Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids
Characterization of the 6-methyl isoxanthopterin (6-MI) base analog dimer, a spectroscopic probe for monitoring guanine base conformations at specific sites in nucleic acids
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DOI：
10.1093/nar/gkr858
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发表时间：
2012-02-01
影响因子：
14.9
通讯作者：
von Hippel, Peter H.
中科院分区：
文献类型：
--
作者：
Datta, Kausiki;Johnson, Neil P.;von Hippel, Peter H.
我们在此利用6 - 甲基异黄蝶呤（6 - MI）作为构象探针，对RNA和DNA中特异性定位的鸟嘌呤（G）残基对的局部构象进行了表征。6 - MI是G的一种碱基类似物，从相邻的6 - MI残基对获得的光谱信号反映了碱基 - 碱基相互作用，这种相互作用对序列环境、局部DNA构象以及探针碱基的溶剂环境敏感。圆二色性（CD）信号显示在双链（ds）DNA中堆叠的6 - MI碱基之间存在强激子耦合；这种耦合在单链（ss）DNA序列中减弱。溶剂相互作用在ssDNA中比在dsDNA中更有效地降低二聚体探针的荧光，而6 - MI碱基之间的自猝灭在dsDNA中增强。6 - MI二聚体探针与相邻的GG残基非常相似，因为这些探针对dsDNA的稳定性以及与溶剂添加剂甜菜碱的相互作用影响极小。它们也可作为有效的模板碱基，尽管DNA引物在6 - MI模板碱基之后的进一步依赖聚合酶的延伸受到显著抑制。这些探针还用于监测模型复制叉处的DNA“呼吸”作用。6 - MI二聚体探针在许多情况下可作为一种有用的工具，用于研究溶液中功能性大分子机器的核酸框架内特定位点的GG构象。
We here characterize local conformations of site-specifically placed pairs of guanine (G) residues in RNA and DNA, using 6-methyl isoxanthopterin (6-MI) as a conformational probe. 6-MI is a base analog of G and spectroscopic signals obtained from pairs of adjacent 6-MI residues reflect base-base interactions that are sensitive to the sequence context, local DNA conformation and solvent environment of the probe bases. CD signals show strong exciton coupling between stacked 6-MI bases in double-stranded (ds) DNA; this coupling is reduced in single-stranded (ss) DNA sequences. Solvent interactions reduce the fluorescence of the dimer probe more efficiently in ssDNA than dsDNA, while self-quenching between 6-MI bases is enhanced in dsDNA. 6-MI dimer probes closely resemble adjacent GG residues, in that these probes have minimal effects on the stability of dsDNA and on interactions with solvent additive betaine. They also serve as effective template bases, although further polymerase-dependent extension of DNA primers past 6-MI template bases is significantly inhibited. These probes are also used to monitor DNA 'breathing' at model replication forks. The 6-MI dimer probe can serve in many contexts as a useful tool to investigate GG conformations at specific sites within the nucleic acid frameworks of functioning macromolecular machines in solution.