Published on Web 11/13/2007
Measurement of the Effect of Monovalent Cations on RNA Hairpin Stability Jeffrey Vieregg,* Wei Cheng, Carlos Bustamante,† and Ignacio Tinoco, Jr. Contribution from the Department of Physics and Department of Chemistry, UniVersity of California, Berkeley, and Physical Biosciences DiVision, Lawrence Berkeley National Laboratory, Berkeley, California 94720, and Howard Hughes Medical Institute, UniVersity of California, Berkeley, California Received June 29, 2007; E-mail:
[email protected] Abstract: Using optical tweezers, we have measured the effect of monovalent cation concentration and species on the folding free energy of five large (49-124 nt) RNA hairpins, including HIV-1 TAR and molecules approximating A‚U and G‚C homopolymers. RNA secondary structure thermodynamics are accurately described by a model consisting of nearest-neighbor interactions and additive loop and bulge terms. Melting of small (
