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Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding.

Tamara M Okonogi·Stephen C Alley·Eric A Harwood·Paul B Hopkins·Bruce H Robinson
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Abstract

An important component of protein-DNA recognition is the charge neutralization of DNA backbone phosphates and subsequent protein-induced DNA bending. Replacement of phosphates by neutral methylphosphonates has previously been shown to be a model for protein-induced bending. In addition to bending, the neutralization process may change the inherent flexibility of the DNA--a feature never before tested. We have developed a method to measure the differential flexibility of duplex DNA when methylphosphonate substitutions are made and find that the local flexibility is increased up to 40%. These results imply that backbone-neutralization-dependent DNA flexibility augments DNA-binding motifs in protein-DNA recognition processes.

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Base SequenceDNAMolecular Sequence DataPhosphatesProtein BindingThermodynamicsJournal ArticleResearch Support, U.S. Gov't, P.H.S.

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Tamara M Okonogi, Stephen C Alley, Eric A Harwood, Paul B Hopkins, Bruce H Robinson. 2002-04-02. Phosphate backbone neutralization increases duplex DNA flexibility: a model for protein binding.. https://doi.org/10.1073/pnas.072067799

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