Biopolym. Cell. 2010; 26(5):360-372.
Variability of DNA structure and protein-nucleic acid reconginition
1Boryskina O. P., 1Tkachenko M. Yu., 1Shestopalova A. V.
  1. A. Usikov Institute of Radio Physics and Electronics, NAS of Ukraine
    12, Proskura Str., Kharkov, Ukraine, 61085


Revealing molecular mechanisms of sequence-specific recognition of DNA by proteins is one of the key tasks of biology. The current review presents the results of statistical analysis of the structural databases obtained by different scientific groups studying the conformational features of free and protein-bound DNA fragments that could be used for clarifying the mechanisms of protein-nucleic acid recognition. The analysis of the published data allowed us to make the following generalizations. The ability of DNA double helix to adopt alternative conformations, including the ones of sugar-phosphate backbone, is an intrinsic characteristic of certain DNA sequences. Such conformational transitions are the potential sources of formation of unique geometry of the dinucleotide steps and/or individual nucleotides and lead to alteration of base stacking and/or changes of the assessable surface area of atoms, and can be the criteria of recognition of DNA by protein as well. Changes in the physical properties that depend on the DNA structure, i. e. the polar/unpolar profile and electrostatic potential of the grooves, can also be used by protein for DNA readout.
Keywords: protein-nucleic acid recognition, variability of DNA structure, sugar-phosphate DNA backbone, alternative conformations


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