Graduate School of Engineering, Nagoya University, Furocho, Chikusa, Nagoya, 464-8603, Japan.
Org Biomol Chem. 2011 Dec 21;9(24):8313-20. doi: 10.1039/c1ob06325a. Epub 2011 Nov 8.
In this study, we investigated the stability and structure of artificial base pairs that contain cyclohexyl rings. The introduction of a single pair of isopropylcyclohexanes into the middle of DNA slightly destabilized the duplex. Interestingly, as the number of the "base pairs" increased, the duplex was remarkably stabilized. A duplex with six base pairs was even more stable than one containing six A-T pairs. Thermodynamic analysis revealed that changes in entropy and not enthalpy contributed to duplex stability, demonstrating that hydrophobic interactions between isopropyl groups facilitated the base pairing, and thus stabilized the duplex. NOESY of a duplex containing an isopropylcyclohexane-methylcyclohexane pair unambiguously demonstrated its "pairing" in the duplex because distinct NOEs between the protons of cyclohexyl moieties and imino protons of both of the neighboring natural base pairs were observed. CD spectra of duplexes tethering cyclohexyl moieties also showed a positive-negative couplet that is characteristic of the B-form DNA duplex. Taken together, these results showed that cyclohexyl moieties formed base pairs in the DNA duplex without severely disturbing the helical structure of natural DNA. Next, we introduced cyclohexyl base pairs between pyrene and nucleobases as an "insulator" that suppresses electron transfer between them. We found a massive increase in the quantum yield of pyrene due to the efficient shielding of pyrene from nucleobases. The cyclohexyl base pairs reported here have the potential to prepare highly fluorescent labeling agents by multiplying fluorophores and insulators alternately into DNA duplexes.
在这项研究中，我们研究了含有环己基环的人工碱基对的稳定性和结构。在 DNA 中间引入一对异丙基环己烷会略微降低双链体的稳定性。有趣的是，随着“碱基对”数量的增加，双链体的稳定性显著提高。含有六个碱基对的双链体甚至比含有六个 A-T 对的双链体更稳定。热力学分析表明，熵的变化而不是焓的变化对双链体的稳定性有贡献，这表明异丙基之间的疏水相互作用促进了碱基配对，从而稳定了双链体。包含异丙基环己烷-甲基环己烷对的双链体的 NOESY 明确证明了其在双链体中的“配对”，因为在环己基部分的质子和两个相邻天然碱基对的亚氨基质子之间观察到了明显的 NOE。连接环己基部分的双链体的 CD 光谱也显示出 B 型 DNA 双链体的特征正-负偶联。总之，这些结果表明环己基部分在 DNA 双链体中形成碱基对，而不会严重干扰天然 DNA 的螺旋结构。接下来，我们在芘和碱基之间引入环己基碱基对作为“绝缘体”，以抑制它们之间的电子转移。我们发现由于芘有效地被碱基屏蔽，芘的量子产率大大提高。这里报道的环己基碱基对有可能通过将荧光团和绝缘体交替引入 DNA 双链体来制备高荧光标记试剂。
