Title: Scar-less multi-part DNA assembly design automation

Abstract

The present invention provides a method of a method of designing an implementation of a DNA assembly. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding flanking homology sequences to each of the DNA oligos. In an exemplary embodiment, the method includes (1) receiving a list of DNA sequence fragments to be assembled together and an order in which to assemble the DNA sequence fragments, (2) designing DNA oligonucleotides (oligos) for each of the DNA sequence fragments, and (3) creating a plan for adding optimized overhang sequences to each of the DNA oligos.

Inventors:

Hillson, Nathan J.

Issue Date:

Tue Aug 06 00:00:00 EDT 2019

Research Org.:

Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Org.:

USDOE

OSTI Identifier:

1568675

Patent Number(s):

10373703

Application Number:

15/147,764

Assignee:

The Regents of the University of California (Oakland, CA)

Patent Classifications (CPCs):

G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

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G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY

G16B15/00 - ICT specially adapted for analysing two-dimensional or three-dimensional molecular structures, e.g. structural or functional relations or structure alignment
G16B20/00 - ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
G16B20/20 - Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
G16B25/00 - ICT specially adapted for hybridisation
G16B25/20 - Polymerase chain reaction [PCR]
G16B30/00 - ICT specially adapted for sequence analysis involving nucleotides or amino acids
G16B30/20 - Sequence assembly

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DOE Contract Number:  

AC02-05CH11231

Resource Type:

Patent

Resource Relation:

Patent File Date: 05/05/2016

Country of Publication:

United States

Language:

English