Helix rigidity of DNA: The meroduplex as an experimental paradigm
Helix rigidity of DNA: The meroduplex as an experimental paradigm
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DOI：
10.1006/jmbi.1996.0393
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发表时间：
1996-07-12
影响因子：
5.6
通讯作者：
Hagerman, PJ
中科院分区：
文献类型：
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作者：
Hagerman, KR;Hagerman, PJ
DNA螺旋的固有刚性通常被认为主要来自垂直碱基-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的实验信息相对较少。为了解决这个问题，研究了腺嘌呤(A)或N-6-甲基腺嘌呤((Me)A)单体与不同长度的脱氧胸腺苷(DT(N))聚合物(It=40、60、81和110)形成的络合物的溶液构象。已知这样的络合物以扩展的手性结构存在，其中嘌呤单体以广泛堆积的阵列存在。因此，在化学计量(磷酸盐)电荷没有任何变化的情况下，原则上可以检查碱基对堆叠形成的结构后果。目前的方法利用了对核酸构象变化高度敏感的瞬变电双折射(TEB)方法。在DT(N)物种中添加毫摩尔浓度的A或(Me)A会导致形成相对刚性的手性络合物，其尺寸严格受聚合物链长度的限制。对于腺嘌呤，主要的物种似乎是[A](近似于n/2)-dt(N)，其中聚合物链加倍形成两个连续的络合物链(三聚体)。在腺嘌呤((Me)A)的N-6位上加甲基导致向双链形式[(Me)A](近似于n)-dt(N)的转变，其固有刚性几乎与相应双链的刚性da(N)-dt(N)相同，尽管双链的化学计量电荷仅为全双链的一半。因此，目前的结果支持这样一个模型，即螺旋刚性主要是由于碱基-堆积相互作用对变形的内在抵抗；变形能与堆积能本身一样，预计将非常依赖于序列。磷酸盐-磷酸盐(排斥性)相互作用，其贡献既是盐依赖的，也是相对独立的，似乎在建立螺旋刚性方面发挥了次要作用。特别是，在没有磷酸盐相互作用的情况下，DNA螺旋可能具有实质性的刚性。因此，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，还可能通过碱基的溶剂化来促进这种扭曲。(C)1996年学术出版社有限公司
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 ((me)A) monomer and deoxythymidylate (dT(n)) polymers of varying length (it = 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 (me)A to the dT(n) 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](approximate to n/2)-dT(n) 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 ((me)A) results in a shift to a meroduplex form, [(me)A](approximate to n)-dT(n), with an intrinsic rigidity that is nearly identical to the rigidity of the corresponding duplex, dA(n)-dT(n), 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. (C) 1996 Academic Press Limited