Quantifying the temperature dependence of glycine-betaine RNA duplex destabilization.
Glycine-betaine (GB) stabilizes folded protein structure because of its unfavorable thermodynamic interactions with amide oxygen and aliphatic carbon surface area exposed during protein unfolding. However, GB can attenuate nucleic acid secondary structure stability, although its mechanism of destabilization is not currently understood. Here we quantify GB interactions with the surface area exposed during thermal denaturation of nine RNA dodecamer duplexes with guanine-cytosine (GC) contents of 17-100%. Hyperchromicity values indicate increasing GB molality attenuates stacking. GB destabilizes higher-GC-content RNA duplexes to a greater extent than it does low-GC-content duplexes due to greater accumulation at the surface area exposed during unfolding. The accumulation is very sensitive to temperature and displays characteristic entropy-enthalpy compensation. Since the entropic contribution to the m-value (used to quantify GB interaction with the RNA solvent-accessible surface area exposed during denaturation) is more dependent on temperature than is the enthalpic contribution, higher-GC-content duplexes with their larger transition temperatures are destabilized to a greater extent than low-GC-content duplexes. The concentration of GB at the RNA surface area exposed during unfolding relative to bulk was quantified using the solute-partitioning model. Temperature correction predicts a GB concentration at 25 °C to be nearly independent of GC content, indicating that GB destabilizes all sequences equally at this temperature.
Department of Chemistry, St. Olaf College , Northfield, Minnesota 55057, United States.
Jeffrey J
JJ
Schwinefus
Ryan J
RJ
Menssen
James M
JM
Kohler
Elliot C
EC
Schmidt
Alexandra L
AL
Thomas
D000465:Algorithms; D001622:Betaine / Q000737:chemistry / Q000494:pharmacology*; D019277:Entropy; D020862:GC Rich Sequence / Q000187:drug effects; D006358:Hot Temperature; D007202:Indicators and Reagents / Q000737:chemistry / Q000494:pharmacology*; D008958:Models, Molecular; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D009843:Oligoribonucleotides / Q000737:chemistry*; D009994:Osmolar Concentration; D059370:RNA Folding / Q000187:drug effects; D020871:RNA Stability / Q000187:drug effects; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013499:Surface Properties / Q000187:drug effects; D044366:Transition Temperature / Q000187:drug effects
D007202:Indicators and Reagents; D009843:Oligoribonucleotides; D012330:RNA, Double-Stranded; D001622:Betaine