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Author Topic: base stacking  (Read 31490 times)

Offline maryatx3dna

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base stacking
« on: July 10, 2015, 05:40:19 am »
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?


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Offline xiangjun

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Re: base stacking
« Reply #1 on: July 10, 2015, 07:51:52 am »
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
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Offline maryatx3dna

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Re: base stacking
« Reply #2 on: July 14, 2015, 03:03:23 am »
ok sir, i wil try.
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Funded by the NIH R24GM153869 grant on X3DNA-DSSR, an NIGMS National Resource for Structural Bioinformatics of Nucleic Acids

Created and maintained by Dr. Xiang-Jun Lu, Department of Biological Sciences, Columbia University