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The energetics of small internal loops in RNA
Author(s) -
Schroeder Susan J.,
Burkard Mark E.,
Turner Douglas H.
Publication year - 1999
Publication title -
biopolymers
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.556
H-Index - 125
eISSN - 1097-0282
pISSN - 0006-3525
DOI - 10.1002/1097-0282(1999)52:4<157::aid-bip1001>3.0.co;2-e
Subject(s) - energetics , chemistry , stacking , base pair , rna , hydrogen bond , internal energy , sequence (biology) , chemical physics , crystallography , dna , thermodynamics , molecule , physics , biochemistry , organic chemistry , gene
The energetics of small internal loops are important for prediction of RNA secondary and tertiary structure, selection of drug target sites, and understanding RNA structure–function relationships. Hydrogen bonding, base stacking, electrostatic interactions, backbone distortion, and base‐pair size compatibility all contribute to the energetics of small internal loops. Thus, the sequence dependence of these energetics are idiosyncratic. Current approximations for predicting the free energies of internal loops consider size, asymmetry, closing base pairs, and the potential to form GA, GG, or UU pairs. The database of known three‐dimensional structures allows for comparison with the models used for predicting stability from sequence. © 2001 John Wiley & Sons, Inc. Biopoly (Nucleic Acid Sci) 52: 157–167, 1999/2000