Theoretical examination of two opposite mechanisms proposed for hepatitis delta virus ribozyme

Article Abstract:

Various methodologies, including the quantum mechanics, molecular mechanics and molecular dynamics are used to provide a theoretical examination of the two opposite mechanisms that were developed for the hepatitis delta virus (HDV) ribozyme. The results show that the active-site cytosine residue (C75) when used as an acid exhibit unfavorable starting geometry, though it has a lower energy barrier, as compared to its base mechanism.

Genetic aspects, Binding sites (Biochemistry), Active sites (Biochemistry), Molecular dynamics, Catalytic RNA, Delta-associated agent, Hepatitis delta virus, Report

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Significant effects of phosphorylation on relative stabilities of DNA and RNA sugar radicals: Remarkably high susceptibility of H-2' abstraction in RNA

Article Abstract:

Nucleoside 3',5'-biphosphates are chosen as model compounds for DNA and RNA, in which the effects of both the nucleobase and phosphorylation are taken into consideration. The C2'-H bond of the phosphorylated RNA is found to be extraordinarily vulnerable to H-abstraction due to the hydrogen-bonding interaction between the 2'-OH and 3'-phosphate groups.

Phosphorylation, Radicals (Chemistry), Properties

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Development of an ONIOM-G3B3 method to accurately predict C-H and N-H bond dissociation enthalpies of ribonucleosides and deoxyribonucleosides

Article Abstract:

An ONIOM-G3B3 method is developed so as to reliably predict the bond dissociation enthalpies (BDEs) of nucleosides. It is found that the accuracy of the ONIOM-G3B3 method is about 1.4 kcal/mol for BDE calculations.

Chemical bonds, Dissociation, Dissociation reactions

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