Abstract
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.
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