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SiteOut: an online tool to design binding site-free DNA sequences

Javier Estrada, Teresa Ruiz-Herrero, Clarissa Scholes, Zeba Wunderlich, Angela H. DePace
doi: https://doi.org/10.1101/029645
Javier Estrada
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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Teresa Ruiz-Herrero
School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA.
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Clarissa Scholes
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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Zeba Wunderlich
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.Current address: Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, USA.
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Angela H. DePace
Department of Systems Biology, Harvard Medical School, Boston, MA, USA.
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  • For correspondence: depace@hms.harvard.edu
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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/.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted October 22, 2015.
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SiteOut: an online tool to design binding site-free DNA sequences
Javier Estrada, Teresa Ruiz-Herrero, Clarissa Scholes, Zeba Wunderlich, Angela H. DePace
bioRxiv 029645; doi: https://doi.org/10.1101/029645
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SiteOut: an online tool to design binding site-free DNA sequences
Javier Estrada, Teresa Ruiz-Herrero, Clarissa Scholes, Zeba Wunderlich, Angela H. DePace
bioRxiv 029645; doi: https://doi.org/10.1101/029645

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