Cherstvy A G, Kornyshev A A, Leikin S
Institut für Festkörperforschung (IFF), Forschungszentrum Jülich, D-52425 Jülich, Germany, Department of Chemistry, Faculty of Physical Sciences, Imperial College London SW7 2AY, U.K., and National Institute of Child Health and Human Development, National Institutes of Health, Department of Health and Human Services, Bethesda, Maryland 20892.
J Phys Chem B. 2004 May 20;108(20):6508-18. doi: 10.1021/jp0380475.
We incorporate sequence-dependent twisting between adjacent base pairs and torsional elasticity of double helix into the theory of DNA-DNA interaction. The results show that pairing and counterion-induced-aggregation of nonhomologous DNA are accompanied by considerable torsional deformation. The deformation tunes negatively charged phosphate strands and positively charged grooves on opposing molecules to stay "in register", substantially reducing nonideality of the helical structure of DNA. Its cost, however, makes interaction between nonhomologous DNA less energetically favorable. In particular, interaction between double helical DNA may result in sequence homology recognition and selective pairing of homologous fragments containing more than 100-200 base pairs. We also find a weak, but potentially measurable, increase in the expected counterion concentration required for aggregation of nonhomologous DNA and slightly higher solubility of such DNA above the critical concentration.
我们将相邻碱基对之间的序列依赖性扭曲以及双螺旋的扭转弹性纳入DNA-DNA相互作用理论。结果表明，非同源DNA的配对和反离子诱导聚集伴随着相当大的扭转变形。这种变形调整了相反分子上带负电的磷酸链和带正电的凹槽，使其保持“对齐”，大大降低了DNA螺旋结构的非理想性。然而，其代价使得非同源DNA之间的相互作用在能量上不太有利。特别是，双螺旋DNA之间的相互作用可能导致序列同源性识别以及包含100 - 200个以上碱基对的同源片段的选择性配对。我们还发现，非同源DNA聚集所需的预期反离子浓度有微弱但可能可测量的增加，并且此类DNA在临界浓度以上的溶解度略高。
