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Design, synthesis and assembly of synthetic nucleic acids

a technology of nucleic acids and design, applied in the field of nucleic acid design and synthesizing, can solve the problems of increasing the cost and time taken to synthesize polynucleotides, prone to errors in the chemical synthesis of oligonucleotides, and reducing the number of polynucleotides. the effect of coupling efficiency and improving the subsequent assembly of polynucleotides

Inactive Publication Date: 2013-08-01
DNA TWOPOINTO
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

This patent describes methods for designing and synthesizing oligonucleotides with high efficiency. The methods involve selecting an initial polynucleotide sequence that codes for a polypeptide and modifying its codon choice based on various design criteria such as excluding certain sequences, incorporating certain elements, and avoiding certain features. The methods also include optimizing the assembly of polynucleotides from shorter fragments. The patent also describes a computer program product and a computer system for automating the design and synthesis process. The technical effects of the patent include improved efficiency in synthesizing oligonucleotides and better control over their assembly.

Problems solved by technology

The assembly of polynucleotides from oligonucleotides is an error-prone process.
Errors arise from the chemical synthesis of oligonucleotides, and the enzymatic processes used to assemble these oligonucleotides into longer polynucleotides.
These errors increase the cost and time taken to synthesize polynucleotides.

Method used

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  • Design, synthesis and assembly of synthetic nucleic acids
  • Design, synthesis and assembly of synthetic nucleic acids
  • Design, synthesis and assembly of synthetic nucleic acids

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Embodiment Construction

[0083]Before the present invention is described in detail, it is to be understood that this invention is not limited to the particular methodology, devices, solutions or apparatuses described, as such methods, devices, solutions or apparatuses can, of course, vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to limit the scope of the present invention.

5.1 Definitions

[0084]Use of the singular forms “a,”“an,” and “the” include plural references unless the context clearly dictates otherwise. Thus, for example, reference to “a polynucleotide” includes a plurality of polynucleotides, reference to “a substrate” includes a plurality of such substrates, reference to “a variant” includes a plurality of variants, and the like.

[0085]Terms such as “connected,”“attached,”“linked,” and “conjugated” are used interchangeably herein and encompass direct as well as indirect connection, attachment, linka...

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Abstract

Methods of synthesizing oligonucleotides with high coupling efficiency (>99.5%) are provided. Methods for purification of synthetic oligonucleotides are also provided. Instrumentation configurations for oligonucleotide synthesis are also provided. Methods of designing and synthesizing polynucleotides are also provided. Polynucleotide design is optimized for subsequent assembly from shorter oligonucleotides. Modifications of phosphoramidite chemistry to improve the subsequent assembly of polynucleotides are provided. The design process also incorporates codon biases into polynucleotides that favor expression in defined hosts. Design and assembly methods are also provided for the efficient synthesis of sets of polynucleotide variants. Software to automate the design and assembly process is also provided.

Description

CROSS-REFERENCES TO RELATED APPLICATIONS[0001]This application is a continuation under 37 C.F.R. §1.53(b) of copending U.S. patent application Ser. No. 11 / 579,704, filed Feb. 27, 2009, which claims priority to PCT Patent Application No. PCT / US05 / 15593, filed on May 4, 2005. U.S. patent application Ser. No. 11 / 579,704 also claims benefit under 35 U.S.C. §119(e) to U.S. Provisional Patent application No. 60 / 567,460, filed on May 4, 2004 and to U.S. Provisional Patent Application No. 60 / 666,909, filed on Mar. 31, 2005, the disclosures of which are hereby incorporated by reference in their entireties.STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT[0002]The research described in this application was funded in part by NIH grant R43 HG003507 from NHGRI.1. FIELD OF THE INVENTION[0003]This invention relates to methods for designing and synthesizing nucleic acids.2. BACKGROUND OF THE INVENTION[0004]Several methods have been described for the synthe...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12N15/10G16B25/20
CPCC12Q1/6806C12N15/1089C12N15/1027G06F19/20G16B25/00G16B25/20
Inventor GOVINDARAJAN, SRIDHARMINSHULL, JEREMY S.NESS, JON E.
Owner DNA TWOPOINTO
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