Reentrant Melting of RNA with Quenched Sequence Randomness

Abstract

The effect of quenched sequence disorder on the thermodynamics of RNA secondary structure formation is investigated for two- and four-letter alphabet models using the constrained annealing approach, from which the temperature behavior of the free energy, specific heat, and helicity is analytically obtained. For competing base pairing energies, the calculations reveal reentrant melting at low temperatures, in excellent agreement with numerical results. Our results suggest an additional mechanism for the experimental phenomenon of RNA cold denaturation.

Theoretical treatment of helix–coil transition of complexes DNA with two different ligands having different binding parameters

“…"Cold" denaturation phenomenon was observed experimentally for proteins and nucleic acids (Dubins et al, 2001;Mikulecky & Feig, 2002;Privalov, 1990). The mechanism of "cold" denaturation was addressed in a huge amount of publications (Badasyan et al, 2014;Hayrapetyan et al, 2014;Mikulecky & Feig, 2004;Privalov, 1990). The "cold" denaturation of DNA-ligand complex is accompanied by redistribution of ligands, bound with molten regions of DNA (see Figure 3, curve 3).…”

Cold denaturation of RNA secondary structures with loop entropy and quenched disorder

“…The explicit diagrams for the latter are showed in the second row and are obtained by considering the sum over all non-nested backbones with associated statistical weight given by eq. (11).…”

“…The molecule folding can be qualitatively and quantitatively addressed via the experimentally observable helicity degree defined as the average fraction of paired bases, which increases when lowering the temperature in the standard scenario. Here we will focus on a two-letter alphabet binding energy model with symbols chosen from the subset {U,A}, in the spirit of [3,11,17,23,27] which physically corresponds to the hydrophilic-hydrophobic model for protein folding [13]. Although this approximation is an oversimplification, it has proven to reproduce in a reasonable fashion the thermodynamics of these molecules and it is able to capture the essential physics behind the folding as well as the glass transition [23].…”

An Integrated Web-based Interactive Data Platform for Molecular Dynamics Simulations

“…Such large-scale simulations require HPC platform and massively parallelized MD computations. The main research focus of MolPhys YSU is the single and double-stranded nucleic, which require validation using MD simulations [18,19,20]. The combination of experimental and various computational methods can give us a deep understanding of the complex processes, behind the nucleic acids hybridization.…”