Hagerman K R, Hagerman P J
Department of Biochemistry, Biophysics and Genetics, University of Colorado Health Sciences Center, Denver, USA.
J Mol Biol. 1996 Jul 12;260(2):207-23. doi: 10.1006/jmbi.1996.0393.
The intrinsic rigidity of the DNA helix is generally believed to arise primarily from vertical base-stacking interactions; however, relatively little experimental information exists regarding the relationship between the thermodynamic stability of base-stacking interactions and the mechanical rigidity imparted by such interactions. To address this issue, the solution conformations of complexes formed between adenine (A) or N-6-methyladenine (meA) monomer and deoxythymidylate (dTn) polymers of varying length (n = 40, 60, 81, and 110) have been examined. Such complexes are known to exist as extended, chiral structures in which the purine monomers exist as extensively stacked arrays. Thus, one can in principle examine the structural consequences of base-pair stack formation in the absence of any change in stoichiometric (phosphate) charge. The current approach has utilized the method of transient electric birefringence (TEB), which is highly sensitive to changes in nucleic acid conformation. Addition of millimolar concentrations of either A or meA to the dTn species leads to the formation of relatively rigid, chiral complexes whose dimensions are strictly limited by the length of the polymer strand. For adenine, the principal species appears to be [A] approximately n/2-dTn in which the polymer strand doubles back to form the two continuous strands of the complex (merotriplex). The addition of a methyl group to the N-6 position of adenine (meA) results in a shift to a meroduplex form, [meA] approximately n-dTn, with an intrinsic rigidity that is nearly identical to the rigidity of the corresponding duplex, dAn-dTn, despite the fact that the stoichiometric charge of the meroduplex is only one-half of that of the full duplex. The current results thus support a model in which helix rigidity is primarily due to the intrinsic resistance to deformation of base-stacking interactions; the deformation energies, as with the stacking energies themselves, are expected to be quite sequence-dependent. Phosphate-phosphate (repulsive) interactions, whose contributions are both salt-dependent and relatively sequence-independent, appear to play a secondary role in establishing helix rigidity. In particular, the DNA helix is likely to possess substantial rigidity in the absence of phosphate interactions. Thus, proteins whose interactions with DNA lead to substantial bending of the helix axis may facilitate such distortions through solvation of bases in addition to partial charge neutralization.
一般认为，DNA螺旋的固有刚性主要源于碱基垂直堆积相互作用；然而，关于碱基堆积相互作用的热力学稳定性与这种相互作用所赋予的机械刚性之间的关系，相对而言实验信息较少。为了解决这个问题，研究了腺嘌呤（A）或N - 6 - 甲基腺嘌呤（meA）单体与不同长度（n = 40、60、81和110）的脱氧胸苷酸（dTn）聚合物形成的复合物的溶液构象。已知此类复合物以伸展的手性结构存在，其中嘌呤单体以广泛堆积的阵列形式存在。因此，原则上可以在化学计量（磷酸盐）电荷无任何变化的情况下，研究碱基对堆积形成的结构后果。目前的方法采用了瞬态电双折射（TEB）方法，该方法对核酸构象的变化高度敏感。向dTn物种中加入毫摩尔浓度的A或meA会导致形成相对刚性的手性复合物，其尺寸严格受聚合物链长度的限制。对于腺嘌呤，主要物种似乎是[A]约n/2 - dTn，其中聚合物链折回形成复合物的两条连续链（部分三链体）。在腺嘌呤的N - 6位添加一个甲基（meA）会导致转变为部分双链体形式，[meA]约n - dTn，其固有刚性与相应双链体dAn - dTn的刚性几乎相同，尽管部分双链体的化学计量电荷仅为完整双链体的一半。因此，目前的结果支持这样一种模型，即螺旋刚性主要归因于碱基堆积相互作用对变形的固有抗性；与堆积能本身一样，变形能预计在很大程度上依赖于序列。磷酸 - 磷酸（排斥）相互作用的贡献既依赖于盐又相对不依赖于序列，似乎在建立螺旋刚性中起次要作用。特别是，在没有磷酸盐相互作用的情况下，DNA螺旋可能具有相当大的刚性。因此，那些与DNA相互作用导致螺旋轴大幅弯曲的蛋白质，除了部分电荷中和外，可能通过碱基的溶剂化作用来促进这种扭曲。
