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

The critical behavior of ribonucleic acid (RNA) secondary structures with quenched sequence randomness is studied by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In addition to the expected melting at high temperature, a cold-melting transition appears when the disorder strength induces competition between favorable and unfavorable base pairs. Our results suggest that the cold denaturation of RNA found experimentally might be triggered by quenched sequence disorder. We calculate hot- and cold-melting critical temperatures for competing favorable and unfavorable base-pair energies and present a folding phase diagram as a function of the loop exponent and temperature

Osmotic pressure induced coupling between cooperativity and stability of a helix-coil transition

Most helix-coil transition theories can be characterized by a set of three parameters: energetic, describing the (free) energy cost of forming a helical state in one repeating unit; entropic, accounting for the decrease of entropy due to the helical state formation; and geometric, indicating how many repeating units are affected by the formation of one helical state. Depending on their effect on the helix-coil transition, solvents or co-solutes can be classified with respect to their action on these parameters. Solvent interactions that alter the entropic cost of helix formation by their osmotic action can affect both the stability (transition temperature) and the cooperativity (transition interval) of the helix-coil transition. A consistent inclusion of osmotic pressure effects in a description of helix-coil transition for poly(L-glutamic acid) in solution with polyethylene glycol can offer an explanation of the experimentally observed linear dependence of transition temperature on osmotic pressure as well as the concurrent changes in the cooperativity of the transition.Comment: 5 pages, 3 figures. To be submitted to Phys.Rev.Let

Microscopic formulation of the Zimm-Bragg model for the helix-coil transition

A microscopic spin model is proposed for the phenomenological Zimm-Bragg model for the helix-coil transition in biopolymers. This model is shown to provide the same thermophysical properties of the original Zimm-Bragg model and it allows a very convenient framework to compute statistical quantities. Physical origins of this spin model are made transparent by an exact mapping into a one-dimensional Ising model with an external field. However, the dependence on temperature of the reduced external field turns out to differ from the standard one-dimensional Ising model and hence it gives rise to different thermophysical properties, despite the exact mapping connecting them. We discuss how this point has been frequently overlooked in the recent literature.Comment: 11 pages, 2 figure

Reentrant Melting of RNA with Quenched Sequence Randomness

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

Competition for hydrogen-bond formation in the helix-coil transition and protein folding

The problem of the helix-coil transition of biopolymers in explicit solvents, such as water, with the ability for hydrogen bonding with a solvent is addressed analytically using a suitably modified version of the Generalized Model of Polypeptide Chains. Besides the regular helix-coil transition, an additional coil-helix or reentrant transition is also found at lower temperatures. The reentrant transition arises due to competition between polymer-polymer and polymer-water hydrogen bonds. The balance between the two types of hydrogen bonding can be shifted to either direction through changes not only in temperature, but also by pressure, mechanical force, osmotic stress, or other external influences. Both polypeptides and polynucleotides are considered within a unified formalism. Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a significant level of agreement is obtained