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首页> 外文期刊>Journal of Molecular Biology >Sequence-dependent DNA structure: The role of the sugar-phosphate backbone
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Sequence-dependent DNA structure: The role of the sugar-phosphate backbone

机译：依赖序列的DNA结构：糖磷酸骨架的作用

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A detailed analysis of the coupling between the conformational properties of the sugar-phosphate backbone and the base stacking interactions in dinucleotide steps of double helical DNA is described. Ln X-ray crystal structures of oligonucleotides, the backbone shows one major degree of freedom, consisting of the torsion angles chi, delta, zeta and the pseudorotation phase angle, P. The remaining torsion angles (beta, epsilon, alpha and gamma) comprise two less important degrees of freedom. The base stacking interactions show three degrees of freedom: slide-roll-twist, shift-tilt, and rise (which is more or less constant). Coupling is observed between the base and backbone degrees of freedom. The major base stacking mode, slide-roll-twist, is coupled to the major backbone mode, X-P-F-I. The secondary base stacking mode, shift-tilt, is coupled to epsilon and zeta and to a lesser extent to the chi-P-delta-zeta mode. We show that the length of the backbone, C, given by the same strand C1'-C1' separation, is an excellent single parameter descriptor for the conformation of the backbone and the way in which it is coupled to the base stacking geometry. The slide-roll-twist motion relates to changes in the mean backbone length, C, and the shift-tilt motion to the difference between the lengths of the two backbone strands, Delta C. We use this observation to develop a simple virtual bond model which describes the coupling of the backbone conformations and the base stacking geometry. A semi-flexible bond is used to connect the same strand C1'-C1' atoms. Analysis of the X-ray crystal structure database, simple geometric considerations and model building experiments all show that this bond is flexible with respect to slide, shift and propeller but rigid with respect to the other 14 local base stacking parameters. Using this simple model for the backbone in conjunction with potential energy calculations of the base stacking interactions, we show that it is possible to predict accurately the values of these 14 base step parameters, given values of slide, shift and propeller. We also show that the base step parameters fall into three distinct groups: roll, tilt and rise are determined solely by the base stacking interactions and are independent of the backbone; twist is insensitive to the base stacking interactions and is determined solely by the constraints of a relatively rigid fixed length backbone; slide and shift are the primary degrees of freedom and cannot be predicted accurately at the dinucleotide level because they are influenced by the conformations of neighbouring steps in a sequence. We have found that the context effect on slide is mediated by the chi torsion angles while the context effect on shift results from a BI to BII transition in the backbone. We have therefore reduced the dimensionality of the dinucleotide step problem to two parameters, slide and shift. (C) 1998 Academic Press. [References: 38]
机译：详细分析了糖-磷酸骨架的构象性质与双螺旋DNA双核苷酸步骤中的碱基堆积相互作用之间的偶联。寡核苷酸的Ln X射线晶体结构，骨架显示一个主要的自由度，由扭角chi，δ，ζ和伪旋转相角P组成。其余的扭角（β，ε，α和γ）包括两个不太重要的自由度。基本堆叠交互显示三个自由度：滑动-滚动-扭曲，移位-倾斜和上升（或多或少是恒定的）。在基本和主干自由度之间观察到耦合。主要的基本堆叠模式“滑转扭曲”耦合到主要的主干模式X-P-F-I。次要基本堆叠模式移位倾斜耦合到epsilon和zeta，并在较小程度上耦合到chi-P-delta-zeta模式。我们显示，由相同链C1'-C1'分隔给出的骨架C的长度，是骨架构型及其耦合至基本堆叠几何结构的出色单参数描述符。滑转扭转运动与平均骨架长度C的变化有关，而移位倾斜运动与两条骨架链的长度Delta C之间的差有关。我们利用这一观察结果建立了一个简单的虚拟键合模型描述了骨架构型与基础堆叠几何结构的耦合。半挠性键用于连接相同的链C1'-C1'原子。对X射线晶体结构数据库的分析，简单的几何考虑和模型构建实验都表明，这种结合对于滑动，移动和螺旋桨是灵活的，而对于其他14个局部基础堆放参数则是刚性的。使用此简单的主干模型，并结合基础堆叠相互作用的势能计算，我们表明，在给定滑动，移动和螺旋桨值的情况下，可以准确预测这14个基本步骤参数的值。我们还表明，基本步长参数分为三个不同的组：滚动，倾斜和上升完全由基本堆叠交互作用确定，并且独立于骨架。扭曲对基础堆叠相互作用不敏感，并且仅由相对刚性的固定长度骨架的约束条件决定。滑动和移位是主要的自由度，不能在二核苷酸水平上准确预测，因为它们受序列中相邻步骤构象的影响。我们已经发现，滑移的上下文效应是由扭转角介导的，而移位的上下文效应是从骨架中的BI过渡到BII的结果。因此，我们将二核苷酸步骤问题的维数减少为两个参数，即滑动和移位。 （C）1998年学术出版社。 [参考：38]

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