The role of DNA shape in protein–DNA recognition

Remo Rohs, Sean M. West, Alona Sosinsky, Peng Liu, Richard S. Mann () and Barry Honig ()
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Remo Rohs: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
Sean M. West: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
Alona Sosinsky: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
Peng Liu: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA
Richard S. Mann: Columbia University, 701 West 168th Street, HHSC 1104, New York, New York 10032, USA
Barry Honig: Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA

Nature, 2009, vol. 461, issue 7268, 1248-1253

Abstract: Abstract The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein–DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein–DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.

Date: 2009
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DOI: 10.1038/nature08473

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