Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

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Improvement of DNA and RNA Sugar Pucker Profiles from Semiempirical Quantum Methods

Neglect of diatomic differential overlap (NDDO) and self-consistent density-functional tight-binding (SCC-DFTB) semiempirical models commonly employed in combined quantum mechanical/molecular mechanical simulations fail to adequately describe the deoxyribose and ribose sugar ring puckers. This failure limits the application of these methods to RNA and DNA systems. In this work, we provide bench...

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15 صفحه اول

Activated Ribonucleotides Undergo a Sugar Pucker Switch upon Binding to a Single-Stranded RNA Template

Template-directed polymerization of chemically activated ribonucleotide monomers, such as nucleotide 5'-phosphorimidazolides, has been studied as a model for nonenzymatic RNA replication during the origin of life. Kinetic studies of the polymerization of various nucleotide monomers on oligonucleotide templates have suggested that the A-form (C3'-endo sugar pucker) conformation is optimal for bo...

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ژورنال

عنوان ژورنال: Journal of Chemical Theory and Computation

سال: 2014

ISSN: 1549-9618,1549-9626

DOI: 10.1021/ct401013s