Ulyanov N B, Zhurkin V B
Institute of Molecular Biology, Academy of Science of the USSR, Moscow.
J Biomol Struct Dyn. 1984 Oct;2(2):361-85. doi: 10.1080/07391102.1984.10507573.
Bending flexibility of the six tetrameric duplexes was investigated d(AAAA):d(TTTT), d(AATT)2, d(TTAA)2, d(GGGG):d(CCCC), d(GGCC)2 and d(CCGG)2,. The tetramers were extended in the both directions by regular double helices. The stiffness of the B-DNA double helix when bent into the both grooves proved to be less than that in the perpendicular direction by an order of magnitude. Such an anisotropy is a property of the sugar-phosphate backbone structure. The calculated fluctuations of the DNA bending along the dyad axis, 5-7 degree, are in agreement with experimental value of the DNA persistence length. Anisotropy of the double helix is sequence-dependent: most easily bent into the minor groove are the tetramers with purine-pyrimidine dimer (RY) in the middle. In contrast, YR dinucleotides prefer bending into the major groove. Moreover, they have an equilibrium bend of 6-12 degree into this groove. The above inequality is caused by stacking interaction of the bases. The bend in the central dimer is distributed to some extent between the adjacent links, though the main fraction of the bend remains within the central link. Variation of the sugar-phosphate geometry in the bent helix is inessential, so that DNA remains within the B-family of forms: namely, when the helical axis is bent by 20 degree. the backbone dihedral angles vary by no more than 15 degree. The obtained results are in accord with x-ray structure of the B-DNA dodecamer; they further substantiate our early model of DNA wrapping in the nucleosome by means of "mini-kinks" separated by a half-pitch of the double helix, i.e. by 5-6 b.p. Sequence-dependent anisotropy of DNA presumably dictates the three-dimensional structure of DNA in solution as well. We have found that nonrandom allocation of YR dimers leads to the systematic bends in equilibrium structure of certain DNA fragments.
研究了六种四聚体双链体d(AAAA):d(TTTT)、d(AATT)₂、d(TTAA)₂、d(GGGG):d(CCCC)、d(GGCC)₂和d(CCGG)₂的弯曲柔韧性。这些四聚体在两个方向上都由规则的双螺旋延伸。当B - DNA双螺旋弯曲到两个沟槽时，其刚度被证明比垂直方向的刚度小一个数量级。这种各向异性是糖 - 磷酸主链结构的一种特性。沿二元轴计算的DNA弯曲波动为5 - 7度，与DNA持久长度的实验值一致。双螺旋的各向异性取决于序列：中间带有嘌呤 - 嘧啶二聚体（RY）的四聚体最容易弯曲到小沟中。相反，YR二核苷酸更喜欢弯曲到大沟中。此外，它们向该沟槽的平衡弯曲为6 - 12度。上述不等式是由碱基的堆积相互作用引起的。中心二聚体中的弯曲在一定程度上分布在相邻链之间，尽管弯曲的主要部分仍在中心链内。弯曲螺旋中糖 - 磷酸几何形状的变化并不重要，因此DNA仍处于B型构象家族中：即当螺旋轴弯曲20度时，主链二面角的变化不超过15度。所得结果与B - DNA十二聚体的x射线结构一致；它们进一步证实了我们早期关于DNA通过双螺旋半间距（即5 - 6个碱基对）分隔的“小扭结”包裹在核小体中的模型。DNA的序列依赖性各向异性可能也决定了溶液中DNA的三维结构。我们发现YR二聚体的非随机分布导致某些DNA片段的平衡结构出现系统性弯曲。
