Conformational and solvent entropy contributions to the thermal response of nucleic acid-based nanothermometers.
With device miniaturization comes the need to measure temperature changes on molecular scales. Recent experiments show that thermoresponsive devices may be constructed based on the temperature-dependence of the relative populations of left- and right-handed nucleic acid helical conformations: upon an increase in temperature, particular sequences of DNA oligonucleotide duplexes in high salt conditions switch from a left-handed (Z) form to a right-handed (B) one, while RNA responds inversely by switching from a right- (A) to a left-handed (Z) form. We use existing temperature-dependent circular dichroism experimental data [Tashiro and Sugiyama, 2005] and a two-state model to extract the entropic contribution to the free energy difference between left- and right-handed form. Then, to address the microscopic origin of the inverse temperature response of RNA and DNA, we perform all-atom molecular dynamics simulations from which we compute both configurational nucleic acid and solvent entropies for a number of RNA and DNA systems; because the ionic conditions in the experiments are outside the physiological range, we cover a wider landscape of sequence, salt conditions, and helical direction. Calculations reveal a complex interplay between configurational, water, and ionic entropies, which, combined with the sequence-dependence, rationalize the experimentally observed transitions from A- to Z-RNA and Z- to B-DNA in high salt concentrations and provide insight that may aid future developments of the use of nucleic acids oligomers for thermal sensing at the nanoscale in physiological conditions.
Wereszczynski
Jeff
J
Department of Chemistry, University of California, Irvine, California 92697, USA.
Andricioaei
Ioan
I
D004247:DNA / Q000737:chemistry*; D019277:Entropy; D056004:Molecular Dynamics Simulation; D036103:Nanotechnology; D012313:RNA / Q000737:chemistry*; D013696:Temperature
D012313:RNA; D004247:DNA