The role of DNA shape in protein|[ndash]|DNA recognition Export

@article{citeulike:6021858, 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.}, author = {Rohs, Remo and West, Sean M. and Sosinsky, Alona and Liu, Peng and Mann, Richard S. and Honig, Barry}, booktitle = {Nature}, citeulike-article-id = {6021858}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature08473}, citeulike-linkout-1 = {http://www.f1000.com/article/id/1166633}, citeulike-linkout-2 = {http://dx.doi.org/10.1038/nature08473}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/19865164}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=19865164}, day = {29}, doi = {10.1038/nature08473}, issn = {0028-0836}, journal = {Nature}, keywords = {biophysics, dna\_shape, protein\_dna\_interactions}, month = {October}, number = {7268}, pages = {1248--1253}, posted-at = {2009-11-07 16:49:13}, priority = {2}, publisher = {Nature Publishing Group}, title = {The role of DNA shape in protein|[ndash]|DNA recognition}, url = {http://dx.doi.org/10.1038/nature08473}, volume = {461}, year = {2009} }

TY - JOUR ID - citeulike:6021858 L3 - citeulike-article-id:6021858 N2 - 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. IS - 7268 JF - Nature SN - 0028-0836 EP - 1253 TI - The role of DNA shape in protein|[ndash]|DNA recognition PB - Nature Publishing Group VL - 461 T2 - Nature SP - 1248 KW - biophysics KW - dna_shape KW - protein_dna_interactions AU - Rohs, Remo AU - West, Sean AU - Sosinsky, Alona AU - Liu, Peng AU - Mann, Richard AU - Honig, Barry PY - 2009/10/29/ UR - http://dx.doi.org/10.1038/nature08473 ER -