title: SiteOut: An Online Tool to Design Binding Site-Free DNA Sequences.
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/.
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.
authors.forename: Javier
authors.initials: J
authors.lastname: Estrada
authors.affiliation: John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, United States of America.
authors.forename: Teresa
authors.initials: T
authors.lastname: Ruiz-Herrero
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.
authors.forename: Clarissa
authors.initials: C
authors.lastname: Scholes
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.
authors.forename: Zeba
authors.initials: Z
authors.lastname: Wunderlich
authors.affiliation: Department of Systems Biology, Harvard Medical School, Boston, MA, United States of America.
authors.forename: Angela H
authors.initials: AH
authors.lastname: DePace
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D004247:DNA / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000235:genetics; D020407:Internet; D011485:Protein Binding / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software; D014158:Transcription, Genetic
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA