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Naphthalene, Phenanthrene, and Pyrene as DNA Base Analogues: Synthesis, Structure, and Fluorescence in DNA.萘、菲和芘作为DNA碱基类似物：DNA中的合成、结构与荧光
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Minor Groove Interactions between Polymerase and DNA: More Essential to Replication than Watson-Crick Hydrogen Bonds?聚合酶与DNA之间的小沟相互作用：对于复制而言，其比沃森-克里克氢键更重要？
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Difluorotoluene, a Nonpolar Isostere for Thymine, Codes Specifically and Efficiently for Adenine in DNA Replication.二氟甲苯，胸腺嘧啶的一种非极性生物电子等排体，在DNA复制中特异性且高效地编码腺嘌呤。
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NMR structure of the chimeric hybrid duplex r(gcaguggc).r(gcca)d(CTGC) comprising the tRNA-DNA junction formed during initiation of HIV-1 reverse transcription.包含HIV-1逆转录起始过程中形成的tRNA-DNA连接的嵌合杂交双链r（gcaguggc）.r（gcca）d（CTGC）的NMR结构
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Nucleotide analogs facilitate base conversion with 3' mismatch primers.核苷酸类似物可促进与3'错配引物的碱基转换。
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NMR solution structures of [d(GCGAAT-3'-3'-alphaT-5'-5'-CGC)2] and its unmodified control.[d(GCGAAT-3'-3'-αT-5'-5'-CGC)2]及其未修饰对照的核磁共振溶液结构
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Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair.包含可复制二氟甲苯-腺嘌呤对的DNA双链体的溶液结构。
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含核苷类似物1-(2'-脱氧-β-D-呋喃核糖基)-3-硝基吡咯的DNA双链体的核磁共振结构及未修饰对照的结构。

NMR structure of a DNA duplex containing nucleoside analog 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole and the structure of the unmodified control.

作者信息

Klewer D A, Hoskins A, Zhang P, Davisson V J, Bergstrom D E, LiWang A C

机构信息

Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843-2128, USA.

出版信息

Nucleic Acids Res. 2000 Nov 15;28(22):4514-22. doi: 10.1093/nar/28.22.4514.

DOI:10.1093/nar/28.22.4514
PMID:11071940
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC113877/
Abstract

The three-dimensional structures of two DNA duplexes d(CATGAGTAC). d(GTACXCATG) (1) and d(CATGAGTAC).d(GTACTCATG) (2), where X represents 1-(2'-deoxy-beta-D-ribofuranosyl)-3-nitropyrrole, were solved using high resolution nuclear magnetic resonance spectroscopy and restrained molecular dynamics. Good convergence was observed between final structures derived from A- and B-form starting geometries for both 1 and 2. Structures of 1 and 2 are right-handed duplexes within the B-form conformational regime. Furthermore, the structures of 1 and 2 are highly similar, with differences in the structures localized to the vicinity of residue 14 (X versus T). The pyrrole group of 1 is in the syn conformation and it is displaced towards the major groove. Furthermore, unlike T14 in 2, the base of X14 has reduced pi-pi stacking interactions with C13 and C15 and the nitro group of X14 is pointing out of the major groove. The structures presented here establish the basis of the thermal data of DNA duplexes containing X and should be informative during the design of improved wild card nucleobase analogs.

摘要

使用高分辨率核磁共振光谱法和受限分子动力学方法解析了两条DNA双链体d(CATGAGTAC).d(GTACXCATG) (1) 和d(CATGAGTAC).d(GTACTCATG) (2) 的三维结构，其中X代表1-(2'-脱氧-β-D-呋喃核糖基)-3-硝基吡咯。对于1和2，从A-型和B-型起始几何结构导出的最终结构之间观察到良好的收敛性。1和2的结构是处于B-型构象范围内的右手双链体。此外，1和2的结构高度相似，结构差异局限于残基14（X与T）附近。1的吡咯基团处于顺式构象，并且它向大沟方向移位。此外，与2中的T14不同，X14的碱基与C13和C15的π-π堆积相互作用减弱，并且X14的硝基指向大沟外部。此处呈现的结构为含X的DNA双链体的热数据奠定了基础，并且在设计改进的通配核苷类似物时应具有参考价值。