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Cis Watson-Crick/Watson-Crick base pairs in DNA： A Density Functional Theory(DFT) Study

Chinese Journal of Structural Chemistry 2017年第8期36卷 1251-1263页

作者：金能智张志斐张其斌者建武李葆光孙一桐 Gansu Computing Center School of Pharmacy North China University of Science and Technology

The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^（＊＊） basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis（NBO） was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick（WC） edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.

关键词： cis Watson-Crick/Watson-Crick(cis WC/WC) base pairs hydrogen bond

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Evaluation of RNA secondary structure prediction for both base-pairing and topology

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Biophysics Reports 2018年第3期4卷 123-132页

作者： Yunjie Zhao Jun Wang Chen Zeng Yi Xiao Institute of Biophysics School of Physics and Key Laboratory of Molecular Biophysics of the Ministry of EducationHuazhong University of Science and Technology Institute of Biophysics and Department of Physics Central China Normal University Department of Physics The George Washington University

Secondary structures of RNAs are crucial to the understanding of their tertiary structures and functions. At present, many theoretical methods are widely used to predict RNA secondary structures. The performance of these methods has been evaluated but only for their ability of base-pairing ***, the topology of a RNA secondary structure is more important for understanding its tertiary structure and function, especially for long RNAs. In this paper, we constructed a new non-redundant RNA database containing 73 RNA with lengths of 50–300 nucleotides and benchmarked four popular algorithms for both base pairing and topology. The results show that the prediction accuracy of secondary structure topology is only 38%, in contrast to 70% for that of base pairing. Furthermore, the topological consistency is not strongly correlated to the base-pairing consistency. Our results will be helpful to understand the limitations of RNA secondary structure prediction methods from a different point of view and also to their improvements in future.

关键词： Prediction accuracy RNA secondary structure prediction base pairs Structural topology

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Special Issue of ＂DNA Nanotechnology＂

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Chinese Journal of Chemistry 2016年第3期34卷 251-251页

作者： Chunai Fan Hao Pei CAS Key Laboratory of Interfacial Physics and Technology Shanghai Institute of Applied Physics Chinese Academy of Sciences Shanghai China Department of Chemistry School of Chemistry and Molecular Engineering East China Normal University Shanghai China

The term ＂DNA nanotechnology＂ describes the de- sign and fabrication of self-assembled nucleic acid nanostructures for various applications. Since Nadrian Seeman pioneered this area in the early 1980s, there has been tremendous interest in creating DNA nanostruc- tures with controlled geometry and topology by utilizing the unique precision in base-pairing of nucleic acids. Along with the rapid emergence and merging of bio- technology and nanotechnology in recent years, various ＂art-like＂ DNA nanostructures in one, two, or three di- mensions have been designed, constructed and exploited for a wide range of applications, including nanorobots, optical and electronic devices, diagnosis and therapy.

关键词： DNA nanotechnology ELECTRONIC apparatus & appliances base pairs

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