Interactive assembly algorithms for molecular cloning.

TitleInteractive assembly algorithms for molecular cloning.
Publication TypeJournal Article
Year of Publication2014
AuthorsAppleton E, Tao J, Haddock T, Densmore D
JournalNat Methods
Volume11
Issue6
Pagination657-62
Date Published2014 Jun
ISSN1548-7105
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.

DOI10.1038/nmeth.2939
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/24776633?dopt=Abstract
Alternate JournalNat. Methods
PubMed ID24776633