loxP511 (see U.S. Pat. No.
5,851,808); frt sites; frt site mutants, variants or derivatives;
dif sites; dif site mutants, variants or derivatives; psi sites;
psi site mutants, variants or derivatives; cer sites; and cer site
mutants, variants or derivatives.
[0313] These cloning systems are typically based upon the principle
that particular recombination sites will recombine with their
cognate counterparts. Nucleic acid molecules of the invention may
be designed so as they contain recombination sites of different
recombinational cloning systems (e.g., lox sites and att sites). As
an example, a nucleic acid molecule of the invention may contain a
single lox site and two att sites, wherein the att sites do not
recombine with each other.
[0314] Recombination sites for use in the invention may be any
nucleic acid that can serve as a substrate in a recombination
reaction. Such recombination sites may be wild type or naturally
occurring recombination sites, or modified, variant, derivative, or
mutant recombination sites. Examples of recombination sites for use
in the invention include, but are not limited to, phage lambda
recombination sites (such as attP, attB, attL, and attR and mutants
or derivatives thereof) and recombination sites from other
bacteriophage such as phi80, P22, P2, 186, P4 and P1 (including lox
sites such as loxP and loxP511). Mutated att sites (e.g., attB
1-10, attP 1-10, attR 1-10 and attL-1 10) are described in U.S.
Appl. No. 60/136,744, filed May 28, 1999, and U.S. application Ser.
No. 09/517,466, filed Mar. 2, 2000, which are specifically
incorporated herein by reference. Other recombination sites having
unique specificity (i.e., a first site will recombine with its
corresponding site and will not recombine with a second site having
a different specificity) are known to those skilled in the art and
may be used to practice the present invention. Corresponding
recombination proteins for these systems may be used in accordance
with the invention with the indicated recombination sites. Other
systems providing recombination sites and recombination proteins
for use in the invention include the FLP/FRT system from
Saccharomyces cerevisiae, the resolvase family (e.g., TndX, TnpX,
Tn3 resolvase, Hin, Hjc, Gin, SpCCE1, ParA, and Cin), and IS231 and
other Bacillus thuringiensis transposable elements. Other suitable
recombination systems for use in the present invention include the
XerC and XerD recombinases and the psi, dif and cer recombination
sites in Escherichia coli. Other suitable recombination sites may
be found in U.S. Pat. No. 5,851,808 issued to Elledge and Liu which
is specifically incorporated herein by reference. Recombination
proteins and mutant, modified, variant, or derivative recombination
sites which may be used in the practice of the invention include
those described in U.S. Pat. Nos. 5,888,732 and 6,143,557, and in
U.S. application Ser. No. 09/438,358 (filed Nov. 12, 1999), based
upon U.S. provisional application No. 60/108,324 (filed Nov. 13,
1998), and U.S. application Ser. No. 09/517,466 (filed Mar. 2,
2000), based upon U.S. provisional application No. 60/136,744
(filed May 28, 1999), as well as those associated with the
GATEWAY.RTM. Cloning Technology available from Life Technologies
Corp., (Carlsbad, Calif.), the entire disclosures of all of which
are specifically incorporated herein by reference in their
entireties.
[0315] Representative examples of recombination sites which can be
used in the practice of the invention include att sites referred to
above. Au sites which specifically recombine with other att sites
can be constructed by altering nucleotides in and near the 7 base
pair overlap region. Thus, recombination sites suitable for use in
the methods, compositions, and vectors of the invention include,
but are not limited to, those with insertions, deletions or
substitutions of one, two, three, four, or more nucleotide bases
within the 15 base pair core region (GCTTTTTTATACTAA (SEQ ID NO:
2)), which is identical in all four wild-type lambda att sites,
attB, attP, attL and attR (see U.S. application Ser. No.
08/663,002, filed Jun. 7, 1996 (now U.S. Pat. No. 5,888,732) and
Ser. No. 09/177,387, filed Oct. 23, 1998, which describes the core
region in further detail, and the disclosures of which are
incorporated herein by reference in their entireties).
Recombination sites suitable for use in the methods, compositions,
and vectors of the invention also include those with insertions,
deletions or substitutions of one, two, three, four, or more
nucleotide bases within the 15 base pair core region
(GCTTTTTTATACTAA (SEQ ID NO: 2)) which are at least 50% identical,
at least 55% identical, at least 60% identical, at least 65%
identical, at least 70% identical, at least 75% identical, at least
80% identical, at least 85% identical, at least 90% identical, or
at least 95% identical to this 15 base pair core region.
[0316] Analogously, the core regions in attB1, attP1, attL1 and
attR1 are identical to one another, as are the core regions in
attB2, attP2, attL2 and attR2. Nucleic acid molecules suitable for
use with the invention also include those which comprising
insertions, deletions or substitutions of one, two, three, four, or
more nucleotides within the seven base pair overlap region
(TTTATAC, which is defined by the cut sites for the integrase
protein and is the region where strand exchange takes place) that
occurs within this 15 base pair core region (GCTTTTTTATACTAA (SEQ
ID NO: 2)).
[0317] Multi-Site GATEWAY.RTM. technology is described in U.S.
Patent Publication No. 2004/0229229 A1, the entire disclosure of
which is incorporated herein by reference, and is effective for
cloning multiple DNA fragments into one vector without using
restriction enzymes. This system can be used to link 1, 2, 3, 4, 5
or more nucleic acid segments, as well as to introduce such
segments into vectors (e.g., a single vector). The GATEWAY.RTM.
(e.g., Multi-Site GATEWAY.RTM.) system allows for combinations of
different promoters, DNA elements, and genes to be studied in the
same vector or plasmid, for efficient gene delivery and expression.
Instead of transfecting multiple plasmids for each gene of
interest, a single plasmid carrying different DNA elements,
referred to as "an expression cassette" can be studied in the same
genomic background.
[0318] The present invention also relates to methods of using one
or more topoisomerases to generate assembled nucleic acid
molecules. Topoisomerases may be used in combination with
recombinational cloning techniques described herein. For example, a
topoisomerase-mediated reaction may be used to attach one or more
recombination sites to one or more nucleic acid segments. The
segments may then be further manipulated and combined using, for
example, recombinational cloning techniques.
[0319] In one aspect, the present invention provides methods for
linking a first and at least a second nucleic acid segment
topoisomerase (e.g., a type IA; type IB, such as Vaccinnia virus
topoisomerase; and/or type II topoisomerase) such that either one
or both strands of the linked segments are covalently joined at the
site where the segments are linked.
[0320] A method for generating a double stranded recombinant
nucleic acid molecule covalently linked in one strand can be
performed by contacting a first nucleic acid molecule which has a
site-specific topoisomerase recognition site (e.g., a type IA or a
type II topoisomerase recognition site), or a cleavage product
thereof, at a 5' or 3' terminus, with a second (or other) nucleic
acid molecule, and optionally, a topoisomerase (e.g., a type IA,
type IB, and/or type II topoisomerase), such that the second
nucleotide sequence can be covalently attached to the first
nucleotide sequence. As disclosed herein, methods of the invention
can be performed using any number of nucleotide sequences,
typically nucleic acid molecules wherein at least one of the
nucleotide sequences has a site-specific topoisomerase recognition
site (e.g., a type IA, type IB or type II topoisomerase), or
cleavage product thereof, at one or both 5' and/or 3' termini.
[0321] Topoisomerase mediated nucleic acid ligation methods are
described in detail in U.S. Patent Publ. No. 2004/0265863 A1, the
entire disclosure of which is incorporated herein by reference.
[0322] Assembled nucleic acid molecules may be cloned may contain a
blunt end to be linked, and the second nucleic acid molecule
involved in the cloning method may contain an overhang at the end
which is to be linked by a site-specific topoisomerase (e.g., a
type IA or a type IB topoisomerase), wherein the overhang includes
a sequence complementary to that comprising the blunt end, thereby
facilitating strand invasion as a means to properly position the
ends for the linking reaction.
[0323] Any number of vectors may be used in the practice of the
invention. Further, the selection of vectors for particular
applications will vary with the specifics of those applications
(e.g., the host cell). In many instances, vectors will be
introduced into host cells in linear form.
[0324] Suitable vectors for use in the present invention also
include prokaryotic vectors such as pcDNAII, pSL301, pSE280,
pSE380, pSE420, pTrcHisA, B, and C, pRSET A, B, and C (Life
Technologies Corp.), pGEMEX-1, and pGEMEX-2 (Promega, Inc.), the
pET vectors (Novagen, Inc.), pTrc99A, pKK223-3, the pGEX vectors,
pEZZ18, pRIT2T, and pMC1871 (Pharmacia, Inc.), pKK233-2 and
pKK388-1 (Clontech, Inc.), and pProEx-HT (Life Technologies Corp.)
and variants and derivatives thereof. Other vectors of interest
include eukaryotic expression vectors such as pFastBac, pFastBacHT,
pFastBacDUAL, pSFV, and pTet-Splice (Life Technologies Corp.),
pEUK-C1, pPUR, pMAM, pMAMneo, pBI101, pBI121, pDR2, pCMVEBNA, and
pYACneo (Clontech), pSVK3, pSVL, pMSG, pCH110, and pKK232-8
(Pharmacia, Inc.), p3'SS, pXT1, pSG5, pPbac, pMbac, pMC1neo, and
pOG44 (Stratagene, Inc.), and pYES2, pAC360, pBlueBacHis A, B, and
C, pVL1392, pBlueBacIII, pCDM8, pcDNA1, pZeoSV, pcDNA3 pREP4,
pCEP4, and pEBVHis (Life Technologies Corp.) and variants or
derivatives thereof.
[0325] Other vectors suitable for use in the invention include
pUC18, pUC19, pBlueScript, pSPORT, cosmids, phagemids, YAC's (yeast
artificial chromosomes), BAC's (bacterial artificial chromosomes),
P1 (Escherichia coli phage), pQE70, pQE60, pQE9 (Qiagen), pBS
vectors, PhageScript vectors, BlueScript vectors, pNH8A, pNH16A,
pNH18A, pNH46A (Stratagene), pcDNA3 (Life Technologies Corp.),
pGEX, pTrsfus, pTrc99A, pET-5, pET-9, pKK223-3, pKK233-3, pDR540,
pRIT5 (Pharmacia), pSPORT1, pSPORT2, pCMVSPORT2.0 and pSV-SPORT1
(Life Technologies Corp.) and variants or derivatives thereof.
[0326] Assembly methods, in addition to other methods described
herein, are capable of being miniaturized and/or automated. In
fact, in many instances, miniaturization will be desirable when the
nucleic acid molecules being assembled and/or introduced into
vectors are present in lower total numbers. One means by which
micro-mixing can be accomplished for assembly and processes such as
insertion of nucleic acid molecules into vectors is by
electrowetting, for example, as described elsewhere herein.
[0327] FIG. 16 is a block diagram of one embodiment of an
instrument for processing nucleic acid molecules of the invention.
On the upper left of this figure is a carrier oil reservoir 1600
and a tube 1601 for transporting oil from this reservoir. Carrier
oil is transported past a series of additional reservoirs 1602 that
contain reagents. The circular structures represent individual
reagents reservoirs. Exemplary reagents are nucleic acid molecules,
PCR enzymes, primers, and vectors, as well as, for example, other
Module 3 related components. The reagents will typically be in the
form of aqueous vesicles transported between oil barriers.
[0328] The reagents transported by the carrier oil are then
transported to a mixing chamber 1603 where mixing occurs. The
reagents then move on to a digital PCR station 1604. The tube 1601
travels between a heating block 1605 where denaturation occurs
followed by a cooling block 1606 where annealing and PCR occurs.
Each time a vesicle travels to the cooling block 1606 after the
first time, a PCR amplification occurs.
[0329] After exiting the digital PCR station 1604, the vesicles
move past additional reagent reservoirs 1607 for the optional
addition of more reagents, (e.g., buffers, error correction
components, etc.), then on to another optional mixing chamber 1608.
The vesicle then move on to an optional storage location 1609. In
instances where more than one nucleic acid molecule is to be
assembled into a larger molecule, the individual nucleic acid
molecules for assembly will often arrive at the storage location
1609 at different times and will need to be sequestered for a
period of time until other components arrive.
[0330] The nucleic acid molecules then move on to another digital
PCR station 1610 and again cycle between cooling and heating
blocks. Error correction reaction may occur in digital PCR station
1610. Finally, assembled nucleic acid molecules are transported to
interface outlets 1611 for collection and waste materials (e.g.,
carrier oil) is collection in a waste reservoir 1612.
[0331] Systems of the type represented in FIG. 16 can process
multiple samples at the same time. These samples can be sequestered
between carrier oil and sent through the system in series. The FIG.
16 block diagram does not show a computer system, optical
components, valves and other components related to system
automation. Optical elements, as well as other elements (e.g.,
electrical elements) can be used to keep track of the location and
identification of reagent vesicles and various points in the flow
system. These reagent vesicles will generally contain nucleic acid
molecules of a predetermined sequence. Thus, the invention include
methods for the simultaneous processing (e.g., sequential
processing) of multiple samples
[0332] Module 4
[0333] Following isolation and treatment, the assembled nucleic
acid molecules can be further transplanted into recipient cells
using methods described herein or known in the art. Methods which
may be used include protoplast and spheroplast fusion, conjugal
transfer (e.g., bacterial conjugation), viral infection,
electroporation and Sendai virus mediated cell fusion. Thus, the
invention includes methods for transferring synthesized and/or
assembled nucleic acid molecules to cells.
[0334] One method for generating yeast protoplast fusions in set
out in Nakazawa and Iwano, Efficient selection of hybrids by
protoplast fusion using drug resistance markers and reporter genes
in Saccharomyces cerevisiae, J. Biosci. Bioeng. 98:353-358 (2004).
Further, methods have been developed for the fusion or prokaryotic
and eukaryotic cells. (See, e.g., Gyuris and Duda, High-efficiency
transformation of Saccharomyces cerevisiae cells by bacterial
minicell protoplast fusion, Mol. Cell. Biol. 6:3295-3297 (1986).
Methods such as these may be used in the practice of the invention
to transfer nucleic acid molecules between cells without exposing
the nucleic acid molecules to an extracellular environment. Other
methods which may be used include natural competence, biolistic
gun, electroporation, Baculovirus mediated transduction, and Type
III secretion systems.
[0335] An exemplary transplantation protocol is described in PCT
Publication WO 2011/109031. One method used to transplant
Mycoplasma genomes from donors to Mycoplasma recipients is
described by Lartigue et al., Genome transplantation in bacteria:
changing one species to another, Science 317:632 (2007). This work
related to the complete replacement of the genome of a bacterial
cell with a genome from another species by genome transplantation
as naked DNA using polyethylene glycol-mediated transformation. The
resulting recipient cells were phenotypically identical to the
donor strain. Such methods can be used to transfer assembled
nucleic acid molecules constructed by methods of the invention to
recipient cells.
[0336] Recipient cells typically will be chosen based on their
ability to support gene expression from the assembled nucleic acid
molecules. For example, after a bacterial genome has been assembled
in a eukaryotic host cell having a suitable genetic manipulation
system (e.g., yeast), then it may be necessary or desirable to
transplant the genome back into a bacterial recipient cell.
Differences in translation and transcription and different codon
usage, among other factors, can prevent expression of the donor
gene products within the host cell. The recipient cell, therefore,
may be of the same species or a similar species as a donor cell or
organism. In many cases, the recipient cells will be of the same
order or kingdom as the donor. However, in cases where expression
in unrelated cell types is required, the initial gene design may
include codon and sequence optimization strategies to allow for
expression in different recipient cells.
[0337] Following isolation of donor nucleic acids in agarose plugs,
host DNA can optionally be removed (e.g., by digest and/or
electrophoresis), and optionally treated with methyltransferases
and/or proteinase.
[0338] Agarose plugs can be melted, for example, by incubation with
.beta.-Agarase I (New England Biolabs) as described in Example
3A(ii)(b) of PCT Publication WO 2011/109031.
[0339] Transplantation can be performed in the presence of
polyethylene glycol (PEG), such as PEG-6000 or PEG-8000 or other
PEG to facilitate transformation. The source, amount, and size of
the PEG can be varied to determine the optimal PEG. In one example,
the PEG is PEG-2000, PEG-40000 PEG-6000, PEG-8000, PEG-10000,
PEG-20000, or other. The concentration of PEG can be varied
depending upon the conditions of the transplantation;
concentrations include those, for example, at or about 5% or at or
about 10%. An example is described in Example 3A(ii)(c) of PCT
Publication WO 2011/109031. Melted plugs can be added to the
recipient cells in the presence of PEG with gentle rocking to mix.
Cells are allowed to recover, centrifuged, and grown in medium
containing appropriate selection medium to select for recipient
cells containing the transplanted donor nucleic acid. In one
aspect, cells are plated on the medium and grown under appropriate
conditions for the recipient cell type until colonies appear.
Colonies can be picked and further grown in selection medium to
produce a desired quantity of recipient cells containing the
transplanted genome or other donor nucleic acid.
[0340] A particular ratio of recipient cells to donor nucleic acid
can be maintained as needed. In one example, a ratio of between at
or about 10.sup.7 and at or about 10.sup.8 recipient cells per 2
.mu.g genomic DNA can be maintained. The provided transplantation
methods can be used to achieve approximately 30 transformants for
200 ng of endogenous genomic DNA, or between 500 and 1500
transplants per reaction, or other appropriate amount that is
obtained from the host or donor cell. In one non-limiting example,
transplantation is carried out with 10.sup.7 recipient cells, 20
picoliters of melted of agarose plug containing donor genome at 100
ng/.mu.l. One would understand that the ratio of recipient cells to
donor nucleic acid may vary depending upon the cell types and that
empirical assessment can be used to optimize the ratio.
[0341] Selection of recipient cells which contain a transplanted
donor nucleic acid can be performed by any number of means. For
example, transplanted donor nucleic acid may contain a positive
selection marker which will allows it to be maintained in recipient
cells. Also, a counter-selectable marker may be introduced in the
recipient cell genome to allow for selection against cells which
retain these nucleic acid molecules. A combination of positive and
counter selection can be employed if one desires an engineered
recipient cell which contains a transplanted donor nucleic acid but
not the original recipient cell genome.
[0342] Further, in some embodiment, a plurality (e.g., two, three,
four, five, etc.) of donor nucleic acid molecules (e.g., genomes
from different organisms), may be introduced into a single host
cell. For example, a diploid yeast strain containing genomes of two
different organisms, such as two Mycoplasma genomes from different
species, can be generated by crossing two different haploid
strains, each carrying one of the genomes. Crossing haploid yeast
strains can be carried out using well-known methods.
[0343] Multiple distinct selection markers can be used in the
respective haploid strains, to allow for selection of cells
containing both genomes after the cross. For example, a HIS3 and
TRP marker can be introduced into two different haploid cells,
respectively, carrying different genomes, followed by selection of
diploid cells on medium lacking histidine and tryptophan, as
described in the Examples of PCT Publication WO 2011/109031.
[0344] Assembled nucleic acid molecules may be used for any number
of purposes. For example, in many instances, it will be desirable
to introduce such molecules into cells for particular applications.
The components of the assembled nucleic acid molecules and the
cells that they are introduced into will vary widely with the
particular application.
[0345] One illustration of an application is a prokaryotic
production cell line for which an assembled nucleic acid molecule
represents the entire genome. This genome may be designed for
minimal functionality with the following features
represent/absent:
[0346] 1. Lack of ability to undergo conjugation or mating (safety
feature).
[0347] 2. Lack of ability to synthesize a critical nutrient (safety
feature).
[0348] 3. Maintain a high energy charge (production efficiency
feature).
[0349] 4. A pathway for generation of a desired end product
(production feature).
[0350] While features included or excluded from cells generated by
methods of the invention can vary greatly, in many instances,
safety features will be included to prevent "escape" of the
organism and limit the ability of the organisms to transfer traits
to other organisms. Production features may be included to tailor
the organisms for a specific application. This tailoring may fine
tuned in a manner not currently possible with a "chasis" organisms.
A chasis organism is an organism which has many of the features the
desired application but requires modification to make it fully
suitable. Typically this modification results from (1) the
inactivation of one or more gene and/or pathway and/or (2) the
introduction of one or more gene. In some instances, assembled
nucleic acid molecules may be introduced into a chasis organism
with or without the ultimate elimination of the chasis organism
genome.
[0351] A recipient cell can be, for example, a bacterial cell, a
yeast cell, a fungal cell, an insect cell, a mammalian cell, a
plant cell or an algal cell.
[0352] The invention includes methods for producing nucleic acid
molecules (e.g., individual coding elements, genomes, etc.)
designed to yield high level production of desired end products, as
well as the nucleic acid molecules themselves and organisms into
which these nucleic acid molecules are introduced. Using amino acid
biosynthesis for purposes of illustration, many organisms can
produce lysine on their own but do so in limited quantities. In
many instances, L-aspartate is a starting compound for L-lysine
production. Further, amino acids which may be produced as part of
the conversion of aspartate to lysine include L-threonine,
L-methionine and L-isoleucine. Further, a number of enzymes are
involved in the conversion of aspartate to lysine, often starting
with aspartate kinase. As would be apparent to one skilled in the
art, pathways associated with the synthesis of L-lysine may also be
altered for high level production of L-threonine, L-methionine
and/or L-isoleucine. Enzymes involved in the production of
L-lysine, L-threonine, L-methionine and L-isoleucine are set out in
U.S. Pat. No. 7,323,321, the entire disclosure of which is
incorporated herein by reference.
[0353] Pathway engineering can be employed to introduce
constitutive, inducible and repressible promoters at specific
points in the metabolic pathway to drive production towards a
designed end product (e.g., L-lysine). Pathway engineering will
often be employed in a manner that allows for the direction of
cellular resources (e.g., energy charge, nutrients) of a cell to be
directed to two functions: (1) Cell growth/division and (2) end
product production. Thus, in some embodiments, the invention
includes methods for designing and constructing cells, as well as
the cells themselves, that channel cellular resources into two
functions: (1) Cell growth/division and (2) end product
production.
[0354] Cells of the invention may be designed to not engage in
activities normally associated with wild-type cells. One of these
activities is mating. Mating consumes cellular resources and
facilitates gene transmission. In many instances, neither of these
effects of mating will be desirable. Further, in some instances,
mating leads to sporulation. Spore formatting may be desirable for
storage of organisms but, in many instances, if sporulation is
desired, then mating genes may be placed under tight regulatory
control or instructed on vectors.
[0355] In some embodiments, the invention includes cells designed
and constructed to have a minimal genome for the desired purpose.
DNA replication, transcription, and translation, as examples,
consume cellular resources. Thus, one method for providing for
efficient cellular resource channeling is to design and/or use a
cell with a minimal genome.
[0356] With respect to cell division, if basic molecules required
for cellular function are decreased below certain levels, then cell
growth and division will generally be impacted. Again using amino
acid production for purposes of illustration, when lysine is the
desired end product there are at least three choices for providing
suitable concentrations of threonine, methionine and isoleucine for
cellular metabolism: (1) Allowing for production of these amino
acids by alternative pathways, (2) using promoters which allow for
some production of these amino acids as side products of lysine
production, and (3) supplying these amino acid exogenously.
[0357] The invention thus include methods for pathway engineering
of cell, such methods comprising:
[0358] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a
microquantity;
[0359] (b) joining some or all of the nucleic acid molecules
present in the pool formed in (a) to form a plurality of larger
nucleic acid molecules; and
[0360] (c) assembling the plurality of larger nucleic acid
molecules to form the nucleic acid molecule which encodes at least
two expression products, wherein at least two of the at least two
expression products are in the same biological pathway that
converts a starting compound (e.g., L-aspartate) to a desired end
product (e.g., L-lysine, L-isoleucine, etc.).
[0361] Various embodiments of the invention include
computer-implemented methods for pathway engineering of cell. These
methods may be implemented by a processor by executing instructions
encoded on a computer-readable medium. According to various
embodiments, the instructions may be for:
[0362] (a) synthesizing a plurality of nucleic acid molecules,
wherein each nucleic acid molecule is prepared in a
microquantity;
[0363] (b) joining some or all of the nucleic acid molecules
present in the pool formed in (a) to form a plurality of larger
nucleic acid molecules; and
[0364] (c) assembling the plurality of larger nucleic acid
molecules to form the nucleic acid molecule which encodes at least
two expression products, wherein at least two of the at least two
expression products are in the same biological pathway that
converts a starting compound (e.g., L-aspartate) to a desired end
product (e.g., L-lysine, L-isoleucine, etc.).
[0365] One application of technology of the invention is in biofuel
production. In many instances, this involves the conversion of a
carbon source to a biofuel or a biofuel precursor. Biofuel or
biofuel precursors vary widely, as do cell suitable for their
production. In many instances, cells used for the production of
biofuel or biofuel precurors will be algal or plant cells.
Exemplary algae which may be used in this and other aspects of the
invention include Anabaena sp., Chlamydomonas reinhardtii,
Chlorella sp., Cyclotella sp., Gloeobacter violaceus,
Nannochloropsis sp., Nodularia sp., Nostoc sp., Prochlorococcus
sp., Synechococcus sp., Oscillatoria sp., Arthrospira sp., Lyngbya
sp., Dunaliella sp., and Synechocystis sp.
[0366] Many species of plants may be cultivated from a single or
small number of plant cells. Thus, plants which contain assembled
nucleic acid molecules in most, if not all of their cells, may be
generated. Exemplary algae which may be used in this and other
aspects of the invention include corn, soybeans, rapeseed, sugar
cane, mustard, switchgrass, and jatropha.
[0367] Biofuels, biofuel precursors and related compounds produced
applications may be useful for applications which include the
following: space heating, lighting, cooking, and running of
automobile engines and generators.
[0368] Exemplary biofuels and biofuel precursors include
normal-chain alcohols (the alcohol group --OH attached to the
terminal carbon) having greater than 3 carbon atoms up to 21 carbon
on. Normal chain alcohols, which may be produced by methods of the
invention, include n-butanol, n-pentanol, n-hexanol, n-heptanol,
n-octanol (capryl alcohol), n-nonanol (pelargonic alcohol),
n-decanol (capric alcohol), n-dodecanol (lauryl alcohol),
n-pentadecanol, n-hexadecanol (cetyl alcohol), n-tetradecanol
(myristyl alcohol), cis-9-hexadecen-1-ol (palmitoleyl alcohol),
n-octadecanol (stearyl alcohol), 9E-octadecen-1-ol (elaidyl
alcohol), cis-9-octadecen-1-ol (oleyl alcohol), 9Z,
12Z-octadecadien-1-ol (linoleyl alcohol), 9E, 12E-octadecadien-1-ol
(elaidolinoleyl alcohol), 9Z, 12Z, 15Z-octadecatrien-1-ol
(linolenyl alcohol), 9E, 12E, 15-E-octadecatrien-1-ol
(elaidolinolenyl alcohol), 12-hydroxy-9-octadecen-1-ol (ricinoleyl
alcohol) and 1-eicosanol (arachidyl alcohol or combinations
thereof. Normal chain alcohols may be saturated or unsaturated.
[0369] n-butanol can be produced by microbial fermentation,
chemically synthesized or obtained from a plant source by bacterial
action (e.g., engineered bacterial generated by methods of the
invention). This includes obtaining butanol from cellulose
containing plants, lignin-containing plants, from sewage and animal
waste, from sugars obtained from plant source and then by
fermentation involving algae (e.g., engineered algae generated by
methods of the invention). Higher alcohols can also be obtained in
similar manner.
[0370] The invention may also be used to produce chemical
intermediates. Example of such intermediates are 1,4-butanediol and
1,3-propanediol. 1,4-butanediol is a bifunctional alcohol with a
broad array of uses in the chemical industry. As examples,
butanediol and its derivatives are used in the production of
plastics, polyurethanes, solvents, electronic chemicals and elastic
fibers. A 1,4-butanediol synthesis pathway is set out in Burk,
International Sugar Journal 112:30-35 (2010). Thus, the invention
includes cells engineered to produce or for increased production of
chemical intermediates (e.g., 1,4-butanediol, 1,3-propanediol,
etc.), as well as methods for designing and producing such
cells.
[0371] Additional Applications
[0372] As one skilled in the art would understand, nucleic acid
molecules produced in microscale quantities (e.g., femtomoles to
nanomoles quantities, such as from about 0.001 femptomole to about
1.0 nanomole, from about 0.01 femptomole to about 1.0 nanomole,
from about 0.1 femptomole to about 1.0 nanomole, from about 0.001
femptomole to about 0.1 nanomole, from about 0.001 femptomole to
about 0.01 nanomole, from about 0.001 femptomole to about 0.001
nanomole, from about 1.0 femptomole to about 1.0 nanomole, from
about 1.0 femptomole to about 0.1 nanomole, from about 1.0
femptomole to about 0.01 nanomole, from about 1.0 femptomole to
about 0.001 nanomole, from about 10 femtomoles to about 1.0
nanomole, from about 10 femtomoles to about 0.001 nanomole, from
about 20 femtomoles to about 1.0 nanomole, from about 100
femtomoles to about 1.0 nanomole, from about 500 femtomoles to
about 1.0 nanomole, from about 1 nanomole to about 800 nanomoles,
from about 40 nanomoles to about 800 nanomoles, from about 100
nanomoles to about 800 nanomoles, from about 200 nanomoles to about
800 nanomoles, from about 500 nanomoles to about 800 nanomoles,
from about 100 nanomoles to about 1,000 nanomoles, etc.).
[0373] The invention may be used to prepare microarrays. Such
microarrays may be generated in multiple ways including by the
depositing of nucleic acid molecules on a support (e.g., a solid
support such as a planar sold support) or by synthesis of nucleic
acid directly on the support. In one embodiment, the plate shown in
FIGS. 2A-2B can be modified so that the base/bottom is designed for
the synthesis of nucleic acid on its surface. Optionally, the base
could be structured to be removable to yield, for example, a planar
microarray. In most such instances, the bead shown in FIGS. 2A-2B
would be omitted during nucleic acid synthesis. Thus, the invention
includes methods for the generation of microarrays.
[0374] Methods for printing microarrays are set out in U.S. Pat.
Nos. 5,807,522 and 7,211,148, the disclosure of which is
incorporated herein by reference. Such methods may be used in the
practice of the invention to produce, for example, microarrays by
the deposition of nucleic acid molecules produced as described
herein.
[0375] One advantage of methods described herein is their
modularity. As an example, nucleic acid molecules which form
sub-portions of different larger nucleic acid molecules may be
produced on the same plate to array. Thus, methods of the invention
allow for the simultaneous production of nucleic acid molecules,
followed by selection of individual synthesized nucleic acid
molecules for later processes (e.g., pooling, cleavage
deprotection, and assembly). Thus, methods of the invention include
those where nucleic acid molecules are simultaneously produced
(e.g., chemically synthesized), followed by assembly into two or
more (e.g., two to ten, three to ten, four to ten, five to ten, two
to thirty, five to thirty, ten to thirty, five to fifty, etc.)
larger nucleic acid molecules.
[0376] In certain embodiments, nucleic acid molecules or plurality
of nucleic acid molecules synthesized by the methods of the present
invention may be primers and/or probes. Primers and/or probes can
be generated in microquantity using, for example, a solid support
as described herein. Primers prime nucleic acid extension reactions
that can be part of an amplification reaction. Probes are used to
detect a target nucleic acid sequence. Accordingly, probes are used
in detection methods to directly or indirectly detect a target
nucleic acid sequence. Primers and probes typically have a
predetermined nucleotide sequence that hybridize with or otherwise
bind to a target nucleic acid sequence. Probes in illustrative
embodiments include a label, such as a fluorescent label. For
example, a control mechanism may be connected to a solid support or
an array of solid supports used in the methods of the present
invention, wherein a target nucleotide sequence is input into the
control mechanism. The control mechanism may be used to direct the
sequence of addition of reactants for nucleic acid synthesis, such
that a nucleic acid molecule having the target nucleotide sequence
is synthesized.
[0377] Probes and primers hybridize with or otherwise bind to a
target nucleic acid sequence because of sequence identity they
share with the target nucleic acid sequence. For example, a primer
or probe can share 80, 85, 90, 95, 96, 97, 98, 99, 99.5, or 100%
contiguous sequence identity with a target nucleic acid sequence.
Primers and probes hybridize with their target nucleic acid
sequence under stringent and typically highly stringent conditions,
as are known in the art.
[0378] A label can be attached to the 5' terminal nucleotide, the
3' terminal nucleotide, or any internal nucleotide of the primers
and/or probes of the present invention. The label in certain
illustrative embodiments, is a fluorophore. A vast array of
fluorophores are known to those of skill in the art and can be
included in the methods and compositions of the present invention.
See, for example, Cardullo et al, Proc. Natl. Acad. Sci. USA
85:8790-8794 (1988); Dexter, D. L, J. of Chemical Physics
21:836-850 (1953); Hochstrasser et al., Biophysical Chemistry
45:133-141 (1992); Selvin, R, Methods in Enzymology 246:300-334
(1995); Steinberg, I., Ann. Rev. Biochem, 40:83-114 (1971); Stryer,
L., Ann. Rev. Biochem, 47:819-846 (1978); Wang et al., Tetrahedron
Letters 31:6493-6496 (1990); Wang et al., Anal. Chem. 67:1197-1203
(1995). For example, the fluorophore can be Biosearch Blue, FAM,
TET, a CAL Fluor dye, JOE, VIC, HEX, a Quasar dye, a Cy dye, NED,
TAMRA, ROX, Texas Red, or a Pulsar dye. These dyes and nucleic acid
synthesis reactants that include these dyes are commercially
available, for example, from Biosearch Technologies, Inc., Glen
Research, or Life Technologies.
[0379] In illustrative embodiments, primers synthesized by methods
provided herein, are PCR primers. In certain embodiments, primers
are labeled with a label on their 5' end or 3' end. For example,
primers can be LUX primers, Scorpion primers, Amplifluor primers,
and/or Plexor primers.
[0380] In certain embodiments, the present invention provides a
method for synthesizing a plurality of primer and probe sets (e.g.,
pairs). The primer and probe sets (e.g., pairs) can be generated in
microquantity using a plate described herein (e.g., a plate of the
general format shown in FIGS. 2A-2B). A primer and probe set (e.g.,
pair) includes one or more primers that prime an extension reaction
that generates a nucleic acid extension product that is a target
nucleic acid sequence for one or more probes of the primer and
probe set (e.g., pair). In other words, in a primer and probe set
(e.g., pair), the probe typically binds to the amplification
product generated by the primer(s). In illustrative embodiments,
the primer and probe set (e.g., pair) include a pair of PCR primers
and a probe that binds to an amplification product generated by an
amplification reaction that uses the pair of primers. For example,
the primer and probe set (e.g., pair) can include two PCR primers
and one 5' nuclease probe or one Molecular Beacons probe that binds
to the amplification product generated when the PCR primers are
used in a PCR reaction.
[0381] As noted above, methods of the present invention can
generate an array of nucleic acid molecules, such as primers,
probes, and/or primer and probe sets (e.g., pairs). For example,
nucleic acid molecules can be synthesized in an array of positions
such that each position includes one or a plurality of nucleic acid
molecules such as primers, probes, and/or primer and probe sets
(e.g., pairs). Array can include primers, probes, and primer and
probe sets (e.g., pairs) at a density of 100, 200, 250, 500, 1000,
10,000, 100,000, 1,000,000, or 10,000,000 per cm.sup.2. The total
number of nucleic acid molecules in an array of nucleic acid
molecules generated using methods of the present invention can
include, for example, 100, 200, 250, 500, 1000, 10,000, 100,000,
1,000,000, 10,000,000, 100,000,000, 1,000,000,000, or
10,000,000,000 primer, probes, and/or primer and probe sets (e.g.,
pairs). More than one primer and probe set (e.g., pair) can be
included in an array position such that the primer and probe set
(e.g., pair) are designed to perform a multiplex reaction, such as
a multiplex PCR reaction.
[0382] Probes of the invention can be labeled with a single dye,
such as a single fluorophore. Probes of the invention can be FISH
probes.
[0383] Probes of the invention can be probes used in amplification
reactions. For example, these probes can be dual-labeled probes.
Dual-labeled probes in certain illustrative embodiments include
labels that are donor-acceptor energy transfer pairs, such as FRET
pairs. When the donor (fluorophore) is a component of a probe that
utilizes donor-acceptor energy transfer, the donor fluorescent
moiety and the quencher (acceptor) of the invention are preferably
selected so that the donor and acceptor moieties exhibit
donor-acceptor energy transfer when the donor moiety is excited.
One factor to be considered in choosing the fluorophore-quencher
pair is the efficiency of donor-acceptor energy transfer between
them. In many instances, the efficiency of FRET between the donor
and acceptor moieties is at least 10%, at least 50%, or at least
80%. The efficiency of FRET can easily be empirically tested using
the methods both described herein and known in the art.
[0384] In some instances, the donor-acceptor pair may include a
fluorophore and a quencher. The quencher can be a dark quencher. As
such, probes of the present invention can include a BHQ dye or a DQ
dye (Epoch) as the quencher. The quencher in other embodiments may
be DABCYL or TAMRA.
[0385] Primers and probes synthesized using methods and systems of
the present invention can include can include moieties that
stabilize hybridization of nucleic acids (e.g., intercalators,
minor groove binding moieties, bases modified with a stabilizing
moiety (e.g., alkynyl moieties, and fluoroalkyl moieties)), and
conformational stabilizing moieties, such as those disclosed in
U.S. Patent Application Publication No. 2007/0059752, the
disclosure of which is incorporated herein by reference. The
primers and probes can include intercalating agents such as
acridine. In other embodiment, primers and probes synthesized using
methods and systems of the present invention can be locked nucleic
acid (LNA) probes, or peptide nucleic acid (PNA) probes.
[0386] Dual-labeled probes synthesized using methods and systems of
the present invention can be used in amplification reactions such
as real-time PCR reactions. The dual-labeled probes in illustrative
examples are hydrolysis probes, such as 5' nuclease probes (see
e.g., Livak et al, PCR Methods Appl., 4:357-562 (1995); and U.S.
Pat. No. 5,538,848), molecular beacons (see e.g., Mhlanga, Methods,
25:463-472 (2001)), scorpions (see e.g., Saha, J. Virol. Methods,
93:33-42 (2001)), or hybridizing probes (see e.g., U.S. Pat. No.
7,670,832). In certain embodiments the primers and probes of the
present invention are used in digital amplification reactions such
as digital PCR reactions.
[0387] Primers synthesized by methods of the present invention can
be between 5 and 50 nucleotides in length and are typically between
10 and 30 and more typically 15 and 30 nucleotides in length.
Probes of the present invention can be between 5 and 100, 10 and
50, 10 and 30, or 15 and 30 nucleotides in length.
[0388] Methods of the present invention can utilize general
chemistries and chemical methods known in the art for synthesizing
nucleic acid molecules that include one, two, or more labels, such
as a fluorescent labels. For example, such methods can utilize
phosphoramidites and/or solid supports that are modified to include
such labels. Exemplary solid supports, for example, can include at
least one quencher bound through a linker to the solid support.
Additional exemplary embodiments can utilize a solid support or a
phosphoramidite functionalized moiety that stabilizes a duplex,
triplex or higher order aggregation (e.g., hybridization) of a
nucleic acid molecule synthesized according to the present
invention with a target nucleic acid molecule.
[0389] In certain embodiments, the primers and/or probes of the
present invention are used in real-time PCR assays such as gene
expression assays or genotyping assays, for example SNP genpotyping
assays. The probes can be generated using methods provided herein,
at a concentration, for example, of between 1 nM and 1 M, 1 mM and
1 M. An exemplary concentration can be 100 mM. The probes and/or
especially the primers generated by methods provided herein can be
lyophilized. For example, 1-1,000,000 picomole of primer can be
lyophilized in a reaction vessel, such as a tube, or a well, or can
be dried on a spot of an array of positions.
[0390] In one embodiment, the present invention provides a method
for nucleic acid synthesis that includes combining nucleic acid
synthesis reactants inside a microwell and generating the nucleic
acid molecule inside the microwell. The microwell can be linked to
a controller, such as a computer processor, wherein a nucleotide
sequence for one or more nucleic acid molecules is input into the
controller or otherwise present in a computer memory of the
controller. The controller can be connected to or otherwise in
communication with a nucleic acid molecule design and ordering
functionality that can be provided over a wide-area network. For
example, nucleic acid molecule design and ordering functionality
can be provided over the Internet.
[0391] In certain embodiments, methods of the present invention
include an HPLC-purification step. In addition, methods of the
present invention can be performed under ISO and/or GMP-certified
conditions. In some embodiment, nucleic acid molecule synthesis is
performed using a microwell plate.
[0392] Methods and apparatus of the invention may also be used for
the preparation of libraries. These libraries may contain one or
more point mutations or highly divergent molecules (e.g., nucleic
acid molecules which encode proteins with different functional
activities). Along these lines, the invention includes methods for
the generation of libraries where all or some of the library
members are chemical synthesized and thus not generated from
cellular nucleic acid. Library types which may be generated by
methods of the invention include cDNA libraries, genomic libraries,
combinatorial libraries, point mutation libraries, and combinations
of one or more of such libraries.
[0393] As noted above, in some embodiments, the invention includes
methods or producing cDNA library equivalents generated, as well as
the libraries themselves, using bioinformatic information. Using
the schematic shown in FIG. 11 for purposes of illustration, a
library may be synthesized and, if necessary, assembled according
to methods described herein. The library members may then be
inserted into a non-library nucleic acid molecule (e.g., a vector,
a cellular chromosome, etc.). Insertion may be facilitated by any
number of means such as ligation (e.g., "sticky end" ligation).
[0394] The invention includes methods for generating library, as
well as the libraries themselves. Some of these libraries are of
types which are difficult or impossible to produce by standard
library production methods. One such type is a partial cDNA
library. Partial cDNA libraries (also referred to as "cDNA
equivalent" libraries) may be generated by bioinformatically
selecting specific cDNAs for inclusion in the library. Nucleic acid
molecules may then be synthesized and, if necessary, assembled to
form the library.
[0395] cDNA libraries typically contain DNA molecules which
correspond to RNA transcripts within a cell. In many cases, such
libraries are biased towards transcripts which contain polyA tails.
mRNAs represented in such libraries typically contain multiple
cDNAs corresponding to individual coding regions. This is true when
splice variants of a genomics coding region are generated by
splicing events. The present invention allows for the production of
cDNA libraries (as well as genomic libraries) with "exclusive"
representation. For example, since nucleic acid molecules are
selected for inclusion, as compared to exclusion, the DNA molecules
corresponding to the following may be excluded from libraries:
ribosomal RNAs, globin RNAs, tRNAs, and specified mRNAs. Thus, the
invention includes methods for producing member biased and
exclusive member inclusion cDNA and genomic libraries, as well as
the libraries themselves.
[0396] Further, libraries of the invention include those which
contain specified nucleic acid molecules. For example, the
invention includes methods for producing cDNA libraries containing
a subset of member represented in cDNA libraries generated by
standard methods. For purposes of illustration, assume that a
particular mammalian cell type has on average 15,000 different mRNA
transcripts including splice variants and one seeks to use a cDNA
library which contains 125 cDNA molecules corresponding to all of
the known splice variants of transcripts corresponding to 35
different kinases. In another instance, one seeks to screen a
collection of nucleic acid molecules that encode variants of the
same wild-type coding sequence. Using FIG. 12A for purposes of
illustration, amino acids 85 through 95, and the coding sequence of
a wild-type cDNA is shown at the top of the figure. Amino acids 88
through 91 represent a region which is predicted to be a flexible
linker connecting two functional domains. In this instance, a
collection of nucleic acid molecules is produced encoding proteins
with different, but specified, amino acids at positions 88 through
91 (the linker region). Collections of nucleic acid molecules such
as those shown in FIG. 12A may be generated in number of ways.
[0397] One way will generally be over inclusive in that additional
nucleic acid molecules will normally be generated. This method
employs "dirty bottle" synthesis. To generate variant molecules
such as those shown in FIG. 12A reagents for the addition of bases
at particular positions are mixed. Thus, when the base at the first
and second positions of codon 88 are to be added, a mixture of
reagents for addition of a C and G could be used. The ratio of
these reagents may be adjusted to favor either C or G addition or
the ratio may be adjusted so that equal amounts of C and G are
introduced. In a portion of the population, the codon CGT
(arginine) would also be generated.
[0398] Another method by which collections of nucleic acid
molecules such as those shown in FIG. 12A may be generated is by
synthesizing the individual variant sequences as separate nucleic
acid segments. This allows for the generation of only nucleic acid
molecules (except for synthesis errors) which encode the desired
variant population members.
[0399] The invention also includes individual and collections of
nucleic acid molecules with codon alterations as compared to
wild-type molecules, as well as methods for producing such
molecules. In some aspects, a codon altered library is generated
where some or all (in many cases all or most) of the nucleic acid
molecules in the collection are codon altered as compared to
naturally wild-type coding sequences. This shows one substantial
advantage of methods of the invention over standard library
construction methods. With standard library construction methods,
libraries are built from naturally occurring nucleic acid molecules
(e.g., genomic DNA, mRNA, etc.). Methods of the invention allow for
efficient construction of libraries using bioinformatic
information. The result being that individual nucleic acid
molecules in any collection generated can be generated with
"tailored" nucleotide sequences.
[0400] Using FIG. 12B for purposes of illustration, a collection of
nucleic acid molecules that contain different codons for the same
coding sequence may be generated and then screened for desired
features (e.g., increased or decreased expressions levels).
Decreased expression levels may be desired when over expression of
a protein is delirious to cells or host organisms that the protein
is produced in. Thus, codon selection can be used as an expression
regulation mechanism.
[0401] Methods of the invention may also be used to generate large
numbers of primers for multiplex amplification (e.g., PCR).
Typically such primers will be between 15 and 100 (e.g., from 15 to
90, from 25 to 90, from 25 to 80, from 25 to 70, from 25 to 60,
from 25 to 50, from 30 to 90, from 30 to 60, etc.) nucleotides in
length. Further, primers may also contain bar codes to allow for
the tagging of amplified nucleic acid molecules for, for example,
later identification as well as tracking of primers and primer
pairs during and subsequent to synthesis runs.
[0402] In some instances, between 500 and 50,000, between 1,000 and
50,000, between 2,000 and 50,000, between 5,000 and 50,000, between
5,000 and 40,000, between 5,000 and 30,000, between 5,000 and
100,000, between 5,000 and 300,000, between 5,000 and 500,000,
between 5,000 and 1,000,000, between 5,000 and 5,000,000, between
10,000 and 100,000, between 10,000 and 500,000, between 10,000 and
800,000, between 20,000 and 100,000, between 20,000 and 500,000,
etc. primers pairs will be generated.
[0403] The invention includes the preparation of primers which may
be used in processes such as Life Technology Corporation's
AMPLISEQ.TM. products (see, e.g., cat. no. 4472395). Products such
as this employ multiplex PCR for the amplification of specific
nucleic acid molecules. The amplified nucleic acid molecules may
then be used in downstream processes such as sequencing to identify
nucleic acids present in a starting sample. In some cases, modified
nucleic acid bases and/or natural bases not typically associated
with DNA (e.g., deoxyuridine) are synthetically incorporated into
the primer sequences as a "fifth (or greater) bottle" to impart
particular properties into the individual primer(s) and/or primer
set to facilitate downstream processing of the amplified products
prior to sequencing or to further impart encoding of the individual
primer(s) and/or primer set in the manner of barcoding to
facilitate and resolve complex sequence analysis typically from a
mixture of samples.
[0404] The invention thus provides methods for producing primer
pools, as well as the primer pools themselves. Primer pools may be
used to amplify RNA and/or DNA populations or subpopulation. As an
example, primer pools may be produced that allow for the
amplification of genomic DNA representing the entire nuclear genome
of a cell, a single nuclear chromosome, a set of nuclear genes or
regions (e.g., a set of chromosomal loci), a mitochondrial genome,
or a chloroplast genome, as well as combinations thereof. The
invention thus includes the bioinformatic design of primers for
specific applications (e.g., the applications set out immediately
above).
[0405] The invention also provides methods for producing primer
pools for the amplification of specific RNA populations. In one
embodiment of the invention, a primer pool is designed to amplify
all mRNA molecules or a subpopulation of mRNA molecules (e.g.,
mRNAs encoding kinases, phosphatases, etc.) produced by a cell but,
optionally, not other RNA molecules (e.g., tRNA, rRNA, hnRNA,
etc.). Such primer pools may then be used for expression analysis
(e.g., measuring the level of expression under various conditions).
Expression analysis may be performed using, for example,
microarrays or sequencing platforms. The invention thus includes
expression analysis methods. In some embodiments, such methods
include one or more of the following steps: (a) designing
bioinformatically a primer pool, (b) synthesizing primer pairs of
the primer pool, (c) contacting the primer pool to a sample derived
from a cell containing nucleic acids (e.g., mRNA), (d) amplifying
nucleic acid molecules in the sample corresponding to the primer
pairs, and (e) analyzing the resulting amplified nucleic acid
molecules.
[0406] The reduction or elimination of nucleic acid molecules
corresponding to rDNA is desirable in many expression analysis
applications because of the abundance of rRNA in many samples.
Other rRNA amplification reduction methods are set out in U.S.
Patent Publication No. 2008/0187969, the disclosure of which is
incorporated herein by reference.
[0407] The invention also includes variations of the above for
additional applications such as multiplex methods of the
identification of mutations in genomic nucleic acid. Thus, the
invention further includes methods and compositions for the
identification of mutations, including cancer screens.
[0408] The invention includes methods for producing various numbers
of primer (in many instances in primer pairs). The number of
primers which may be prepared by methods of the invention as
separate entities and/or in mixed populations range from five to
500,000, from 500 to 500,000, from 1,000 to 500,000, from 5,000 to
500,000, from 10,000 to 500,000, from 20,000 to 500,000, from
30,000 to 500,000, from 5,000 to 250,000, from 5,000 to 100,000,
from five to 5,000, from five to 50,000, from 5,000 to 800,000,
from 5,000 to 1,000,000, from 5,000 to 2,000,000, from 10,000 to
2,000,000, from 20,000 to 1,000,000, from 30,000 to 2,000,000,
etc.
[0409] The invention thus provides methods for the rapid design,
configuration and synthesis of defined sets of primers for the
specifically determining genetic compositions and characterization
of regions for a wide variety of analyses, sample sets and
experimental designs. This aspect of the invention partially flows
from the use of bioinformatics in conjunction with nucleic acid
molecule synthesis methods described herein. In particular, the
complete sequences of a considerable number of genomes have been
sequenced. This sequence information, combined with nucleic acid
synthesis methods (as well as other methods) described herein allow
for detailed genome and transcriptome analyses. Multiplex methods,
such as those set out above, provide one means for performing such
analyses.
Representative Embodiments
[0410] Numerous variations of the invention are feasible and may be
employed to achieve the desired results. Many such variations may
be directed to design features. In some instances, such design
features may be used for operator convenience and/or cost savings
(e.g., decreased reagent usage).
[0411] FIG. 9 shows one embodiment of an electrical coil that may
be used in specific embodiments of the invention. Numerous
variations of such coils, a number of which are described elsewhere
herein, may be used with the invention.
[0412] An electrical coil such as that shown in FIG. 9 may be
designed with the following exemplary structural an operation
parameters: Maximum current density 3 Amps/mm.sup.2, double layer
flat coil, wire cross section 5.times.2 .mu.m, 10 turns, inner
diameter (Di).about.10 .mu.m, outer diameter (Da).about.180 .mu.m,
and wire length .about.6 mm
TABLE-US-00006 TABLE 6 Mag. Field Strength current (A) (A/m)
(approx. short coil) 0.00003 6.314390318 current (.mu.A) Mag. Flux
Density (T) 30 7.9349E-06
[0413] FIG. 9 and TABLE 6 show exemplary specifications of a flat
double layer coil that can be build up on a wafer. A coil such as
that shown in FIG. 9 may be designed such that contact is made with
each well in a synthesis platform. Further, the generation of a
magentic field may be used to lift beads from synthesis sites
(e.g., wells). Exemplary magnetic field strength/flux density
figures are shown in TABLE 6. A FEM-program like Comsol
(www.comsol.com) may be used to calculate parameters for specific
systems and formats.
[0414] Several materials, and properties associated with these
materials, that may be used in electrodes used in various aspects
of the invention are set out in TABLE 7. The selection of electrode
materials will be determined by numerous factors including costs
and various design specifications and power requirements.
TABLE-US-00007 TABLE 7 Specific Resistance Coil Resistance DC Power
Voltage Material ((.OMEGA.*mm.sup.2)/m) (.OMEGA.) (.mu.W) (V)
Copper 1.68E-02 10.068 0.009061 0.000302 Aluminum 2.65E-02 15.9
0.01431 0.000477 Gold 2.21E-02 13.284 0.011956 0.000399
[0415] Electrodes (e.g., electrical coils) used in the practice of
the invention will be designed so as to meet the particular
applications for which they are used. As an example, when
electrodes are used to generate EGA, they will generally be
designed with the following in mind: (1) The application (e.g.,
local application) of sufficient current to allow for the
generation of an effective amount of EGA within a specified time
period, (2) limitation of heating associated with the application
of current. Thus, will generally be desirable to limit the amount
of current used to reach a local pH of 1.0 with the addition of
little excess current. TABLE 8 provides calculations for achieving
this with specific well parameters. Further, the generation of pH 1
in a well as set out below will require that 727 pA of current be
applied for about 1 second. This results in a current density of
115A/m.sup.2 on the working electrode.
TABLE-US-00008 TABLE 8 Current/pH generation for a cylindrical well
using a 2.8 .mu.m bead Input Parameter Well Diameter (.mu.m) 4 Well
Height (.mu.m) 3 Desired pH 1 Buffer Concen. (mol/L) 0.1 Area
(.mu.m.sup.2) 6.3 Well Vol. (.mu.m.sup.3) 37.68 Protons Generated
4.52 .times. 10.sup.9 Charge (pAs) 727 Current Density WE
(A/m.sup.2) 115
[0416] The shape of an electrode may vary greatly and may be a coil
as shown in FIG. 9, a disk, a thin film, etc. Further, electrodes
used in the practice of the invention may be composed of any number
of compounds, including platinum, palladium, copper, gold,
aluminum, niobium, niobium oxide, tungsten, titanium, tantalum,
molybdenum, nickel, platinum, silver, manganese, neodymium, carbon,
and silicon, and an alloy material or a compound material
containing one or more of the above-described elements, as well as
other elements.
[0417] FIG. 10 shows an exemplary apparatus format of the
invention. This figure shows two pumps 1000 that deliver fluids, as
well as gases when appropriate, through tubes 1001 to fluidic
channels 1002, which is bounded at the top by a plate 1007. Fluids
delivered to the apparatus are removed through drainage channels
1003 to drainage tubes 1004 which lead to waste collection 1005.
The pumps 1000 are connected to fluid reservoirs (not shown), or
gas reservoirs when appropriate, and a control device (not shown)
that regulate what fluid or gas is delivered to the apparatus.
[0418] The control device also regulates the length of time that
fluids or gasses contact nucleic acid synthesis "chips" 1006. Three
nucleic acid synthesis "chips" 1006 are visible in FIG. 10 resting
on an electrode 1008. Fluids and/or gases are put in contact with
the chips and current passes through particular locations on the
chips where it is desirable for chemical reactions to occur. As
described elsewhere herein, any number of reagents and washing
materials may be used in the practice of the invention. In many
instances, the reagents and materials used will be those which
allow for the production of nucleic acid molecules.
[0419] The lower electrode 1008, as shown in FIG. 9, covers the
entire base of the apparatus. This need not be the case and one or
more electrodes may be associated with one end of each well or more
than one well. Opposite this electrode (shown as a lower electrode
1008 in FIG. 10), there will typically be one or more second
electrodes (not shown in FIG. 10) that allows for current to flow
through entire chips or through wells of the chips. In many
instances, these second electrodes will be positioned over
individual wells of the chip to allow for current to be directed
through the wells on an individual basis (see FIGS. 2A-2B).
[0420] Fluid channel 1002 can be formed in a surface layer. The
surface layer can be formed of a polymeric material, inorganic
material, or a combination thereof. For example, the surface layer
can be formed of a polymeric material. An exemplary polymeric
material includes acrylic, fluoropolymer, ethylene vinyl acetate
(EVA), or any combination thereof. In an example, the polymeric
material is a fluoropolymer. An exemplary fluoropolymer includes
polyvinylidene fluoride (PVDF), polyvinyl fluoride (PVF),
fluorinated ethylene propylene (FEP) copolymer, ethylene
chlorotrifluoroethylene (ECTFE) copolymer, a copolymer of
tetrafluoroethylene, hexafluoropropylene, and vinylidene fluoride
(THV), a copolymer of tetrafluoroethylene and perfluoro
methylvinylether (PFA or MFA), a fluoropolymer having a fluorinated
oxolane in its backbone, perfluoroether, or any combination
thereof. In particular, the fluoropolymer can be a fluoropolymer
having fluorinated oxolane in its backbone, for example, Cytop.
Further, the polymer coating can be amorphous, exhibiting little or
no crystallinity. In another example, the surface layer is formed
of an inorganic insulator. For example, the inorganic insulator can
include an oxide of silicon, aluminum, hafnium, tantalum,
zirconium, or any combination thereof, can include
tetraorthosilicate, can include a nitride of silicon, or can
include any combination thereof. In an example, the inorganic
insulator can include an oxide of silicon. In another example, the
inorganic insulator includes a nitride of silicon.
[0421] The surface layer can have a thickness in a range of 0.3
micrometers to 10 micrometers, such as a range of 0.5 micrometers
to 6 micrometers.
[0422] Individual wells used in the practice of the invention may
be of any number of shapes and sizes. One example of well
parameters is set out in TABLE 9. Of course, well volume and other
factors will change with well dimensions.
TABLE-US-00009 TABLE 9 Exemplary cylindrical well parameters Input
Parameter Well Diameter 40 .mu.m Well Height 35 .mu.m pH 1 Buffer
Concen. (mol/l) 0.1 mol/l Area/Well 1256 .mu.m.sup.2 Output
Parameter Well Volume 43,960 .mu.m.sup.3 Generated Protons/Well
(incl. buffer) 5.28 .times. 10.sup.12 Charge 848 nAs Current
Density/Well 675 A/m.sup.2
TABLE-US-00010 TABLE 10 Input Output Number of Oligos/ 1.0 .times.
10.sup.8 Required Buffer 1,666,667 Bead Vol. (pl) Number of beads
with 1 same oligo sequence Oligonucleotide 0.10 Concentration
(.mu.mol/l) Bead Diameter (.mu.m) 30 Bead Vol. (.mu.m.sup.3)
14,137.17
[0423] TABLE 10 shows some bead parameters and estimate buffer
volume and concentration for a particular bead size.
[0424] After completion of nucleic acid molecules production steps,
the substrates (e.g., beads) containing the nucleic acid molecules
may be collected, separated from the synthesis substrates, and
further processed.
[0425] An exemplary work flow is one such as the following: (1)
Beads are prepared with functional (hydroxyl or amine) groups, (2)
the beads are derivatized in batch off-line forming amide with
pre-synthesized universal primers with rare type IIs restriction
site for enzymatic cleavage of synthesized nucleic acid molecules
off the beads, (3) the beads are loaded by flowing suspension into
chip, application of current secures beads in wells, (4) the loaded
beads are in or near physical contact with an anode and EGA is
generated at anode and on the bead surface for deprotection, (5)
synthesis steps as described herein are performed, (6) after
synthesis, digitally electro-eject of desired beads from well is
accomplished by reversing the current, (7) ejected beads are
collected and pooled from the liquid flow out of chip, and (8)
other beads are held in wells until later in time by the
application of weak current in initial anode/cathode
orientation.
[0426] Those skilled in the art will recognize that the operations
of the various embodiments may be implemented using hardware,
software, firmware, or combinations thereof, as appropriate. For
example, some processes can be carried out using processors or
other digital circuitry under the control of software, firmware, or
hard-wired logic. (The term "logic" herein refers to fixed
hardware, programmable logic and/or an appropriate combination
thereof, as would be recognized by one skilled in the art to carry
out the recited functions.) Software and firmware can be stored on
computer-readable media. Some other processes can be implemented
using analog circuitry, as is well known to one of ordinary skill
in the art. Additionally, memory or other storage, as well as
communication components, may be employed in embodiments of the
invention.
[0427] FIG. 15 is a block diagram that illustrates a computer
system 1500 that may be employed to carry out processing
functionality, according to various embodiments, upon which
embodiments of a thermal cycler system 500 of FIG. 5 may utilize.
Computing system 1500 can include one or more processors or
controllers, such as a processor 1504. Processor 1504 can be
implemented using a general or special purpose processing engine
such as, for example, a microprocessor, controller or other control
logic. In this example, processor 1504 is connected to a bus 1502
or other communication medium. For example, processor 1504 may be a
current controller as described above with reference to FIGS.
2A-2B.
[0428] Further, it should be appreciated that a computing system
1500 of FIG. 12 may be embodied in any of a number of forms, such
as a rack-mounted computer, mainframe, supercomputer, server,
client, a desktop computer, a laptop computer, a tablet computer,
hand-held computing device (e.g., PDA, cell phone, smart phone,
palmtop, etc.), cluster grid, netbook, embedded systems, or any
other type of special or general purpose computing device as may be
desirable or appropriate for a given application or environment.
Additionally, a computing system 1500 can include a conventional
network system including a client/server environment and one or
more database servers, or integration with LIS/LIMS infrastructure.
A number of conventional network systems, including a local area
network (LAN) or a wide area network (WAN), and including wireless
and/or wired components, are known in the art. Additionally,
client/server environments, database servers, and networks are well
documented in the art.
[0429] Computing system 1500 may include bus 1502 or other
communication mechanism for communicating information, and
processor 1504 coupled with bus 1502 for processing
information.
[0430] Computing system 1500 also includes a memory 1506, which can
be a random access memory (RAM) or other dynamic memory, coupled to
bus 1502 for storing instructions to be executed by processor 1504.
Memory 1506 also may be used for storing temporary variables or
other intermediate information during execution of instructions to
be executed by processor 1504. Computing system 1500 further
includes a read only memory (ROM) 1508 or other static storage
device coupled to bus 1502 for storing static information and
instructions for processor 1504.
[0431] Computing system 1500 may also include a non-transitory
storage device 1510, such as a magnetic disk, optical disk, or
solid state drive (SSD) is provided and coupled to bus 1502 for
storing information and instructions. Storage device 1510 may
include a media drive and a removable storage interface. A media
drive may include a drive or other mechanism to support fixed or
removable storage media, such as a hard disk drive, a floppy disk
drive, a magnetic tape drive, an optical disk drive, a CD or DVD
drive (R or RW), flash drive, or other removable or fixed media
drive. As these examples illustrate, the storage media may include
a computer-readable storage medium having stored there in
particular computer software, instructions, or data.
[0432] In alternative embodiments, storage device 1510 may include
other similar instrumentalities for allowing computer programs or
other instructions or data to be loaded into computing system 1500.
Such instrumentalities may include, for example, a removable
storage unit and an interface, such as a program cartridge and
cartridge interface, a removable memory (for example, a flash
memory or other removable memory module) and memory slot, and other
removable storage units and interfaces that allow software and data
to be transferred from the storage device 1510 to computing system
1500.
[0433] Computing system 1500 can also include a communications
interface 1518. Communications interface 1518 can be used to allow
software and data to be transferred between computing system 1500
and external devices. Examples of communications interface 1518 can
include a modem, a network interface (such as an Ethernet or other
NIC card), a communications port (such as for example, a USB port,
a RS-232C serial port), a PCMCIA slot and card, Bluetooth, etc.
Software and data transferred via communications interface 1518 are
in the form of signals which can be electronic, electromagnetic,
optical or other signals capable of being received by
communications interface 1518. These signals may be transmitted and
received by communications interface 1518 via a channel such as a
wireless medium, wire or cable, fiber optics, or other
communications medium. Some examples of a channel include a phone
line, a cellular phone link, an RF link, a network interface, a
local or wide area network, and other communications channels.
[0434] Computing system 1500 may be coupled via bus 1502 to a
display 1512, such as a cathode ray tube (CRT) or liquid crystal
display (LCD), for displaying information to a computer user. An
input device 1514, including alphanumeric and other keys, is
coupled to bus 1502 for communicating information and command
selections to processor 1504, for example. An input device may also
be a display, such as an LCD display, configured with touch screen
input capabilities. Another type of user input device is cursor
control 1516, such as a mouse, a trackball or cursor direction keys
for communicating direction information and command selections to
processor 1504 and for controlling cursor movement on display 1512.
This input device typically has two degrees of freedom in two axes,
a first axis (e.g., x) and a second axis (e.g., y), that allows the
device to specify positions in a plane. A computing system 1500
provides data processing and provides a level of confidence for
such data. Consistent with certain implementations of embodiments
of the present teachings, data processing and confidence values are
provided by computing system 1500 in response to processor 1504
executing one or more sequences of one or more instructions
contained in memory 1506. Such instructions may be read into memory
1506 from another computer-readable medium, such as storage device
1510. Execution of the sequences of instructions contained in
memory 1506 causes processor 1504 to perform the process states
described herein. Alternatively hard-wired circuitry may be used in
place of or in combination with software instructions to implement
embodiments of the present teachings. Thus implementations of
embodiments of the present teachings are not limited to any
specific combination of hardware circuitry and software.
[0435] The term "computer-readable medium" and "computer program
product" as used herein generally refers to any media that is
involved in providing one or more sequences or one or more
instructions to processor 1504 for execution. Such instructions,
generally referred to as "computer program code" (which may be
grouped in the form of computer programs or other groupings), when
executed, enable the computing system 1500 to perform features or
functions of embodiments of the present invention. These and other
forms of computer-readable media may take many forms, including but
not limited to, non-volatile media, volatile media, and
transmission media. Non-volatile media includes, for example, solid
state, optical or magnetic disks, such as storage device 1510.
Volatile media includes dynamic memory, such as memory 1506.
Transmission media includes coaxial cables, copper wire, and fiber
optics, including the wires that comprise bus 1502.
[0436] Common forms of computer-readable media include, for
example, a floppy disk, a flexible disk, hard disk, magnetic tape,
or any other magnetic medium, a CD-ROM, any other optical medium,
punch cards, paper tape, any other physical medium with patterns of
holes, a RAM, PROM, and EPROM, a FLASH-EPROM, any other memory chip
or cartridge, a carrier wave as described hereinafter, or any other
medium from which a computer can read.
[0437] Various forms of computer readable media may be involved in
carrying one or more sequences of one or more instructions to
processor 1504 for execution. For example, the instructions may
initially be carried on magnetic disk of a remote computer. The
remote computer can load the instructions into its dynamic memory
and send the instructions over a telephone line using a modem. A
modem local to computing system 1500 can receive the data on the
telephone line and use an infra-red transmitter to convert the data
to an infra-red signal. An infra-red detector coupled to bus 1502
can receive the data carried in the infra-red signal and place the
data on bus 1502. Bus 1502 carries the data to memory 1506, from
which processor 1504 retrieves and executes the instructions. The
instructions received by memory 1506 may optionally be stored on
storage device 1510 either before or after execution by processor
1504.
[0438] It will be appreciated that, for clarity purposes, the above
description has described embodiments of the invention with
reference to different functional units and processors. However, it
will be apparent that any suitable distribution of functionality
between different functional units, processors or domains may be
used without detracting from the invention. For example,
functionality illustrated to be performed by separate processors or
controllers may be performed by the same processor or controller.
Hence, references to specific functional units are only to be seen
as references to suitable means for providing the described
functionality, rather than indicative of a strict logical or
physical structure or organization.
Oligonucleotide Synthesis Exemplary Embodiments
[0439] The following reagents are purchased and prepared for use in
the oligonucleotide synthesis methods set out herein:
[0440] Amidite A: DMT-dA(bZ) Phosporamidite >99% (SIGMA
Aldrich)
[0441] Amidite C: DMT-dC(bZ) Phosphoramidite >99% (SIGMA
Aldrich)
[0442] Amidite G: DMT-dG(iB) Phosporamidite >99% (SIGMA
Aldrich)
[0443] Amidite T: DMT-dT Phoshpramidite >99% (SIGMA Aldrich)
[0444] ACN: Acetonitrile for DNA synthesis <10 ppm water
[0445] Capping A: Cap A for DNA Synthesis (Acetic
Anhydrid/Tetrahydrofuran 9.1/90.1) (SIGMA Aldrich)
[0446] Capping B: Cap B for DNA Synthesis
(Tetrahydrofuran/N-Methylimidazole/Pyridine 8/1/1) (SIGMA
Aldrich)
[0447] Oxidizer: Oxidizer (Tetrahydrofuran/Water/Pyridin/Iodine
77/2/21/2.52 (v/v/v/w)) (SIGMA Aldrich)
[0448] Activator: DCI activator configured for Perkin Elmer 8900
(Dicyanoimidazole/Acetonitril 3/100 (w/v)<30 ppm water) (SIGMA
Aldrich)
[0449] Deblock (DEB): TCA-Deblock 3/100 (v/v)<200 ppm water
(SIGMA Aldrich)
[0450] EGA: Electrochemical generated Acid: 5.5 g hydroquinone and
7.5 g tetraethyl ammonium p-toluene sulfonate is solubilized in 500
ml acetonitrile. The solution is electrochemically treated by a
range of 14-20V until a pH 1-2 is reached, then adjust to pH 2.2
with acetonitrile. The solution is treated in an electrochemical
cell where the anode and cathode compartment are separated by a
Nafion membrane (Dupont, type N117, CAS Nr. 31175-20-9). A direct
current by a range of 14-20V is applied until a pH 1-2 is reached
in the anode compartment, then the electrolyte is adjusted to pH
2.2 with acetonitrile.
[0451] Oligonucleotide synthesis is performed by the steps set out
below in Set-up: A synthesis package consisting of a bottom frit,
solid support (60 nmol scale) mounted with a first base
(corresponding to the 3'-end) and a top frit is provided.
[0452] Pre-processing: 40-110 .mu.l ACN is dispensed onto the
synthesis package, incubate for 15-20 sec. and ACN is removed.
40-110 .mu.l of ACN is applied and immediately removed. 22-55 .mu.l
EGA is pipette onto the package, incubated for 22-30 sec. and then
removed.
[0453] Synthesis cycles: (a) 22-55 .mu.l of EGA is dispensed,
incubated for 56-75 sec., then removed. This step is repeated once.
Next, 40-110 .mu.l of ACN is applied and removed without
incubation. This step is repeated twice. 10-30 .mu.l solution of
Amidite/Activator (50/50) is dispensed and incubated for 50-60
sec., then removed. This step is repeated once. 40-110 .mu.l ACN is
pipette and removed. 10-35 .mu.l CAP A/B (50/50) is dispensed and
incubated for 30-40 sec., then removed. 40-110 .mu.l ACN is applied
without incubation and then removed. 20-50 .mu.l Oxidizer is
dispensed and incubated for 30-40 sec., then removed. 40-110 .mu.l
ACN is added, then immediately removed. 10-35 .mu.l CAP A/B (50/50)
is dispensed and incubated for 30-40 sec., this removed. (b) 50-110
.mu.l is applied CAN, then removed without incubation. Steps (a) to
(b) are repeated for each base to be added to the nascent
oligonucleotide chain. After the final base is coupled, the
following steps complete the synthesis process: 40-110 .mu.l ACN is
dispensed and then removed. 22-55 .mu.l EGA is added, incubated for
53-70 sec., then removed. The EGA step is repeated once. 40-110
.mu.l ACN is pipette, then removed without incubation. The ACN step
is repeated once.
[0454] After the synthesis process was completed, a post processing
of the oligonucleotides was done: The deprotection and cleavage of
the oligonucleotides from the solid support was performed in an
ammonia atmosphere at 80.degree. C. applying pressure of at least 3
bar for 2 hours. Subsequently, the synthesis package was washed
with ACN two times using 100 .mu.l ACN. Finally, the
oligonucleotides were eluted with 200 .mu.l 10 mM TRIS buffer pH
7.5.
[0455] In order to determine the concentration of each
oligonucleotide, the optical density (O.D.) is measured using a
standard photometer at a wave length of 260 nm. Specification of
the oligonucleotide concentration is required, in order to be able
to prepare a mix of all oligonucleotides required for the synthesis
of a given DNA fragment, so that each oligonucleotide has the same
final concentration of 0.1 .mu.mol in this mix.
TABLE-US-00011 TABLE 11 Sequence of Oligonucleotides SEQ ID Oligo
Sequence Coupling NO: AL1
GAGGTACCGTCAATTTAATTAATTTTCAGGATGACGCGGAACTTGCCACACG 51 3 AL10
TGAAATTCTTGGCTATTACAACAGACTGCCTTCAGATCTTAGCTTATGGCAAT 52 4 AL11
CAAGAGAGCAAGCTCATCATTCTGGCCAGTGGTGGACCCCAAGCCTTAGTAAA 52 5 AL12
CATAATGAGGACCTACACTTATGAGAAGCTTCTGTGGACCACAAGCAGAGTGC 52 6 AL13
TGAAGGTGCTGTCTGTCTGCTCTAGCAACAAGCCGGCCATTGTAGAAGCTGGT 52 7 AL14
GGGATGCAGGCACTGGGGCTTCATCTGACAGACCCAAGTCAGCGACTTGTTCA 52 8 AL15
AAACTGTCTTTGGACTCTCAGAAACCTTTCAGATGCAGCGACTAAGCAGGAAG 52 9 AL16
GGATGGAAGGCCTCCTTGGGACTCTAGTGCATTGTCTTCTTGGCGCGCCCAAC 52 10 AL2
TGCAATTCCTGAGGCGACAAAAGCGCTAAACGATGAGGCCCAGGTGGTAGTT 51 11 AL3
AATAAAGCTGCTGTTATGGTCCATCAGCTTTCCAAAAAGGAAGCTTCCAGAC 51 12 AL4
ATGCCATCATGCGCTCCCCTCAGATGGTGTCTGCCATTGTACGCACCATGCA 51 13 AL5
GAATACAAATGATGTAGAGACAGCTCGTTGTACTGCTGGGACTCTGCACAAC 51 14 AL6
CTTTCTCACCACCGCGAGGGCTTGCTGGCCATCTTTAAGTCTGGTGGCATCC 51 15 AL7
CAGCGCTGGTGAAAATGCTTGGGTCACCAGTGGATTCTGTACTGTTCTACGCC 52 16 AL8
ATCACGACACTGCATAATCTCCTGCTCCATCAGGAAGGAGCTAAAATGGCAGT 52 17 AL9
GCGCCTAGCTGGTGGACTGCAGAAAATGGTTGCTTTGCTCAACAAAACAAACG 52 18 Am1
TCGCCTCAGGAATTGCACGTGTGGCAAGTTCCGC 33 19 Am10
TGATGAGCTTGCTCTCTTGATTGCCATAAGCTAAGATCTG 39 20 Am11
CATAAGTGTAGGTCCTCATTATGTTTACTAAGGCTTGGGGTCC 42 21 Am12
CAGACAGACAGCACCTTCAGCACTCTGCTTGTGGTCC 36 22 Am13
CCCAGTGCCTGCATCCCACCAGCTTCTACAATGGCC 35 23 Am14
CTGAGAGTCCAAAGACAGTTTTGAACAAGTCGCTGACTTG 39 24 Am15
CAAGGAGGCCTTCCATCCCTTCCTGCTTAGTCGCTG 35 25 Am2
GGACCATAACAGCAGCTTTATTAACTACCACCTGGGCCTC 39 26 Am3
GGAGCGCATGATGGCATGTCTGGAAGCTTCCTTTTTGG 37 27 Am4
GCTGTCTCTACATCATTTGTATTCTGCATGGTGCGTACAATGG 42 28 Am5
TCGCGGTGGTGAGAAAGGTTGTGCAGAGTCCCAGC 34 29 Am6
GCATTTTCACCAGCGCTGGGATGCCACCAGACTTAAAG 37 30 Am7
GAGATTATGCAGTGTCGTGATGGCGTAGAACAGTACAGAATC 41 31 Am8
CCACCAGCTAGGCGCACTGCCATTTTAGCTCCTTC 34 32 Am9
CTGTTGTAATAGCCAAGAATTTCACGTTTGTTTTGTTGAGCAAAG 44 33 Apb
GTCTTGTGCTCCAGGCGCGCCAAGAAGACAATGCACTA 37 34 Apf
CGTGTCTTGTCCAGGTACCGTCAATTTAATTAATTTTC 37 35
[0456] Materials Used For Oligonucleotide Assembly
[0457] PCR master-mix (prepared freshly for 50 reactions): 1 ml
H2O, 50 .mu.l dNTPs (100 mM each), 250 .mu.l 10.times. reaction
buffer, 50 .mu.l PAN Polymerase mix (PAN, Aidenbach, Germany) are
mixed and spin down, then stored at 2-8.degree. C.
[0458] TE buffer: 10 mM Tris/HCl, 1 mM ethylenediamine tetraacetic
acid (EDTA), pH 8.
[0459] 10.times. Loading Dye: 250 mg bromophenol blue (Merck,
Darmstadt, Germany), 250 mg xylene cyanol (Merck), 58 ml glycerine
(86%, Roth, Karlsruhe, Germany) in 42 ml H.sub.2O is mixed and
aliquoted.
[0460] Agarose gel running buffer: TAE buffer (40 mM Tris/HCl pH
8.0, 20 mM NaAc, 2 mM EDTA)
[0461] ZERO BLUNT.TM. TOPO PCR Cloning Kit (Life Technologies,
Carlsbad, Calif.)
[0462] LB (Luria Bertani) medium: In 1 liter of H.sub.2O, 10 g
Bacto-trypton (Sigma-Aldrich, Deisenhofen, Germany), 5 g yeast
extract (Sigma-Aldrich), 10 g NaCl, is mixed, adjusted to pH 7.0
with NaOH, autoclave and stored at 4.degree. C.
[0463] Methods Used For Oligonucleotide Assembly
[0464] Oligonucleotide assembly. 5 .mu.l of the
oligonucleotide-pool containing all oligonucleotides of the
oligonucleotide are mixed and adjusted to a final concentration of
15 nM, 18 .mu.l H.sub.2O and 27 .mu.l PCR master-mix and subject to
PCR using the protocol described in TABLE 11. For further
amplification of the elongated oligonucleotides, 7 .mu.l of the
first PCR reaction is mixed with each 2 .mu.l of the terminal
amplification primer Apf and Apb (at a concentration of 15 .mu.M,
each), 27 .mu.l PCR master-mix and 14 .mu.l H2O, and subjected to
PCR using the protocol of TABLE 12.
[0465] Fragment analysis. An aliquot of the PCR reaction is mixed,
usually 1/10th of the reaction volume, diluted in H.sub.2O or TE if
necessary, with 1 volume of Loading Dye per 9 volumes of purified
DNA sample for gel analysis. The mixture is then loaded on a 1%
agarose gel. The gel is run at a constant current and voltage
(5V/cm2, 50V-150V) in TAE buffer.
[0466] Blunt cloning. 0.5-4 .mu.l of the fresh PCR product is mixed
with 1 .mu.l of the pCR II-Blunt-TOPO and adjusted the volume to 6
.mu.l with H2O, then incubated for 5 min at 22.degree. C., then
placed on ice.
[0467] Transformation. Competent E. coli (e.g., XL1-gold from
Invitrogen Life Technologies, Carlsbad, Calif.) are transformed
with the Blunt cloning mix. 100 .mu.l of competent E. coli is
thawed on ice, 2 .mu.l of the Blunt cloning is added and mixed to
the cells, then incubated for 20 min on ice. To apply a heat shock,
the reaction tube is incubated for 60 sec at 42.degree. C. using a
water bath or a thermomixer (Thermomixer comfort, for 1.5 ml
reaction tubes, Eppendorf, Hamburg, Germany) Immediately after the
heat shock, the cells are put on ice for 5 min. If using ampicillin
for selection, the cells are plated directly on ampicillin
containing LB-plates (100 mg/1) and incubated at 37.degree. C.
overnight. For other selection agents (e.g., kanamycin or
tetracycline), it is necessary to incubate the transformed bacteria
with LB-medium without antibiotics for at least 30 min. at
37.degree. C. in a shaker in order to provide time for recovery and
expression of the respective resistance gene.
[0468] Colony picking. The required number of colonies are picked
from the selection plate using a sterile tooth pick and perform a
colony PCR (cPCR) using the PCR master mix and respective
amplification primer (PCR protocol 2). The PCR product is analyzed
on a 1% agarose gel as described to checked for the correct insert
length.
[0469] Sequence analysis. The PCR products with the correct insert
size are subjected to a sequencing reaction (e.g., using
BIGDYE.RTM. Direct Cycle Sequencing Kit and a Genetic Analyzer from
Invitrogen), according to the manufacturer's instructions, and the
sequencing results are compared with the original oligonucleotide
sequence to evaluate error classes and error rates.
TABLE-US-00012 TABLE 11 PCR Protocol 1 Cycle Number Step .degree.
C. Time 1 1 1 95 04:00 2 30 1 95 00:30 2 60 .fwdarw.40* 00:30 3 72
01:00 3 1 1 72 04:00 4 1 1 4 .infin. *use a touch down program
TABLE-US-00013 TABLE 12 PCR Protocol 2 Cycle Number Step .degree.
C. Time 1 1 1 95 04:00 2 30 1 95 00:30 2 58 00:30 3 72 01:00 3 1 1
72 04:00 4 1 1 4 .infin.
EXPERIMENTAL DESCRIPTION AND RESULTS
Experiment 1
[0470] The oligonucleotide with the nucleotide sequences set shown
in TABLE 13 are synthesized twice, one set using DEB as a
deblocking reagent the other set using EGA, as described. With each
deblocking reagent two fragment sets have been synthesized. The
detailed sequences of the oligonucleotides are shown in TABLE
13.
[0471] After determination of the concentration the
oligonucleotides are pooled as described. Oligonucleotide mixes
contain oligonucleotides from the synthesis with DEB except for one
oligonucleotide, that is produced using EGA. Eight different
oligonucleotide mixes are been prepared and analysed. For each
oligonucleotide set a different EGA-originated oligonucleotide is
replaced. The oligonucleotides Am1 (2.times.), Am3, Am5, Amb
(3.times.), Am13 are replaced. The oligonucleotide set are
assembled as described in FIG. 23 and the sequence is analyzed. In
total, sequence information derived from 49 colonies is evaluated.
All oligonucleotide regions that corresponded to the EGA derived
oligonucleotide have the correct sequences. From 1715 sequenced
bases no errors are detected.
Experiment 2
[0472] In this experiment oligonucleotide sets (see TABLE 11 for
the sequence information) are synthesized with the described
process. For all sets, EGA is used as the deblocking reagent using
the described standard oligonucleotide synthesis process. The
average oligonucleotide concentration is 49.21 .mu.M.
[0473] After cloning and transformation of the assembled
oligonucleotides, assembled nucleic acid molecules from 5 colonies
are analyzed by sequencing. The error rate (detected errors/1000
base pairs) of the synthesized oligonucleotides is as follows. A
total of 16 insertions, 1.7 deletions and 1.2 substitutions per
1000 bp are detected.
Oligonucleotide Stitching Assembly (OSA) Exemplary Embodiments
[0474] A series of OSA reactions were performed to identify
operational parameters of assembly methods. The resulting data is
set out in FIG. 20 and in tables below.
[0475] Cell extracts for use if OSA methods were prepared as
follows: DH10B E. coli strain (Life Technologies) was grown
overnight at 37.degree. C. in 5 ml LB media. Two ml of the
overnight culture was then transferred to 100 ml fresh LB media and
then grown at 37.degree. C. until the OD.sub.600 nm, reached
approximately 0.6. The cells were harvested by centrifugation at
5000.times.g for 20 minutes at 4.degree. C. Cell pellets
(.about.0.92 g wet weight) were washed once with 200 ml deionized
H.sub.2O and then resuspended into 1.2 ml CELLYTIC.TM. B Cell Lysis
Reagent (Sigma Chemical Co.), followed by incubation for 10 minutes
at room temperature. The cell suspension was centrifuged at
20,000.times.g for 2 min. at room temperature and the supernatant
was transferred to a 1.5 ml micrcentrifuge tube. The cell extract
was then mixed with equal volume of 100% glycerol. Aliquots of
.about.50 .mu.l cell lysate were stored at -80.degree. C. in 50%
glycerol.
[0476] The OSA protocol was as follows: The reaction mixture
components were added to a 1.5 ml tube in the order set out below
in TABLE 14, then the final reaction mixture was mixed well and
incubated at room temperature for 30 min (additional time point at
45 min for precloned fragment). Four .mu.l was used for
transformation into TOP10 chemically competent cells and 50 to 100
.mu.l of cells were plated on corresponding LB agar selection
plates. Transformation conditions were as follows: An aliquot from
the assembly reaction and cells were mixed and incubate on ice for
at least 5 min, then heat shocked at 42.degree. C. for 30 sec. The
transformation reaction was placed on ice and at least 250 .mu.l of
SOC medium was added. Cells were allowed to recover on a shaker for
1 hour at 37.degree. C.
[0477] pUC19 derivatives (AmpR vectors) were mainly used. Inserts
were either (1) digested from existing vectors harboring an
antibiotic resistance marker other than AmpR (e.g., Kanamycin,
Spectinomycin) or (2) PCR amplified using a template lacking an
AmpR marker. Data was generate using inserts ranging from 500 bp up
to several kb in length.
TABLE-US-00014 TABLE 14 Exemplary OSA Reaction Mixture 100 ng
PCR-amplified vector (2.3 kb) x inserts (molar ratio of inserts to
vector = 2:1) y 5x reaction buffer 4 .mu.l stitching oligos (0.4
.mu.M) 1 .mu.l H.sub.2O (up to 17 .mu.l total) (12 - x - y) .mu.l
Mix well Extract 1 .mu.l 10x Enzyme Mixture 2 .mu.l Total Volume 20
.mu.l
[0478] TABLE 15 shows the composition of reagents used in used in
the OSA reactions set out herein.
TABLE-US-00015 TABLE 15 10X Enzyme Mix 5X Buffer Mix T7exo 0.3
U/.mu.l Tris pH 7.5 100 mM T4 Gene 32 Protein 5 .mu.g/.mu.l NaCl
125 mM BSA 5 mg/ml MgCl2 50 mM Tris pH 8 20 mM PEG-8000 25% NaCl 60
mM DTT 3.5 mM B-Mercaptoethanol 0.25 mM EDTA 1 mM Glycerol 50%
[0479] As shown below in TABLE 16, efficient assembly requires the
presence of the cell extract.
TABLE-US-00016 TABLE 16 Oligonucleotides and Cell Extract Result in
Efficient Assembly Extract Oligos CE (%) STDEV CFU/plate STDEV - -
2.8 0.9 288.7 58.8 - + 40.6 5.6 160.7 80.9 + - 2.5 0.6 327.0 91.1 +
+ 93.7 1.5 514.0 145.5 Oligos: PS (partially phosphorothioated
oligonucleotides) complementary Extract: redET cells Configuration:
1 vector + 1 PCR insert
[0480] In some instances partially phosphorothioated
oligonucleotides (a sulfur atom for a non-bridging oxygen in the
phosphate backbone of an oligo) were used in which phosphorothioate
bonds close to the 5' terminus of the oligonucleotides were
introduced to render these oligonucleotides resistant to
exonuclease degradation.
[0481] As shown below in TABLE 17, the manner in which the insert
is prepared has little effect on cloning efficiency.
TABLE-US-00017 TABLE 17 PCR-Amplified DNA vs Precloned and
Restriction Enzyme Excised Fragments Conditions CE (%) STDEV
CFU/plate STDEV (-) oligos 2.6 3.7 225.0 84.9 PCR fragment 95.7 0.2
4995.0 551.5 BglII 94.4 1.4 1650.0 403.1 PacI 94.7 4.5 1695.0 636.4
Oligos: PS complementary Extract: redET cells Configuration: 1
vector + 1 insert (PCR or restriction enzyme digested)
[0482] RedET cells, as referred to herein, are E. coli cells that
express redET genes. The data shown in TABLE 18 demonstrates that
the redET gene products are not required for efficient OSA, at
least for the assembly of two inserts. In some instances, the
presence of redET gene products may be beneficial in that they may
increase assembly efficiency or be necessary for complex assemblies
(e.g., assemblies involving five or more inserts).
TABLE-US-00018 TABLE 18 redET Genes are not Required for OSA
Extract Oligos CE (%) STDEV CFU/plate STDEV DH10B - 0.0 0.0 125.0
49.5 DH10B + 88.0 5.2 715.0 162.6 redET - 0.0 0.0 150.0 14.1 redET
+ 79.4 11.3 675.0 162.6 Oligos: PS offset (Offset here refers to 30
overlapped nt (dsDNA) and 2x 30 nt (ssDNA)) Extract: redET or DH10B
cells Configuration: 1 vector + 2 inserts
[0483] The data shown in TABLE 19 demonstrates that OSA can be used
to assemble at least three insert nucleic acid molecules.
TABLE-US-00019 TABLE 19 Up to Three Inserts, at Least 50% Cloning
Efficiency Type CE (%) STDEV CFU/plate STDEV 1 insert redET 93.7
1.5 5140.0 1455.2 2 inserts 88.0 5.2 715.0 162.6 3 inserts 45 min
inc 51.6 14.1 50.0 2.8 Oligos: PS complementary or offset Extract:
redET or DH10B Configuration: 1 vector + 1 to 3 inserts
Low Volume PCR Based Nucleic Acid Assembly
TABLE-US-00020 [0484] TABLE 20 PCR Amplification Conditions used to
Miniaturize the Gene Synthesis Reactions Sample 1 2 3 4 1.sup.st
Rxn Vol. 50 .mu.l 33 nl 50 .mu.l 33 nl PCR PCR 0.2 ml PCR OA plate
0.2 ml PCR OA plate Chamber tube (IOM48) tube (IOM48) PCR Veriti
.RTM. Applied Veriti .RTM. Applied Machine Thermal Biosystems .RTM.
Thermal Biosystems .RTM. Cycler GeneAmp .RTM. Cycler GeneAmp .RTM.
PCR System PCR System 9700 9700 Stage 1 98.degree. C., 30 sec
98.degree. C., 30 sec 98.degree. C., 30 sec 98.degree. C., 30 sec
Stage 2 95.degree. C., 10 sec 95.degree. C., 10 sec 95.degree. C.,
10 sec 95.degree. C., 10 sec (.times.15 (40% (40% (40% (40% cycles)
ramping) ramping) ramping) ramping) 60.degree. C., 30 sec
55.degree. C., 30 sec 60.degree. C., 30 sec 55.degree. C., 30 sec
72.degree. C., 1 min 67.degree. C., 1 min 72.degree. C., 1 min
67.degree. C., 1 min Stage 3 72.degree. C., 2 min 67.degree. C., 2
min 72.degree. C., 2 min 67.degree. C., 2 min 4.degree. C., .infin.
4.degree. C., .infin. 4.degree. C., .infin. 4.degree. C., .infin.
Heat Cover Yes Yes* Yes Yes* 2.sup.nd Rxn vol. 50 .mu.l 50 .mu.l 33
nl 33 nl PCR PCR 0.2 ml PCR 0.2 ml PCR OA plate OA plate Chamber
tube tube (IOM49) (IOM50) PCR Veriti .RTM. Veriti .RTM. Applied
Applied Machine Thermal Thermal Biosystems .RTM. Biosystems .RTM.
Cycler Cycler GeneAmp .RTM. GeneAmp .RTM. PCR System PCR System
9700 9700 Stage 1 98.degree. C., 30 sec 98.degree. C., 30 sec
98.degree. C., 30 sec 98.degree. C., 30 sec Stage 2 95.degree. C.,
10 sec 95.degree. C., 10 sec 95.degree. C., 10 sec 95.degree. C.,
10 sec (.times.15 (40% (40% (40% (40% cycles) ramping) ramping)
ramping) ramping) 60.degree. C., 30 sec 60.degree. C., 30 sec
55.degree. C., 30 sec 55.degree. C., 30 sec 72.degree. C., 1 min
72.degree. C., 1 min 67.degree. C., 1 min 67.degree. C., 1 min
Stage 3 72.degree. C., 5 min 72.degree. C., 5 min 67.degree. C., 5
min 67.degree. C., 5 min 4.degree. C., .infin. 4.degree. C.,
.infin. 4.degree. C., .infin. 4.degree. C., .infin. Heat Cover Yes
Yes Yes* Yes* *Paper cushion was located between heat cover and OA
plate
[0485] The data shown in FIGS. 24A-24B was generated using nucleic
acid molecules assembled by the methods shown in TABLE 20 and shows
nucleic acid assembly in volumes as low as 33 nanoliters. Specific
reaction conditions details are set out above. One item not shown
for the assembly reactions are the specific sequences of the
assembled nucleic acid molecules. It is believed that the sequences
of the nucleic acid molecules assembled will not significantly
impact assembly data. However, in some instances, cycling
conditions may need to be adapted for optimal efficiency.
[0486] Embodiments may be in accordance with following numbered
clauses:
[0487] 1. A multiwell plate for non-template directed synthesis of
nucleic acid molecules, the plate comprising: [0488] (a) at least
one bead located in each of a plurality of wells of the plate, and
[0489] (b) an electrochemically generated acid being present in one
or more well, wherein the bead is between 0.1 .mu.m and 100 .mu.m
in diameter.
[0490] 2. The multiwell plate of clause 1, wherein the number of
wells in the plate is between 10 and 10,000,000.
[0491] 3. The multiwell plate of any one of the preceding clauses,
wherein the total volume of each well is between 0.1 .mu.l and 50
.mu.l.
[0492] 4. The multiwell plate of any one of the preceding clauses,
wherein each well is operably connected to a pair of
electrodes.
[0493] 5. The multiwell plate of any one of the preceding clauses,
wherein the wells of the plate are connected to microfluidic
channels for the introduction and removal of reagents.
[0494] 6. A method for the generation of an assembled nucleic acid
molecule, the method comprising: [0495] (a) synthesizing a
plurality of nucleic acid molecules, wherein each nucleic acid
molecule is prepared in a well of a plate in an average amount of
from about 0.001 nanomoles to about 1,000 nanomoles; [0496] (b)
combining the nucleic acid molecules generated in (a) to produce a
pool; [0497] (c) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules; [0498] (d) eliminating nucleic acid
molecules which contain sequence errors from the plurality of
larger nucleic acid molecules formed in (c) to produce an error
corrected nucleic acid molecule pool; and [0499] (e) assembling the
nucleic acid molecules in the error corrected nucleic acid molecule
pool to form the assembled nucleic acid molecule.
[0500] 7. The method of clause 6, wherein the joining in (c) is
mediated by polymerase chain reaction and/or ligases.
[0501] 8. The method of any one of clauses 6 or 7, wherein the
assembled nucleic acid molecule is composed of at least five
nucleic acid molecules.
[0502] 9. The method of any one of clauses 6 to 8, wherein the
assembled nucleic acid molecule is composed of between five and
five thousand nucleic acid molecules.
[0503] 10. The method of any one of clauses 6 to 9, wherein the
assembled nucleic acid molecule is at least 20 kilobases.
[0504] 11. The method of any one of clauses 6 to 10, wherein the
assembled nucleic acid molecule is between 10 kilobases and 1
megabase.
[0505] 12. The method of any one of clauses 6 to 11, wherein the
assembled nucleic acid molecule is closed, circular.
[0506] 13. The method of any one of clauses 6 to 12, wherein the
assembled nucleic acid molecule is a plasmid.
[0507] 14. The method of any one of clauses 6 to 13, wherein two or
more assembled nucleic acid molecule are simultaneously formed.
[0508] 15. The method of any one of clauses 6 to 14, wherein
assembly of the nucleic acid molecules in the error corrected
nucleic acid molecule pool occurs in a fungal cell.
[0509] 16. The method of any one of clauses 6 to 15, wherein step
(b) further comprises combining nucleic acid molecules generated in
(a) with nucleic acid molecules obtained by other means to form a
pool, wherein said other means include PCR, restriction enzyme
digest or exonuclease treatment.
[0510] 17. The method of any one of clauses 6 to 16, wherein the
assembled nucleic acid molecule generated in (e) is assembled and
introduced into a cloning vector.
[0511] 18. A method for producing a product nucleic acid molecule,
the method comprising: [0512] (a) designing the product nucleic
acid molecule of between 0.1 kilobases and 500 kilobases in size,
wherein the product nucleic acid molecule is defined by nucleotide
sequence; [0513] (b) synthesizing a plurality of individual nucleic
acid molecules which differ in nucleotide sequence, wherein each
individual nucleic acid molecule is synthesized to prepare a
quantity of between 1.0.times.10.sup.3 and 1.0.times.10.sup.9
copies and wherein the individual nucleic acid molecules are
capable of hybridizing with one or more of the other individual
nucleic acid molecules; [0514] (c) combining the individual nucleic
acid molecules synthesized in [0515] (b) under conditions which
allow for hybridization of the individual nucleic acid molecules
under conditions which allow for the formation of at least one
larger nucleic acid molecule; and [0516] (d) combining the at least
one larger nucleic acid molecule formed in (c) with one or more
additional nucleic acid molecules to form the product nucleic acid
molecule, wherein the product nucleic acid molecule contains less
than one sequence error per kilobase.
[0517] 19. The method of clause 18, wherein the product nucleic
acid molecule is of a size selected from the groups consisting of:
[0518] (a) between 0.1 kilobases and 300 kilobases; [0519] (b)
between 10 kilobases and 200 kilobases; [0520] (c) between 10
kilobases and 100 kilobases; and [0521] (d) between 10 kilobases
and 50 kilobases.
[0522] 20. The method of any one of clauses 18 or 19, wherein an
error correction process is employed after step (b) or after step
(d).
[0523] 21. The method of any one of clauses 18 to 20, wherein each
individual nucleic acid molecule is synthesized to prepare a
quantity selected from the group consisting of: [0524] (a) between
5.0.times.10.sup.3 and 1.0.times.10.sup.9 copies; [0525] (b)
between 1.0.times.10.sup.6 and 1.0.times.10.sup.9 copies; [0526]
(c) between 1.0.times.10.sup.7 and 1.0.times.10.sup.8 copies;
[0527] (d) between 2.0.times.10.sup.7 and 1.0.times.10.sup.9
copies; [0528] (e) between 5.0.times.10.sup.7 and
1.0.times.10.sup.9 copies; [0529] (f) between 7.0.times.10.sup.7
and 1.0.times.10.sup.9 copies; [0530] (g) between
2.0.times.10.sup.7 and 8.0.times.10.sup.8 copies; and [0531] (h)
between 2.0.times.10.sup.7 and 5.0.times.10.sup.8 copies.
[0532] 22. The method of any one of clauses 18 to 21, wherein
polymerase chain reactions are used to amplify the at least one
larger nucleic acid molecule formed in step (c).
[0533] 23. The method of any one of clauses 18 to 22, wherein the
product nucleic acid molecule is self replicable.
[0534] 24. The method of any one of clauses 18 to 23, wherein the
self replicable nucleic acid molecule is a plasmid.
[0535] 25. The method of any one of clauses 18 to 24, wherein the
individual nucleic acid molecules are synthesized on beads, wherein
each bead is containing in a well.
[0536] 26. The method of any one of clauses 18 to 25, wherein the
beads are of a size selected from the group consisting of: [0537]
(a) between 5 .mu.m and 100 .mu.m in diameter; [0538] (b) between
20 .mu.m and 100 .mu.m in diameter; [0539] (c) between 28 and 32
.mu.m in diameter; [0540] (d) between 5 .mu.m and 60 .mu.m in
diameter; and [0541] (e) between 10 .mu.m and 100 .mu.m in
diameter.
[0542] 27. A method for the generation of a self replicating
nucleic acid molecule, the method comprising: [0543] (a)
synthesizing a plurality of nucleic acid molecules, wherein each
nucleic acid molecule is prepared in a microquantity in the well of
a plate; [0544] (b) joining some or all of the nucleic acid
molecules present in the pool formed in (a) to form a plurality of
larger nucleic acid molecules; and [0545] (c) assembling the
plurality of larger nucleic acid molecules to form the self
replicating nucleic acid molecule.
[0546] 28. The method of clause 27, wherein the self replicating
nucleic acid molecule is a chromosome or a plasmid.
[0547] 29. The method of any one of clauses 27 or 28, wherein the
self replicating nucleic acid molecule is a genome.
[0548] 30. The method of any one of clauses 27 to 29, wherein the
genome is a viral genome, a nuclear genome, an organelle genome, or
a genome of a prokaryotic cell.
[0549] 31. A method for synthesizing and assembling a nucleic acid
molecule which encodes more than one expression product, the method
comprising: [0550] (a) synthesizing a plurality of nucleic acid
molecules, wherein each nucleic acid molecule is prepared in a
microquantity; [0551] (b) joining some or all of the nucleic acid
molecules present in the pool formed in (a) to form a plurality of
larger nucleic acid molecules; and [0552] (c) assembling the
plurality of larger nucleic acid molecules to form the nucleic acid
molecule which encodes more than one expression product.
[0553] 32. The method of clause 31, wherein the more than one
expression products are proteins that are involved in the same
biological pathway.
[0554] 33. The method of any one of clauses 31 or 32, wherein the
more than one expression products are proteins which are involved
in the same biological pathway are enzymes that catalyze a series
of chemical reactions in a biological pathway.
[0555] 34. The method of any one of clauses 31 to 33, wherein the
chemical reactions in the same biological pathway are sequential
reactions.
[0556] 35. The method of any one of clauses 31 to 34, wherein the
biological pathway results in an end product selected from the
group consisting of: [0557] (a) a biofuel precursor; [0558] (b) an
antibiotic or antibiotic precursor; [0559] (c) a food component;
and [0560] (d) an industrial enzyme.
[0561] 36. The method of any one of clauses 31 to 35, wherein the
biofuel precursor is an alcohol selected from the group consisting
of: [0562] (a) butanol; [0563] (b) pentanol; [0564] (c) hexanol;
[0565] (d) heptanol; and [0566] (e) octanol.
[0567] 37. The method of any one of clauses 31 to 36, wherein the
food component is an amino acid selected from the group consisting
of: [0568] (a) L-lysine; [0569] (b) L-threonine; [0570] (c)
L-methionine; [0571] (d) L-leucine; [0572] (e) L-isoleucine: [0573]
(f) L-valine, and [0574] (g) Homoserine.
[0575] 38. The method of any one of clauses 31 to 37, wherein the
assembled nucleic acid molecule is introduced into a prokaryotic
cell.
[0576] 39. The method of any one of clauses 31 to 38, wherein the
prokaryotic cell is a Corynebacterium.
[0577] 40. The method of any one of clauses 31 to 39, wherein the
Corynebacterium is Corynebacterium glutamicum.
[0578] 41. A non-transitory computer-readable storage medium
encoded with instructions, executable by a processor, for
generating assembled nucleic acid molecule, the instructions
comprising instructions for: [0579] (a) synthesizing a plurality of
nucleic acid molecules, wherein each nucleic acid molecule is
prepared in a microquantity in the well of a plate; [0580] (b)
combining the nucleic acid molecules generated in (a) to produce a
pool; [0581] (c) joining some or all of the nucleic acid molecules
present in the pool formed in (b) to form a plurality of larger
nucleic acid molecules; [0582] (d) eliminating nucleic acid
molecules which contain sequence errors from the plurality of
larger nucleic acid molecules formed in (c) to produce an error
corrected nucleic acid molecule pool; and [0583] (e) assembling the
nucleic acid molecules in the error corrected nucleic acid molecule
pool to form the assembled nucleic acid molecule.
[0584] 42. A system for generating assembled nucleic acid molecule,
the system comprising: [0585] a processor; and a memory encoded
with processor-executable instructions for: [0586] (a) synthesizing
a plurality of nucleic acid molecules, wherein each nucleic acid
molecule is prepared in a microquantity in the well of a plate;
[0587] (b) combining the nucleic acid molecules generated in (a) to
produce a pool; [0588] (c) joining some or all of the nucleic acid
molecules present in the pool formed in (b) to form a plurality of
larger nucleic acid molecules; [0589] (d) eliminating nucleic acid
molecules which contain sequence errors from the plurality of
larger nucleic acid molecules formed in (c) to produce an error
corrected nucleic acid molecule pool; and [0590] (e) assembling the
nucleic acid molecules in the error corrected nucleic acid molecule
pool to form the assembled nucleic acid molecule.
[0591] All publications, patents and patent applications mentioned
in this Specification are indicative of the level of skill of those
of ordinary skill in the art and are herein incorporated by
reference to the same extent as if each individual publication,
patent, or patent applications was specifically and individually
indicated to be incorporated by reference.
[0592] The invention being thus described, one skilled in the art
would recognize that the invention may be varied in many ways. Such
variations are not to be regarded as a departure from the spirit
and scope of the invention, and all such modifications as would be
obvious to one of ordinary skill in the art are intended to be
included within the scope of the following claims.
Sequence CWU 1
1
44110DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 1atcgcatgcg 10215DNAEnterobacteria phage
lambda 2gcttttttat actaa 15352DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 3gaggtaccgt
caatttaatt aattttcagg atgacgcgga acttgccaca cg 52453DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 4tgaaattctt ggctattaca acagactgcc ttcagatctt
agcttatggc aat 53553DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 5caagagagca agctcatcat
tctggccagt ggtggacccc aagccttagt aaa 53653DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 6cataatgagg acctacactt atgagaagct tctgtggacc
acaagcagag tgc 53753DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 7tgaaggtgct gtctgtctgc
tctagcaaca agccggccat tgtagaagct ggt 53853DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 8gggatgcagg cactggggct tcatctgaca gacccaagtc
agcgacttgt tca 53953DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 9aaactgtctt tggactctca
gaaacctttc agatgcagcg actaagcagg aag 531053DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 10ggatggaagg cctccttggg actctagtgc attgtcttct
tggcgcgccc aac 531152DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 11tgcaattcct
gaggcgacaa aagcgctaaa cgatgaggcc caggtggtag tt 521252DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 12aataaagctg ctgttatggt ccatcagctt tccaaaaagg
aagcttccag ac 521352DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 13atgccatcat gcgctcccct
cagatggtgt ctgccattgt acgcaccatg ca 521452DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 14gaatacaaat gatgtagaga cagctcgttg tactgctggg
actctgcaca ac 521552DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 15ctttctcacc accgcgaggg
cttgctggcc atctttaagt ctggtggcat cc 521653DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 16cagcgctggt gaaaatgctt gggtcaccag tggattctgt
actgttctac gcc 531753DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 17atcacgacac
tgcataatct cctgctccat caggaaggag ctaaaatggc agt 531853DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 18gcgcctagct ggtggactgc agaaaatggt tgctttgctc
aacaaaacaa acg 531934DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 19tcgcctcagg
aattgcacgt gtggcaagtt ccgc 342040DNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 20tgatgagctt
gctctcttga ttgccataag ctaagatctg 402143DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 21cataagtgta ggtcctcatt atgtttacta aggcttgggg tcc
432237DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 22cagacagaca gcaccttcag cactctgctt
gtggtcc 372336DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 23cccagtgcct gcatcccacc
agcttctaca atggcc 362440DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 24ctgagagtcc
aaagacagtt ttgaacaagt cgctgacttg 402536DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 25caaggaggcc ttccatccct tcctgcttag tcgctg
362640DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 26ggaccataac agcagcttta ttaactacca
cctgggcctc 402738DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 27ggagcgcatg atggcatgtc
tggaagcttc ctttttgg 382843DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 28gctgtctcta
catcatttgt attctgcatg gtgcgtacaa tgg 432935DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 29tcgcggtggt gagaaaggtt gtgcagagtc ccagc
353038DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 30gcattttcac cagcgctggg atgccaccag
acttaaag 383142DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 31gagattatgc agtgtcgtga
tggcgtagaa cagtacagaa tc 423235DNAArtificial SequenceDescription of
Artificial Sequence Synthetic oligonucleotide 32ccaccagcta
ggcgcactgc cattttagct ccttc 353345DNAArtificial SequenceDescription
of Artificial Sequence Synthetic oligonucleotide 33ctgttgtaat
agccaagaat ttcacgtttg ttttgttgag caaag 453438DNAArtificial
SequenceDescription of Artificial Sequence Synthetic
oligonucleotide 34gtcttgtgct ccaggcgcgc caagaagaca atgcacta
383538DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 35cgtgtcttgt ccaggtaccg tcaatttaat
taattttc 383669DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotide 36acccgtaaag cgagtttagt
tttgaaaaac aaatgacata atgacatcat cccctgattg 60tgttttaca
693736DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 37aattctaccc gtaaagcgag tttagttttg aaaaac
363836DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotide 38aatgacatca tcccctgatt gtgttttaca agtaga
363933DNAArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotideDescription of Combined DNA/RNA Molecule
Synthetic oligonucleotideCDS(1)..(33) 39ttc ctt cct gct act ggt ggc
gtt ttc cgu aat 33Phe Leu Pro Ala Thr Gly Gly Val Phe Arg Asn1 5
104011PRTArtificial SequenceDescription of Artificial Sequence
Synthetic oligonucleotideDescription of Combined DNA/RNA Molecule
Synthetic oligonucleotide 40Phe Leu Pro Ala Thr Gly Gly Val Phe Arg
Asn1 5 104133DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotideCDS(1)..(33) 41ttc ctc ccc gcc
acc ggc ggc gtc ttc aga aat 33Phe Leu Pro Ala Thr Gly Gly Val Phe
Arg Asn1 5 104233DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotideCDS(1)..(33) 42ttc cta cca gcc
act gga ggc gtc ttc agg aat 33Phe Leu Pro Ala Thr Gly Gly Val Phe
Arg Asn1 5 104333DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotideCDS(1)..(33) 43ttc ctt ccg gca
aca ggt ggg gtg ttc cgc aat 33Phe Leu Pro Ala Thr Gly Gly Val Phe
Arg Asn1 5 104433DNAArtificial SequenceDescription of Artificial
Sequence Synthetic oligonucleotideDescription of Combined DNA/RNA
Molecule Synthetic oligonucleotideCDS(1)..(33) 44ttc ctt ccc gcg
acc ggt ggg gta ttc cgu aac 33Phe Leu Pro Ala Thr Gly Gly Val Phe
Arg Asn1 5 10
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