Gotfredsen C H, Spielmann H P, Wengel J, Jacobsen J P
Department of Chemistry, Odense University, Denmark.
Bioconjug Chem. 1996 Nov-Dec;7(6):680-8. doi: 10.1021/bc960061f.
Two-dimensional 1H NMR spectroscopy was used to determine the solution structure of the double-stranded DNA oligonucleotide d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3'), where X is 1-(2-O-methyl-beta-D-arabinofuranosyl)thymine. The structure determination was based on a total relaxation matrix analysis of NOESY cross-peak intensities using the MARDIGRAS program. The improved RANDMARDI procedure was used during the calculations to include the experimental "noise" in the NOESY spectra. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the modified DNA duplex from both A-form and B-form DNA starting structures. The root-mean-square deviation of the coordinates for the 40 structures was 0.82 A. The duplex adopts a normal B-DNA-type helix, and the spectra as well as the structure show that the modified nucleotide X adopts a C2'-endo (S) sugar conformation. There are no significant changes in the helix originating from the modified nucleotide. The CH3O group on X is directed toward the major groove, and there seems to be free space for further modifications at this position.
采用二维¹H核磁共振光谱法测定双链DNA寡核苷酸d(5'-CGCATATAGCC-3'): d(5'-GGCTAXATGCG-3')的溶液结构，其中X为1-(2-O-甲基-β-D-阿拉伯呋喃糖基)胸腺嘧啶。结构测定基于使用MARDIGRAS程序对NOESY交叉峰强度进行的全弛豫矩阵分析。计算过程中使用了改进的RANDMARDI程序，以纳入NOESY谱中的实验“噪声”。将源自NOE的距离约束应用于受限分子动力学计算。从A-型和B-型DNA起始结构分别为修饰的DNA双链体生成了20个最终结构。这40个结构的坐标的均方根偏差为0.82 Å。该双链体采用正常的B-DNA型螺旋，光谱和结构均表明修饰的核苷酸X采用C2'-内型（S）糖构象。修饰的核苷酸未使螺旋发生显著变化。X上的CH₃O基团朝向大沟，此位置似乎有进一步修饰的自由空间。
