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

Romina Oliva*, Luigi Cavallo, Anna Tramontano

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

76 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)865-879
Number of pages15
Issue number3
StatePublished - 2006
Externally publishedYes

Bibliographical note

Funding Information:
This work was supported by University ‘La Sapienza’ of Rome (C26A039249) and by the Biosapiens Network of Excellence, European Commission FP6 Programme, contract number LHSG-CT-203-503265. R.O. is recipient of a postdoctoral grant from Centro Linceo Interdisciplinare ‘Beniamino Segre’, Accademia dei Lincei. Funding to pay the Open Access publication charges for this article was provided by EU.

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'Accurate energies of hydrogen bonded nucleic acid base pairs and triplets in tRNA tertiary interactions'. Together they form a unique fingerprint.

Cite this