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4273531 
Journal Article 
The influence of sugar-phosphate backbone on the stacking interaction in B-DNA helix formation 
Mittal, S; Mishra, BK; Sathyamurthy, N 
2015 
Yes 
Current Science
ISSN: 0011-3891
EISSN: 0011-3905 
108 
6 
1126-1131 
WOS:000352802600026 
The influence of sugar-phosphate backbone on the stacking interaction in the adenine...thymine base-pair dimer (A...T)(2) has been studied using the density functional theoretic method and the dispersion-corrected density functional BLYP-D3 and the triplezeta quality basis set def2-TZVP. In the absence of the sugar-phosphate backbone, several stacked conformers were obtained with a small difference in their stabilization energy values (-20 to -25 kcal/mol). However, the presence of the sugar-phosphate backbone limits the movement of the two A...T units, and yet the stacking interaction remains significant (-19.4 kcal/mol). Despite the constraints imposed by the backbone, the dimer (A...T)(2) is found to retain its favourable geometry. The influence of sodium ions on the geometry and the interaction energy is found to be negligible. 
B-DNA helix formation; BLYP-D3; stacking interaction; sugar-phosphate backbone