Abstract

MARIN RAY, M.  and  DAZA, Édgar E.. tRNA ACCEPTOR STEM CHARACTERIZATION BY MEANS OF LOCAL DESCRIPTORS BASED ON PARTIAL CHARGES. Rev.Colomb.Quim. [online]. 2008, vol.37, n.1, pp.31-44. ISSN 0120-2804.

In this work the charge distribution of the tRNA acceptor stem is characterized, considering all the possible Watson- Crick base pair combinations. 256 RNA fragments modeled by 10 nucleotides were used in order to model the first three pairs of the acceptor stem, the discriminator base and the CCA end. We propose two local charge descriptors based on the charge distribution of the nitrogenated base to characterize each nucleotide. These descriptors were computed from atomic partial charges derived from HF/6-31G calculations. From the characterization and classification of the stems according to the proposed descriptors, we found a special behavior for the discriminator base (in contrast to the other positions) and a strong effect of this position on the CCA end. The classification of nine variations of the tRNAAla acceptor stem showed a good structure-activity relationship that makes evident the usefulness of the proposed descriptors to characterize the local charge distributions of these biomolecules.

Keywords : tRNA acceptor stem; discriminator base; aminoacylation; identity elements; charge distribution; partial charges; local charge descriptors.

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