Banks K M, Hare D R, Reid B R
Department of Chemistry, University of Washington, Seattle 98195.
Biochemistry. 1989 Aug 22;28(17):6996-7010. doi: 10.1021/bi00443a033.
A three-dimensional solution structure for the self-complementary dodecanucleotide [d-(GCCTGATCAGGC)]2 has been determined by distance geometry with further 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 BclI, 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 distance measurements, distance geometry calculations, and NOESY spectra back-calculation) to generate experimentally self-consistent solution structures for short DNA sequences.
已通过距离几何学确定了自互补十二聚体核苷酸[d-(GCCTGATCAGGC)]2的三维溶液结构，并在对NOESY谱进行反计算后进行了进一步优化。该DNA十二聚体包含被限制性内切酶BclI识别并切割的六聚体[d(TGATCA)]2，确定其结构是为了更好地理解蛋白质与DNA之间发生的序列特异性相互作用。对该结构的初步检查表明，相对于理想化的B型DNA，该结构存在负超螺旋，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族类型的结构。这项研究证明了生成短DNA序列的实验自洽溶液结构所需的条件（共振归属、质子间距离测量、距离几何学计算和NOESY谱反计算）。
