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首页> 外文期刊>Journal of Molecular Biology >Sequence-dependent DNA structure: tetranucleotide conformational maps.
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Sequence-dependent DNA structure: tetranucleotide conformational maps.

机译：依赖序列的DNA结构：四核苷酸构象图。

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A database of X-ray crystal structures of double helical DNA oligomers has been used to analyse the role of the sugar-phosphate backbone in coupling the conformational properties of neighbouring dinucleotide steps. The base step parameters which are most strongly coupled to the backbone degrees of freedom are slide and shift, and these are the two dinucleotide step parameters which show strong correlations along a sequence: the value of slide follows the values in the neighbouring steps, whereas shift tends to alternate. This conformational coupling is mediated by the shared furanose rings at the step junctions: a change in the value of slide causes a change in the mean value of the same strand 3' and 5'-chi torsion angle, and a change in the mean value of the 3' and 5' sugar pseudo-rotation phase angle, P; a change in the value of shift causes a difference between the same strand 3' and 5'-chi in A-DNA and a difference between the 3' and 5'-P in B-DNA. We have used a database of tetranucleotide X-ray crystal structures to parameterise a simple model for the coupling of slide and shift. Using this junction model together with our dinucleotide step potential energy maps described previously, we can in principle calculate the structure of any DNA oligomer. The parameterisation indicates that the rotational step parameters are accurate to within 5 degrees, and the translational step parameters are accurate to within 0.5 A. The model has been used to study the potential energy surfaces of all possible tetranucleotide sequences, and the calculations agree well with the experimental data from X-ray crystal structures. Some dinucleotide steps are context independent (AA/TT, AT and TA), because the conformational properties of all possible neighbouring steps are compatible. When the conformational properties of the neighbours are not compatible, the behaviour of a step cannot be understood at the dinucleotide level. Thus the conformations of CG, GC and GG/CC are all strongly context dependent. The remaining mixed sequence steps show weakly context-dependent behaviour. The approach allows the calculation of the relative stability and flexibility of tetranucleotide sequences, and the results indicate why TATA is used as an origin of replication. Clear predictions are made about sequences which have not yet been characterised crystallographically. In particular, poly(CCA).poly(TGG) is predicted to have an unusual structure which lies between the C and D-DNA polymorphs. Copyright 2000 Academic Press.
机译：双螺旋DNA低聚物的X射线晶体结构数据库已用于分析糖-磷酸骨架在偶联相邻二核苷酸步骤的构象特性中的作用。与骨架自由度最紧密耦合的基本步长参数是滑动和移位，这是两个二核苷酸步长参数，它们沿着一个序列显示出很强的相关性：滑动值遵循相邻步长中的值，而移位倾向于交替。这种构象偶联是由台阶连接处的共用呋喃糖环介导的：滑动值的变化会导致相同链3'和5'-chi扭转角的平均值发生变化，而平均值也会发生变化3′和5′糖的假旋转相位角P;位移值的变化会导致A-DNA的相同链3'和5'-chi之间存在差异，而B-DNA的3'和5'-P之间存在差异。我们已经使用四核苷酸X射线晶体结构数据库来参数化滑动和移位耦合的简单模型。使用该连接模型以及前面所述的我们的二核苷酸阶梯势能图，我们原则上可以计算任何DNA寡聚物的结构。参数化表明旋转步长参数精确到5度以内，平移步长参数精确到0.5 A以内。该模型已用于研究所有可能的四核苷酸序列的势能面，并且计算与X射线晶体结构的实验数据。一些二核苷酸步骤是上下文无关的（AA / TT，AT和TA），因为所有可能的相邻步骤的构象性质都是兼容的。当邻居的构象特性不兼容时，在二核苷酸水平上不能理解一个步骤的行为。因此，CG，GC和GG / CC的构象都与上下文密切相关。其余的混合序列步骤显示出弱上下文相关的行为。该方法可以计算四核苷酸序列的相对稳定性和灵活性，结果表明了为什么将TATA用作复制起点。对于尚未结晶表征的序列做出了明确的预测。特别地，预测poly（CCA）.poly（TGG）具有位于C和D-DNA多晶型物之间的不寻常结构。版权所有2000学术出版社。

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