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. 2000 Mar;26(1):43-50.
doi: 10.1023/A:1005250718139.

Structure based sequence dependent stiffness scale for trinucleotides: a direct method

M M Gromiha  1
Affiliations

Structure based sequence dependent stiffness scale for trinucleotides: a direct method

M M Gromiha. J Biol Phys. 2000 Mar.

Abstract

A new set of stiffness parameters for all the 32trinucleotide units has been set up directly from thethree dimensional structures of DNA molecules. It wasobserved that GAC/GTC is the stiffest trinucleotideand ACC/GGT is the most flexible one. The averagestiffness values computed for a set of operatorsequences using the new parameters correlate very wellwith the protein-DNA binding specificity and bindingfree energy change of 434 repressor and Cro repressor,respectively. The new structure based stiffness scalecan explain the protein-DNA binding specificity to thelevel of 0.92.

Keywords: DNA structure; Young's modulus; protein-DNA binding; sequence dependent; stiffness scale.

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