The recognition of specific DNA sequences by proteins is thoughtto depend on two types of mechanisms: one that involves theformation of hydrogen bonds with specific bases, primarily in themajor groove, and one involving sequence-dependent deformations ofthe DNA helix. By comprehensively analyzing the three-dimensionalstructures of protein-DNA complexes, we show that the binding ofarginines to narrow minor grooves is a widely used mode forprotein-DNA recognition. This readout mechanism exploits thephenomenon that narrow minor grooves strongly enhance the negativeelectrostatic potential of the DNA. The nucleosome core particleoffers a striking example of this effect. Minor groove narrowing isoften associated with the presence of A-tracts, AT-rich sequencesthat exclude the flexible TpA step. These findings suggest that theability to detect local variations in DNA shape and electrostaticpotential is a general mechanism that enables proteins to useinformation in the minor groove, which otherwise offers fewopportunities for the formation of base-specific hydrogen bonds, toachieve DNA binding specificity
1. What three properties of the major groove are advantageous toalpha helix insertion?
2. Which nucleotides are prevalent in narrow minor grooves?
3. Which amino acid tends to bind to the minor groove and howare minor groove width and electrostatic potential correlated?
The recognition of specific DNA sequences by proteins is thoughtto depend on two types of mechanisms: one that involves theformation of hydrogen bonds with specific bases, primarily in themajor groove, and one involving sequence-dependent deformations ofthe DNA helix. By comprehensively analyzing the three-dimensionalstructures of protein-DNA complexes, we show that the binding ofarginines to narrow minor grooves is a widely used mode forprotein-DNA recognition. This readout mechanism exploits thephenomenon that narrow minor grooves strongly enhance the negativeelectrostatic potential of the DNA. The nucleosome core particleoffers a striking example of this effect. Minor groove narrowing isoften associated with the presence of A-tracts, AT-rich sequencesthat exclude the flexible TpA step. These findings suggest that theability to detect local variations in DNA shape and electrostaticpotential is a general mechanism that enables proteins to useinformation in the minor groove, which otherwise offers fewopportunities for the formation of base-specific hydrogen bonds, toachieve DNA binding specificity
1. What three properties of the major groove are advantageous toalpha helix insertion?
2. Which nucleotides are prevalent in narrow minor grooves?
3. Which amino acid tends to bind to the minor groove and howare minor groove width and electrostatic potential correlated?
