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首页> 外文期刊>Journal of Biomolecular Structure and Dynamics >A new peculiar DNA structure : NMR solution structure of a DNA kissing complex.
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A new peculiar DNA structure : NMR solution structure of a DNA kissing complex.

机译：一种新的特殊DNA结构：DNA接吻复合物的NMR溶液结构。

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摘要

The deoxyoligoribonucleotide d(CTTGCTGAAGCGCGCACGGCAAG) (dSL1) corresponding to the reverse transcripted sequence of the dimerization initiation site SL1 of HIV- 1(Lai) RNA was synthesized using phosphoramidite chemistry. Like its oligoribonucleotide counterpart, dSL1 dimerized spontaneously in solution. Here we report the first NMR solution structure of a kissing complex formed with two DNA strands. The melting point of the DNA dimer (35 degreeC) was found slightly higher than the one of the corresponding RNA dimer (32 degreeC). Despite this only slight difference in melting point, several structural differences were observed between the ribo- and the deoxyribo- dimers. The solution structure of the deoxy- dimer was a symmetric homodimer with a loop-loop interaction stabilized by four central G-C base-pairs, a head to tail A-A base-pair arrangement between the A8 residues of the two strands and a stacking of A9 with C15. As a consequence, G10 was not paired and occupied a position outside the stem and the loop. Each stem was formed by seven base-pairs whose axis made an angle of about 100 degree with the plane of the loops. The distortion of the helix at the junction of the stem and of the loop induced a fold up of the A8pA9 step with a phosphate-phosphate distance lowered to 4.5A. The plane of the non-canonical A-A base-pair was oriented perpendicularly to the axis of the stems. The four central base-pairs formed an open fan-shaped motif with an angle of 20 degree between the bases and each of them was oriented perpendicularly to the A8-A8 plane. The deviation of the computed chemical shifts and the experimental ones for the aromatic proton was always less than 0.25ppm for each of the 16 converged solution structures and their average less than 0.1ppm.
机译：利用亚磷酰胺化学合成了与HIV-1（Lai）RNA的二聚化起始位点SL1的逆转录序列相对应的脱氧寡核糖核苷酸d（CTTGCTGAAGCGCGCACGGCAAG）（dSL1）。像其寡核糖核苷酸对应物一样，dSL1在溶液中自发二聚。在这里，我们报告了由两条DNA链形成的接吻复合物的第一个NMR溶液结构。发现DNA二聚体的熔点（35℃）比相应的RNA二聚体之一的熔点（32℃）稍高。尽管熔点仅有微小差异，但在核糖和脱氧核糖二聚体之间仍观察到一些结构差异。脱氧二聚体的溶液结构是对称的同型二聚体，其环-环相互作用由四个中央GC碱基对稳定，两个链的A8残基之间的头尾AA碱基对排列和A9与C15。结果，G10未配对，并占据了茎和环之外的位置。每个茎由七个碱基对形成，它们的轴与环的平面成约100度角。茎和环的交界处的螺旋变形导致A8pA9步骤折叠，而磷酸盐-磷酸盐距离降低至4.5A。非规范A-A碱基对的平面垂直于茎轴定向。四个中央碱基对形成一个开放的扇形图案，两个碱基之间的夹角为20度，每个碱基对均垂直于A8-A8平面。对于16个聚合溶液结构，芳香族质子的化学位移与实验值的偏差始终小于0.25ppm，其平均值小于0.1ppm。

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