The role of DNA shape in protein-DNA recognition

Nature. 2009 Oct 29;461(7268):1248-53. doi: 10.1038/nature08473.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • AT Rich Sequence / genetics
  • Animals
  • Arginine / metabolism
  • Base Sequence
  • DNA / chemistry*
  • DNA / genetics
  • DNA / metabolism*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism*
  • Databases, Factual
  • Hydrogen Bonding
  • Lysine
  • Nucleic Acid Conformation*
  • Nucleosomes / chemistry
  • Nucleosomes / metabolism
  • Protein Binding
  • Saccharomyces cerevisiae
  • Static Electricity

Substances

  • DNA-Binding Proteins
  • Nucleosomes
  • DNA
  • Arginine
  • Lysine