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Nucleic Acids Research 2006 34(3):865-879; doi:10.1093/nar/gkj491
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Published online 6 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Article

Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions

Romina Oliva1,2,*, Luigi Cavallo3 and Anna Tramontano2

1Centro Linceo Interdisciplinare ‘Beniamino Segre’, Accademia dei Lincei I-00165 Rome, Italy 2Dipartimento di Scienze Biochimiche ‘A. Rossi Fanelli’, Università di Roma ‘La Sapienza’ I-00185 Rome, Italy 3Dipartimento di Chimica, Università di Salerno Via Salvador Allende, Baronissi (SA), I-84081, Italy

*To whom correspondence should be addressed. Tel: +39 06 49910957; Fax: +39 06 4440062; Email: romina.oliva{at}uniroma1.it

Received December 4, 2005. Revised January 19, 2006. Accepted January 19, 2006.

Tertiary interactions are crucial in maintaining the tRNA structure and functionality. We used a combined sequence analysis and quantum mechanics approach to calculate accurate energies of the most frequent tRNA tertiary base pairing interactions. Our analysis indicates that six out of the nine classical tertiary interactions are held in place mainly by H-bonds between the bases. In the remaining three cases other effects have to be considered. Tertiary base pairing interaction energies range from –8 to –38 kcal/mol in yeast tRNAPhe and are estimated to contribute roughly 25% of the overall tRNA base pairing interaction energy. Six analyzed posttranslational chemical modifications were shown to have minor effect on the geometry of the tertiary interactions. Modifications that introduce a positive charge strongly stabilize the corresponding tertiary interactions. Non-additive effects contribute to the stability of base triplets.


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