Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.
Three-dimensional solution structure of a DNA duplex containing the BclI restriction sequence: two-dimensional NMR studies, distance geometry calculations, and refinement by back-calculation of the NOESY spectrum.
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含有 BclI 限制序列的 DNA 双链体的三维溶液结构：二维 NMR 研究、距离几何计算以及通过 NOESY 谱反算进行细化。
DOI：
10.1021/bi00443a033
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发表时间：
1989
期刊：
影响因子：
2.9
通讯作者：
Reid,BR
中科院分区：
文献类型：
--
作者：
Banks,KM;Hare,DR;Reid,BR
摘要：通过距离几何学确定了自互补十二核苷酸[d-（GCCTGATCAGGC）] 2的三维溶液结构，并在反算NOESY谱后进行了进一步的改进。这种DNA十二聚体含有被限制性内切酶Bell识别和切割的六聚体[d（TGATCA）] 2，确定其结构是为了更好地理解蛋白质和DNA之间发生的序列特异性相互作用。结构的初步检查表明，该结构相对于理想化的B型DNA是欠绕的，尽管一些局部结构参数（糖基扭转角和假旋转角）表明存在B家族类型的结构。这项研究表明的要求（共振分配，interproton distancemassumption，距离几何计算，和NOESY光谱反算），以产生实验自洽solutionstructures短的DNA序列。蛋白质对短DNA序列的识别（阻遏物对操纵子序列的识别，RNA聚合酶对启动子序列的识别，内切酶对限制性序列的识别）是非常特异的（Ohlendorf和马修斯，1983）。已知这些DNA序列与其特异性蛋白质之间的亲和力受许多高度敏感的分子间力调节，所述分子间力包括带正电荷的氨基酸与带负电荷的磷酸骨架之间的静电相互作用、序列特异性分子间氢键和货车范德华相互作用（贝格&布隆贝格，1978;贝格等人，1981年; Takeda
Revised Manuscript Received May 10, 1989 abstract: A three-dimensional solutionstructure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)] 2 has been determined by distance geometry withfurther refinements being performed after back-calculation of the NOESY spectrum. This DNA dodecamer contains the hexamer [d (TGATCA)] 2 recognized and cut by the restriction endonuclease Bell, and its structure was determined in hopes of obtaining a better understanding of the sequence-specific interactions which occur between proteins and DNA. Preliminary examination of the structure indicates the structure is underwound with respect to idealized B-form DNA though some of the local structural parameters (glycosyl torsion angle and pseudorotation angle) suggest a B-family type of structure is present. This research demonstrates the requirements (resonance assignments, interproton distancemeasurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solutionstructures for short DNA sequences. e recognition of short DNA sequences by proteins (operator sequences by repressors, promoter sequences by RNA polymerase, and restriction sequences by endonucleases) is remarkably specific (Ohlendorf & Matthews, 1983). The affinities between these DNA sequences and their specific proteins are known to be regulated by a number of highly sensitive intermolecular forces, which include electrostatic interactions between the positively charged amino acidsand the negatively charged phosphate backbone, sequence-specific intermolecular hydrogen bonding, and van der Waals inter-actions (Berg & Blomberg, 1978; Berg et al., 1981; Takeda