Thermal stability of RNA hairpins containing a four-membered loop and a bulge nucleotide.
Fourteen RNA hairpins containing a four-membered loop and a bulge nucleotide were synthesized and their thermal stabilities determined. The combined contribution of a four-membered loop and bulge A to the free energy of a hairpin is calculated to be 9.3 kcal/mol at 37 degrees C and successfully predicts the stability of an independent RNA hairpin. The introduction of a bulge nucleotide to the helical stem of an RNA hairpin destabilizes the molecule in a sequence-dependent manner. The individual thermodynamic contributions of a four-membered loop and bulge A, G, and U residues to the stability of an RNA hairpin loop are presented.
Groebe
D R
DR
Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215.
Uhlenbeck
O C
OC
D001483:Base Sequence; D002851:Chromatography, High Pressure Liquid; D002855:Chromatography, Thin Layer; D004355:Drug Stability; D008433:Mathematics; D008962:Models, Theoretical; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009843:Oligoribonucleotides / Q000138:chemical synthesis; D012313:RNA / Q000138:chemical synthesis; D012259:Ribonuclease, Pancreatic; D013816:Thermodynamics
D009843:Oligoribonucleotides; D012313:RNA; D012259:Ribonuclease, Pancreatic