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Nat Methods. 2014 Jun;11(6):657-62. doi: 10.1038/nmeth.2939. Epub 2014 Apr 28.

Interactive assembly algorithms for molecular cloning.

Author information

1
1] Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, USA. [2] Center of Synthetic Biology, Boston University, Boston, Massachusetts, USA.
2
Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, California, USA.
3
Center of Synthetic Biology, Boston University, Boston, Massachusetts, USA.
4
1] Graduate Program in Bioinformatics, Boston University, Boston, Massachusetts, USA. [2] Center of Synthetic Biology, Boston University, Boston, Massachusetts, USA. [3] Department of Electrical and Computer Engineering, Boston University, Boston, Massachusetts, USA.

Abstract

Molecular biologists routinely clone genetic constructs from DNA segments and formulate plans to assemble them. However, manual assembly planning is complex, error prone and not scalable. We address this problem with an algorithm-driven DNA assembly planning software tool suite called Raven (http://www.ravencad.org/) that produces optimized assembly plans and allows users to apply experimental outcomes to redesign assembly plans interactively. We used Raven to calculate assembly plans for thousands of variants of five types of genetic constructs, as well as hundreds of constructs of variable size and complexity from the literature. Finally, we experimentally validated a subset of these assembly plans by reconstructing four recombinase-based 'genetic counter' constructs and two 'repressilator' constructs. We demonstrate that Raven's solutions are significantly better than unoptimized solutions at small and large scales and that Raven's assembly instructions are experimentally valid.

PMID:
24776633
DOI:
10.1038/nmeth.2939
[Indexed for MEDLINE]

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