SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences
View/ Open
Published Version
https://doi.org/10.1371/journal.pone.0151740Metadata
Show full item recordCitation
Estrada, Javier, Teresa Ruiz-Herrero, Clarissa Scholes, Zeba Wunderlich, and Angela H. DePace. 2016. “SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.” PLoS ONE 11 (3): e0151740. doi:10.1371/journal.pone.0151740. http://dx.doi.org/10.1371/journal.pone.0151740.Abstract
DNA-binding proteins control many fundamental biological processes such as transcription, recombination and replication. A major goal is to decipher the role that DNA sequence plays in orchestrating the binding and activity of such regulatory proteins. To address this goal, it is useful to rationally design DNA sequences with desired numbers, affinities and arrangements of protein binding sites. However, removing binding sites from DNA is computationally non-trivial since one risks creating new sites in the process of deleting or moving others. Here we present an online binding site removal tool, SiteOut, that enables users to design arbitrary DNA sequences that entirely lack binding sites for factors of interest. SiteOut can also be used to delete sites from a specific sequence, or to introduce site-free spacers between functional sequences without creating new sites at the junctions. In combination with commercial DNA synthesis services, SiteOut provides a powerful and flexible platform for synthetic projects that interrogate regulatory DNA. Here we describe the algorithm and illustrate the ways in which SiteOut can be used; it is publicly available at https://depace.med.harvard.edu/siteout/.Other Sources
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795680/pdf/Terms of Use
This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAACitable link to this page
http://nrs.harvard.edu/urn-3:HUL.InstRepos:26318714
Collections
- FAS Scholarly Articles [18292]
- HMS Scholarly Articles [17922]
Contact administrator regarding this item (to report mistakes or request changes)