Department of Chemistry, Wayne State University , Detroit, Michigan 48202, United States.
J Am Chem Soc. 2014 Jan 8;136(1):282-90. doi: 10.1021/ja409515v. Epub 2013 Dec 19.
The DNA i-motif conformation was discovered in (CCG)•(CGG)n trinucleotide repeats, which are associated with fragile X syndrome, the most widespread inherited cause of mental retardation in humans. The DNA i-motif is a four-stranded structure whose strands are held together by proton-bound dimers of cytosine (C(+)•C). The stronger base-pairing interactions in C(+)•C proton-bound dimers as compared to Watson-Crick G•C base pairs are the major forces responsible for stabilization of i-motif conformations. Methylation of cytosine results in silencing of the FMR1 gene and causes fragile X syndrome. However, the influence of methylation or other modifications such as halogenation of cytosine on the base-pairing energies (BPEs) in the i-motif remains elusive. To address this, proton-bound heterodimers of cytosine and 5-methylcytosine, 5-fluorocytosine, 5-bromocytosine, and 5-iodocytosine are probed in detail. Experimentally, the BPEs of proton-bound heterodimers of cytosine and modified cytosines are determined using threshold collision-induced dissociation (TCID) techniques. All modifications at the 5-position of cytosine are found to lower the BPE and therefore would tend to destabilize DNA i-motif conformations. However, the BPEs in these proton-bound heterodimers still significantly exceed those of the Watson-Crick G•C and neutral C•C base pairs, suggesting that C(+)•C mismatches are still energetically favored such that i-motif conformations are preserved. Excellent agreement between TCID measured BPEs and B3LYP calculated values is found with the def2-TZVPPD and 6-311+G(2d,2p) basis sets, suggesting that calculations at these levels of theory can be employed to provide reliable energetic predictions for related systems.
DNA i 型结构在（CCG）·（CGG）n 三核苷酸重复序列中被发现，该序列与脆性 X 综合征有关，这是人类最常见的遗传性智力障碍原因。DNA i 型结构是一种四链结构，其链由质子结合的胞嘧啶二聚体（C(+)·C）连接在一起。与 Watson-Crick G·C 碱基对相比，C(+)·C 质子结合二聚体中的更强碱基配对相互作用是稳定 i 型结构的主要力量。胞嘧啶的甲基化导致 FMR1 基因沉默，并导致脆性 X 综合征。然而，甲基化或其他修饰（如胞嘧啶的卤化）对 i 型结构中碱基对能（BPE）的影响仍然难以捉摸。为了解决这个问题，详细研究了胞嘧啶和 5-甲基胞嘧啶、5-氟胞嘧啶、5-溴胞嘧啶和 5-碘胞嘧啶的质子结合杂二聚体。实验上，使用阈碰撞诱导解离（TCID）技术确定质子结合杂二聚体中胞嘧啶和修饰胞嘧啶的 BPE。在 5 位上的所有修饰都被发现降低了 BPE，因此倾向于破坏 DNA i 型结构的稳定性。然而，这些质子结合杂二聚体中的 BPE 仍然显著超过 Watson-Crick G·C 和中性 C·C 碱基对，这表明 C(+)·C 错配仍然在能量上是有利的，从而保持了 i 型结构的稳定性。TCID 测量的 BPE 与 B3LYP 计算值之间存在极好的一致性，这表明在这些理论水平上的计算可以用于为相关系统提供可靠的能量预测。
