C-H.O hydrogen bonds in minor groove of A-tracts in DNA double helices.
Analysis of available B-DNA type oligomeric crystal structures as well as protein-bound DNA fragments (solved using data with resolution <2.6 A) indicates that in both data sets, a majority of the (3'-Ade) H2..O2(3'-Thy/Cyt) distances in AA.TT and GA.TC dinucleotide steps, are considerably shorter than their values in a uniform fibre model, and are smaller than their optimum separation distance. Since the electropositive C2-H2 group of adenine is in close proximity of the electronegative keto oxygen atoms of both pyrimidine bases in the antiparallel strand of the double-helical DNA structures, it suggests the possibility of intra-base-pair as well as cross-strand C-H..O hydrogen bonds in the minor groove. The C2-H2..O2 hydrogen bonds within the A.T base-pairs could be a natural consequence of Watson-Crick pairing. However, the close cross-strand interactions between the bases at the 3'-ends of the AA.TT and GA.TC steps arise due to the local sequence-dependent geometry of these steps. While the base-pair propeller twist in these steps is comparable to the fibre model, some of the other local parameters such as base-pair opening angle and inter-base-pair slide show coordinated changes, leading to these shorter C2-H2..O2 distances. Hence, in addition to the well-known minor groove hydration, it appears that favourable C2-H2..O2 cross-strand interactions may play a role in imparting a characteristic geometry to AA.TT and GA.TC steps, as well as An.Tn and GAn.TnC tracts, which leads to a narrow minor groove in these regions.
Ghosh
A
A
Molecular Biophysics Unit, Indian Institute of Science, Bangalore, 560012, India.
Bansal
M
M
D020029:Base Pairing; D001483:Base Sequence; D002244:Carbon / Q000378:metabolism*; D003460:Crystallization; D004247:DNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006859:Hydrogen / Q000378:metabolism*; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010100:Oxygen / Q000378:metabolism*
D002244:Carbon; D006859:Hydrogen; D004247:DNA; D010100:Oxygen