Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy
Structure and dynamics of the DNA hairpins formed by tandemly repeated CTG triplets associated with myotonic dystrophy
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DOI：
10.1093/nar/24.4.775
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发表时间：
1996-02-15
影响因子：
14.9
通讯作者：
Gupta, G
中科院分区：
文献类型：
--
作者：
Mariappan, SVS;Garcia, AE;Gupta, G
DNA三联体（CTG）n的异常扩增导致强直性肌营养不良。为了更好地理解重复扩增的分子机制，对（CTG）n重复序列进行了结构研究。NMR和凝胶电泳研究证明溶液中存在（CTG）（5）和（CTG）（6）的发夹结构。单体发夹结构在宽范围的盐浓度（10-200 mM NaCl）、DNA浓度（DNA链中的微摩尔至毫摩尔）和pH（6.0-7.5）下保持不变。当n为奇数时，（CTG）发夹在环中含有三个碱基，当n为偶数时，含有四个碱基。对于奇数和偶数n，茎中的堆叠和配对保持相同，即两个氢键T。T对与相邻的G C对堆叠。（CTG）5和（CTG）（6）中的核苷酸均为C2 ′-内反构象。全弛豫矩阵分析已被执行，以获得NOE距离约束NOESY实验在七个不同的混合时间（25，50，75，100，125，200和500毫秒）。NOESY衍生的距离约束，随后被用于约束分子动力学模拟，以获得一个家庭的结构与NMR数据一致。通过采用Lipari-Szabo形式主义，计算了（CTG）5和（CTG）（6）的H5-H6（胞嘧啶）和H2 '-H2“偶极相关的理论序参数。实验数据表明，（CTG）（5）发夹环中的胞嘧啶比茎中的胞嘧啶稍微更灵活。（CTG）（6）发夹环中的胞嘧啶非常灵活，这意味着四碱基环的动力学本质上不同于三碱基环。
Anomalous expansion of the DNA triplet (CTG)n causes myotonic dystrophy. Structural studies have been carried out on (CTG)n repeats in an attempt to better understand the molecular mechanism of repeat expansion. NMR and gel electrophoretic studies demonstrate the presence of hairpin structures for (CTG)(5) and (CTG)(6) in solution. The monomeric hairpin structure remains invariant over a wide range of salt concentrations (10-200 mM NaCl), DNA concentrations (micromolar to millimolar in DNA strand) and pH (6.0-7.5). The (CTG) hairpin contains three bases in the loop when n is odd and four bases when n is even. For both odd and even n the stacking and pairing in the stem remain the same, i.e. two hydrogen bond T . T pairs stack with the neighboring G C pairs. All the nucleotides in (CTG)5 and (CTG)(6) adopt C2'-endo, anti conformations. Full-relaxation matrix analysis has been performed to derive the NOE distance constraints from NOESY experiments at seven different mixing times (25, 50, 75, 100, 125, 200 and 500 ms). NOESY-derived distance constraints were subsequently used in restrained molecular dynamics simulations to obtain a family of structures consistent with the NMR data. The theoretical order parameters are computed for H5-H6 (cytosines) and H2'-H2'' dipolar correlations for both (CTG)5 and (CTG)(6) by employing the Lipari-Szabo formalism. Experimental data show that the cytosine in the loop of the (CTG)(5) hairpin is slightly more flexible than those in the stem. The cytosine in the loop of the (CTG)(6) hairpin is extremely flexible, implying that the dynamics of the four base loop is intrinsically different from that of the three base loop.