Programmable iterated elongation: a method for manufacturing synthetic genes and combinatorial DNA and protein libraries

• US 8,962,532 B2
• Filed: 06/19/2007
• Issued: 02/24/2015
• Est. Priority Date: 06/19/2006
• Status: Expired due to Fees

• Current Assignee: Yeda Research and Development Co. Ltd. (Weizmann Institute of Science)
• Original Assignee: Yeda Research and Development Co. Ltd. (Weizmann Institute of Science)
• Inventors: Shapiro, Ehud Y., Linshiz, Gregory, Ben-Yehezkel, Tuval, Kaplan, Shai, Adar, Rivka, Gronau, Ilan, Tuvi, Sivan
• Primary Examiner(s): Babic, Christopher M.
• Assistant Examiner(s): Flinders, Jeremy C
• Application Number:
  US12/308,557
• Publication Number:
  US 20100240538A1
• Time in Patent Office: 2,807 Days
• US Class Current: 506/24
• CPC Class Codes: C12N 15/1031 mutagenesis by gene assembly, e.g. assembly by oligonucleotide extension PCR
• CPC Class Codes: C12N 15/1089 Design, preparation, screening or analysis of libraries using computer algorithms
• CPC Class Codes: C12N 15/66 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
• CPC Class Codes: C12Q 1/686 Polymerase chain reaction [PCR]
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids
• CPC Class Codes: G16B 30/20 Sequence assembly
• CPC Class Codes: G16B 35/00 ICT specially adapted for in silico combinatorial libraries of nucleic acids, proteins or peptides
• CPC Class Codes: G16B 35/10 Design of libraries
• CPC Class Codes: G16C 20/60 In silico combinatorial chemistry

Abstract

A method for manufacturing synthetic genes and combinatorial DNA and protein libraries, termed here Divide and Conquer-DNA synthesis (D&C-DNA synthesis) method. The method can be used in a systematic and automated way to synthesize any long DNA molecule and, more generally, any combinatorial molecular library having the mathematical property of being a regular set of strings. The D&C-DNA synthesis method is an algorithm design paradigm that works by recursively breaking down a problem into two or more sub-problems of the same type. The division of long DNA sequences is done in silico. The assembly of the sequence is done in vitro. The D&C-DNA synthesis method protocol consists of a tree, in which each node represents an intermediate sequence. The internal nodes are created in elongation reactions from their daughter nodes, and the leaves are synthesized directly. After each elongation only one DNA strand passes to the next level in the tree until receiving the final product. Optionally and preferably, error correction is performed to correct any errors which may have occurred during the synthetic process.

Claims

1. A method for at least semi-automatically manufacturing a biopolymer, comprising:

a. analyzing the biopolymer to be constructed to determine a plurality of potentially faulty subcomponents for collectively defining the biopolymer;

wherein said subcomponents are selected from the group consisting of nucleotides, polynucleotide, oligonucleotide, double stranded or single stranded DNA or RNA, a synthetic gene, an oligonucleotide of at least about 100 bases in length, an oligonucleotide of at least about 200 bases in length, an oligonucleotide of at least about 400 bases in length, or combinations thereof;

b. determining a hierarchical process for recursively constructing the biopolymer from said potentially faulty subcomponents, said determining comprising

decomposing said hierarchical process into a plurality of sub-processes by searching for an optimal and valid division point of said hierarchical process, and then selecting an optimal set of sub-processes to construct the biopolymer for said hierarchical process, said hierarchical process comprising a plurality of stages, each stage comprising a plurality of sub-processes such that an output of said sub-processes of said stage is a plurality of sub-components to be combined as an output of said stage, wherein said output of a previous stage is an input to a subsequent stage of said hierarchical process, wherein a first stage and a first plurality of sub-processes are defined according to said division point, which determines a starting point for said hierarchical process, such that all subsequent stages and sub-processes are determined according to said first stage and said first plurality of sub-processes;

wherein said sub-processes are collectively optimized and wherein at least one sub-process for combining a plurality of subcomponents is selected according to one or more criteria selected from the group consisting of;

time, energy input, by-products, monetary expense, number of subcomponents, sub-processes required, and any combination thereof, wherein said valid division point is at least partially determined according to at least one constraint selected from the group consisting of availability of at least one subcomponent, characterization of at least one subcomponent and cost of performing an associated sub-process;

wherein said hierarchical process is determined at least partially according to an optimal protocol wherein said optimal protocol is determined based on a set of constraints and a set of cost parameters wherein said set of constraints comprises a plurality of subcomponents to be synthesizable as oligo-primers, size of oligonucleotides, number of oligonucleotides, number of reactions, number of sub-processes, number of levels in the construction hierarchy, availability of oligonucleotides having defined sequences, and use of natural DNA or RNA; and

c. constructing a set of instructions for assembling the biopolymer according to said plurality of potentially faulty subcomponents and according to said hierarchical process; and

d. recursively constructing the biopolymer according to said set of instructions from a plurality of subcomponents, wherein at least one subcomponent has an error and wherein at least one sub-process of said hierarchical process corrects said error providing a final biopolymer product not featuring an error, wherein said biopolymer is a polynucleotide or oligonucleotide;

wherein said subcomponents comprise single stranded DNA and at least one oligonucleotide primer, and said plurality of sub-processes comprise elongation, phosphorylation and degradation by a DNA degrading enzyme, such that said recursively constructing the biopolymer comprises performing an elongation reaction with two input overlapping ssDNA fragments to form a dsDNA;

phosphorylating a primer at the 5′

end;

amplifying the dsDNA with said primer; and

degrading said phosphate-labeled PCR strand with said DNA degrading enzyme, yielding an elongated ssDNA fragment as output;

wherein said stages are repeated to form said biopolymer.

2. The method of claim 1, wherein said at least one sub-process for correcting said error combines a plurality of erroneous subcomponents, together having a complete set of error free parts.

3. The method of claim 1, further comprising constructing a library of biopolymers.

4. The method of claim 1, wherein said biopolymer is manufactured or synthesized automatically.

5. The method of claim 1 wherein said determining said hierarchical process further comprises:

determining an efficient path for recursively constructing the final cut from said first stage and said first sub-processes according to a branch and bound algorithm.

6. The method of claim 5, wherein said analyzing further comprises constructing each subcomponent separately.

7. The method of claim 3 for constructing a library of final biopolymers, further comprising:

a. Analyzing the plurality of final biopolymers to detect at least one shared subcomponent between the final biopolymers; and

b. Determining a recursive, hierarchical construction process with a minimal number of sub-processes by using said at least one shared subcomponent.

8. The method of claim 1, wherein said two input overlapping ssDNA fragments comprise two oligonucleotide primers the first time said stages are performed.

9. The method of claim 8, wherein said recursively constructing the biopolymer according to set of instructions from said plurality of subcomponents comprises determining whether an error free ssDNA fragment is generated by a subprocess;

if not, repeating said processes of elongation, phosphorylation and degradation with one or more potentially faulty subcomponents until said error free ssDNA fragment is generated.