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首页> 外文期刊>Biochemistry >Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex
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Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex

机译：包含非核苷酸接头的分子内DNA三链体的溶液构象：与DNA双链体的比较

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摘要

The solution properties of the parallel intramolecular DNA triplex d(GAGAGA-oct-TCTCTC-oct-CTCTCT) (oct = -O-(CH2)8-O-PO2-O-(CH2)8-O-PO2-) and the duplex d(GAGAGA-oct-TCTCTC) have been examined by UV melting and high-resolution nuclear magnetic resonance spectroscopy (NMR). All nucleotides were primarily in the S conformation (i.e. near C2'-endo) in both the duplex and the triplex. However, the sugars of the Hoogsteen pyrimidine strand had a lower fraction of the S state than the Watson-Crick strands. Glycosidic torsion angles derived from nuclear Overhauser effect (NOE) build-up curves were found in the range -103 degrees to -133 degrees, with a clear alternation in magnitude along the GAGAGA strand in the triplex, whereas the glycosidic torsion angles were more similar in the duplex. Internucleotide NOEs were also consistent with an overall B-like geometry, rather than the A family. However, particularly in the Hoogsteen strand, some sequential NOE intensities were intermediate between those of the B and A forms. Distance and torsion constraints derived from NMR experiments were used to generate structures and were refined by restrained molecular dynamics. Extensive chemical shift differences between residues in the triplex and duplex were found for the purine strand, and there were remarkable differences in the pattern of shift differences for the A and G residues that correlated with differences in glycosidic torsion angles. Although there are differences in structure between the free duplex and that in the triplex, they are in important respects similar, indicating that only small conformational adjustments are needed to make parallel triple helices.
机译：平行分子内DNA三链体d（GAGAGA-oct-TCTCTC-oct-CTCTCT）（oct = -O-（CH2）8-O-PO2-O-（CH2）8-O-PO2-）和双相d（GAGAGA-oct-TCTCTC）已通过紫外熔融和高分辨率核磁共振波谱（NMR）进行了检查。在双链体和三链体中，所有核苷酸均主要为S构型（即，在C2'-末端附近）。但是，Hoogsteen嘧啶链的糖的S状态分数比Watson-Crick链的低。发现从核Overhauser效应（NOE）累积曲线得出的糖苷扭转角在-103度至-133度范围内，沿着GAGAGA链在三元组中的幅度明显不同，而糖苷扭转角则更相似在双工中。核苷酸间NOE也与总体B样几何形状一致，而不是与A族一致。但是，特别是在Hoogsteen链中，一些连续的NOE强度介于B和A形式的中间。来自NMR实验的距离和扭转约束用于生成结构，并通过受约束的分子动力学加以完善。发现嘌呤链在三链体和双链体中的残基之间存在广泛的化学位移差异，并且与糖苷扭转角的差异相关的A和G残基的位移差异模式存在显着差异。尽管游离双链体和三链体之间在结构上存在差异，但它们在重要方面相似，这表明仅需很小的构象调整即可制备平行的三链螺旋。

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