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Albany 2015:Book of Abstracts

Albany 2015
Conversation 19
June 9-13 2015
©Adenine Press (2012)

Force and temperature dependent folding of a 2-base-pair RNA kissing complex

The stability and function of proteins from thermophilic species can vary with temperature in a complex manner. However, in considering nucleic acids, ΔH is typically assumed to be constant when interpreting thermal melting results. Here we use temperature controlled optical tweezers or "thermal tweezers" to mechanically characterize the folding thermodynamics of a 2-base-pair kissing complex from the Moloney murine leukemia virus (MMLV) at temperatures ranging from 22°C to 42°C. At each temperature the folding free energy is directly determined from the reversible mechanical work to unfold the kissing complex. Surprisingly, the folding free energy of this basic RNA tertiary interaction depends non-linearly on temperature, indicating that ΔH changes with temperature. Based on mutational perturbation and molecular dynamics simulations, this non-linearity is attributed to the presence of a multi-step, temperature-sensitive, unfolding pathway. Specifically, at elevated temperatures, the unpaired flanking adenine bases in the hairpin loops are flipped out of their respective stacking positions, exposing the underlying kissing base pairs to water, thus reducing their stability. Our study suggests that at mesophilic temperatures, single-stranded residues can be thermally influenced, which may provide profound insights into temperature-dependent RNA folding and conformational dynamics.

William Stephenson1
Ashely Colvin2
Alan A. Chen 2, 3
Pan T.X. Li 2, 4

1 College of Nanoscale Science and Engineering
SUNY Polytechnic Institute
257 Fuller Rd.
Albany, NY 12203
2 The RNA Institute,
3 Department of Chemistry,
4Depatment of Biological Sciences
University at Albany
Albany, NY 12222

wstephenson@albany.edu