Helical structure of xylose-DNA.
Helical structure of xylose-DNA.
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DOI：
10.1021/ja9065877
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发表时间：
2010-01
影响因子：
15
通讯作者：
Amutha Ramaswamy;M. Froeyen;P. Herdewijn;A. Ceulemans
中科院分区：
文献类型：
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作者：
Amutha Ramaswamy;M. Froeyen;P. Herdewijn;A. Ceulemans
合成生物学和系统化学显示出对修饰核苷酸以获得酶促稳定的人工核酸的日益增长的兴趣。一种潜在的候选系统是木糖-DNA，其中2 ′-脱氧-β-D-呋喃核糖被2 ′-脱氧-β-D-呋喃木糖取代。我们在这里提出的螺旋结构和木糖-DNA的构象分析的基础上的35 ns的MD模拟的29个碱基对的DNA双链体。从右旋木糖-DNA螺旋开始，我们观察到从右旋到左旋螺旋的显著构象转变。左旋木糖-DNA是高度动态的，涉及螺旋的旋拧和旋拧运动。糖折叠引起的螺旋变化影响主链采用木糖-DNA的主链角度，同时保留Watson-Crick碱基配对和堆叠相互作用。结果证明了基于核糖和木糖的附加体的手性正交性。就信息存储的稳定性和紧凑性而言，基于核糖的天然DNA是无与伦比的。
Synthetic biology and systems chemistry demonstrate a growing interest in modified nucleotides to achieve an enzymatically stable artificial nucleic acid. A potential candidate system is xylose-DNA, in which the 2'-deoxy-beta-D-ribo-furanose is substituted by 2'-deoxy-beta-D-xylo-furanose. We present here the helical structure and conformational analysis of xylose-DNA on the basis of 35 ns MD simulations of a 29-base-pair DNA duplex. Starting from a right-handed xylose-DNA helix, we observe a remarkable conformational transition from right- to left-handed helix. The left-handed xylose-DNA is highly dynamic, involving screwing and unscrewing motion of the helix. The sugar pucker induced helical changes influence the backbone to adopt the backbone angles for xylose-DNA while retaining the Watson-Crick base pairing and stacking interactions. The results demonstrate the chiral orthogonality of the ribose and xylose based episomes. As far as stability and compactness of information storage is concerned, the ribose based natural DNA is unsurpassed.