base stacking

[maryatx3dna]

sir,

Does any helical parameter is directly related to base stacking so that we can a give an account of relative base stacking strength other than visual observation with mstacking or base overlap?

[xiangjun]

The base-overlap area is an intuitive parameter to quantify stacking interactions that matches visual  observations. As regard to the correlation between base-stacking interactions and helical parameters, why not you have a try with some examples? I guess the correlation would depend on DNA conformations. Among other parameters, slide should be a related one.

HTH,

Xiang-Jun

[maryatx3dna]

ok sir, i wil try.