RT Journal Article
SR Electronic
T1 SiteOut: an online tool to design binding site-free DNA sequences
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 029645
DO 10.1101/029645
A1 Javier Estrada
A1 Teresa Ruiz-Herrero
A1 Clarissa Scholes
A1 Zeba Wunderlich
A1 Angela H. DePace
YR 2015
UL http://biorxiv.org/content/early/2015/10/22/029645.abstract
AB 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/.