Hsu S T, Chou M T, Chou S H, Huang W C, Cheng J W
Division of Structural Biology and Biomedical Science Department of Life Science, National Tsing Hua University, Hsinchu 300, Taiwan, ROC.
J Mol Biol. 2000 Feb 4;295(5):1129-37. doi: 10.1006/jmbi.1999.3388.
We have studied the hydration and dynamics of RNA C2'-OH in a DNA. RNA hybrid chimeric duplex d(CGC)r(aaa)d(TTTGCG). Long-lived water molecules with correlation time tau(c) larger than 0.3 ns were found close to the RNA adenine H2 and H1' protons in the hybrid segment. A possible long-lived water molecule was also detected close to the methyl group of 7T in the RNA-DNA junction but not to the other two thymine bases (8T and 9T). This result correlates with the structural studies that only DNA residue 7T in the RNA-DNA junction adopts an O4'-endo sugar conformation (intermediate between B-form and A-form), while the other DNA residues including 3C in the DNA-RNA junction, adopt C1'-exo or C2'-endo conformations (in the B-form domain). Based on the NOE cross-peak patterns, we have found that RNA C2'-OH tends to orient toward the O3' direction, forming a possible hydrogen bond with the 3'-phosphate group. The exchange rates for RNA C2'-OH were found to be around 5-20 s(-1), compared to 26.7(+/-13.8) s(-1) reported previously for the other DNA.RNA hybrid duplex. This slow exchange rate may be due to the narrow minor groove width of d(CGC)r(aaa)d(TTTGCG), which may trap the water molecules and restrict the dynamic motion of hydroxyl protons. The distinct hydration patterns of the RNA adenine H2 and H1' protons and the DNA 7T methyl group in the hybrid segment, as well as the orientation and dynamics of the RNA C2'-OH protons, may provide a molecular basis for further understanding the structure and recognition of DNA.RNA hybrid and chimeric duplexes.
我们研究了DNA·RNA杂交嵌合双链体[d(CGC)r(aaa)d(TTTGCG)]₂中RNA C2'-OH的水合作用和动力学。在杂交片段中，发现与RNA腺嘌呤的H2和H1'质子相邻存在相关时间τc大于0.3 ns的长寿命水分子。在RNA-DNA连接处靠近7T的甲基处也检测到一个可能的长寿命水分子，但在其他两个胸腺嘧啶碱基（8T和9T）处未检测到。这一结果与结构研究相关，即RNA-DNA连接处只有DNA残基7T采用O4'-内式糖构象（介于B型和A型之间），而包括DNA-RNA连接处的3C在内的其他DNA残基采用C1'-外式或C2'-内式构象（处于B型结构域）。基于NOE交叉峰模式，我们发现RNA C2'-OH倾向于朝向O3'方向排列，与3'-磷酸基团形成可能的氢键。发现RNA C2'-OH的交换速率约为5 - 20 s⁻¹，相比之前报道的其他DNA·RNA杂交双链体的26.7(±13.8) s⁻¹较慢。这种缓慢的交换速率可能是由于[d(CGC)r(aaa)d(TTTGCG)]₂的小沟宽度较窄，这可能会捕获水分子并限制羟基质子的动态运动。杂交片段中RNA腺嘌呤H2和H1'质子以及DNA 7T甲基独特的水合模式，以及RNA C2'-OH质子的取向和动力学，可能为进一步理解DNA·RNA杂交体和嵌合双链体的结构和识别提供分子基础。
