Effects of non-nearest neighbors on the thermodynamic stability of RNA GNRA hairpin tetraloops.

Biochemistry
Pamela L VanegasBrent M Znosko

Abstract

Currently, several models for predicting the secondary structure of RNA exist, one of which is free energy minimization using the Nearest Neighbor Model. This model predicts the lowest-free energy secondary structure from a primary sequence by summing the free energy contributions of the Watson-Crick nearest neighbor base pair combinations and any noncanonical secondary structure motif. The Nearest Neighbor Model also assumes that the free energy of the secondary structure motif is dependent solely on the identities of the nucleotides within the motif and the motif's nearest neighbors. To test the current assumption of the Nearest Neighbor Model that the non-nearest neighbors do not affect the stability of the motif, we optically melted different stem-loop oligonucleotides to experimentally determine their thermodynamic parameters. In each of these oligonucleotides, the hairpin loop sequence and the adjacent base pairs were held constant, while the first or second non-nearest neighbors were varied. The experimental results show that the thermodynamic contributions of the hairpin loop were dependent upon the identity of the first non-nearest neighbor, while the second non-nearest neighbor had a less obvious effect. These results...Continue Reading

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Citations

Jul 27, 2012·Current Opinion in Structural Biology·J P Bida, Rijhu Das
Sep 25, 2015·Nucleic Acids Research·Simon KettererMatthias Meier
Jul 13, 2016·Proceedings of the National Academy of Sciences of the United States of America·Fang-Chieh ChouRhiju Das
Aug 19, 2016·Dalton Transactions : an International Journal of Inorganic Chemistry·Srijana GhimireDavid R McMillin
Oct 11, 2013·Biochemistry·Zexiang Chen, Brent M Znosko
Jun 6, 2013·The Journal of Physical Chemistry. B·Lashan De SilvaShoujun Xu
Feb 2, 2018·Physical Chemistry Chemical Physics : PCCP·Carolyn E Carr, Luis A Marky
Jul 10, 2018·Nucleic Acids Research·Luigi D'AscenzoPascal Auffinger

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