WO2010059763A1 - Compositions and methods for the assembly of polynucleotides - Google Patents

Compositions and methods for the assembly of polynucleotides Download PDF

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Publication number
WO2010059763A1
WO2010059763A1 PCT/US2009/065048 US2009065048W WO2010059763A1 WO 2010059763 A1 WO2010059763 A1 WO 2010059763A1 US 2009065048 W US2009065048 W US 2009065048W WO 2010059763 A1 WO2010059763 A1 WO 2010059763A1
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Prior art keywords
annealable linker
nucleic acid
linker sequence
restriction
restriction site
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PCT/US2009/065048
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English (en)
French (fr)
Inventor
Zach Serber
Raymond Lowe
Jeffrey A. Ubersax
Sunil S. Chandran
Erik Jedediah Dean
Darren M. Platt
Kenneth Toshiki Takeoka
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Amyris Biotechnologies, Inc.
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Publication date
Application filed by Amyris Biotechnologies, Inc. filed Critical Amyris Biotechnologies, Inc.
Priority to JP2011537596A priority Critical patent/JP2012509084A/ja
Priority to SG2011036274A priority patent/SG171760A1/en
Priority to CA2744153A priority patent/CA2744153C/en
Priority to AU2009316660A priority patent/AU2009316660B2/en
Priority to MX2011005195A priority patent/MX2011005195A/es
Priority to EP09764127.8A priority patent/EP2358875B1/en
Priority to KR1020117014144A priority patent/KR101794298B1/ko
Priority to BRPI0922187-5A priority patent/BRPI0922187B1/pt
Priority to CN200980154897.0A priority patent/CN102282255B/zh
Publication of WO2010059763A1 publication Critical patent/WO2010059763A1/en
Priority to ZA2011/03637A priority patent/ZA201103637B/en

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    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C12N15/1034—Isolating an individual clone by screening libraries
    • C12N15/1093—General methods of preparing gene libraries, not provided for in other subgroups
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/10—Processes for the isolation, preparation or purification of DNA or RNA
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/64—General methods for preparing the vector, for introducing it into the cell or for selecting the vector-containing host
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/66—General methods for inserting a gene into a vector to form a recombinant vector using cleavage and ligation; Use of non-functional linkers or adaptors, e.g. linkers containing the sequence for a restriction endonuclease
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B40/00—Libraries per se, e.g. arrays, mixtures
    • C40B40/04—Libraries containing only organic compounds
    • C40B40/06—Libraries containing nucleotides or polynucleotides, or derivatives thereof
    • C—CHEMISTRY; METALLURGY
    • C40—COMBINATORIAL TECHNOLOGY
    • C40B—COMBINATORIAL CHEMISTRY; LIBRARIES, e.g. CHEMICAL LIBRARIES
    • C40B50/00—Methods of creating libraries, e.g. combinatorial synthesis
    • C40B50/06—Biochemical methods, e.g. using enzymes or whole viable microorganisms

Definitions

  • the present invention relates generally to the field of recombinant DNA technology and, more particularly, to improved methods for the ordered assembly of a plurality of DNA segments into an assembled polynucleotide.
  • Recombination of polynucleotides can be carried out using many methods known in the art. Traditional techniques for recombining nucleic acids have utilized restriction enzymes and ligating enzymes for the creation of novel nucleic acid molecules.
  • Recombinant molecules such as cloning and expression vectors can be utilized to integrate a nucleic acid sequence of interest into the genome of a host cell, and/or drive the expression of one or more genes of interest. Utilization of a vector to drive expression of a gene of interest in the cell, for example a yeast cell, requires that the vector contain requisite genetic elements that enable replication and expression of the gene of interest. These elements may include, for example, the gene or genes of interest, a promoter sequence, a terminator sequence, selectable markers, integration loci, and the like.
  • PCR polymerase chain reaction
  • splicing by overlap extension facilitates the assembly of DNA molecules at precise junctions without the use of restriction enzymes or ligase.
  • Component fragments to be recombined are generated in separate polymerase chain reactions using uniquely designed primers which produce amplicons having complementary termini to one another.
  • primers which produce amplicons having complementary termini to one another.
  • strands having complementary sequences at their 3' ends overlap and act as primers for each other.
  • Extension of this overlap by DNA polymerase produces a nucleic acid molecule in which the original sequences are "spliced" together.
  • SOE while more efficient than traditional ligation enzyme-based methods for combining a plurality of nucleic acid fragments, does require time to optimize primer sequences and amplification conditions to produce desired products.
  • Each junction between the fragments to be spliced together must be individually considered, and a pair of primers must be designed for each fragment in order to make the ends compatible.
  • Traditional considerations for the design of PCR primers e.g., melting temperature, G-C content, avoidance of hairpin and dimer formation, and stringency for false priming sites, must be considered even more carefully as the number of fragments to be spliced in the SOE reaction increases.
  • compositions and methods provided herein allow for rapid and ordered assembly, or "stitching," of component polynucleotides into assembled polynucleotides.
  • the methods provided herein utilize circular nucleic acid assembly vectors.
  • an assembly vector comprises a component polynucleotide wherein the component polynucleotide comprises a DNA segment flanked by: (i) an annealable linker on the 3' end; (ii) a primer binding segment on the 5' end and an annealable linker on the 3' end; (iii) an annealable linker on both the 3' end and on the 5' end; (vi) an annealable linker on the 5' end and primer binding segment on the 3' end; or (v) an annealable linker on the 5 'end.
  • a plurality of component polynucleotides can be stitched together by providing a plurality of assembly vectors in a single reaction vessel.
  • component polynucleotides can be excised from their assembly vectors within the reaction vessel.
  • the component polynucleotides can then be denatured, annealable linker sequences can be annealed to complementary strands on an adjacent component polynucleotide, and the component polynucleotides can be stitched together into an assembled polynucleotide by splicing by overlap extension (SOE) followed by PCR.
  • SOE overlap extension
  • component polynucleotides excised from assembly vectors can be assembled into an assembled polynucleotide in vivo by homologous recombination within a host cell transformed with the component polynucleotides. Assembled polynucleotides can be further combined in vivo by host cell mediated homologous recombination.
  • the efficiency of polynucleotide assembly can be enhanced by the provision of a standard set of annealable linker sequences that are used within the assembly vector, for example, those described herein as SEQ ID NOS: 1 to 23.
  • the annealable linker sequences provide sequence overlap between adjacent component polynucleotides in the assembly reaction.
  • the annealable linker sequences lack appreciable secondary structure both at the RNA and at the DNA level, do not cross react in an undesirable manner with one another, and have relatively high melting temperatures (T m ). Consequently, a number of component polynucleotides can be stitched together without the need for designing unique primers for each component polynucleotide, thereby saving time and labor.
  • Compositions and methods provided herein can be used to assemble many types of polynucleotides, including synthetic genes, constructs, cloning vectors, expression vectors, chromosomes, genomes, peptide libraries, and the like.
  • a vector i.e., an assembly vector, that can be used in the assembly of one or more assembled polynucleotides from a plurality of component polynucleotides.
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA- LA-D-LB-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-D-LB-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, and a restriction site RB (i.e., 5'- RA-LA-D-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-PA-D-LB-RB-S').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, a primer binding segment PB, and a restriction site RB (i.e., 5'- RA-LA-D-PB-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-LA-D-LB-RB-3'). Exemplary assembly vectors are provided in FIG. IB and FIG. 2.
  • a primer binding segment (i.e., PA or PB) can be any nucleotide sequence that is not complementary with any of the annealable linker sequences that are used to make an assembled polynucleotide.
  • a primer binding segment includes a restriction endonuclease recognition site and/or cleavage site.
  • a primer binding segment comprises a nucleic acid sequence of one of the available linker sequences (e.g., one of SEQ ID NOS: 1 to 23), or complements thereof, not being used in the particular assembly reaction.
  • the nucleic acid sequence of primer binding segment PA is selected from the group consisting of SEQ ID NOS: 24, 25, and complements thereof.
  • the nucleic acid sequence of primer binding segment PB is selected from the group consisting of SEQ ID NOS: 24, 25, and complements thereof.
  • primer binding segment PA and primer binding segment PB are not identical in sequence.
  • the two or more annealable linker sequences are at least 24 nucleotides in length and have a T m of at least 60 0 C.
  • two or more annealable linker sequences have a G-C content of at least 70% and a T m of at least 70 0 C, and do not form appreciable secondary DNA structures.
  • the nucleic sequence of annealable linker sequence LA is selected from the group consisting of SEQ ID NOS: 1 to 8, and complements thereof.
  • the nucleic sequence of annealable linker sequence LB is selected from the group consisting of SEQ ID NOS: 1 to 8, and complements thereof.
  • the nucleic sequences of annealable linker sequence LA and annealable linker sequence LB are selected from the group consisting of SEQ ID NOS: 1 to 8, and complements thereof.
  • two or more annealable linker sequences have an A-T content of at least 30% and a T m of at least 65 0 C, and do not form appreciable secondary DNA or RNA structures.
  • two or more annealable linker sequences have a low G-C content and a T m of at least 65 0 C, and comprise the sequence motif 5 '- ANNNNNNNNANNNAANTANNTTNANA-S', wherein A stands for adenine, N for any nucleotide, and T for thymine.
  • the nucleic sequence of annealable linker sequence LA is selected from the group consisting of SEQ ID NOS: 9 to 23, and complements thereof.
  • nucleic sequence of annealable linker sequence LB is selected from the group consisting of SEQ ID NOS: 9 to 23, and complements thereof. In some embodiments, the nucleic sequences of annealable linker sequence LA and annealable linker sequence LB are selected from the group consisting of SEQ ID NOS: 9 to 23, and complements thereof.
  • the ordered assembly of the plurality of component polynucleotides can be controlled by the selection of annealable linker sequences that flank a DNA segment within the assembly vector. Accordingly, in some embodiments, to ensure that component polynucleotides can be assembled in an ordered fashion, the sequences of an annealable linker sequence/annealable linker sequence pair within a particular assembly vector are not complementary. Similarly, in some embodiments, the sequences of a primer binding segment/annealable linker sequence pair within a particular assembly vector are not complementary.
  • restriction sites RA and RB are cleavable by the same restriction endonuclease so as to facilitate the excision of the component polynucleotide from the assembly vector.
  • restriction site RA or RB is cleavable by a restriction endonuclease that leaves a 5' or 3' overhang.
  • restriction site RA or RB is cleavable by a restriction endonuclease that leaves a blunt end.
  • restriction sites RA and RB are cleavable by the same restriction endonuclease.
  • the restriction sites RA and RB are cleavable by a Type IIS restriction endonuclease. In some embodiments, the restriction sites RA and RB are cleavable by the same Type IIS restriction endonuclease. In a particular embodiment, restriction sites RA and RB are cleavable by Sapl or Lgul restriction endonucleases. [0020] In another aspect, the invention provides an entry vector useful in the preparation of an assembly vector comprising a DNA segment.
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-RY-D-RZ-LB-RB-S').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, and a restriction site RB (i.e., 5'-RA-LA-RY-D-RZ-RB-S').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5 '-RA- L A-RY-D- RZ-LB-RB-3').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-PA-RY-D-RZ-LB-RB-S ').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, a primer binding segment PB, and a restriction site RB (i.e., 5'-RA- LA-RY-D-RZ-PB-RB-3').
  • An exemplary entry vector is provided in FIG. IA.
  • Digestion of an entry vector with one or more restriction endonucleases capable of cleaving RY and RZ can create a linearized vector capable of acceptance of a DNA segment.
  • restriction sites RY and RZ of the entry vector are cleavable by the same restriction endonuclease.
  • restriction sites RY and RZ of the entry vector are cleavable by a Type IIS restriction endonuclease.
  • restriction sites RY and RZ of the entry vector are cleavable by the same Type IIS restriction endonuclease.
  • the Type IIS restriction endonuclease is Schl or MIyI.
  • restriction sites RA and RB of the entry vector are cleavable by the same restriction endonuclease. In some embodiments, restriction sites RA and RB of the entry vector are cleavable by a Type IIS restriction endonuclease. In some embodiments, restriction sites RA and RB of the entry vector are cleavable by the same Type IIS restriction endonuclease. In particular embodiments, the Type IIS restriction endonuclease is Sapl or Lgul.
  • the invention provides an assembly composition comprising a plurality of assembly vectors for use in the assembly of one or more assembled polynucleotides from a plurality of component polynucleotides.
  • the assembly composition comprises:
  • each first nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RAo, any DNA segment selected from the group D 0 , an annealable linker sequence LBo, and a second restriction site RBo;
  • each intermediate nucleic acid molecule n is circular and comprises, in a 5' to 3' orientation, a first restriction site RA n , a first annealable linker sequence LA n , any DNA segment selected from the group D n , a second annealable linker sequence LB n , and a second restriction site RB n , and wherein n represents an integer from one to the number of intermediate nucleic acid molecules;
  • each last nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RA m , an annealable linker sequence LA m , any DNA segment selected from the group D m , a second restriction site RB m wherein m represents an integer one greater than the number of intermediate nucleic acid molecules; whereupon cleavage of restriction sites RAo through RB m and denaturation of the resulting linear nucleic acid molecules, each annealable linker sequence LB (P- D is capable of hybridizing to the complement of annealable linker sequence LA P , wherein n is an integer that varies from 1 to (m-1), wherein p represents an integer from 1 to m, and wherein each group D 0 ,...
  • one or more first nucleic acid molecules further comprises a primer binding segment PA positioned 5' to the DNA segment selected from the group D 0 .
  • one or more last nucleic acid molecules further comprises a primer binding segment PB positioned 3' to the DNA segment selected from the group D m .
  • the assembly composition comprises two or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises three or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises four or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises five or more intermediate nucleic acid molecules.
  • the composition comprises six or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises seven or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises eight or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises nine or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises ten or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises fifteen or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises twenty or more intermediate nucleic acid molecules. [0027] In certain embodiments, m is equal to 1. In certain embodiments, m is equal to 2. In certain embodiments, m is equal to 3. In certain embodiments, m is equal to 4.
  • m is equal to 5. In certain embodiments, m is equal to 6. In certain embodiments, m is equal to 7. In certain embodiments, m is equal to 8. In certain embodiments, m is equal to 9. In certain embodiments, m is equal to 10. In certain embodiments, m is equal to or greater than 10.
  • each annealable linker sequence LB( P- i) is capable of selectively hybridizing to the complement of annealable linker sequence LA P compared to the other annealable linker sequneces, or their complements, in the assembly composition.
  • each annealable linker sequence L( P- i ) is identical in sequence to annealable linker sequence LA P .
  • the restriction sites RAo through RB m are cleavable by the same restriction endonuclease so as to facilitate excision of the component polynucleotides from the assembly vectors.
  • the restrictions sites RAo through RB m are cleavable by Sapl and/or Lgul restriction endonucleases.
  • the invention provides a components composition comprising a plurality of linear nucleic acid molecules wherein the linear nucleic acid molecules can be formed by digesting an assembly composition with one or more restriction endonucleases capable of cleaving restriction sites RA 0 through RB m wherein the assembly composition comprises:
  • each first nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RAo, any DNA segment selected from the group Do, an annealable linker sequence LBo, and a second restriction site RBo;
  • each intermediate nucleic acid molecule n is circular and comprises, in a 5' to 3' orientation, a first restriction site RA n , a first annealable linker sequence LA n , any DNA segment selected from the group D n , a second annealable linker sequence LB n , and a second restriction site RB n , and wherein n represents an integer from one to the number of intermediate nucleic acid molecules;
  • each last nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RA m , an annealable linker sequence LA 111 , any DNA segment selected from the group D m , a second restriction site RB m wherein m represents an integer one greater than the number of intermediate nucleic acid molecules; whereupon cleavage of restriction sites RAo through RB m and denaturation of the resulting linear nucleic acid molecules, each annealable linker sequence LB (p- i) is capable of hybridizing to the complement of annealable linker sequence LA P , wherein n is an integer that varies from 1 to (m-1), wherein p represents an integer from 1 to m, and wherein each group Do,...
  • one or more first nucleic acid molecules further comprises a primer binding segment PA positioned 5' to the DNA segment selected from the group Do.
  • one or more last nucleic acid molecules further comprises a primer binding segment PB positioned 3' to the DNA segment selected from the group D m .
  • the components composition comprises two or more intermediate nucleic acid molecules. In certain embodiments, the components components composition comprises three or more intermediate nucleic acid molecules. In certain embodiments, the components composition comprises four or more intermediate nucleic acid molecules. In certain embodiments, the components composition comprises five or more intermediate nucleic acid molecules.
  • the components composition comprises six or more intermediate nucleic acid molecules. In certain embodiments, the components composition comprises seven or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises eight or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises nine or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises ten or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises fifteen or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises twenty or more intermediate nucleic acid molecules.
  • m is equal to 1. In certain embodiments, m is equal to 2. In certain embodiments, m is equal to 3. In certain embodiments, m is equal to 4. In certain embodiments, m is equal to 5. In certain embodiments, m is equal to 6. In certain embodiments, m is equal to 7. In certain embodiments, m is equal to 8. In certain embodiments, m is equal to 9. In certain embodiments, m is equal to 10. In certain embodiments, m is equal to or greater than 10.
  • kits useful for assembling a plurality of polynucleotides in accordance with the methods provided herein comprises: (a) one or more entry vectors described herein; (b) one or more restriction endonucleases capable of cleaving restriction sites RA and RB of the entry vectors; and (c) one or more restriction endonucleases capable of cleaving restriction sites RY and RZ of the entry vectors.
  • the invention provides a library of nucleic acid molecules.
  • a nucleic acid molecule of the library comprises a first restriction site RA, a DNA segment D, an annealable linker sequence LB, and a second restriction site RB.
  • a nucleic acid molecule of the library comprises a first restriction site RA, a primer binding segment PA, a DNA segment D, an annealable linker sequence LB, and a second restriction site RB.
  • a nucleic acid molecule of the library comprises a first restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a second restriction site RB.
  • a nucleic acid molecule of the library comprises a first restriction site RA, an annealable linker sequence LA, a DNA segment D, and a second restriction site RB. In some embodiments, a nucleic acid molecule of the library comprises a first restriction site RA, an annealable linker sequence LA, a DNA segment D, a primer binding segment PB, and a second restriction site
  • the library comprises at least one of each of the following vectors:
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, and a restriction site RB 0 .
  • the library comprises at least one of each of the following vectors:
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5 " to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, a primer binding segment PB, and a restriction site RB 0 .
  • the DNA segment D comprises a nucleic sequence selected from the group consisting of a selectable marker, a promoter, genomic targeting sequence, a nucleic acid sequence encoding an epitope tag, and a nucleic acid sequence encoding a gene of interest, a nucleic acid sequence encoding a termination codon and lacZ.
  • the library comprises at least one of each of the following nucleic acid molecules:
  • n represents an integer from one to the number of intermediate nucleic acid molecules
  • each annealable linker sequence LB( P- i) is capable of hybridizing to the complement of annealable linker sequence L A p wherein p represents the integers from 1 to m.
  • a first nucleic acid molecule further comprises a primer binding segment PA positioned 5' to the DNA segment selected from the group D 0 .
  • a last nucleic acid molecules further comprises a primer binding segment PB positioned 3' to the DNA segment selected from the group D m .
  • the library comprises two or more intermediate nucleic acid molecules. In certain embodiments, the library comprises three or more intermediate nucleic acid molecules. In certain embodiments, the library comprises four or more intermediate nucleic acid molecules. In certain embodiments, the library comprises five or more intermediate nucleic acid molecules. In certain embodiments, the library comprises six or more intermediate nucleic acid molecules. In certain embodiments, the library comprises seven or more intermediate nucleic acid molecules.
  • the assembly composition comprises eight or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises nine or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises ten or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises fifteen or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises twenty or more intermediate nucleic acid molecules. [0041] In certain embodiments, m is equal to 1. In certain embodiments, m is equal to 2. In certain embodiments, m is equal to 3. In certain embodiments, m is equal to 4. In certain embodiments, m is equal to 5. In certain embodiments, m is equal to 6. In certain embodiments, m is equal to 7. In certain embodiments, m is equal to 8. In certain embodiments, m is equal to 9. In certain embodiments, m is equal to 10. In certain embodiments, m is equal to or greater than 10.
  • each first nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RAo, any primer binding segment selected from the group PA, any DNA segment selected from the group D 0 , an annealable linker sequence LBo, and a second restriction site RB 0 ;
  • each intermediate nucleic acid molecule n is circular and comprises, in a 5' to 3' orientation, a first restriction site RA n , a first annealable linker sequence LA n , any DNA segment seleted from the group D n , a second annealable linker sequence LB n , and a second restriction site RB n , and wherein n represents an integer from one to the number of intermediate nucleic acid molecules;
  • each last nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RA m , an annealable linker sequence LA n ,, a DNA segment selected from the group D m , any primer binding segment selected from the group PB, a second restriction site RB m wherein m represents an integer one greater than the number of intermediate nucleic acid molecules; whereupon cleavage of restriction sites RA 0 through RB m and denaturation of the resulting linear nucleic acid molecules, each annealable linker sequence LB( P- i ) is capable of hybridizing to the complement of annealable linker sequence LA n , wherein n is an integer that varies from 1 to (m-1), wherein p represents an integer from 1 to m, and wherein each group Do,...
  • D n ,...and D m consists of one or more DNA segments; wherein the one or more restriction endonucleases are capable of cleaving the restriction sites RA 0 through RB m ; and (b) contacting the components composition with DNA polymerase, deoxyribonucleoside triphosphates and one or more first primers and one or more second primers, under conditions suitable for denaturation of the nucleic acid molecules, annealing of annealable linker sequence LB( P- j) to annealable linker sequence LA P , and extension therefrom; wherein each said first primer is capable of hybridizing to one of said primer binding segments selected from the group PA and each said second primer is capable of hybridizing to one of said primer binding segments selected from the group PB; and subjecting the components composition to polymerase chain reaction, wherein a polynucleotide is assembled which comprises, in a 5' to 3' orientation, one DNA segment selected from each of the groups Do,... D n ,...and D
  • the assembly composition comprises two or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises three or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises four or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises five or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises six or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises seven or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises eight or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises nine or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises ten or more intermediate nucleic acid molecules.
  • the assembly composition comprises fifteen or more intermediate nucleic acid molecules. In certain embodiments, the assembly composition comprises twenty or more intermediate nucleic acid molecules. [0044] In certain embodiments, m is equal to 1. In certain embodiments, m is equal to 2. In certain embodiments, m is equal to 3. hi certain embodiments, m is equal to 4. In certain embodiments, m is equal to 5. In certain embodiments, m is equal to 6. In certain embodiments, m is equal to 7. In certain embodiments, m is equal to 8. In certain embodiments, m is equal to 9. In certain embodiments, m is equal to 10. In certain embodiments, m is equal to or greater than 10.
  • the assembly composition comprises one first nucleic acid molecule and one last nucleic acid molecule. In other embodiments, the assembly composition comprises more than one first nucleic acid molecule and more than one last nucleic acid molecule, and the assembly methods provide for the ordered assembly of multiple component polynucleotides into a plurality of assembled polynucleotides in a combinatorial fashion.
  • the assembly composition comprises comprises at least two nucleic acid molecules that comprise the same annealable linker sequence LA or LB, or the same primer binding segment PA or PB, or the same pair of annealable linker sequences LA and LB, or the same pair of annealable linker sequence / primer binding segment LA and PB, or LB and PA.
  • the methods comprise transforming a host cell with an assembled polynucleotide generated by the methods of polynucleotide assembly described herein. In other embodiments, the methods comprise transforming a host cell with a plurality of assembled polynucleotides generated by the methods of polynucleotide assembly described herein. In a particular embodiment, the host cell combines two or more assembled polynucleotides into one or more combined polynucleotide by homologous recombination. In yet other embodiments, the methods comprise transforming a host cell with a plurality of component polynucleotides and allowing the host cell to generate one or more assembled or combined polynucleotides by homologous recombination.
  • the present invention provides methods for generating a plurality of host cells comprising a plurality of assembled polynucleotides.
  • the plurality of host cells are generated by transforming host cells with a composition comprising a plurality of assembled polynucleotides generated by combinatorial assembly of component polynucleotides.
  • the plurality of host cells are generated by transforming host cells with a composition comprising a plurality of assembled polynucleotides of which at least two assembled polynucleotides comprise non- functional segments of a selectable marker that upon host cell mediated homologous recombination generate a functional selectable marker, and by selecting host cells comprising a combined polynucleotide.
  • the plurality of host cells are generated by combinatorial methods by transforming host cells with a component composition comprising multiple component polynucleotides of which at least two component polynucleotides comprise the same annealable linker sequence LA or LB or the same pair of annealable linker sequences LA and LB, and by selecting host cells comprising an assembled polynucleotide.
  • polynucleotide comprising one or more sequences selected from the group consisting of SEQ ID NOS: lto 25.
  • FIG. IA provides a schematic of an entry vector useful for the preparation of an assembly vector of the invention.
  • the vector contains a restriction site RAo, a primer binding segment PA or an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB.
  • FIG. IB provides an exemplary method of preparing an entry vector for acceptance of a DNA segment to form an assembly vector.
  • Digestion with Schl a Type IIS restriction endonuclease that is capable of producing blunt ends allows for isolation of the vector with the linker sites open to be fused to the DNA segment (D). Blunt-end ligation of D into the entry vector can be performed by traditional methods using, e.g., T4 DNA ligase.
  • FIG. 2 presents a schematic of an assembly composition
  • a plurality of assembly vectors (first, intermediate, and last), each comprising a DNA segment of interest (D 0 , D n , D m ).
  • the first nucleic acid molecule comprises a first restriction site RAo, a primer binding segment PA, a DNA segment D 0 , an annealable linker sequence LB 0 , and a second restriction site RB 0 .
  • the one or more intermediate nucleic acid molecules comprise a first restriction site RA n , a first annealable linker sequence LA n , a DNA segment D n , a second annealable linker sequence LB n , and a second restriction site RB n wherein n represents an integer from one to the number of intermediate nucleic acid molecules; and the last nucleic acid molecule comprises a first restriction site RA m , an annealable linker sequence LA m , a DNA segment D m , a primer binding segment PB, a second restriction site RB n , wherein m represents an integer one greater than the number of intermediate nucleic acid molecules.
  • Assembly vectors comprising DNA segments to be assembled are pooled in a single tube and digested with Sapl to release component polynucleotide fragments from the assembly vector backbones. Following heat inactivation of Sapl, the component polynucleotide fragments are subjected to denaturing conditions, followed by annealing conditions sufficient for hybridization of the complementary annealable linker pairs. Following primer extension in the presence of DNA polymerase and dNTPs, primers complementary to PA and PB are added, followed by traditional PCR amplification. An assembled polynucleotide comprising component polynucleotides D 0 , Di, D 2 , and D 3 assembled in a 5' to 3' direction is produced as a result of the assembling reaction.
  • FIG. 4 shows a map of the pRYSE vector.
  • FIG. 5 shows assembled polynucleotides obtained by assembling 2 to 4 component polynucleotides (Assemblies 1 through 6 in Table 7) using different methods for removing the Sapl restriction endonuclease (column purification or heat inactivation), different assembly vector DNA concentrations (5 ng (low DNA concentration) or 50 ng (high DNA concentration) of smallest fragment with equal molar concentration of all other fragments, and different annealing temperatures for PCR amplification (54 0 C and 72 0 C).
  • FIG. 1 shows assembled polynucleotides obtained by assembling 2 to 4 component polynucleotides (Assemblies 1 through 6 in Table 7) using different methods for removing the Sapl restriction endonuclease (column purification or heat inactivation), different assembly vector DNA concentrations (5 ng (low DNA concentration) or 50 ng (high DNA concentration) of smallest fragment with equal molar concentration of all other fragments, and different annealing temperatures for PCR a
  • FIG. 6 shows assembled polynucleotides obtained by assembling 6 or 9 component polynucleotides (Assemblies 7, and 13 through 16 in Table 7) using different DNA polymerases (Phusion (New England Biolabs, Ipswich, MA) and PfuUltraII (Stratagene/Agilent, La Jolla, CA)).
  • FIG. 7 shows a map of the pMULE vector.
  • the pMULE entry vector differs from the pRYSE entry vector in that it lacks a primer binding segments or annealable linker sequences.
  • FIG. 8 present an exemplary method of combining assembled polynucleotides into a combined polynucleotide by host cell mediated homologous recombination, and integrating the combined polynucleotide into a chromosome of the host cell.
  • Assembled polynucleotide A comprises a DNA segment D m i encoding a first non-functional segment of a selectable marker and a DNA segment D 0 1 encoding an upstream genomic targeting sequence.
  • Assembled polynucleotide B comprises a DNA segment D m2 encoding a second non-functional segment of the selectable marker and a DNA segment D 02 encoding a downstream genomic targeting sequence.
  • the host cell recombines assembled polynucleotide A and assembled polynucleotide B at the region of homology in DNA segments D m i and D m2 to form a combined polynucleotide comprising a functional selectable marker, and uses the genomic targeting sequences encoded by DNA segments Doi and Do 2 to insert the combined polynucleotide by homologous recombination into its chromosome.
  • FIG. 9 presents an exemplary method of generating an assembled polynucleotide by homologous recombination in a host cell and integration of the assembled polynucleotide into the chromosome of the host cell.
  • an assembly composition comprising assembly vectors is digested with a restriction endonuclease, resulting in the excision of component polynucleotides from the assembly vector backbones.
  • the component polynucleotides are introduced into a host cell where they are recombined at the regions of homology in the annealable linker sequences to form an assembled polynucleotide, and the assembled polynucleotide is integrated into the chromosome of the host cell.
  • FIG. 10 presents an exemplary method of assembling a plurality of assembled polynucleotide from seven (7) component polynucleotides in the same reaction.
  • Assembly vectors comprising DNA segments to be assembled are pooled in a single tube and digested with Sapl to release component polynucleotides from the assembly vector backbones.
  • Sapl the component polynucleotide fragments are subjected to denaturing conditions, followed by annealing conditions sufficient for hybridization of the complementary annealable linker pairs.
  • primers complementary to PA and PB are added, followed by traditional PCR amplification.
  • the assembly reaction results in the production of an assembled polynucleotide comprising component polynucleotides D O i / o 2 , Di /2 , D 3 , and D 4 i /42 assembled in a 5' to 3' direction.
  • FIG. 11 presents an exemplary method of generating a plurality of host cells comprising combinatorially combined polynucleotides.
  • Assembled polynucleotides Al and A2, each comprising the same upstream genomic targeting sequence and the same first nonfunctional portion of a selectable marker, and assembled polynucleotides Bl and B2, each comprising the same downstream genomic targeting sequence and the same second nonfunctional portion of a selectable marker are combinatorially combined by host cell mediated homologous recombination to generate four different combined polynucleotides, Al /Bl, A1/B2, A2/B1, and A2/B2, each comprising a functional selectable marker, that can be inserted into a chromosome to generate four different host cells.
  • FIG. 12A shows the component polynucleotides used in Example 10 for the high-throughput generation of combinatorially assembled polynucleotides and yeast cells comprising combinatorially assembled and combined polynucleotides, and the expected assembled and combined polynucleotides.
  • US upstream genomic targeting sequence
  • DS downstream genomic targeting sequence
  • P various promoter sequences
  • G various protein coding sequences
  • URA 5' segment of selectable marker
  • RA3 3' segment of selectable marker
  • PA primer binding segment PmeI-5"
  • PB primer binding segment PmeI-3'
  • LB 0 annealable linker sequence RYSE 2
  • LA n i annealable linker sequence RYSE 2
  • LB n ] annealable linker sequence RYSE 15
  • LA n2 annealable linker sequence RYSE 3
  • LB n2 annealable linker sequence RYSE 16
  • LA n3 annealable linker sequence RYSE 15
  • LB n3 annealable linker sequence RYSE 3
  • LA 114 annealable linker sequence RYSE 16
  • LB n4 annealable linker sequence RYSE 4
  • LA n , j annealable linker sequence RYSE
  • FIG. 12B shows exemplary assembled polynucleotides (boxed) generated as described in Example 10 and resolved on a 1% agarose gel.
  • FIG. 12C shows restriction analysis for exemplary cell colonies obtained as described in Example 10.
  • FIG. 13A shows the assembled polynucleotide and component polynucleotides used in Example 11 , and the expected chromosomal locus obtained upon assembly and chromosomal integration by the host cells.
  • FIG. 13B shows cPCR analysis results obtained for yeast cell transformants generated in Example 11 that comprise chromosomally integrated assembled polynucleotides.
  • FIG. 14 shows the component polynucleotides used in Example 12 for the high-throughput generation of yeast cells comprising chromosomally integrated combinatorially assembled and combinatorially combined polynucleotides, and the expected combined polynucleotides obtained upon assembly and combination by host cell mediated homologous recombination.
  • US upstream genomic targeting sequence
  • DS downstream genomic targeting sequence
  • P various promoter sequences
  • G various protein coding sequences
  • URA 5' segment of selectable marker
  • RA3 3' segment of selectable marker
  • PA primer binding segment PmeI-5'
  • PB primer binding segment PmeI-3'
  • LB 0 annealable linker sequence RYSE 2
  • LA n i annealable linker sequence RYSE 2
  • LB n i annealable linker sequence RYSE 15
  • LA n2 annealable linker sequence RYSE 3
  • LB n2 annealable linker sequence RYSE 16
  • LA n3 annealable linker sequence RYSE 15
  • LB n3 annealable linker sequence RYSE 3
  • LA n4 annealable linker sequence RYSE 16
  • LB n4 annealable linker sequence RYSE 4
  • LA m i annealable linker sequence RYSE 3
  • polynucleotide refers to a polymer composed of nucleotide units as would be understood by one of skill in the art.
  • Preferred nucleotide units include but are not limited to those comprising adenine (A), guanine (G), cytosine (C), thymine (T), and uracil (U).
  • Useful modified nucleotide units include but are not limited to those comprising 4-acetylcytidine, 5-(carboxyhydroxylmethyl)uridine, 2-O-methylcytidine, 5-carboxymethylaminomethyl-2-thiouridine, 5-carboxymethylamino-methyluridine, dihydrouridine, 2-O-methylpseudouridine, 2-O-methylguanosine, inosine, N6- isopentyladenosine, 1 -methyladenosine, 1 -methylpseudouridine, 1 -methylguanosine, 1- methylinosine, 2,2-dimethylguanosine, 2-methyladenosine, 2-methylguanosine, 3- methylcytidine, 5-methylcytidine, N6-methyladenosine, 7-methylguanosine, 5- methylaminomethyluridine, 5-methoxyaminomethyl-2-thiouridine, 5-methoxyuridine, 5- methoxycarbonyl
  • Polynucleotides include naturally occurring nucleic acids, such as deoxyribonucleic acid (“DNA”) and ribonucleic acid (“RNA”), as well as nucleic acid analogs.
  • Nucleic acid analogs include those that include non-naturally occurring bases, nucleotides that engage in linkages with other nucleotides other than the naturally occurring phosphodiester bond or that include bases attached through linkages other than phosphodiester bonds.
  • nucleotide analogs include, for example and without limitation, phosphorothioates, phosphorodithioates, phosphorotriesters, phosphoramidates, boranophosphates, methylphosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs), and the like.
  • a “component polynucleotide” refers to a polynucleotide sequence that can be assembled together to form a "assembled polynucleotide” using the methods of polynucleotide assembly described herein.
  • the resulting population of component polynucleotides can comprise the totality of DNA segments to be assembled into a assembled polynucleotide.
  • an "assembled polynucleotide” refers to a polynucleotide produced by the methods of polynucleotide assembly described herein.
  • the assembled polynucleotide can be comprised of the two or more component polynucleotides.
  • the assembled polynucleotide comprises 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 or more component polynucleotides.
  • Assembled polynucleotide length can range from about 100 to about 20,000 nucleotides, or more.
  • the assembled polynucleotide length ranges from about 200 to about 10,000, about 200 to about 8000, about 200 to about 5000, about 200 to about 3000, or about 200 to about 1000 nucleotides. In other embodiments, the assembled polynucleotide length can range from about 200 to about 2000, about 2000 to about 5000, about 5000 to about 10,000, about 10,000 to about 20,000, or greater than 20,000 nucleotides.
  • DNA segment refers to any isolated or isolatable molecule of DNA.
  • Useful examples include but are not limited to a protein-coding sequence, reporter gene, fluorescent marker coding sequence, promoter, enhancer, terminator, intron, exon, poly-A tail, multiple cloning site, nuclear localization signal, mRNA stabilization signal, selectable marker, integration loci, epitope tag coding sequence, degradation signal, or any other naturally occurring or synthetic DNA molecule.
  • the DNA segment can be of natural origin.
  • a DNA segment can be completely of synthetic origin, produced in vitro.
  • a DNA segment can comprise any combination of isolated naturally occurring DNA molecules, or any combination of an isolated naturally occurring DNA molecule and a synthetic DNA molecule.
  • a DNA segment may comprise a heterologous promoter operably linked to a protein coding sequence, a protein coding sequence linked to a poly-A tail, a protein coding sequence linked in-frame with a epitope tag coding sequence, and the like.
  • Complementary refers to the topological compatibility or matching together of interacting surfaces of two polynucleotides as understood by those of skill in the art. Thus, two sequences are “complementary” to one another if they are capable of hybridizing to one another to form a stable anti-parallel, double-stranded nucleic acid structure.
  • a first polynucleotide is complementary to a second polynucleotide if the nucleotide sequence of the first polynucleotide is substantially identical to the nucleotide sequence of the polynucleotide binding partner of the second polynucleotide, or if the first polynucleotide can hybridize to the second polynucleotide under stringent hybridization conditions.
  • the polynucleotide whose sequence 5'-TATAC-3' is complementary to a polynucleotide whose sequence is 5 '- GTATA-3 1 .
  • Primer refers to a polynucleotide sequence that is capable of specifically hybridizing to a polynucleotide template sequence, e.g., a primer binding segment, and is capable of providing a point of initiation for synthesis of a complementary polynucleotide under conditions suitable for synthesis, i.e., in the presence of nucleotides and an agent that catalyzes the synthesis reaction (e.g., a DNA polymerase).
  • the primer is complementary to the polynucleotide template sequence, but it need not be an exact complement of the polynucleotide template sequence.
  • a primer can be at least about 80, 85, 90, 95, 96, 97, 98, or 99% identical to the complement of the polynucleotide template sequence.
  • a primer can be of variable length but generally is at least 15 bases. In some embodiments, the primer is between 15 and 35 bases long. In some embodiments, the primer is more than 35 bases long.
  • the primer has a melting temperature (T m ), i.e., the temperature at which one half of the DNA duplex will dissociate to become single stranded, of at least 5O 0 C. In other embodiments, the primer has a T m between about 5O 0 C and 7O 0 C. In still other embodiments, the primer does not form appreciable DNA or RNA secondary structures so as to not impact the efficiency of hybridization to the polynucleotide template sequence.
  • the term "primer binding segment” is a polynucleotide sequence that binds to a primer so as to provide a point of initiation for synthesis of a complementary polynucleotide under conditions suitable for synthesis.
  • the primer binding sequence is one of the annealable linkers of the present invention.
  • a sequence is a primer binding sequence instead of an annealable linker by the absence of a complementary linker within a given set of assembly vectors or component polynucleotides within an assembly composition.
  • the primer binding segment can function as a genomic targeting sequence, e.g., an upstream or downstream genomic targeting sequence.
  • linker sequence and "annealable linker sequence” are used interchangeably and refer to a polynucleotide sequence contained within an entry vector and assembly vector described herein.
  • an annealable linker sequence flanks a DNA segment within an entry vector or assembly vector.
  • an annealable linker Upon excision of a component polynucleotide from an assembly vector, and denaturation of the component polynucleotide, an annealable linker is capable of specifically hybridizing to a complementary annealable linker sequence of an adjacent component polynucleotide in a polynucleotide assembly reaction, as described herein.
  • An annealable linker upon annealing with a complementary linker strand, can provide a point of initiation for synthesis of a complementary polynucleotide.
  • vector is used in reference to extrachromosomal nucleic acid molecules capable of replication in a cell and to which an insert sequence can be operatively linked so as to bring about replication of the insert sequence.
  • Useful examples include but are not limited to circular DNA molecules such as plasmid constructs, phage constructs, cosmid vectors, etc., as well as linear nucleic acid constructs (e.g., lambda phage constructs, bacterial artificial chromosomes (BACs), yeast artificial chromosomes (YACs), etc.).
  • a vector may include expression signals such as a promoter and/or a terminator, a selectable marker such as a gene conferring resistance to an antibiotic, and one or more restriction sites into which insert sequences can be cloned.
  • Vectors can have other unique features (such as the size of DNA insert they can accommodate).
  • the term "entry vector” refers to a cloning vector plasmid that can serve as a parental vector for the preparation of an assembly vector to be used in the polynucleotide assembly methods provided herein.
  • An entry vector comprises two annealable linker sequences, or an annealable linker sequence and a primer binding segment, which flank restriction sites that can be utilized for the introduction of a DNA segment to form an assembly vector.
  • an "assembly vector” refers to an entry vector to which a DNA segment has been introduced.
  • An assembly vector can be used in the polynucleotide assembly methods described herein to provide a component polynucleotide to be assembled into a assembled polynucleotide.
  • assembly vector refers to a vector comprising one annealable linker sequence, two annealable linker sequences, or an annealable linker sequence and a primer binding segment, and a DNA segment.
  • restriction enzyme or “restriction endonuclease” refers to a member or members of a classification of catalytic molecules that bind a cognate sequence of DNA and cleave the DNA molecule at a precise location within that sequence.
  • Restriction endonucleases include Type IIS restriction endonucleases. This class of enzymes differs from other restriction endonucleases in that the recognition sequence is separate from the site of cleavage.
  • Type IIS restriction enzymes include AIwI, Bsal, Bbsl, Bbul, BsmAI, Bsrl, Bsml, BspMI, Earl, Esp3I, Fokl, Hgal, Hphl, Lgul, MboII, MnII, PIeI, Sapl, Schl, SfaNi, and the like. Many of these restriction endonucleases are available commercially and are well known to those skilled in the art. [0081] As used herein, the term "annealable linker sequence duplex" refers to one annealable linker sequence strand aligned with a substantially complementary annealable linker sequence strand in antiparallel association.
  • annealable linker sequence duplexes may contain mismatched base pairs or unmatched bases, although in particular embodiments, the annealable linker sequence duplex comprises two annealable linker sequence strands having perfect complementarity.
  • genomic targeting sequence refers to a nucleotide sequence that is present in the genome of a host cell at a site at which a polynucleotide of the invention is to be inserted by host cell mediated homologous recombination.
  • upstream genomic targeting sequence and downstream genomic targeting sequence refer to genomic targeting sequences that are located upstream and downstream of each other in the genome of a host cell.
  • chromosomal targeting sequence refers to a nucleotide sequence that is present in a chromosome of a host cell at a site at which a polynucleotide of the invention is to be inserted by host cell mediated homologous recombination.
  • upstream chromosomal targeting sequence and “downstream chromosomal targeting sequence” refer to chromosomal targeting sequences that are located upstream and downstream of each other in a chromosome of a host cell.
  • the present invention provides rapid, robust, and high- throughput methods for the ordered assembly of a plurality of component polynucleotides into one or more assembled polynucleotides.
  • the methods of the invention utilize circular nucleic acid vectors, termed assembly vectors, that each comprise a DNA segment, D, flanked by an annealable linker sequence (i.e., LA or LB), a pair of annealable linker sequences (i.e., LA and LB), or an annealable linker sequence and a primer binding segment (i.e., LA and PB or LB and PA), and a pair of restriction sites, RA and RB (FIG. IB).
  • assembly vectors that each comprise a DNA segment, D, flanked by an annealable linker sequence (i.e., LA or LB), a pair of annealable linker sequences (i.e., LA and LB), or an annealable linker sequence and a primer binding segment (i.e
  • Restriction endonuclease digestion of a plurality of assembly vectors at restriction sites RA and RB generates a plurality of component polynucleotides comprising the elements 5'-LA- D-3 ⁇ 5'-D-LB-3 ⁇ 5'-LA-D-LB-3', 5'-LA-D-PB-3 ⁇ or 5'-LB-D-P A-3' (FIG. 3).
  • annealable linker sequences LA and LB provide the component polynucleotides with complementary termini that are utilized in a splice overlap extension assembly reaction followed by polymerase chain reaction (SOE/PCR) to assemble the component polynucleotides into an assembled polynucleotide with an ordered sequence.
  • the methods can provide for assembly into a single assembled polynucleotide of a number of functional DNA elements, including but not limited to protein- coding sequences, reporter genes, fluorescent marker coding sequences, promoters, enhancers, terminators, introns, exons, poly-A tails, multiple cloning sites, nuclear localization signals, mRNA stabilization signals, selectable markers, integration loci, epitope tag coding sequences, and degradation signals.
  • the methods can be used for the assembly of any type of assembled polynucleotide, including but not limited to synthetic genes, constructs, cloning vectors, expression vectors, chromosomes, genomic integration constructs, genomes, and DNA libraries.
  • the methods can be used to assemble DNA segments in a single reaction without need for manipulation and characterization of intermediate products.
  • the methods can also provide for the assembly of an assembled polynucleotide from a plurality of component polynucleotides not originating from an assembly vector (i.e., DNA segments obtained by standard procedures known in the art, such as for example, PCR amplification, chemical synthesis, and the like, that are flanked by one or two annealable linker sequences, LA and/or LB, or by an annealable linker sequence and a primer binding segment (i.e., LA and PB or LB and PA).
  • an assembly vector i.e., DNA segments obtained by standard procedures known in the art, such as for example, PCR amplification, chemical synthesis, and the like, that are flanked by one or two annealable linker sequences, LA and/or LB, or by an annealable linker sequence and a primer binding segment (i.e., LA and PB or LB and PA).
  • the component polynucleotides not originating from an assembly vector may be added to the assembly reaction at any stage prior to the SOE/PCR reaction or host cell mediated homologous recombination for assembly into the assembled polynucleotide.
  • the assembly methods can be used to assemble:(l) component polynucleotides derived from assembly vectors comprising one or two annealable linker sequences, or an annealable linker sequence and a primer binding segment, and generated by digestion of the assembly vectors; (2) vectorless DNA fragments flanked by one or two annealable linker sequences, or by an annealable linker sequence and a primer binding segment ; and (3) combinations thereof.
  • provided herein are methods of assembling a plurality of component polynucleotides into one or more assembled polynucleotides, comprising the steps of:
  • each first nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RAo, any primer binding segment selected from the group PA, any DNA segment selected from the group D 0 , an annealable linker sequence LBo, and a second restriction site RB 0 ;
  • each intermediate nucleic acid molecule n is circular and comprises, in a 5' to 3' orientation, a first restriction site RA n , a first annealable linker sequence LA n , any DNA segment seleted from the group D n , a second annealable linker sequence LB n , and a second restriction site RB n , and wherein n represents an integer from one to the number of intermediate nucleic acid molecules;
  • each last nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RA m , an annealable linker sequence LA m , a DNA segment selected from the group D m , any primer binding segment selected from the group PB, a second restriction site RB m wherein m represents an integer one greater than the number of intermediate nucleic acid molecules; whereupon cleavage of restriction sites RA 0 through RB m and denaturation of the resulting linear nucleic acid molecules, each annealable linker sequence LB (P- i ) is capable of hybridizing to the complement of annealable linker sequence LA P , wherein n is an integer that varies from 1 to (m-1), wherein p represents an integer from 1 to m, and wherein each group D 0 ,... D n ,...and D n , consists of one or more DNA segments; wherein the one or
  • each said first primer is capable of hybridizing to one of said primer binding segments selected from the group PA and each said second primer is capable of hybridizing to one of said primer binding segments selected from the group PB; and subjecting the components composition to polymerase chain reaction, wherein a polynucleotide is assembled which comprises, in a 5' to 3' orientation, one DNA segment selected from each of the groups Do,...
  • FIG. 3 depicts one embodiment of the assembly methods of the invention for illustrative purposes.
  • a total of four component polynucleotides are assembled to yield an assembled polynucleotide.
  • the assembly methods provided herein can be used to assemble any number of component polynucleotides into one or more assembled polynucleotides.
  • the methods provided herein result in the assembly of 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, or more component polynucleotides into one or more assembled polynucleotides.
  • the assembly composition from which the assembled polynucleotide is generated comprises four input assembly vectors, denoted "first,” “intermediate 1 (inti),” “intermediate 2 (UIt 2 ),” and "last.”
  • Each assembly vector comprises a DNA segment flanked either by an annealable linker sequence and a primer binding segment, or by two annealable linker sequences.
  • DNA segment D 0 is flanked by 5' primer binding segment PA and 3' annealable linker sequence LBo.
  • DNA segment Di is flanked by 5' and 3' annealable linker sequences LAi and LBi
  • DNA segment D 2 is flanked by 5' and 3' annealable linker sequences LA 2 and LB 2
  • DNA segment D 3 is flanked by 3' primer binding segment PB and 5' annealable linker sequence LA 3 .
  • the 5'-PA-D-LB-3 ⁇ 5'-LA-D-LB-3', or 5'-LA-D-PB-3' elements in the assembly vectors are further flanked by Sapl restriction endonuclease sites.
  • the assembly composition is digested with Sapl, resulting in the excision of component polynucleotides, comprising the elements 5'-PA-D-LB-3' , 5'LA-D-LB-3 ⁇ or 5'-LA-D-PB-3 ⁇ from the assembly vector backbones into a components composition.
  • Sap I is a Type IIS restriction endonuclease, its recognition site is distal to its cleavage site, and cleavage occurs outside of its recognition sequence.
  • Type IIS restriction endonucleases particularly useful in the assembly of a polynucleotide according to the methods provided herein, since polynucleotides can be assembled which do not comprise a restriction-site scar, which may otherwise result from cleavage of restriction sites RA and RB with a non-TypeIIS restriction endonuclease.
  • the Type IIS recognition site is 5' of the corresponding cleavage site for each of RAo, RA n , and RA m , and 3' of its cleavage site RB 0 , RA n , and RA m .
  • restriction sites RA 0 through RB m are oriented so that cleavage by one or more Type IIS restriction endonucleases capable of cleaving RAo through RB m results in separation of RA 0 from Do, LBo from RB 0 , RA n , from LA n , LB n from RB n , RA m from LA m , and D m from RB m , wherein resultant linearized nucleic acid molecules comprising Do, LB 0 , RA n , LB n , LA m or D m do not comprise any of RAo through RB m .
  • the resulting component polynucleotides do not include any trace of either the restriction enzyme's recognition or cleavage sites.
  • the inventive methods of polynucleotide assembly can be used to transform host cells multiple times without the introduction of sequence repeats which may cause genetic instability.
  • the restriction endonuclease is optionally inactivated.
  • any method known in the art for inactivating endonuclease enzyme activity may be employed, including column or gel-based purification methods.
  • One convenient method is heat inactivation, e.g., at 65° for 20 minutes, which requires little or no manipulation of the components composition outside of the reaction tube.
  • Assembly of the component polynucleotides into an assembled polynucleotide is enabled by sequence duplexes formed by overlapping strands of complementary termini among the component polynucleotides.
  • the annealable linker sequences are designed such that annealable linker sequence LBo can hybridize to the complement of annealable linker sequence LAi, annealable linker sequence LBi can hybridize to the complement of annealable linker sequence LA 2 , and annealable linker sequence LB 2 can hybridize to the complement of annealable linker sequence LA 3 .
  • the component polynucleotides are subjected to denaturing conditions (e.g., heat) to generate single-stranded component polynucleotides, which concomitant with or subsequent to the denaturation step of the assembly reaction are contacted with a thermostable DNA polymerase and deoxyribonucleoside triphosphates.
  • denaturing conditions e.g., heat
  • the thermostable DNA polymerase can be any thermostable DNA polymerase deemed suitable by those of skill in the art.
  • Thermostable DNA polymerases suitable for use in the present methods include but are not limited to Thermus thermophilus (Tth) DNA polymerase, Thermus aquaticus (Taq) DNA polymerase, Thermotoga neopolitana (Tne) DNA polymerase, Thermotoga maritima (Tma) DNA polymerase, Therm°C°Ccus litoralis (TIi or VENTTM) DNA polymerase, Pyr°C°Ccus fitriosus (Pfu or DEEPVENTTM) DNA polymerase, ,PVr 0 C 0 CcWj 1 woosii (Pwo) DNA polymerase, Bacillus ster other mophilus (Bst) DNA polymerase, Sulfolobus acid°Caldarius (SAC) DNA polymerase, Thermoplasma acidophilum (Tac) DNA polymerase, Thermus flavus (Tfl/Tub) DNA polymerase, The
  • Thermostable DNA polymerases having high fidelity (i.e., proofreading properties) and low error rates are preferred.
  • the DNA polymerase is PhusionTM DNA Polymerase (New England Biolabs, Ipswich, MA).
  • the DNA Polymerase is PfuUltraTM II Fusion DNA Polymerase (Strategene / Agilent, La Jolla, CA).
  • the assembly reaction is then subjected to conditions that allow for strand elongation from the 3'-hydroxyl portions of the overlapping annealable linker sequences, during which the thermostable DNA polymerase fills in the portion between the overlapping annealable linker sequences.
  • the assembly reaction is subjected to a limited number of repeating cycles of denaturation / annealing / extension (e.g., for 5-15 cycles) during which a substantial amount of double-stranded assembled polynucleotides are formed.
  • the component polynucleotides act as both primers and template to generate a full length template for the assembled polynucleotide.
  • the annealing and extension steps of the PCR can both be performed at 72 0 C.
  • the primer binding segments PA and PB are designed to not overlap with each other or any of the annealable linker sequences or DNA segments, but rather serve as binding sites for primers used to amplify the full length assembled polynucleotide.
  • primers complementary to primer binding segments PA and PB are added, and the composition is subjected to traditional PCR amplification conditions.
  • the PCR amplification conditions can be any PCR amplification conditions deemed suitable by those of skill in the art, including those described in PCi? Technology: Principles and Applications for DNA Amplification, ed. HA Erlich, Stockton Press, New York, N. Y.
  • the PCR step of the assembly reaction comprises about 35 cycles of denaturation, annealing, and extension in the presence of primers complementary to primer binding segments PA and PB.
  • the annealing and extension steps of the PCR can both be performed at 72°.
  • optimal conditions for successful amplification will depend on the thermostable DNA polymerase and the annealable linker sequences utilized, and these conditions may be adjusted accordingly.
  • the assembled polynucleotide can be purified by any technique apparent to one of skill in the art, e.g., gel electrophoresis purification methods and used for a variety of purposes.
  • the assembled polynucleotide can be inserted into an expression vector backbone for sequence verification.
  • the present invention provides methods for generating host cells comprising assembled polynucleotides.
  • the assembled polynucleotide is at least 3 kb in size. In other embodiments, the assembled polynucleotide is at least 5 kb in size. In still other embodiments, the assembled polynucleotide is at least 6, 7, 8, 9, or 10 kb in size. In still other embodiments, the assembled polynucleotide is greater than 10 kb in size. In still other embodiments, the assembled polynucleotide is greater than 15 kb in size. In still other embodiments, the assembled polynucleotide is greater than 20 kb in size.
  • methods comprise transforming a host cell with an assembled polynucleotide generated by the methods of polynucleotide assembly described herein.
  • the assembled polynucleotide can be circularized prior to transformation or can be transformed as a linear molecule.
  • the assembled polynucleotide can be maintained in the host cell as an extrachromosomal polynucleotide.
  • the assembled polynucleotide can be integrated into the genome of the host cell, e.g., by host cell mediated homologous recombination.
  • an assembled polynucleotide that is to be integrated into a chromosome of a host cell is generated from an assembly composition comprising a first nucleic acid molecule comprising an upstream chromosomal targeting sequence and a last nucleic acid molecule comprising a downstream chromosomal targeting sequence, each chromosomal targeting sequence being of sufficient length to initiate homologous recombination by the host cell with its chromosome.
  • the methods comprise transforming a host cell with a plurality of assembled polynucleotides generated by the methods of polynucleotide assembly described herein.
  • the host cell combines two or more assembled polynucleotides into a single combined polynucleotide by homologous recombination.
  • Host cell transformants comprising the combined polynucleotides are selected by virtue of expressing a selectable marker that is generated in the process of combining the assembled polynucleotides.
  • the method is particularly useful for inserting relatively large pieces of polynucleotide into a target polynucleotide by homologous recombination.
  • Genomic integration includes chromosomal integration, i.e., integration of a polynucleotide into a chromosome of a host cell. Suitable chromosomal integration sites in Saccharomyces cerevisiae include but are not limited to the NDT80, HO, GAL2, and GALl -GAL 10-GAL7 locus.
  • the method can also be useful for generating host cells comprising an extrachromosomally maintained polynucleotide, e.g., vectors and expression plasmids.
  • the stability of either a chromosomally integrated or an extrachromosomally maintained combined polynucleotide is increased when the combined polynucleotide does not comprise identical annealable linker sequences or DNA segments arranged as direct repeats that can otherwise initiate additional homologous recombination events resulting in the excision of segments of the component polynucleotide. Therefore, in some embodiments, the assembled polynucleotides comprise unique annealable linker sequences and DNA segments. In other embodiments, the assembled polynucleotides contain one or more identical annealable linker sequences or DNA segments that upon combination of the assembled polynucleotides are arranged as inverted repeats in the combined polynucleotide.
  • FIG. 8 The generation of an exemplary combined polynucleotide and integration of the combined polynucleotide into a chromosome of the host cell by homologous recombination is illustrated in FIG. 8. Two assembled polynucleotides A and B are taken up by a host cell that is capable of homologous recombination.
  • Each assembled polynucleotide comprises a DNA segment D m that encodes a segment of a selectable marker, wherein DNA segment D m i of assembled polynucleotide A encodes a first segment of a selectable marker and DNA segment D m2 of assembled polynucleotide B encodes a second segment of the selectable marker, wherein DNA segment D m i and DNA segment O n ⁇ comprise a region of homology sufficient to initiate host cell mediated homologous recombination, and wherein neither DNA segment D m i nor DNA segment D m2 produces a functional selectable marker, but whereupon homologous recombination by the host cell a functional selectable marker is generated.
  • Each assembled polynucleotide further comprises a DNA segment D 0 encoding a chromosomal targeting sequence of sufficient length to initiate host mediated homologous recombination, wherein DNA segment Doi of assembled polynucleotide A encodes an upstream chromosomal targeting sequence and DNA segment D 02 of assembled polynucleotide B encodes a downstream chromosomal targeting sequence.
  • the host cell recombines assembled polynucleotide A and assembled polynucleotide B at the region of homology in DNA segments D m i and D 012 to form a combined polynucleotide.
  • the host cell uses the chromosomal targeting sequences encoded by DNA segments Doi and Do 2 to insert the combined polynucleotide by homologous recombination into its chromosome.
  • Host cells comprising the combined polynucleotide can be readily identified based on the functional selectable marker generated.
  • the methods comprise transforming a host cell with a plurality of component polynucleotides and allowing the host cell to generate one or more assembled polynucleotides by homologous recombination.
  • the assembled polynucleotide can be extrachromosomally maintained in the host cell or integrated into the chromosome of the host cell.
  • the generation of an exemplary assembled polynucleotide by homologous recombination in a host cell and integration of the assembled polynucleotide into the chromosome of the host cell is illustrated in FIG. 9.
  • an assembly composition comprising assembly vectors is digested with a Type IIS restriction endonuclease such as Sapl or Lgul, resulting in the excision from the assembly vector backbones of component polynucleotides.
  • a Type IIS restriction endonuclease such as Sapl or Lgul
  • Do and D 3 can be the upstream and downstream chromosomal targeting sequence, in which case the presence of a primer binding segment in the first and last assembly vectors is optional.
  • the two primer binding segments could function as the upstream and downstream genomic targeting sequences.
  • each excised component polynucleotide comprises an annealable linker sequence LB that is homologous to an annealable linker sequence LA of another component polynucleotide and that is of sufficient length to initiate host mediated homologous recombination.
  • the component polynucleotide excised from the first assembly vector further comprises an upstream chromosomal targeting sequence
  • the component polynucleotide excised from the last assembly vector further comprises a downstream chromosomal targeting sequence, wherein both chromosomal targeting sequences are of sufficient length to initiate host mediated homologous recombination with a chromosome of the host cell.
  • the restriction endonuclease can subsequently be inactivated.
  • the components composition is introduced into a host cell capable of homologous recombination.
  • the host cell recombines the component polynucleotides at the regions of homology between the annealable linker sequences to form an assembled polynucleotide, and the assembled polynucleotide is integrated into the chromosome.
  • Host cells comprising the assembled polynucleotide can be readily identified based on a selectable marker encoded by a DNA segment of the assembled polynucleotide. [00103] Any host cell can be used in the methods describe herein.
  • suitable host cells are host cells that are capable of recombining polynucleotides based on complementary sequence stretches such as provided by the selectable marker segments, genomic targeting sequences, and annealable linker sequences provided herein.
  • Illustrative examples of such host cells include but are not limited to Saccharomyces cerevisiae. Conditions suitable for uptake of DNA by such host cells are well known in the art.
  • Host cell transformants comprising an assembled or combined polynucleotide can be readily identified by virtue of expressing a selectable marker encoded by the assembled polynucleotide or by the combined polynucleotide that permits selection for or against the growth of the cells.
  • the selectable marker may be encoded by a single DNA segment present in an assembly vector of an assembly composition.
  • nonfunctional segments of the selectable marker may be encoded by DNA segments present in multiple assembly vectors of an assembly composition or in multiple assembled polynucleotides such that a functional selectable marker is generated only upon generation of an assembled polynucleotide or upon generation of a combined polynucleotide, respectively.
  • a wide variety of selectable markers are known in the art (see, for example,
  • the selectable marker is a drug resistant marker.
  • a drug resistant marker enables cells to detoxify an exogenous drug that would otherwise kill the cell.
  • drug resistant markers include but are not limited to those which confer resistance to antibiotics such as ampicillin, tetracycline, kanamycin, bleomycin, streptomycin, hygromycin, neomycin, ZeocinTM, and the like.
  • the selectable marker is an auxotrophic marker.
  • An auxotrophic marker allows cells to synthesize an essential component (usually an amino acid) while grown in media that lacks that essential component.
  • Selectable auxotrophic gene sequences include, for example, hisD, which allows growth in histidine free media in the presence of histidinol.
  • selectable markers include a bleomycin-resistance gene, a metallothionein gene, a hygromycin B-phosphotransferase gene, the AURI gene, an adenosine deaminase gene, an aminoglycoside phosphotransferase gene, a dihydro folate reductase gene, a thymidine kinase gene, a xanthine-guanine phosphoribosyltransferase gene, and the like.
  • Auxotrophy can also be used to identify host cell transformants comprising a chromosomally integrated assembled or combined polynucleotide when the integration of the assembled or combined polynucleotide results in the disruption of a gene that the host cell requires to synthesize a component essential for cell growth, thus rendering the cell auxotrophic.
  • Host cell transformants comprising a chromosamlly integrated assembled or combined polynucleotide can also be identified by selecting host cell transformants exhibiting other traits encoded by individual DNA segments or by combinations of DNA segments, e.g., expression of peptides that emit light, or by molecular analysis of individual host cell colonies, e.g., by restriction enzyme mapping, PCR amplification, or sequence analysis of isolated assembled polynucleotides or chromosomal integration sites.
  • the present invention provides rapid, robust, and high- throughput methods for the ordered assembly of multiple component polynucleotides into a plurality of assembled polynucleotides.
  • the methods rely on the use of an assembly composition comprising assembly vectors that each comprise a DNA segment D, flanked by an annealable linker sequence LA or LB, a pair of annealable linker sequences LA and LB, or by an annealable linker sequence and a primer binding segment, i.e., LA and PB or LB and PA, flanked by a pair of restriction sites RA and RB (FIG. IB).
  • the assembly composition comprises at least two assembly vectors that have the same annealable linker sequence LA or LB or the same primer binding segment PA or PB, but differ with respect to the DNA segment.
  • the assembly composition comprises at least two assembly vectors that have the same pair of annealable linker sequences LA and LB, or the same annealable linker sequence and primer binding segment pair, i.e., LA and PB or LB and PA but differ with respect to the DNA segment.
  • FIG. 10 presents an exemplary method of generating a plurality of assembled polynucleotides from seven (7) component polynucleotides in the same reaction.
  • Assembly vectors comprising DNA segments to be assembled are pooled in a single tube and digested with Sapl to release component polynucleotide fragments from the assembly vector backbones.
  • the component polynucleotides are subjected to denaturing conditions, followed by annealing conditions sufficient for hybridization of the complementary annealable linker pairs.
  • primers complementary to primer binding segments PA and PB are added to PCR amplify eight (8) different full-length assembled polynucleotides that comprise DNA segments Do 1/02, D1/2, D 3 , and D 41 ⁇ 2 assembled in various possible combinations.
  • Individual assembled polynucleotides can be isolated from the composition of mixed assembled polynucleotides, e.g., by another round of PCR amplification using primers complementary to regions of DNA segments D 01 , D 02 , D 41 , and D42.
  • a set of assembled polynucleotides can be isolated by first and last assembly vectors comprising one of a group of primer binding segments PA and/or PB and using primers for PCR amplification that hybridize to only a select subgroup of primer binding segments PA and PB.
  • the isolated assembled polynucleotides can be used, e.g., to transform host cells to generate a plurality of host cells comprising assembled polynucleotides.
  • host cells can be directly transformed with the composition of mixed assembled polynucleotides and host cell transformants comprising each assembled polynucleotide can be isolated, e.g., by molecular analysis of individual host cell colonies, or by selecting host cell transformants comprising selectable markers or exhibiting other traits encoded by individual DNA segments or by combinations of DNA segments.
  • a plurality of host cells comprising a plurality of polynucleotides assembled by combinatorial methods are generated by transforming host cells with a composition comprising multiple assembled polynucleotides of which at least two assembled polynucleotides comprise non-functional segments of a selectable marker that upon homologous recombination generate a functional selectable marker, and by selecting host cells comprising a combined polynucleotide.
  • FIG. 11 illustrates a combinatorial approach to generating a plurality of host cells comprising combined polynucleotides.
  • assembled polynucleotides Al and A2 each comprising the same upstream chromosomal targeting sequence and the same first portion of a selectable marker
  • assembled polynucleotides Bl and B2 each comprising the same downstream chromosomal targeting sequence and the same second portion of a selectable marker
  • a plurality of host cells comprising a plurality of polynucleotides assembled and combined by combinatorial methods are generated by transforming host cells with a component composition comprising multiple component polynucleotides of which at least two component polynucleotides comprise non-functional segments of a selectable marker that upon host cell mediated homologous recombination generate a functional selectable marker, and by selecting host cells comprising an assembled or combined polynucleotide.
  • an entry vector that can be used to prepare an assembly vector.
  • an entry vector is a circular polynucleotide that comprises a selectable marker, an origin of replication, and a DNA segment immediately flanked by two restriction sites that facilitate the subcloning of different DNA segments to be assembled in the assembly methods provided herein.
  • the entry vector further comprises one or two annealable linker sequences, or an annealable linker sequence and a primer binding segment, flanking the restriction sites.
  • the entry vector further comprises an additional pair of restriction sites positioned at the outer flanks of the DNA segment, e.g., that flank the one or two annealable linker sequences, or the annealable linker sequence and primer binding segment.
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, and a restriction site RB.
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB.
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA or an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB.
  • the sequence of the DNA segment D of the entry vector is the lac Z reporter gene.
  • the lac Z reporter gene is useful for facilitating blue/white selection of colonies transformed with vectors comprising DNA segments other than lac Z, e.g., during the preparation of an assembly vector described herein.
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, and a restriction site RB (i.e., 5'- RA-LA-RY-D-RZ-RB-3').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-RY-D-RZ-LB-RB-S').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5 ' -RA-L A-RY-D- RZ-LB-RB-3').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a restriction site RY, a DNA segment D, a restriction site RZ, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-PA-RY-D-RZ-LB-RB-S ').
  • the entry vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, a primer binding segment PB, and a restriction site RB (i.e., 5'-RA- LA-RY-D-RZ-PB-RB-3').
  • An exemplary entry vector is provided in FIG. IA.
  • the primer binding segment can be any nucleotide sequence that is not complementary with any of the annealable linker sequences that are used to make an assembled polynucleotide.
  • the two primer binding segment includes a restriction endonuclease recognition and cleavage site.
  • the primer binding segment is simply one of the available linker sequences that are not being used in a particular assembly reaction.
  • the nucleic acid sequence of primer binding segment PA is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • the nucleic acid sequence of primer binding segment PB is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • the nucleic acid sequences of primer binding segment PA and primer binding segment PB are selected from the group consisting of SEQ ID NOS: 24 and 25.
  • PA and PB are not identical in sequence.
  • the nucleic acid sequence of annealable linker sequence LA or LB is at least 24 nucleotides and has a T m of at least 60 0 C.
  • the nucleic acid sequence of annealable linker sequence LA is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the nucleic sequence of annealable linker sequence LB is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the nucleic sequences of annealable linker sequence LA and annealable linker sequence LB are selected from the group consisting of SEQ ID NOS: 1 to 23.
  • restriction sites RY and RZ can be utilized as cloning sites to introduce various DNA segments for the generation of an assembly vector.
  • RY and RZ are not identical in sequence.
  • RY and RZ are cleavable by the same restriction endonuclease.
  • RY and RZ are identical in sequence.
  • restriction sites RY and RZ are cleavable by a restriction endonuclease that generates staggered ends, i.e. termini having a 5' or 3' overhang.
  • restriction sites RY and RZ are cleavable by a restriction endonuclease that generates blunt ends.
  • restriction sites RY and RZ can be any restriction site known in the art
  • restriction sites recognized by the Type IIS restriction endonucleases are particularly useful.
  • Type IIS restriction endonucleases have DNA binding domains that are distinct from their cleavage domains. Therefore, they recognize a specific sequence but cleave at a defined distance away.
  • the Type IIS restriction endonuclease Schl (which is also known as MIyI) binds to a recognition site containing the sequence GAGTC and cleaves four (4) base pairs away from the recognition site, creating a blunt ended DNA molecule.
  • Type IIS restriction sites are particularly useful for the preparation of an assembly vector from an entry vector.
  • restriction sites RY and RZ are restriction sites recognizable and cleavable by any Type IIS restriction endonuclease known in the art.
  • Suitable Type IIS restriction endonucleases include but are not limited to the following endonucleases and their isoschizomers, which are indicated in parentheses: Alw26I (BsmAI), AIwI (AcIWI, Binl), AsuHPI (Hphl), Bbvl (Bst71I), Bcefl, BstF5I (BseGI, Fokl), Faul, Hgal, Sapl (Lgul), MboII, PIeI, Sapl, Schl (MIyI), SfaNI, and TspRI, Acelll, Bbsl (BbvII, Bpil, BpuAI), Bce83I, BciVI, Bfil (Bmrl), Bpml (Gsul), Bsal (Eco31I), BseRI, Bsgl, BsmBI (Esp3I), BsmFI, BspMI, BsrDI (Bse3DI), Bsu
  • restriction sites RY and RZ are recognizable and cleavable by the Schl restriction endonuclease.
  • RA and RB are not identical in sequence.
  • RA and RB are cleavable by the same restriction endonuclease.
  • RA and RB are identical in sequence.
  • restriction sites RA and RB are cleavable by a restriction endonuclease that generates staggered ends, i.e. termini having a 5' or 3' overhang.
  • restriction sites RA and RB are cleavable by a restriction endonuclease that generates blunt ends.
  • restriction sites RA and RB can be any restriction sites known in the art, restriction sites that are relatively infrequent in DNA (e.g., cDNA) of one or more organisms (i.e., an infrequent cutter) are particularly useful.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in human DNA.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in mouse DNA.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in yeast DNA, for example, in the DNA of Saccharomyces cerevisiae, Pichia pastoris, Kluyveromyces lactis, Arxula adeninivorans, or Hansenula polymorpha.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively few restriction sites in the DNA of bacteria, for example, in the DNA of Escherichia coli or Bacillus subtilis.
  • restriction sites RA and RB are recognizable and cleavable by a Type IIS restriction endonuclease wherein the recognition site is distal to the polynucleotide sequence comprising, e.g., PA/LA-D-PB/LB.
  • each restriction site RA and RB is independently recognizable and cleavable by a restriction endonuclease selected from the group consisting of Mssl, Nrul (Bsp68I, MluB2I, Sbol3I, Spol), SnaBI (BstSNI, Ecol05I), Srfl, and Swal (BstRZ246I, BstSWI, MspSWI, Smil), Hpal, Hindi, PshAI, OHI, AIuI, Alw26I, Ball, Dral, Dpnl, EcoR47III, EcoRCRI, EcoRV, Fokl, Haelll, Hindi, Mbol, MspAlI, Nad, Rsal, PvuII, Seal, Smal, Sspl, Stul, Xmnl, EcaBC3I, Scil, Hindi, Dral, BsaBI, Cac8I, Hpy8I, MIyI, PshAI,
  • restriction sites RA and RB are recognizable and cleavable by the Sapl or Lgul restriction endonuclease.
  • Lgul is an isoschizomer of Sapl having the same recognition and cleavage specificity.
  • the entry vector provided herein also comprises one or more nucleic acid sequences that generally have some function in the replication, maintenance, or integrity of the vector (e.g., origins of replication) as well as one or more selectable markers.
  • Replication origins are unique polynucleotides that comprise multiple short repeated sequences that are recognized by multimeric origin-binding proteins and that play a key role in assembling DNA replication enzymes at the origin site.
  • Suitable origins of replication for use in the entry and assembly vectors provided herein include but are not limited to E. coli oriC, colEl plasmid origin, 2 ⁇ and ARS (both useful in yeast systems), sfl, SV40 EBV oriP (useful in mammalian systems), or those found in pSClOl.
  • Selectable markers can be useful elements in vectors as they provide a means to select for or against growth of cells that have been successfully transformed with a vector containing the selectable marker and express the marker.
  • any vector may be used to construct the entry vector as provided herein.
  • vectors known in the art and those commercially available (and variants or derivatives thereof) may be engineered to include a restriction site RA, optionally a primer binding segment PA or an annealable linker sequence LA, a restriction site RY, a DNA segment D, a restriction site RZ, optionally a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB, for use in the methods provided herein.
  • vectors may be obtained from, for example, Vector Laboratories Inc., InVitrogen, Promega, Novagen, NEB, Clontech, Boehringer Mannheim, Pharmacia, EpiCenter, OriGenes Technologies Inc., Stratagene, Perkin Elmer, Pharmingen, Life Technologies, Inc., and Research Genetics.
  • General classes of vectors of particular interest include prokaryotic and/or eukaryotic cloning vectors, expression vectors, fusion vectors, two-hybrid or reverse two-hybrid vectors, shuttle vectors for use in different hosts, mutagenesis vectors, transcription vectors, vectors for receiving large inserts, and the like.
  • vectors of interest include viral origin vectors (M 13 vectors, bacterial phage ⁇ vectors, adenovirus vectors, and retrovirus vectors), high, low and adjustable copy number vectors, vectors that have compatible replicons for use in combination in a single host (PACYC 184 and pBR322) and eukaryotic episomal replication vectors (pCDM8).
  • entry vectors for use in accordance with the methods provided herein are the pRYSE vectors, having the nucleotide sequences of SEQ ID NO: 207 through 221.
  • a schematic of the pRYSE vectors is provided in FIG. 4, and the preparation of the pRYSE vectors is described in Example 1 below.
  • an assembly vector that can be used in the assembly of a plurality of component polynucleotides into one or more assembled polynucleotides.
  • an assembly vector is a circular polynucleotide that comprises a selectable marker, an origin of replication, and a DNA segment flanked by an annealable linker sequence, an annealable linker sequence pair, or by an annealable linker sequence / primer binding segment pair, flanked by a pair of restriction sites.
  • the restriction sites can serve to facilitate excision of the component polynucleotide from the assembly vector backbone during the assembly reaction.
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA or an annealable linker sequence LA, a DNA segment D, and a restriction site RB.
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a DNA segment D, a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB.
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA or an annealable linker sequence LA, a DNA segment D, a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB.
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, and a restriction site RB (i.e., 5'-RA-LA-D-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-D-LB-RB-3').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-LA-D-LB-RB-S').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB (i.e., 5'-RA-PA-D-LB-RB-S').
  • the assembly vector is a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, a primer binding segment PB, and a restriction site RB (i.e., 5'-RA-LA-D-PB-RB-S'). Exemplary assembly vectors are provided in FIG. IB and FIG. 2.
  • nucleic acid sequence of primer binding segment [00128] In some embodiments, the nucleic acid sequence of primer binding segment
  • nucleic acid sequence of primer binding segment PB is selected from the group consisting of SEQ ID NOS: 24 and 25. In some embodiments, the nucleic acid sequences of primer binding segment PA and primer binding segment PB are selected from the group consisting of SEQ ID NOS: 24 and 25. In preferable embodiments, the nucleic acid sequences of primer binding segment PA and primer binding segment PB are not identical. [00129] In some embodiments, the nucleic acid sequence of annealable linker sequence LA or LB is at least 24 nucleotides and has a T m of at least 60 0 C.
  • the nucleic acid sequence of annealable linker sequence LA is selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequence of annealable linker sequence LB is selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequences of annealable linker sequence LA and annealable linker sequence LB are selected from the group consisting of SEQ ID NOS: 1 to 23.
  • RA and RB are not identical in sequence. In some embodiments, RA and RB are cleavable by the same restriction endonuclease. In some embodiments, RA and RB are identical in sequence. In some embodiments, restriction sites RA and RB are cleavable by a restriction endonuclease that generates staggered ends, i.e. termini having a 5' or 3' overhang. In other embodiments, restriction sites RA and RB are cleavable by a restriction endonuclease that generates blunt ends.
  • restriction sites RA and RB can be any restriction sites known in the art, restriction sites that are relatively infrequent in DNA (e.g., cDNA) of one or more organisms (i.e., an infrequent cutter) are particularly useful.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in human DNA.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in mouse DNA.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively infrequent restriction sites in yeast DNA, for example, in the DNA of Saccharomyces cerevisiae, Pichia pastoris, Khiyveromyces lactis, Arxula adeninivorans, or Hansenula polymorpha.
  • restriction sites RA and RB are recognizable and cleavable by a restriction endonuclease that has relatively few restriction sites in the DNA of bacteria, for example, in the DNA of Escherichia coli or Bacillus subtilis.
  • restriction sites RA and RB are recognizable and cleavable by a Type IIS restriction endonuclease.
  • suitable Type IIS restriction endonucleases include but are not limited to: Mssl, Nrul (Bsp68I, MluB2I, Sbo 131, Spol), SnaBI (BstSNI, Ecol05I), Srfl, and Swal (BstRZ246I, BstSWI, MspSWI, Smil), Hpal, Hindi, PshAI, Olil, AIuI, Alw26I, Ball, Dral, Dpnl, EcoR47III, EcoRCRI, EcoRV, Fokl, Haelll, Hindi, Mbol, MspAlI, Nad, Rsal, PvuII, Seal, Smal, Sspl, Stul, Xmnl, EcaBC3I, Scil, Hindi, Dral,
  • restriction sites RA and RB are recognizable and cleavable by the Sapl or Lgul restriction endonuclease.
  • the DNA segment of an assembly vector does not comprise a nucleic acid sequence that can be recognized and cleaved by a restriction endonuclease that can cleave any of restriction sites RA and RB within the assembly vector. This ensures that the DNA segment remains intact during the first stage of the assembly reaction, during which the component polynucleotide is excised from the assembly vector backbone.
  • the DNA segment does not comprise a Sapl/Lgul site and RA and RB are cleavable by Sapl or Lgul.
  • Site-directed mutagenesis see Carter, BfChem. J. 237:1-7 (1986); Zoller and Smith, Methods Enzymol. 154:329-50 (1987)
  • cassette mutagenesis restriction selection mutagenesis (Wells et ai, Gene 34:315-323 (1985))
  • oligonucleotide- mediated (site-directed) mutagenesis PCR mutagenesis, or other known techniques can be performed to modify any such sequence within the DNA segment either before or after ligation of the DNA segment to the entry vector.
  • the assembly vector provided herein also comprises one or more nucleic acid sequences that generally have some function in the replication, maintenance, or integrity of the vector ⁇ e.g., origins of replication) as well as one or more selectable markers.
  • Replication origins are unique polynucleotides that comprise multiple short repeated sequences that are recognized by multimeric origin-binding proteins and that play a key role in assembling DNA replication enzymes at the origin site.
  • Suitable origins of replication for use in the entry and assembly vectors provided herein include but are not limited to E.
  • coli oriC coli oriC, colEl plasmid origin, 2 ⁇ and ARS (both useful in yeast systems), sfl, SV40 EBV oriP (useful in mammalian systems), or those found in pSClOl.
  • Selectable markers can be useful elements in vectors as they provide a means to select for or against growth of cells that have been successfully transformed with a vector containing the selectable marker and express the marker.
  • any vector may be used to construct the assembly vector as provided herein.
  • vectors known in the art and those commercially available (and variants or derivatives thereof) may be engineered to include a restriction site RA, a primer binding segment PA or an annealable linker sequence LA, a DNA segment D, a primer binding segment PB or an annealable linker sequence LB, and a restriction site RB, for use in the methods provided herein.
  • vectors may be obtained from, for example, Vector Laboratories Inc., InVitrogen, Promega, Novagen, NEB, Clontech, Boehringer Mannheim, Pharmacia, EpiCenter, OriGenes Technologies Inc., Stratagene, Perkin Elmer, Pharmingen, Life Technologies, Inc., and Research Genetics.
  • General classes of vectors of particular interest include prokaryotic and/or eukaryotic cloning vectors, expression vectors, fusion vectors, two-hybrid or reverse two-hybrid vectors, shuttle vectors for use in different hosts, mutagenesis vectors, transcription vectors, vectors for receiving large inserts, and the like.
  • An assembly vector can be prepared from an entry vector.
  • the entry vector can be digested with one or more restriction endonucleases capable of cleaving RY and RZ thereby linearizing the vector such that it can accept a DNA segment.
  • the DNA segment can be ligated into RY and RZ sites using standard cloning techniques to generate an assembly vector of the invention.
  • the DNA segment may be obtained by standard procedures known in the art from cloned DNA (e.g., a DNA "library"), by chemical synthesis, by cDNA cloning, or by the cloning of genomic DNA, or fragments thereof, purified from the desired cell, or by PCR amplification and cloning. See, for example, Sambrook et ah, Molecular Cloning, A Laboratory Manual, 3d. ed., Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York (2001); Glover, D.M. (ed.), DNA Cloning: A Practical Approach, 2d. ed., MRL Press, Ltd., Oxford, U.K. (1995).
  • An assembly vector can also be prepared from another vector that does not comprise an annealable linker sequence, an annealable linker sequence pair, or an annealable linker sequence / primer binding segment pair flanking the site of insertion of the DNA segment.
  • the vector can be digested with one or more restriction endonucleases capable of cleaving the vector at a site suitable for insertion of a DNA fragment, e.g., at a multiple cloning site, thereby linearizing the vector such that it can accept a DNA fragment.
  • the DNA fragment to be inserted can be obtained by standard procedures known in the art such as, for example, cloning, chemical synthesis, or PCR amplification.
  • the DNA fragment comprises a DNA segment flanked by an annealable linker sequence, an annealable linker sequence pair or an annealable linker sequence / primer binding segment pair.
  • the DNA fragment comprises, in a 5' to 3 ' orientation, an annealable linker sequence LA or a primer binding segment PA, a DNA segment D, and an annealable linker sequence LB or a primer binding segment PB (i.e., 5'- LA-D-LB-3' or 5'-PA-D-LB-3' or 5'-LA-D-PB-3').
  • the DNA fragment comprises, in a 5' to 3' orientation, a DNA segment D, and an annealable linker sequence LB or a primer binding segment PB (i.e., 5'-D-LB-3' or 5'-D-PB-3').
  • the DNA fragment comprises, in a 5' to 3' orientation, an annealable linker sequence LA or a primer binding segment PA, and a DNA segment D, (i.e., 5'-LA-D-3' or 5'-PA-D-3').
  • the DNA fragment can further comprise a pair of restriction sites that flank the annealable linker sequence, the annealable linker sequence pair or the annealable linker sequence / primer binding segment pair and that upon cleavage by a restriction endonuclease produce termini that are compatible with termini produced by linearising the vector into which the DNA fragment is to be inserted.
  • the DNA fragment can generated such that it contains such compatible termini and does not require additional digestion with a restriction endonuclease to produce the compatible termini.
  • the restriction sites used to generate the compatible termini may be preserved to serve as restriction sites RA and RB of the assembly vector.
  • the ligation may remove the original restriction sites but additional restriction sites may be present in the linearised vector that can serve as restriction sites RA and RB of the assembly vector.
  • Example 6 a pRYSE vector or from another vector (i.e., a pMULE vector) are provided in Example 6 below.
  • annealable linker sequences that flank the DNA segment located within entry vectors and assembly vectors.
  • Annealable linker sequences provide sequence overlap between adjacent component polynucleotides in an assembly reaction, and thus serve to prime a component polynucleotide for assembly into an assembled polynucleotide.
  • the annealable linker sequences LA and LB of the entry and assembly vectors are optimized to provide efficient and accurate priming to complementary annealable linker sequences during an assembly reaction.
  • the length of an annealable linker sequence is long enough to provide adequate specificity with its complement annealable linker sequence, yet short enough to readily anneal to its complement annealable linker sequence at the annealing temperature of the assembly reaction. In some embodiments the length of an annealable linker sequence is long enough to allow for host cell mediated homologous recombination with its complement annealable linker sequence.
  • the annealable linker sequence is about 5, 10, 15, 20,
  • the annealable linker sequence is at least 10, 12, 14, 16, 18, 20, 22, 24, 26, 28, or 30 nucleotides in length. In some embodiments, the anealable linker sequence is greater than 30, 40, 50, 60, 70, 80, 90, 100, 500, 1000, 5000, or 10,000 nucleotides in length. In some embodiments, the annealable linker is at least 18 nucleotides in length and is a number divisible by three, so as to facilitate read-through transcription of the linker when ligated to an encoding DNA segment.
  • the annealable linker is 18, 21, 24, 27, 30, 33, 36, 39, 42, 45, 48, 51, 54, 57, or 60 nucleotides in length.
  • an annealable linker sequence has a relatively high melting temperature (T 111 ), i.e., the temperature at which one half of an annealed annealable linker sequence duplex will dissociate to become single stranded.
  • T 111 melting temperature
  • the T m of an annealable linker can be calculated according to SantaLucia, PNAS, 95:- 1460- 1465 (1998) using a nearest neighbor algorithm.
  • a relatively high T m may provide for more specific priming during an assembly reaction.
  • an annealable linker sequence duplex has a T m of about 60 0 C - 80 0 C. In some embodiments, an annealable linker sequence duplex has a T m of about 65 0 C - 75 0 C.
  • an annealable linker sequence duplex has a T m of greater than 50 0 C, 55 0 C, 60 0 C, 65 0 C, 70 0 C, 75 0 C, 80 0 C, 85 0 C, or 90 0 C.
  • annealable linker sequences do not form appreciable secondary structures (e.g., hairpins, self-dimers) produced via intramolecular (i.e., within the same molecule) interactions under the conditions of the methods described herein, either at the DNA level or at the RNA level or at both the DNA and the RNA level. The presence of secondary structures in DNA can lead to poor or no assembled polynucleotide yield of the assembly reaction.
  • RNA can lead to decreased translation efficiencies, which are of particular concern when the annealable linker sequence is used to assemble component polynucleotides comprising a promoter and a protein coding sequence inco a assembled polynucleotide in which the annealable linker sequence is positioned between the promoter and the protein coding sequence.
  • annealable linker sequences useful in the assembly methods of the invention are designed to not form secondary RNA and/or DNA structures.
  • the ability of an annealable linker sequence to form secondary RNA or DNA structures can be determined using software tools such as, for example, IDT Oligo Analyzer (Integrated DNA Technologies, Coralville, IA), mFold (Zuker 2003 Nucleic Acids Res.
  • RNAfold (Hofacker & Stadler (2006) Bioinformatics 22 (10): 1 172-6).
  • these tools calculate the Gibbs free energy ( ⁇ G) for transition of a sequence from the linear to the folded state.
  • ⁇ G Gibbs free energy
  • annealable linker sequences are designed to have large ⁇ G values for the transition from linear to folded states.
  • annealable linker sequences are designed to have ⁇ G values for the transition from linear to folded states that are equal to or greater than the ⁇ G values for the transition from linear to folded states of the n-bases that lie immediately upstream of the coding sequences of highly expressed genes in the Saccharomyces cerevisiae genome, wherein n represents an integer that corresponds to the number of bases in the annealable linker sequence.
  • annealable linker sequences are 36 bases long and have a ⁇ G value for the transition from linear to folded states of -1 or greater.
  • annealable linker sequences are also designed to avoid unintended intermolecular interactions (i.e., between different molecules).
  • an annealable linker sequence does not anneal substantially with any other sequences within the assembly vector that contains the annealable linker sequence (e.g., vector backbone sequences) and/or with any other sequences within other assembly vectors of the assembly compositions aside from the complementary annealable linker sequences required for polynucleotide assembly by the methods provided herein.
  • an annealable linker sequence does not anneal substantially with other annealable linker sequences within assembly vectors of the assembly compositions provided herein.
  • an annealable linker sequence has a high G-C content, i.e., the number of guanine and cytosine nucleotides in the annealable linker sequence as a percentage of the total number of bases in the annealable linker sequence.
  • Annealable linker sequences that have a high G-C content are generally useful in the methods of the invention because a high G-C content generally provides for a high T m , which in turn may provide for more specific priming during an assembly reaction and for time and process savings by allowing combination of the annealing and extension steps of SOE/PCR.
  • the G-C content of the annealable linker sequence is between about 20-80%.
  • the G-C content of the annenalable linker sequence is between about 40-60%. In some embodiments, the G-C content of the annealable linker sequence is about 40, 45, 50, 55, 60, or 70%. In particular embodiments, an annealable linker sequence has a G-C content of greater than 70%.
  • Illustrative examples of annealable linker sequences that have a high G-C content, do not form appreciable secondary DNA structures, and have a T m of 70 0 C or greater are SEQ ID NOS: 1 to 8.
  • an annealable linker sequence has a high A-T content, i.e., the number of adenine and thymine nucleotides in the annealable linker sequence as a percentage of the total number of bases in the annealable linker sequence.
  • a high A-T content may provide for reduced propensity of the annealable linker sequence to form substantial secondary structures, which may be of particular concern when the annealable linker sequence is used to assemble component polynucleotides comprising a promoter and a protein coding sequence into a assembled polynucleotide in which the annealable linker sequence is positioned between the promoter and the protein coding sequence.
  • the A-T content of the annealable linker sequence is between about 20-80%. In some embodiments, the A-T content of the annealable linker sequence is between about 40-60%. In some embodiments, the A-T content of the annealable linker sequence is about 30, 35, 40, 45, 50, 55, or 60%. In some embodiments, the annealable linker sequence has an A-T content of greater than 30%. In some embodiments, the sequence of the 3 '-most 26 bases of an annealable linker sequence fulfills the following consensus motif: 5'- ANNNNNNNNANNNAANTANNTTNANA-3', wherein A stands for adenine, N for any nucleotide, and T for thymine.
  • an annealable linker sequence comprises one or more restriction sites. Incorporation of restriction sites into an annealable linker sequence allows for the excision of a DNA segment from an entry or assembly vector while maintaining the restriction sites RA and RB within the entry vector or assembly vector.
  • Restriction sites within the annealable linker sequence also facilitate directional subcloning of DNA segments into other entry or assembly vectors.
  • This feature facilitates the efficient construction of assembly vectors comprising the same DNA segment but having different annealable linker sequence pairs or primer binding segment / annealable linker sequence pairs, for instance, to generate a library of assembly vectors comprising different annealable linker sequence pairs as described below.
  • This feature can also obviate the need to re-amplify and sequence a DNA segment to create additional assembly vectors comprising the DNA segment.
  • the annealable linker sequence comprises a unique restriction site.
  • the restriction site is a 7-base pair restriction site, i.e., is cleavable by a restriction endonuclease that recognizes a 7-base pair nucleotide sequence.
  • the restriction site is a 8-base pair restriction site.
  • the restriction site within the annealable linker sequence is recognized and cleavable by Mrel, Fsel, Sbfl, AsiSI, Notl, Ascl, or BbvCI.
  • the annealable linker sequence comprises a sequence that allows for read-through transcription once the linker is ligated to an encoding DNA segment.
  • an annealable linker sequence allows for read-through transcription in both the 5' to 3' and 3' to 5' orientation.
  • the length of the annealable linker sequence preferably, is a number of nucleotides divisible by three (3).
  • an annealable linker sequence does not comprise codons that are rarely used in Escherichia coli (E. coli) or Saccharomyces cerevisiae (S. cerevisiae). Efficient expression of heterologous genes in E.
  • an annealable linker sequence that comprises a read-through sequence preferably does not comprise rare codons used in E. coli or S. cerevisiae, so as to enable efficient expression of proteins encoded by a assembled polynucleotide comprising the annealable linker sequence.
  • the set of annealable linker sequences are unique sequences that are not found in an intended host organism. In some embodiments, the set of annealable linker sequences are unique sequences that are not found in E. coli. In other embodiments, the set of annealable linker sequences are unique sequences that are not found in S. cerevisiase.
  • suitable annealable linker sequences are identified in a test assembled polynucleotide.
  • a test assembled polynucleotide comprises the annealable linker sequence to be tested and additional elements that permit testing of the annealable linker sequence.
  • a test assembled polynucleotide can be assembled from the first component polynucleotide comprising, in a 5' to 3' orientation, a primer binding segment or an annealable linker sequence, a DNA segment comprising the promoter, and the annealable linker sequence to be tested, and the second component polynucleotide comprising, in a 5' to 3' orientation, the annealable linker sequence to be tested, a DNA segment encoding a reporter gene (e.g., green fluourescent protein (GFP)), and a primer binding segment or annealable linker sequence.
  • a reporter gene e.g., green fluourescent protein (GFP)
  • test assembled polynucleotide can be tested in vivo or in vitro for the efficiency of expression of the reporter gene. Similar test assembled polynucleotides can be assembled to test the suitability of annealable linker sequences for assembling component polynucleotides comprising DNA segments comprising other elements, such as an enhancer, terminator, poly-A tail, nuclear localization signal, mRNA stabilization signal, selectable marker, epitope tag coding sequence, degradation signal, and the like.
  • the test assembled polynucleotide may comprise additional component polynucleotides that enable testing, such as for example, genomic targeting sequences and selectable markers that enable introduction of the test assembled polynucleotide into host cells and selection of positive transformants for in vivo testing.
  • Table 1 presents the T 111 , restriction sites, and read-through amino acids of exemplary annealable linker sequences corresponding to SEQ ID NOS: 1-23.
  • a library comprising a plurality of assembly vectors.
  • the library can serve to facilitate the efficient assembly of a plurality of component polynucleotides into one or more assembled polynucleotides that are functional in prokaryotes or eukaryotes, and thus facilitate the generation of unique organisms, e,g,, recombinant strains of bacteria or yeast, without the need for time-consuming restriction endonuclease and ligase enzyme based cloning techniques.
  • the assembly methods and compositions provided herein can facilitate the efficient replacement or introduction of functional DNA units, e.g., promoters, enhancers, origins of replication, etc., within an expression construct, and thus can provide for efficient optimization of the replication of, and/or expression from, the expression construct within a host organism.
  • the library may comprise a plurality of assembly vectors assembled within a single composition or container, e.g., a composition or container suitable for performing the assembly methods provided herein.
  • the library may comprise a plurality of assembly vectors that are not assembled within the same composition or container.
  • the library comprises at least 3, at least 6, at least 10, at least 20, at least 50, or more than 50 assembly vectors, each comprising a DNA segment.
  • the library comprises a plurality of assembly vectors wherein each of the assembly vectors comprises, in a 5' to 3' orientation, a first restriction site RA, a DNA segment D, an annealable linker sequence LB, and a second restriction site RB.
  • the library comprises a plurality of assembly vectors wherein each of the assembly vectors comprises, in a 5' to 3' orientation, a first restriction site RA, a primer binding segment PA or a first annealable linker sequence LA, a DNA segment D, and a second restriction site RB.
  • the library comprises a plurality of assembly vectors wherein each of the assembly vectors comprises, in a 5' to 3' orientation, a first restriction site RA, a first annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB or a primer binding segment PB, and a second restriction site RB.
  • the annealable linker sequence pair or annealable linker sequence / primary binding segment pair within each assembly vector of the library does not comprise the same sequence.
  • the nucleic acid sequence of the annealable linker sequence LA and/or LB within each assembly vector is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the nucleic acid sequence of the primer binding segment PA or PB within each assembly vector is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • the library comprises at least one of each of the following vectors:
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3 ' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, and a restriction site RB 0 .
  • the library comprises at least one of each of the following vectors:
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, a primer binding segment PA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, an annealable linker sequence LB, and a restriction site RB;
  • a vector that consists of a circular polynucleotide that comprises, in a 5' to 3 ' orientation, a restriction site RA, an annealable linker sequence LA, a DNA segment D, a primer binding segment PB, and a restriction site RB 0 .
  • nucleic acid sequence of primer binding segment is the nucleic acid sequence of primer binding segment
  • PA is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequence of primer binding segment PB is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequences of primer binding segment PA and primer binding segment PB are selected from the group consisting of SEQ ID NOS: 24 and 25.
  • the nucleic acid sequence of any of the annealable linker sequences LA and annealable linker sequneces LB in the library are selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequences of at least one of the annealable linker sequences LA and at least one of the annealable linker sequences LB in the library are selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequence of each of the annealable linker sequences LA and annealable linker sequences LB in the library is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the DNA segment D comprises a nucleic sequence selected from the group consisting of a selectable marker, a promoter, a genomic targeting sequence, a nucleic acid sequence encoding an epitope tag, a nucleic acid sequence encoding a gene of interest, a nucleic acid sequence encoding a termination codon, and lacZ.
  • the library comprises at least one of each of the following nucleic acid molecules:
  • a first nucleic acid molecule wherein the first nucleic acid molecule is circular and comprises, in a 5' to 3' orientation, a first restriction site RAo, any DNA segment selected from the group D 0 , an annealable linker sequence LB 0 , and a second restriction site RBo;
  • intermediate nucleic acid molecule wherein the intermediate nucleic acid molecule n is circular and comprises, in a 5' to 3' orientation, a first restriction site RA n , a first annealable linker sequence LA n , any DNA segment selected from the group D n , a second annealable linker sequence LB n , and a second restriction site RB n , and wherein n represents an integer from one to the number of intermediate nucleic acid molecules; and
  • each annealable linker sequence LB( P-1) is capable of hybridizing to the complement of annealable linker sequence LA P wherein p represents the integers from 1 to m, and wherein each group Do,...
  • D n consists of one or more DNA segments.
  • a first nucleic acid molecule further comprises a primer binding segment PA positioned 5' to the DNA segment selected from the group D 0 .
  • a last nucleic acid molecules further comprises a primer binding segment PB positioned 3' to the DNA segment selected from the group D m .
  • each annealable linker sequence LB( P- i) upon cleavage of restriction sites RAo through RB m and denaturation of the resulting linear nucleic acid molecules, each annealable linker sequence LB( P- i) is capable of selectively hybridizing to the complement of annealable linker sequence LA P compared to the other annealable linker seuences, or their complements, in the components composition. In some embodiments, each annealable linker sequence LB( P- i) is identical in sequence to annealable linker sequence LA P .
  • the restriction sites RAo through RB m are cleavable by the same restriction endonuclease so as to facilitate excision of the component polynucleotides from the assembly vectors.
  • the restrictions sites RAo through RB m are cleavable by Sapl and Lgul restriction endonucleases.
  • the nucleic acid sequence of primer binding segment is cleavable by the same restriction endonuclease so as to facilitate excision of the component polynucleotides from the assembly vectors.
  • the restrictions sites RAo through RB m are cleavable by Sapl and Lgul restriction endonucleases.
  • nucleic acid sequence of primer binding segment PB is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequences of primer binding segment PA and primer binding segment PB are selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequences of primer binding segment PA and primer binding segment PB are not identical.
  • nucleic acid sequence of any of the annealable linker sequences LA and annealable linker sequences LB in the library is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the nucleic acid sequences of at least one of the annealable linker sequences LA and at least one of the annealable linker sequences LB in the library are selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequence of each of the annealable linker sequences LA and annealable linker sequences LB in the library is selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic acid sequence of each of the annealable linker sequences LA in the composition are not identical to one another. In some embodiments, the nucleic acid sequence of each of the annealable linker sequences LB in the composition are not identical to one another.
  • the library comprises the following nucleic acid molecules:
  • LA p wherein p represents the integers from 1 to m.
  • the library comprises a plurality of assembly vectors wherein each assembly vector comprises the same annealable linker sequence, annealable linker sequence pair or annealable linker sequence / primary binding segment pair but differs in the sequence of their respective DNA fragment D.
  • the library comprises a plurality of assembly vectors wherein each assembly vector comprises the same DNA segment D flanked by a unique annealable linker sequence, annealable linker sequence pair or annealable linker sequence / primer binding segment pair.
  • each assembly vector comprises the same DNA segment D flanked by a unique annealable linker sequence, annealable linker sequence pair or annealable linker sequence / primer binding segment pair.
  • Such a library may serve to facilitate the rapid assembly of DNA segment D into a particular position or orientation relative to the other DNA segments being assembled into the assembled polynucleotide.
  • the members of the library comprise DNA segments that have shared structural or functional characteristics.
  • a library can comprise a plurality of assembly vectors comprising the same functional DNA unit.
  • Exemplary functional DNA units include but are not limited to protein-coding sequences, reporter genes, fluorescent markers, promoters, enhancers, terminators, introns, exons, poly-A tails, multiple cloning sites, nuclear localization signals, nuclear export signals, mRNA stabilization signals, selectable markers, integration loci, epitope tags, and degradation signals.
  • the library comprises a plurality of assembly vectors wherein each assembly vector comprises the same promoter.
  • the assembly vectors can comprise any prokaryotic or eukaryotic promoter sequence known in the art.
  • Exemplary eukaryotic promoters include but are not limited to a metallothionein promoter, a constitutive adenovirus major late promoter, a dexamethasone-inducible MMTV promoter, a S V40 promoter, a MRP po/ /// promoter, a constitutive MPSV promoter, an RSV promoter, a tetracycline-inducible CMV promoter (such as the human immediate-early CMV promoter), and a constitutive CMV promoter.
  • the assembly vectors comprise a yeast promoter sequence.
  • Exemplary yeast promoters include but are not limited to PGAL3, PGAL7, PCTR3, PMET3, PPGKl, PTDHl, PTDH3, PFBAl, PTEFl, PENOl, PENO2, PCYCl, PTDH2, PCUPl, PGAL80, PGAL2, PBNA6, PTMA29, PSBPl, PPUP3, PACS2, PTPOl, PRPTl, PAAT2, PAHPl, PSSEl, PTEF2, PNPL3, PPET9, PTUB2, POLEl, PCPRl, PIPPPl, and PSODl.
  • the library comprises a plurality of assembly vectors wherein each assembly vector comprises the same terminator sequence.
  • the assembly vectors can comprise any prokaryotic or eukaryotic terminator sequence known in the art.
  • the assembly vectors comprise a yeast terminator sequence.
  • Exemplary yeast terminators include but are not limited to TADHl, TENOl, TENO2, TCYCl, TNDT80, TTDH3, TTDHl, and TPGKl.
  • the library comprises a plurality of assembly vectors wherein each assembly vector comprises the same selectable marker.
  • the assembly vectors can comprise any prokaryotic or eukaryotic selectable marker known in the art. Examples of selectable markers include but are not limited to antibiotic resistance markers (e.g., genes encoding resistance to kanamycin, ampicillin, chloramphenicol, gentamycin, or trimethoprim) and metabolic markers (e.g., amino acid synthesis genes or transfer RNA genes).
  • kits for the assembly of a polynucleotide comprising two or more of the following: (a) one or more entry vectors described herein; (b) one or more restriction endonucleases capable of cleaving the restriction sites RA and RB of said one or more entry vectors; (c) one or more restriction endonucleases capable of cleaving the restriction sites RY and RZ of said entry vectors; and (d) oligonucleotide primers capable of annealing to primer binding segments PA and PB of said one or more entry vectors.
  • restriction sites RA and RB of each entry vector of the kit are recognizable and cleavable by Sapl restriction endonuclease, and the kit comprises Sapl restriction endonuclease.
  • restriction sites RY and RZ of each entry vector of the kit are recognizable and cleavable by Schl (or MIyI) restriction endonuclease, and the kit comprises Schl (or MIyI) restriction endonuclease.
  • the nucleic acid sequence of primer binding segment are recognizable and cleavable by Sapl restriction endonuclease, and the kit comprises Sapl restriction endonuclease.
  • restriction sites RY and RZ of each entry vector of the kit are recognizable and cleavable by Schl (or MIyI) restriction endonuclease, and the kit comprises Schl (or MIyI) restriction endonuclease.
  • the nucleic acid sequence of primer binding segment are recognizable and cleavable by Sapl restriction endonuclease
  • PA of one or more entry vectors in the kit is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequence of primer binding segment PB one or more entry vectors in the kit is selected from the group consisting of SEQ ID NOS: 24 and 25.
  • nucleic acid sequences of primer binding segment PA and primer binding segment PB are not identical.
  • nucleic sequence of annealable linker sequence LA of one or more entry vectors in the kit is selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the nucleic sequence of annealable linker sequence LB one or more entry vectors in the kit is selected from the group consisting of SEQ ID NOS: 1 to 23. In some embodiments, the nucleic sequences of annealable linker sequence LA and annealable linker sequence LB of all the entry vectors in the kit are selected from the group consisting of SEQ ID NOS: 1 to 23.
  • the kit comprises pRYSE vector #1, the sequence of which is provided herein as SEQ ID NO: 221.
  • the kit comprises pRYSE vector #2, the sequence of which is provided herein as SEQ ID NO: 207.
  • the kit comprises pRYSE vector #3, the sequence of which is provided herein as SEQ ID NO: 208.
  • the kit comprises pRYSE vector #4, the sequence of which is provided herein as SEQ ID NO: 209.
  • the kit comprises pRYSE vector #5, the sequence of which is provided herein as SEQ ID NO: 210.
  • the kit comprises pRYSE vector #6, the sequence of which is provided herein as SEQ ID NO: 21 1.
  • the kit comprises pRYSE vector #7, the sequence of which is provided herein as SEQ ID NO:212.
  • the kit comprises pRYSE vector #8, the sequence of which is provided herein as SEQ ID NO: 213.
  • the kit comprises pRYSE vector #9, the sequence of which is provided herein as SEQ ID NO: 214.
  • the kit comprises pRYSE vector #10, the sequence of which is provided herein as SEQ ID NO: 215.
  • the kit comprises pRYSE vector #11, the sequence of which is provided herein as SEQ ID NO: 216.
  • the kit comprises pRYSE vector #12, the sequence of which is provided herein as SEQ ID NO: 217. In some embodiments, the kit comprises pRYSE vector #13, the sequence of which is provided herein as SEQ ID NO: 218. In some embodiments, the kit comprises pRYSE vector #14, the sequence of which is provided herein as SEQ ID NO:219. In some embodiments, the kit comprises pRYSE vector #15, the sequence of which is provided herein as SEQ ID NO: 220.
  • the kit further comprises instructions for use that describe the polynucleotide assembly method disclosed herein.
  • a polynucleotide polymerase such as a thermostable DNA polymerase (e.g., Pfu DNA polymerase), and deoxyribonucleoside triphosphates (dNTPs) are also present in the kit.
  • dNTPs deoxyribonucleoside triphosphates
  • two or more assembly vectors each comprising a component polynucleotide to be assembled into an assembled polynucleotide may be provided in the kit.
  • assembly vectors may be provided that comprise a component polynucleotide useful for calibration and/or for use as a positive control to verify correct performance of the kit.
  • assembly vectors comprising as a component polynucleotide a protein-coding sequence, reporter gene, fluorescent marker coding sequence, promoter, enhancer, terminator, intron, exon, poly-A tail, multiple cloning site, nuclear localization signal, niRNA stabilization signal, selectable marker, integration loci, epitope tag coding sequence, and degradation signal.
  • the invention is illustrated by the following examples, which are not intended to be limiting in any way.
  • the Saccharyomices cerevisiae constructs described in the Examples were derived from Saccharyomices cerevisiae strain CEN. PK2. Unlike Saccharyomices cerevisiae strain S288c, the genomic sequence of strain CEN. PK2 is not publically available. Some of the constructs described were sequence-verified, and so the sequences provided are those of the actual CEN.PK2-derived constructs. For constructs that were not sequence-verified, the sequences provided are based on the published genomic sequence of strain S288c, and thus may include polymorphic differences to the sequences of the actual CEN.PK2-derived constructs.
  • pRYSE vectors comprise, in a 5' to 3' orientation, a first Sapl restriction enzyme recognition site, a first annealable linker sequence or primer binding segment, a first Schl restriction enzyme recognition site, a green fluourescent protein (GFP) or lacZ marker gene, a second Schl restriction enzyme recognition site, a second annealable linker sequence or primer binding segment, and a second Sapl restriction enzyme recognition site.
  • pRYSE vectors comprise, in a 5' to 3' orientation, a first Sapl restriction enzyme recognition site, a first annealable linker sequence or primer binding segment, a first Schl restriction enzyme recognition site, a green fluourescent protein (GFP) or lacZ marker gene, a second Schl restriction enzyme recognition site, a second annealable linker sequence or primer binding segment, and a second Sapl restriction enzyme recognition site.
  • GFP green fluourescent protein
  • a DNA fragment encoding ⁇ -lactamase was PCR amplified from the pUC 19 vector (GenBank accession L09137) using primers JCB158-17C (SEQ ID NO: 229) and JCB158-17D (SEQ ID NO: 230) after the Schl restriction enzyme recognition site in the bla gene of pUC19 had been removed by site-directed mutagenesis of pUC19 using PCR primers JCB158-17A (SEQ ID NO: 227) and JCBl 58-17B (SEQ ID NO: 228).
  • the PCR product was gel purified, and then ligated into the TOPO vector (Invitrogen, Carlsbad, CA), from which it was liberated again by digesting the construct to completion using Sphl and Mfel restriction enzymes, yielding the "bla DNA fragment”.
  • DNA fragments 1040 and 1041 were digested to completion using BstXI restriction enzyme, and each digested fragment was ligated with the 2.65 kb vector backbone that was generated by cutting to completion pAM1466 (SEQ ID NO: 223; generated synthetically by Biosearch Technologies, Novato, CA) using restriction enzymes Sad and Kpnl.
  • the 1040_pAM1466 DNA construct was digested to completion using BsmBI and BstXI restriction enzymes, the reaction mixture was resolved by gel electrophoresis, and an approximately 3.5 kb DNA fragment comprising the 1040 DNA fragment was gel purified.
  • the 1041_pAM1466 DNA construct was digested to completion using Bsal and BstXI restriction enzymes, the reaction mixture was resolved by gel electrophoresis, and an approximately 0.9 kb 1041 DNA fragment comprising the 1041 DNA fragment was gel purified. The purified DNA fragments were ligated, yielding DNA construct 1040_1041_pAM1466.
  • DNA fragment 1042 was joined to DNA construct 1040 1041 by a PCR "stitching" reaction using primers JO36 (SEQ ID NO: 69) and JO37 (SEQ ID NO: 70) to generate the 1040 1041 DNA fragment, primers JO38 (SEQ ID NO: 71) and JO39 (SEQ ID NO: 72) to generate the 1042 DNA fragment with a terminal sequence that overlapped a terminal sequence of the 1040 1041 DNA fragment, and primers JO39 (containing a Sphl restriction enzyme recognition site) (SEQ ID NO: 72) and JO36 (containing a Mfel restriction enzyme recognition site) (SEQ ID NO: 69) to join the two PCR products.
  • primers JO36 SEQ ID NO: 69
  • JO37 SEQ ID NO: 70
  • primers JO38 SEQ ID NO: 71
  • JO39 SEQ ID NO: 72
  • primers JO39 containing a Sphl restriction enzyme recognition site
  • JO36 containing a Mfel restriction
  • the 1040_1041_1042 PCR product was digested to completion using Sphl and Mfel restriction enzymes, the reaction mixture was resolved by gel electrophoresis, the approximately 2.4 kb 1040 1041 1042 DNA fragment was gel purified, and the purified DNA fragment was ligated to the gel purified bla fragment, yielding the "1040_1041_1042_bla" DNA construct.
  • the amplified PCR products were gel extracted, then digested to completion using Xhol and Sad restriction enzymes, the restriction enzymes were heat inactivated for 20 minutes at 65 0 C, and the digested PCR products were column purified and then ligated with the gel purified approximately 2.2 kb DNA fragment that resulted from digesting the 1040_1041_1042_bla DNA construct to completion using Xhol and Sad restriction enzymes.
  • the resulting vectors were PCR amplified using PCR primers 5 and 6 (see Table 3), the reaction mixtures were resolved by gel electrophoresis, and the approximately 2.2 kb "'pRYSE vector backbones" were gel purified.
  • lacZ gene was PCR amplified from the pUC 19 vector using primers S027
  • SEQ ID NO: 65 SEQ ID NO: 65
  • S028 SEQ ID NO: 66
  • the reaction mixture was resolved by gel electrophoresis, the approximately 0.5 kb PCR product was gel purified, and the purified PCR product was ligated with each of the pRYSE vector backbones.
  • Site-directed mutagenesis was performed on the resulting vectors using PCR primers L012 (SEQ ID NO: 231) and L013 (SEQ ID NO: 232) to remove a Schl restriction enzyme recognition site from the origin of replication.
  • pRYSE vectors 1 through 15 were synthesized using PCR primers S036 (SEQ ID NO: 67) and S037 (SEQ ID NO: 68) to remove the Schl restriction enzyme recognition site from the lacZ fragment, thus yielding pRYSE vectors 1 through 15 (see FIG. 4 for a plasmid map of the pRYSE vectors, and SEQ ID NOS: 207 through 221 for the nucleotide sequence of pRYSE vectors 1 through 15).
  • This example describes alternative methods for making pRYSE vectors.
  • pRYSE vectors 1 through 15 can be generated synthetically using as template
  • SEQ ID NOS: 207 through 221 e.g., by Biosearch Technologies, Novato, CA. Additional pRYSE vectors comprising different annealable linker sequences can be generated synthetically using as template SEQ ID NO: 221 in which the Pmel-5' primer binding segment and/or the RYSE 1 annealable linker sequence are changed to another suitable annealable linker sequence or primer binding segment (see Table 1).
  • This example describes methods for making a pMULE vector, comprising, in a 5' to 3' orientation, a first Sapl restriction enzyme recognition site, a first Schl restriction enzyme recognition site, a lacZ marker gene, a second Schl restriction enzyme recognition site, and a second Sapl restriction enzyme recognition site.
  • the pMULE vector can be used to clone Mules.
  • Bits are DNA fragments that can be inserted into pRYSE vectors to generate assembly vectors comprising component polynucleotides that can be assembled into assembled polynucleotides using methods disclosed herein.
  • Bits may encode genes or genetic elements of interest (e.g., promoters, terminators, selectable markers, integration loci, epitope tags, localization signals, degradation signals, fluorescent markers, multiple cloning sites). Bits were PCR amplified from a template using primers as described in Table 4.
  • MULEs are DNA fragments that can be inserted into pMULE vectors to generate assembly vectors comprising components polynucleotides that can be assembled into assembled polynucleotides using methods disclosed herein.
  • MULEs may encode genes or genetic elements of interest (e.g., promoters, terminators, selectable markers, integration loci, epitope tags, localization signals, degradation signals, fluorescent markers, multiple cloning sites) flanked by annealable linker sequence pairs or annealable linker sequence / primer binding segment pairs.
  • MULEs were PCR amplified from a template using primers of which the 3' end anneals to the target sequence and the 5' end comprises an annealable linker sequence or a primer binding segment (see Table 1 for suitable annealable linker sequences), as described in Table 5.
  • This example describes methods for inserting Bits into pRYSE vectors or
  • pRYSE vectors 1 through 8 and pRYSE vector 15 were digested to completion using Schl restriction enzyme, and the digested DNA fragments were treated with Antarctic Phosphatase (New England Biolabs, Ipswich, MA). The phosphatase was heat inactivated at 65 0 C for 20 minutes, the reaction mixtures were resolved by gel electrophoresis, and the approximately 2.2 kb pRYSE vector backbones (lacking lacZ) were gel purified. Purified pRYSE vector backbones were ligated with Bits as detailed in Table 6, thus yielding assembly vectors.
  • the pMULE vector is digested to completion using Schl restriction enzyme, the reaction mixture is resolved by gel electrophoresis, and the approximately 2.2 kb pMULE vector backbone (lacking lacZ) is gel purified.
  • the purified pMULE vector backbone is treated with a phosphatase (e.g., Antarctic Phosphatase (New England Biolabs, Ipswich, MA), CIAP (New England Biolabs, Ipswich, MA), SAP (New England Biolabs, Ipswich, MA; Fermentas, Glen Burnie, MD), or FastAP (Fermentas, Glen Burnie, MD)), the phosphatase is heat inactivated ⁇ e.g., 20 min at 65 0 C), and the pMULE vector backbone is ligated with MULEs, thus yielding assembly vectors.
  • a phosphatase e.g., Antarctic Phosphatase (New England Biolabs, I
  • Ligations were performed using 50 ng vector backbone, 3 molar excess Bit, and a ligase (e.g., Quick Ligase (New England Biolabs, Ipswich, MA), T4 DNA ligase (regular and high concentration; vendor, Fermentas, Glen Burnie, MD ), Fast Ligase (Fermentas, Glen Burnie, MD)) as per manufacturer's suggested protocol.
  • a ligase e.g., Quick Ligase (New England Biolabs, Ipswich, MA), T4 DNA ligase (regular and high concentration; vendor, Fermentas, Glen Burnie, MD ), Fast Ligase (Fermentas, Glen Burnie, MD)
  • Bit GAL4 was generated by stitching together Bits GAL4-1 and GAL4-2 (see Table 4) using primers JU-286-275-31-GAL4-F (SEQ ID NO: 140) and JU-287-275-31-GAL4-R (SEQ ID NO: 141).
  • Escherichia coli parent cells (Invitrogen, Carlsbad, CA). Host cell transformants were selected on Luria Bertoni (LB) agar containing 100 ug/mL carbenicillin and 40 ug/mL X-gal. Single white colonies were transferred from LB agar to culture tubes containing 5 niL of LB liquid medium and carbenicillin, and the cultures were incubated overnight at 37°C on a rotary shaker at 250 rpm. Plasmid DNAs were extracted and sequenced to identify clones containing the correct sequence in the correct orientation. The cells were stored at -80 0 C in cryo-vials in 1 mL stock aliquots made up of 400 uL sterile 50% glycerol and 600 uL liquid culture.
  • This example describes methods for assembling component polynucleotides into a assembled polynucleotide using assembly vectors and/or MULEs.
  • Assembly vectors (see Table 7) were placed together in one tube (333 fmole of each RABit) and digested using Lgul restriction enzyme (Fermentas, Glen Burnie, MD). The restriction enzyme was removed by column centrifugation or heat inactivated for 20 minutes at 65 0 C.
  • Lgul restriction enzyme Fermentas, Glen Burnie, MD
  • the restriction enzyme was removed by column centrifugation or heat inactivated for 20 minutes at 65 0 C.
  • 333 fmole of each MULE or assembled polynucleotide were placed together in one tube or were added to the digested assembly vectors.
  • the samples were split into three 30 uL reactions; water, buffer, dNTPs, and DNA polymerase were added to each reaction mixture, and a first round of PCR amplification was initiated. Samples were placed on ice, 0.5 uM of each terminal primer (Table 7) were added to the reaction mixtures, and a second round of PCR amplification was performed. The three PCR reaction mixtures were combined in one tube, the reaction mixtures were resolved by gel electrophoresis, and the PCR products were gel purified.
  • Phase I-A and Phase I-B assembled polynucleotides were cloned into the TOPO Zero Blunt II cloning vector (Invitrogen, Carlsbad, CA), yielding plasmids TOPO-Phase I-A and TOPO-Phase I-B, respectively.
  • the constructs were propagated in TOPlO cells (Invitrogen, Carlsbad, CA) grown on LB agar containing 50 ⁇ g/ml kanamycin.
  • Phase I-A and Phase I-B inserts were gel extracted using a gel purification kit (Qiagen, Valencia, CA), and equal molar ratios of the purified DNA fragments were ligated using T4 DNA ligase (New England Biolabs, Ipswich, MA), yielding the Phase I complete assembled polynucleotide.
  • the Phase I complete assembled polynucleotide was cloned into the TOPO Zero Blunt II cloning vector (Invitrogen, Carlsbad, CA), yielding plasmid TOPO-Phase I.
  • the construct was propagated in TOPlO cells (Invitrogen, Carlsbad, CA) grown on LB agar containing 50 ⁇ g/ml kanamycin.
  • Phase II complete assembled polynucleotide (see Table 7) was cloned into the TOPO Zero Blunt II cloning vector (Invitrogen, Carlsbad, CA), yielding plasmid TOPO- Phase II.
  • the construct was propagated in TOPlO cells (Invitrogen, Carlsbad, CA) grown on LB agar containing 50 ⁇ g/ml kanamycin.
  • Phase III-A and Phase IH-B assembled polynucleotides were cloned into the TOPO Zero Blunt II cloning vector (Invitrogen, Carlsbad, CA), yielding plasmids TOPO-Phase III-A and TOPO-Phase III-B, respectively.
  • the constructs were propagated in TOPlO cells (Invitrogen, Carlsbad, CA) grown on LB agar containing 50 ⁇ g/ml kanamycin.
  • Phase III-A and Phase III-B inserts were gel extracted using a gel purification kit (Qiagen, Valencia, CA), and equal molar ratios of the purified DNA fragments were ligated using T4 DNA ligase (New England Biolabs, Ipswich, MA), yielding the Phase III complete assembled polynucleotide.
  • the Phase III complete assembled polynucleotide was cloned into the TOPO Zero Blunt II cloning vector (Invitrogen, Carlsbad, CA), yielding plasmid TOPO-Phase III.
  • the construct was propagated in TOPlO cells (Invitrogen, Carlsbad, CA) grown on LB agar containing 50 ⁇ g/ml kanamycin.
  • TOPlO cells Invitrogen, Carlsbad, CA
  • LB agar containing 50 ⁇ g/ml kanamycin.
  • yeast cell transformations 25 ml of Yeast Extract Peptone Dextrose
  • YPD YPD medium
  • the culture was grown overnight at 3O 0 C on a rotary shaker at 200 rpm.
  • the OD600 of the culture was measured, and the culture was then used to inoculate 50 ml of YPD medium to an OD600 of 0.15.
  • the newly inoculated culture was grown at 30 0 C on a rotary shaker at 200 rpm up to an OD600 of 0.7 to 0.9, at which point the cells were transformed with 1 ⁇ g of DNA.
  • the cells were allowed to recover in YPD medium for 4 hours before they were plated on agar containing a selective agent to identify the host cell transformants.
  • Starter host strain Yl 198 was generated by resuspending active dry PE-2 yeast
  • strain identities of the colonies were verified by analyzing their chromosomal sizes on a Bio-Rad CHEF DR II system (Bio-Rad, Hercules, CA) using the Bio-Rad CHEF Genomic DNA Plug Kit (Bio-Rad, Hercules, CA) according to the manufacturer's specifications.
  • One colony was picked and stocked as strain Yl 198.
  • Strains Y 1661 , Y 1662, Y 1663 , and Y 1664 were generated from strain Y 1198 by rendering the strain haploid.
  • Strain Yl 198 was grown overnight in 5 mL of YPD medium at 3O 0 C in a glass tube in a roller drum. The OD600 was measured, and the cells were diluted to an OD600 of 0.2 in 5 mL of YP medium containing 2% potassium acetate. The culture was grown overnight at 30 0 C in a glass tube in a roller drum. The OD600 was measured again, and 4 OD600*mL of cells was collected by centrifugation at 5,000g for 2 minutes.
  • the cell pellet was washed once with sterile water, and then resuspended in 3 mL of 2% potassium acetate containing 0.02% raffinose.
  • the cells were grown for 3 days at 30 0 C in a glass tube in a roller drum. Sporulation was confirmed by microscopy. An aliquot of 33 uL of the culture was transferred to a 1.5 mL microfuge tube and was centrifuged at 14,000rpm for 2 minutes.
  • the cell pellet was resuspended in 50 uL of sterile water containing 2 uL of 10 mg/mL Zymolyase IOOT (MP Biomedicals, Solon, OH), and the cells were incubated for 10 minutes in a 30 0 C waterbath. The tube was transferred to ice, and 150 uL of ice cold water was added. An aliquot of 10 uL of this mixture was added to a 12 mL YPD plate, and tetrads were dissected on a Singer MSM 300 dissection microscope (Singer, Somerset, UK).
  • Zymolyase IOOT MP Biomedicals, Solon, OH
  • the YPD plate was incubated at 3O 0 C for 3 days, after which spores were patched out onto a fresh YPD plate and grown overnight at 30 0 C.
  • the mating types of each spore from 8 four-spore tetrads were analyzed by colony PCR.
  • a single 4 spore tetrad with 2 MATA and 2 MATalpha spores was picked and stocked as strains Y 1661 (MATA), Y 1662 (MATA), Y 1663 (MATalpha), and Y 1664 (MATalpha).
  • Host strain 1515 was generated by transforming strain Yl 664 with plasmid
  • Host cell transformants were selected on YPD medium containing 300 ug/mL hygromycin B. [00207] Host strain 1762 was generated by transforming strain Yl 515 with plasmid
  • Host strain 1770 was generated by transforming strain Y 1762 in two steps with expression plasmid pAM404 and plasmid TOPO-Phase III digested to completion using Pmel restriction endonuclease.
  • Expression plasmid pAM404 was derived from plasmid pAM353, which was generated by inserting a nucleotide sequence encoding a ⁇ -farnesene synthase into the pRS425-Gall vector (Mumberg et. al.
  • the nucleotide sequence insert was generated synthetically, using as a template the coding sequence of the ⁇ -farnesene synthase gene of Artemisia annua (GenBank accession number AY835398) codon-optimized for expression in Saccharomyces cerevisiae (SEQ ID NO: 121).
  • the synthetically generated nucleotide sequence was flanked by 5' BamHI and 3 ' Xhol restriction sites, and could thus be cloned into compatible restriction sites of a cloning vector such as a standard pUC or pACYC origin vector.
  • the synthetically generated nucleotide sequence was isolated by digesting to completion the DNA synthesis construct using BamHI and Xhol restriction enzymes.
  • the reaction mixture was resolved by gel electrophoresis, the approximately 1.7 kb DNA fragment comprising the ⁇ -farnesene synthase coding sequence was gel extracted, and the isolated DNA fragment was ligated into the BamHI Xhol restriction site of the pRS425-Gall vector, yielding expression plasmid pAM353.
  • the nucleotide sequence encoding the ⁇ -farnesene synthase was PCR amplified from pAM353 using primers GW-52-84 pAM326 BamHI (SEQ ID NO: 188) and GW-52-84 pAM326 Nhel (SEQ ID NO: 189).
  • the resulting PCR product was digested to completion using BamHI and Nhel restriction enzymes, the reaction mixture was resolved by gel electrophoresis, the approximately 1.7 kb DNA fragment comprising the ⁇ -farnesene synthase coding sequence was gel extracted, and the isolated DNA fragment was ligated into the BamHI Nhel restriction site of vector pAM178 (SEQ ID NO: 122), yielding expression plasmid pAM404.
  • Host cell transformants with pAM404 were selected on Complete Synthetic Medium (CSM) lacking methionine and leucine.
  • CSM Complete Synthetic Medium
  • Host cell transformants with pAM404 and Phase III complete assembled polynucleotide were selected on CSM lacking methionine and leucine and containing 200 ug/mL G418.
  • Host strain 1793 was generated by transforming strain Y 1770 with a URA3 knockout construct (SEQ ID NO: 123).
  • the knockout construct was generated by first generating DNA fragments URA3US (generated from Saccharomyces cerevisiae strain CEN.PK2 genomic DNA using PCR primers KMH33-276-21-URA3 5 ⁇ fwd (SEQ ID NO: 147) and KMH34-276-21-URA3 5'.rev (SEQ ID NO: 148)) and URA3DS (generated from Saccharomyces cerevisiae strain CEN.PK2 genomic DNA using PCR primers KMH35-276- 21-URA3 3'.fwd (SEQ ID NO: 149) and KMH36-276-21-URA3 3 '.rev (SEQ ID NO: 150); followed by stitching the two DNA fragments together using PCR primers KMH33-276-21- URA3 5'.fwd and KMH36-276-21-URA3 3 '.rev. Host cell transformants were selected on YPD medium containing 5-FOA.
  • Host strain YAAA was generated by transforming strain Y 1793 with the
  • Phase I marker recycling assembled polynucleotide (see Table 7). Host cell transformants were selected on CSM lacking methionine and uracil. The URA3 marker was excised by growing the cells overnight in YPD medium at 3O 0 C on a rotary shaker at 200 rpm, and then plating the cells onto agar containing 5-FOA. Marker excision was confirmed by colony PCR.
  • Host strain YBBB was generated by transforming strain YAAA with the
  • Phase II marker recycling assembled polynucleotide (see Table 7). Host cell transformants were selected on CSM lacking methionine and uracil. The URA3 marker was excised by growing the cells overnight in YPD medium at 30 0 C on a rotary shaker at 200 rpm, and then plating the cells onto agar containing 5-FOA. Marker excision was confirmed by colony PCR.
  • Host strain Y1912 was generated by transforming strain YBBB with the Phase
  • Host cell transformants were selected on CSM lacking methionine and uracil.
  • the URA3 marker was excised by growing the cells overnight in YPD medium at 30 0 C on a rotary shaker at 200 rpm, and then plating the cells onto agar containing 5-FOA. Marker excision was confirmed by colony PCR.
  • Host strain Y1913 was generated by transforming strain Y1912 with the STE5 knockout assembled polynucleotide (see Table 7). Host cell transformants were selected on CSM lacking methionine and uracil.
  • Host strain Yl 915 was generated from strain Y1913 by curing the strain from pAM404 and transforming the resulting strain with the IMEl knockout assembled polynucleotide (see Table 7). Strain Y1913 was propagated in non-selective YPD medium at 30 0 C on a rotary shaker at 200 rpm. Approximately 100 cells were plated onto YPD solid media and allowed to grow for 3 days at 30 0 C before they were replica-plated no CSM plates lacking methionine and leucine where they were grown for another 3 days at 30 0 C. Cured cells were identified by their ability to grow on minimal medium containing leucine and their inability to grow on medium lacking leucine. A single such colony was picked and transformed with the IMEl knockout assembled polynucleotide. Host cell transformants were selected on CSM lacking methionine and uracil.
  • This example describes methods for selecting annealable linker sequences to be used to assemble component polynucleotides encoding a promoter and a protein coding sequence into a assembled polynucleotide by the inventive methods disclosed herein.
  • MULEs encoding promoters followed by two different candidate annealable linker sequences annealable linker sequence RYSE 15 (Rl 5; SEQ ID NO: 15) and annealable linker sequence RYSE 7 (R7; SEQ ID NO: 7), as well as MULEs encoding GFP preceded by the two annealable linker sequences, were PCR amplified as described in Table 8.
  • PCR reactions were resolved by gel electrophoresis, the MULEs were gel purified, and the purified MULEs were used to assemble test assembled polynucleotides.
  • MULEs and assembly vectors (see Table 6) to be assembled (see Table 9) were placed together in a tube (333 fmole of each assembly vector, 667 fmole for each MULE) and digested using Lgul restriction enzyme (Fermentas, Glen Burnie, MD). The restriction enzyme was heat inactivated for 20 minutes at 65 0 C.
  • the samples were split into three 30 uL reactions; water, buffer, dNTPs, and DNA polymerase were added to each reaction mixture, and a first round of PCR amplification was initiated.
  • Terminal primers were then added to the reaction mixtures, and a second round of PCR amplification was performed (see Table 9).
  • the three PCR reaction mixtures were combined in one tube, the reaction mixtures were resolved by gel electrophoresis, and the PCR products were gel purified.
  • test assembled polynucleotides were used to transform a Saccharomyces cerevisiae host strain that was URA3 deficient and had a deletion of the GAL80 locus. Host cell transformants were selected on CSM lacking uracil, and correct genomic integration of the assembled polynucleotide was confirmed by colony PCR. Two verified colonies from each transformation were picked into 360 uL Bird Seed Medium (BSM) containing 2% sucrose, and the cultures were incubated for 48 hours at 3O 0 C on a rotary shaker at 999 rpm.
  • BSM Bird Seed Medium
  • annealable linker sequence RYSE 15 enabled increased GALl, TDH3, and CYCl promoter driven expression of the GFP reporter gene in the test assembled polynucleotides compared to annealable linker sequence RYSE 7.
  • This example describes methods for the high-throughput combinatorial assembly of polynucleotides, and methods for the high-throughput generation of host cells comprising combinatorially combined polynucleotides.
  • the component polynucleotides used in this example, and the expected assembled and combined polynucleotides generated from these component polynucleotides, are schematically illustrated in FIG. 12 A.
  • the component polynucleotides comprised DNA segments encoding an upstream and a downstream chromosomal targeting sequence (US and DS), 6 different promoters (P), 35 different proteins (G), and a 5' and a 3' segment of the URA3 selectable marker (URA and RA3, respectively), flanked by annealable linker sequences pairs or primer binding segment / annealable linker sequence pairs.
  • Lgul Digestion Plates 96-well plates
  • the plates were incubated at 37 0 C for 75 min, after which the Lgul restriction endonuclease was heat inactivated at 65 0 C for 20 min in a PCR machine.
  • SOE/PCR Plates triplicate 96-well plates
  • Assembled polynucleotides were PCR amplified. Each SOE/PCR Plate received additional reagent and was thermocycled in a PCR machine as shown in the table below. Corresponding wells on SOE/PCR plates were pooled into 96-deep well blocks, and assembled polynucleotides were purified using the Omega Biotek E-Z 96® Cycle-Pure Kit (Omega Bio-Tek Inc., Norcross, GA) as per manufacturer's suggested protocol (approximate end- volumes of 45 uL).
  • FIG. 12B shows exemplary assembled polynucleotides (boxed) resolved on a
  • Assembled polynucleotides were ligated into a pUC-19 based vector backbone.
  • a pTRC promoter i.e., promoter of the TRC gene of Saccharomyces cerevisiae
  • GIuRS GIuRS
  • 96-well plates (“Ligation Plates") were set up as shown in the table below, and the plates were incubated at 24 0 C for 15 min, and then at 16 0 C overnight. Ligation products were purified using the ZR-96 DNA Clean & ConcentratorTM- 5 (Zymo Research Corporation, Orange, CA) as per manufacturer's suggested protocol.
  • Yeast cells comprising chromosomally integrated combined polynucleotides were generated by host cell mediated homologous recombination between terminal chromosomal targeting sequences and selectable marker segments of the assembled polynucleotides.
  • 96-well PCR plates (“Yeast Transformation Plates”) were set up and heat shock transformations were carried out in a PCR machine as shown in the table below.
  • the Yeast Transformation Plates were spun at 2,00Og for 2 min, supernatants were removed, and cell pellets were washed three times with 200 uL ddH2O. Cell pellets were resuspended with 100 uL cold Bird Seed Media (BSM) taken from previously prepared pre-chilled 96-well culture plates ("Seed Plates") containing 360 uL cold BSM per well. The suspended cells were transferred to the Seed Plates, and were grown overnight at 3O 0 C in a Multitron II Incubator Shaker. The Seed Plates were spun at 3,000g for 5 min, all but 60 uL of the liquid was removed, and covered Seed Plates were shaken at l,000rpm to resuspend the cell pellets.
  • BSM cold Bird Seed Media
  • This example describes methods for generating yeast cells comprising assembled polynucleotides generated by host cell mediated homologous recombination.
  • the assembled polynucleotide and component polynucleotides used in this example, and the expected chromosomal locus obtained upon assembly and chromosomal integration, are schematically illustrated in FIG. 13 A.
  • the cells were spun down, supernatant was removed, cells were resuspended in 400 uL ddH2O, and host cell transformants were selected for by plating 100- 200 uL of the cell suspension on agar lacking uracil.
  • This example describes methods for the high-throughput generation of yeast cells comprising combinatorially assembled and combinatorially combined polynucleotides generated by host cell mediated homologous recombination.
  • the component polynucleotides used in this example, and the expected combined polynucleotides obtained upon assembly and combination by host cell mediated homologous recombination, are schematically illustrated in FIG. 14A.
  • the component polynucleotides comprised DNA segments encoding an upstream and a downstream chromosomal targeting sequence (US and DS), 6 different promoters (P), 35 different proteins (G), and a 5' and a 3' segment of the URA3 selectable marker (URA and RA3, respectively), flanked by annealable linker sequences pairs or primer binding segment / annealable linker sequence pairs.
  • Lgul Digestion Plates 96-well plates
  • the plates were incubated at 37 0 C for 75 min, after which the Lgul restriction endonuclease was heat inactivated at 65 0 C for 20 min in a PCR machine.
  • yeast Transformation Plates 96-well PCR plates
  • Master mix sufficient for 4 PCR plates contains 100 mL 50% PEG, 4 mL boiled (95 0 C for at least 10 min) single-stranded DNA, 15 mL IM LiAc.
  • the Yeast Transformation Plates were spun at 2,00Og for 2 min, supernatants were removed, and cell pellets were washed three times with 200 uL ddH2O. Cell pellets were resuspended with 100 uL cold Bird Seed Media (BSM) taken from previously prepared pre-chilled 96-well culture plates ("Seed Plates") containing 360 uL cold BSM per well. The suspended cells were transferred to the Seed Plates, and were grown overnight at 3O 0 C in a Multitron II Incubator Shaker.
  • BSM cold Bird Seed Media
  • the Seed Plates were spun at 3,000g for 5 min, all but 60 uL of the liquid was removed, and covered Seed Plates were shaken at l,000rpm to resuspend the cell pellets.
  • Various dilutions of cells were plated on agar lacking uracil, and incubated overnight at 37 0 C. Colonies of yeast cell transformants harboring a functional URA3 selectable marker were picked and analyzed.

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