DNA BENDING EFFECT OF REPLACING ADENINE W/ GUANINE NMR & COMPUTER EXPERIMENTS

用鸟嘌呤 NMR 替换腺嘌呤的 DNA 弯曲效应

• 批准号: 6355176
• 负责人: SANTHARAM KAMATH
• 金额: $ 2.68万
• 依托单位: MASSACHUSETTS INSTITUTE OF TECHNOLOGY
• 依托单位国家: 美国
• 财政年份: 2000
• 资助国家: 美国
• 起止时间: 2000-05-01 至 2001-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6355176
• 关键词: biological products; biomedical equipment development; biomedical resource; technology /technique

The width of the minor groove was determined in the following three closely related I I-mer B-DNA duplexes code named AAA, GAA and GGA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G AAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G GAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G GGA III by monitoring the interstrand NOE between the H2 of adenine and Hl' of the 3'-neighboring residue from the complementary strand at 500 MHz. It has been shown that the width of the minor groove was narrow in the GC rich oligonucleotides and that the narrow minor groove was not something endemic to A-tract DNA. The width of the groove is dictated by local sequence contexts and independent of neighboring A-tract DNA. It is also known that DNA bending is associated with nucleotidyl units assuming trans conformation about C4'-C5' at the 5' end of A-tract, and heteronomous structures at the 3' end of the A-tract. In view of our previous observation that DNA bends and kinks also occur in GC rich oligomers GAA and GGA, we have carried out a series of 'H-H, 'H-"P and 'H- 13C COSY NMR experiments to determine 'H-'H, 'H_31 p, 31 p_ I 3C, three bond couplings. The various coupling constants of the sugar phospahte backbone in GAA and GGA along each chain of the duplex are being extracted using computer simulation. In addition to extracting the coupling constants, we have also recorded the NOESY spectra for GAA and GGA at various mixing times. The coupling data and the NOESY distance data on these oligomers will be used to derive an ensemble of spatial configurations in equilibrium. It is believed that these data will lead to a better understanding of the DNA bending problem.

小沟的宽度由以下公式确定： 三个密切相关的II-mer B-DNA双链体，编码为AAA、GAA和 GGA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G AAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G GAA C-C-T-C-A-A-A-C-T-C-C G-G-A-G-T-T-T-G-A-G-G GGA III，通过监测链间NOE 腺嘌呤的H2和来自该序列的3 '-相邻残基的H1'之间的 互补链在500兆赫。 已经表明，宽度 在富含GC的寡核苷酸中，小沟的宽度较窄， 狭窄的小沟不是A道DNA特有的。 凹槽的宽度由局部序列上下文决定， 独立于相邻的A束DNA。 我们也知道DNA 弯曲与假定反式的核苷酸基单元有关 A束5'端C4'-C5'构象， 在A束的3'端的结构。 鉴于我们以前 观察到DNA弯曲和扭结也发生在富含GC的低聚物中 GAA和GGA，我们已经进行了一系列的'H-H，'H-“P和'H-13 C COSY NMR实验以确定'H-' H，'H_31 p，31 p_ I 3C，三个 键合耦合 糖磷酸酯的各种耦合常数 沿着双链体的每条链的GAA和GGA中的主链被 使用计算机模拟提取。 除了提取 耦合常数，我们还记录了NOESY光谱的GAA 和GGA在不同的混合时间。 耦合数据和NOESY 关于这些低聚物的距离数据将用于导出以下的系综： 平衡的空间结构。 据信，这些数据 将有助于我们更好地理解DNA弯曲问题。