R2oDNA Designer: Computational Design of Biologically Neutral Synthetic DNA Sequences

被引：45

作者：

Casini, Arturo ^{[1
,2
]}

Christodoulou, Georgia ^{[2
]}

Freemont, Paul S. ^{[1
,2
]}

Baldwin, Geoff S. ^{[1
,2
]}

Ellis, Tom ^{[1
,3
]}

MacDonald, James T. ^{[1
,2
]}

机构：

[1] Univ London Imperial Coll Sci Technol & Med, Ctr Synthet Biol & Innovat, London SW7 2AZ, England

[2] Univ London Imperial Coll Sci Technol & Med, Dept Life Sci, London SW7 2AZ, England

[3] Univ London Imperial Coll Sci Technol & Med, Dept Bioengn, London SW7 2AZ, England

来源：

ACS SYNTHETIC BIOLOGY | 2014年 / 3卷 / 08期

基金：

英国工程与自然科学研究理事会; 英国生物技术与生命科学研究理事会;

关键词：

software; synthetic biology; biologically neutral sequences; linkers; GENE-EXPRESSION; CONSTRUCTION; CIRCUITS; ELEMENTS;

D O I：

10.1021/sb4001323

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

R2oDNA Designer is a web application that stochastically generates orthogonal sets of synthetic DNA sequences designed to be biologically neutral. Biologically neutral sequences may be used for directing efficient DNA assembly by overlap-directed methods, as a negative control for functional DNA, as barcodes, or potentially as spacer regions to insulate biological parts from local context. The software creates optimized sequences using a Monte Carlo simulated annealing approach followed by the elimination of sequences homologous to host genomes and commonly used biological parts. An orthogonal set is finally determined by using a network elimination algorithm. Design constraints can be defined using either a web-based graphical user interface (GUI) or uploading a file containing a set of text commands.

引用

页码：525 / 528

页数：4

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