Effects of Salt, Polyethylene Glycol, and Locked Nucleic Acids on the Thermodynamic Stabilities of Consecutive Terminal Adenosine Mismatches in RNA Duplexes

Consecutive terminal mismatches add thermodynamic stability to RNA duplexes and occur frequently in microRNA-mRNA interactions. Accurate thermodynamic stabilities of consecutive terminal mismatches contribute to the development of specific, high-affinity siRNA therapeutics. Consecutive terminal aden...

Full description

Saved in:
Bibliographic Details
Published in:The journal of physical chemistry. B 2013-04, Vol.117 (13), p.3531-3540
Main Authors: Gu, Xiaobo, Nguyen, Mai-Thao, Overacre, Abigail, Seaton, Samantha, Schroeder, Susan J.
Format: Article
Language:English
Subjects:
Adenosine - chemistry
Adenosines
Analytical, structural and metabolic biochemistry
Biological and medical sciences
Free energy
Fundamental and applied biological sciences. Psychology
Mathematical models
MicroRNAs - chemistry
Nucleic acids
Nucleic Acids - chemistry
Polyethylene glycol
Polyethylene Glycols - chemistry
Ribonucleic acids
RNA, Messenger - chemistry
Rna, ribonucleoproteins
Salts - chemistry
Sodium Chloride - chemistry
Stability
Terminals
Thermodynamics
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Consecutive terminal mismatches add thermodynamic stability to RNA duplexes and occur frequently in microRNA-mRNA interactions. Accurate thermodynamic stabilities of consecutive terminal mismatches contribute to the development of specific, high-affinity siRNA therapeutics. Consecutive terminal adenosine mismatches (TAMS) are studied at different salt concentrations, with polyethylene glycol cosolutes, and with locked nucleic acid (LNA) substitutions. These measurements provide benchmarks for the application of thermodynamic predictions to different physiological or therapeutic conditions. The salt dependence for RNA duplex stability is similar for TAMS, internal loops, and Watson–Crick duplexes. A unified model for predicting the free energy of an RNA duplex with or without loops and mismatches at lower sodium concentrations is presented. The destabilizing effects of PEG 200 are larger for TAMS than internal loops or Watson–Crick duplexes, which may result from different base stacking conformations, dynamics, and water hydration. In contrast, LNA substitutions stabilize internal loops much more than TAMS. Surprisingly, the average per adenosine increase in stability for LNA substitutions in internal loops is −1.82 kcal/mol and only −0.20 kcal/mol for TAMS. The stabilities of TAMS and internal loops with LNA substitutions have similar favorable free energies. Thus, the unfavorable free energy of adenosine internal loops is largely an entropic effect. The favorable stabilities of TAMS result mainly from base stacking. The ability of RNA duplexes to form extended terminal mismatches in the absence of proteins such as argonaute and identifying the enthalpic contributions to terminal mismatch stabilities provide insight into the physical basis of microRNA–mRNA molecular recognition and specificity.
ISSN:1520-6106
1520-5207
DOI:10.1021/jp312154d