Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate.
Modified nucleotides allow fundamental energetic and kinetic properties of nucleic acids to be probed. Here, we demonstrate that an RNA hairpin containing the nucleotide analogue 8-bromoguanosine (8BrG or G), gcUUCGgc, has enhanced stability relative to the unmodified hairpin, with DeltaDeltaG(37)(degrees)= -0.69 +/- 0.15 kcal mol(-1) and DeltaT(M) = +6.8 +/- 1.4 degrees C. NMR spectroscopic data suggest that the enhanced stability of gcUUCGgc does not arise from the native state; laser temperature-jump experiments support this notion, as gcUUCGgc and gcUUCGgc have similar unfolding rate constants, but the folding rate constant of gcUUCGgc is 4.1-fold faster at 37.5 degrees C and 2.8-fold faster under isoenergetic conditions. On the basis of these findings, we propose that 8BrG reduces the conformational entropy of the denatured state, resulting in an accelerated conformational search for the native state and enhanced stability.
Proctor
David J
DJ
Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania 16802, USA.
Ma
Hairong
H
Kierzek
Elzbieta
E
Kierzek
Ryszard
R
Gruebele
Martin
M
Bevilacqua
Philip C
PC
D020029:Base Pairing; D006151:Guanosine / Q000031:analogs & derivatives* / Q000737:chemistry*; D007700:Kinetics; D007834:Lasers; D008956:Models, Chemical; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry*; D013056:Spectrophotometry, Ultraviolet; D013696:Temperature; D013816:Thermodynamics; D014466:Ultraviolet Rays
D006151:Guanosine; C035169:8-bromoguanosine; D012313:RNA