College of Liberal Arts & Sciences

The Role of DNA Shape in Protein-DNA Recognition

Monday, March 1, 2010

March 1, Mon 2010
11:00 am, MRB 200 Conference Room

Dr. Remo Rohs

Howard Hughes Medical Institute, Columbia University

The Role of DNA Shape in Protein-DNA Recognition

The recognition of specific DNA sequences by proteins is often based on the interplay of two readout mechanisms: one that involves the formation of hydrogen bonds with specific bases (base readout), primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix (shape readout). The comprehensive analysis of the three-dimensional structures of protein–DNA complexes shows 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. The reported 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.



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