Nakano Shu-ichi, Kanzaki Takayuki, Sugimoto Naoki
High Technology Research Center, Konan University, 8-9-1 Okamoto, Higashinada-ku, Kobe, 658-8501, Japan.
J Am Chem Soc. 2004 Feb 4;126(4):1088-95. doi: 10.1021/ja037314h.
To understand the influences of the ribonucleotide on a duplex conformation and its stability, we systematically studied the CD spectra and the thermodynamics of nucleic acid duplexes formed by the chimeric RNA-DNA strand in which ribonucleotides and deoxyribonucleotides were covalently attached. It was found that the duplex stability was context-dependent and independent of the number of ribonucleotides in the chimeric strand, whereas the CD spectra showed less overall structural perturbation by the chimeric junctions. Combining the results of the CD and the thermodynamic data revealed a stability-structure relationship for the duplexes. Importantly, DeltaG(o)37 values estimated for the chimeric junction formation in the RNA-DNA/DNA and the RNA-DNA/RNA duplexes were close to those of RNA/DNA and RNA/RNA interactions, respectively. Furthermore, DeltaG(o)37s of the DNA-RNA/DNA and DNA-RNA/DNA-RNA junctions were similar to those of the DNA duplex, and the values of DNA-RNA/RNA-DNA were similar to those of the DNA/RNA. The thermodynamic analyses suggest that the 5'-nucleotide may be the crucial factor that determines the stability at the chimeric junction. Our results not only suggest influences of the ribonucleotide on a duplex conformation and its stability but also are useful for the design of RNA-DNA chimeric strands applicable to biotechnology.
为了了解核糖核苷酸对双链体构象及其稳定性的影响，我们系统地研究了由核糖核苷酸和脱氧核糖核苷酸共价连接的嵌合RNA-DNA链形成的核酸双链体的圆二色光谱（CD光谱）和热力学性质。结果发现，双链体稳定性取决于上下文，且与嵌合链中核糖核苷酸的数量无关，而CD光谱显示嵌合连接对整体结构的扰动较小。结合CD光谱结果和热力学数据揭示了双链体的稳定性-结构关系。重要的是，RNA-DNA/DNA和RNA-DNA/RNA双链体中嵌合连接形成的ΔG(o)37值分别接近RNA/DNA和RNA/RNA相互作用的值。此外，DNA-RNA/DNA和DNA-RNA/DNA-RNA连接的ΔG(o)37值与DNA双链体的相似，而DNA-RNA/RNA-DNA的值与DNA/RNA的相似。热力学分析表明，5'-核苷酸可能是决定嵌合连接处稳定性的关键因素。我们的结果不仅表明了核糖核苷酸对双链体构象及其稳定性的影响，而且对于设计适用于生物技术的RNA-DNA嵌合链也很有用。
