Nishizaki T, Iwai S, Ohkubo T, Kojima C, Nakamura H, Kyogoku Y, Ohtsuka E
Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-ku, Sapporo 060, Japan.
Biochemistry. 1996 Apr 2;35(13):4016-25. doi: 10.1021/bi9519821.
The solution structures of two DNA duplexes containing a DNA*RNA hybrid region at different sites, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) (DHD, where D and H represent the DNA and DNA x RNA hybrid segments, respectively) and d(GGAGA)r(UGAC) x d(GTCATCTCC) (DDH), were determined by nuclear magnetic resonance spectroscopy to clarify the structural features of the D-H and H-D junctions. All proton-proton distances were derived from the NOESY spectra, with mixing times of 45 ms, and the restrained molecular dynamics were carried out starting from the typical A- and B-form conformations. Both duplexes were converged from the respective initial structures into structures with RMSD values of less than 1.0 angstrom. These structures were subjected to full relaxation matrix refinement to produce the final structures. In the case of the D-H junction, where the ribonucleotide was linked to the 3'-end of the DNA, the H2' and H2" signals of the deoxynucleotide overlapped completely, and the ribonucleotide had a H1'-H2' coupling constant larger than that of the normal C3'-endo sugar pucker. The dihedral angles, the pseudorotation phase angles, and the helical parameters changed at the H-D junction, but not at the D-H junction. A detailed comparison of the two duplexes revealed the structural heterogeneity between the DNA segment and the DNA x RNA hybrid region and the transitions at the junctions.
通过核磁共振光谱法测定了两个在不同位点含有DNA*RNA杂交区域的DNA双链体的溶液结构，即d(GG)r(AGAU)d(GAC)×d(GTCATCTCC)（DHD，其中D和H分别代表DNA和DNA×RNA杂交片段）和d(GGAGA)r(UGAC)×d(GTCATCTCC)（DDH），以阐明D-H和H-D连接的结构特征。所有质子-质子距离均来自混合时间为45毫秒的NOESY光谱，并从典型的A-和B-型构象开始进行受限分子动力学模拟。两个双链体均从各自的初始结构收敛到RMSD值小于1.0埃的结构。对这些结构进行完全弛豫矩阵精修以产生最终结构。在核糖核苷酸连接到DNA 3'-末端的D-H连接情况下，脱氧核苷酸的H2'和H2"信号完全重叠，并且核糖核苷酸的H1'-H2'耦合常数大于正常C3'-内型糖折叠的耦合常数。二面角、假旋转相角和螺旋参数在H-D连接处发生变化，但在D-H连接处未发生变化。对这两个双链体的详细比较揭示了DNA片段与DNA×RNA杂交区域之间的结构异质性以及连接处的转变。
