Sequence-dependent DNA structure: Tetranucleotide conformational maps
Sequence-dependent DNA structure: Tetranucleotide conformational maps
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DOI：
10.1006/jmbi.1999.3237
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发表时间：
2000-01-07
影响因子：
5.6
通讯作者：
Hunter, CA
中科院分区：
文献类型：
--
作者：
Packer, MJ;Dauncey, MP;Hunter, CA
双螺旋DNA低聚物的X-射线晶体结构的数据库已被用来分析糖-磷酸骨架在耦合相邻的二核苷酸步骤的构象特性的作用。与骨架自由度耦合最强的碱基步骤参数是滑动和移位，这是两个二核苷酸步骤参数，它们显示出沿着序列的强相关性：滑动的值遵循相邻步骤中的值，移位往往交替。这种构象偶联是由阶梯连接处共享的呋喃糖环介导的：slide值的变化引起相同链3'和5'-chi扭转角的平均值的变化，以及3'和5'糖假旋转相位角P的平均值的变化;移位值的变化导致A-DNA中相同链3 ′和5 ′-chi之间的差异和B-DNA中3 ′和5 ′-P之间的差异。我们已经使用了一个数据库的四核苷酸X射线晶体结构参数化一个简单的模型耦合的幻灯片和移位。使用这个连接模型与我们先前描述的二核苷酸台阶势能图一起，我们原则上可以计算任何DNA寡聚体的结构。参数化指示旋转步长参数精确到5度内，并且平移步长参数精确到0.5埃内。该模型已被用来研究所有可能的四核苷酸序列的势能面，计算结果与X射线晶体结构的实验数据符合良好。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特性是相容的。当相邻分子的构象性质不相容时，就不能在二核苷酸水平上理解一个步骤的行为。因此，CG，GC和GG/CC的构象都是强上下文依赖的。其余的混合序列步骤显示弱上下文相关的行为。该方法允许四核苷酸序列的相对稳定性和灵活性的计算，结果表明为什么TATA被用作复制起点。对尚未被晶体学表征的序列进行了明确的预测。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。(C)北京大学出版社.
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, 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 Angstrom. 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. (C) 2000 Academic Press.