Structure and conversion kinetics of a Bi-stable DNA i-motif: Broken symmetry in the [d(5mCCTCC)]4 tetramer
Structure and conversion kinetics of a Bi-stable DNA i-motif: Broken symmetry in the [d(5mCCTCC)]4 tetramer
复制标题
DOI：
10.1006/jmbi.1996.0472
复制
发表时间：
1996-08-23
影响因子：
5.6
通讯作者：
Leroy, JL
中科院分区：
文献类型：
--
作者：
Nonin, S;Leroy, JL
在微酸性pH下，富C低聚物的质子化导致形成一个四链结构，由两个平行的双链组成，它们的半质子化的C在头到尾的方向上。嵌入在所谓的i基序中的C+对。在以前报告的所有病例中，双工都是相同的。d（5mCCTCC）低聚物形成的四聚体是不同的。该结构是根据在短混合时间内测量的NOESY交叉峰得出的55个残留间距离计算的。它由两个插入的非等效对称双工组成。基序为C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5，但其中一个双链的胸腺嘧啶基（T3*）环出并位于四聚体的宽凹槽中。胸腺嘧啶碱基T3堆叠成对称的T。序列相邻的C2之间的T对。C2（+）对和C2*。另一个双工的C2*(+)对。大量的交换交叉峰为双工互转换提供了证据。在0℃时，反应速率为1.4 s(-1)，活化能为94 kJ/mol。T3的开通。T3对，T3*闭合。T3对，和C2*的开口。C*(+)对与双工互转换同时发生。这表明胸腺嘧啶碱基的协同打开和关闭驱动了双工相互转换。打开C4。C4（+）和C4*。C4*(+)对和四聚体的解离不是相互转化的一部分，因为它们发生的速度要慢得多。[d(5mCCTCC)]4四聚体内的双相相互转换首次提供了生物聚合物中对称性破缺的结构和动力学表征。d（5mCCUCC）形成的四聚体采用类似的结构，但双相相互转化的速率更快：在0℃时40 s(-1)，在32℃时，相互转化在NMR时间尺度上很快。(C) 1996学术出版社有限公司
At slightly acidic pH protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C . C+ pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical.The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T . T pair between the sequentially adjacent C2 . C2(+) pair and the C2*. C2*(+) pair of the other duplex.Numerous exchange cross-peaks provide evidence for duplex interconversion. The interconversion rate is 1.4 s(-1) at 0 degrees C and the activation energy is 94 kJ/mol.The opening of the T3 . T3 pair, the closing of the T3*. T3 pair, and the opening of the C2*. C*(+) pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4 . C4(+) and C4*. C4*(+) pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer.The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s(-1) at 0 degrees C. At 32 degrees C, interconversion is fast on the NMR time scale. (C) 1996 Academic Press Limited.