Structure, recognition properties, and flexibility of the DNA-RNA hybrid
Structure, recognition properties, and flexibility of the DNA-RNA hybrid
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DOI：
10.1021/ja043293v
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发表时间：
2005-04-06
影响因子：
15
通讯作者：
Orozco, M
中科院分区：
文献类型：
--
作者：
Noy, A;Pérez, A;Orozco, M
利用分子动力学方法研究了室温下DNA-RNA杂交体在水溶液中的性质。杂交体的结构介于A和B形式之间，但通常更接近典型的A型螺旋。所有的核糖都表现出北pucklep，而2 '-脱氧核糖存在于北，东，南pucklep，后者是最常见的一个。DNA-RNA杂交体的分子识别模式是正常DNA和RNA双链体的独特组合。最后，从基本的动力学和刚度分析得到的结果表明，大的和非常不对称的灵活性的混合和强烈的偏好，每一条链（DNA或RNA）在相应的homoduplexes的内在运动的性质。独特的结构和动力学性质的DNA-RNA杂交的切割RNase H的机制的影响进行了讨论。
Molecular dynamics is used to investigate the properties of the DNA-RNA hybrid in aqueous solution at room temperature. The structure of the hybrid is intermediate between A and B forms but, in general, closer to the canonical A-type helix. All the riboses exhibit North puckerings, while 2'-deoxyriboses exist in North, East, and South puckerings, the latter being the most populated one. The molecular recognition pattern of the DNA-RNA hybrid is a unique combination of those of normal DNA and RNA duplexes. Finally, the results obtained from essential dynamics and stiffness analysis demonstrate the large and very asymmetric flexibility of the hybrid and the strong predilection that each strand (DNA or RNA) has on the nature of their intrinsic motions in the corresponding homoduplexes. The implications of the unique structural and dynamic properties of the DNA-RNA hybrid on the mechanism of cleavage by RNase H are discussed.