Structure based sequence dependent stiffness scale for trinucleotides: a direct method.
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.
The Institute of Physical and Chemical Research (RIKEN), Tsukuba Life Science Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan.
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Gromiha
DNA structure; Young's modulus; protein-DNA binding; sequence dependent; stiffness scale