Factors affecting thermodynamic stabilities of RNA 3 x 3 internal loops.
Internal loops in RNA are important for folding and function. The 3 x 3 nucleotide internal loops are the smallest size symmetric loops with a potential noncanonical base pair (middle pair) flanked on both sides by a noncanonical base pair (loop-terminal pair). Thermodynamic and structural insights acquired for 3 x 3 loops should improve approximations for stabilities of 3 x 3 and larger internal loops. Most natural 3 x 3 internal loops are purine rich, which is also true of other internal loops. A series of oligoribonucleotides containing different 3 x 3 internal loops were studied by UV melting and imino proton NMR. Both loop-terminal and middle pairs contribute to the thermodynamic stabilities of 3 x 3 loops. Extra stabilization of -1.2 kcal/mol was found for a GA middle pair when flanked by at least one non-pyrimidine-pyrimidine loop-terminal pair. A penalty of approximately 1 kcal/mol was found for loops with a single loop-terminal GA pair that has a U 3' to the G of the GA pair. A revised model for predicting stabilities of 3 x 3 loops is derived by multiple linear regression.
Chen
Gang
G
Department of Chemistry, University of Rochester, Rochester, New York 14627, USA.
Znosko
Brent M
BM
Jiao
Xiaoqi
X
Turner
Douglas H
DH
D020029:Base Pairing; D001483:Base Sequence; D009682:Magnetic Resonance Spectroscopy; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D011522:Protons; D012313:RNA / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D020871:RNA Stability; D013816:Thermodynamics
D011522:Protons; D012313:RNA