Related papers: Ion Condensation onto Ribozyme is Site-Specific an…
The translocation of structured RNA or DNA molecules through narrow pores necessitates the opening of all base pairs. Here, we study the interplay between the dynamics of translocation and base-pairing theoretically, using kinetic Monte…
RNA-binding proteins form biomolecular condensates with RNA through phase separation, playing crucial roles in various cellular processes. While intrinsically disordered regions (IDRs) are key drivers of phase separation, additional factors…
The structure and dynamics of negatively charged nucleic acids strongly correlate with the concentration and charge of the oppositely charged counter-ions. It is well known that the structural collapse of DNA is favored in the presence of…
The radiation-induced damages in bio-molecules are ubiquitous processes in radiotherapy, radio-biology and critical to space-projects. In this study we present a precise quantification of the fragmentation mechanisms of deoxyribonucleic…
Adsorption of monovalent and multivalent cat- and anions on a deoxyribose nucleic acid (DNA) molecule from a salt solution is investigated by computer simulation. The ions are modelled as charged hard spheres, the DNA molecule as a point…
Non-coding RNA sequences play a great role in controlling a number of cellular functions, thus raising the need to understand their complex conformational dynamics in quantitative detail. In this perspective, we first show that single…
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, structurally disordered RNA-binding domains of virus coat…
Riboswitches, RNA elements found in the untranslated region, regulate gene expression by binding to target metaboloites with exquisite specificity. Binding of metabolites to the conserved aptamer domain allosterically alters the…
In partially ionized plasma, where ions can be in different ionization states, each charge state can be described as a different fluid for the purpose of multi-ion collisional transport. In the case of two charge states, transport pushes…
In the course of our investigations of the adsorption of ions to the air-water interface, we previously reported the surprising result that doubly-charged carbonate anions exhibit a stronger surface affinity than do singly-charged…
The interaction of phosphate groups with ions in an aqueous environment has a strong impact on the structure and folding processes of DNA and RNA. The dynamic variety of ionic arrangements, including both contact pairs and water separated…
Fundamental studies of the effect of specific ions on hydrophobic interactions are driven by the need to understand phenomena such as hydrophobically driven self-assembly or protein folding. Using beta-peptide-inspired nano-rods, we…
Solvation of ions is ubiquitous on our planet. Solvated ions have a profound effect on the behavior of ionic solutions, which is crucial in nature and technology. Experimentally, ions have been classified into "structure makers" or…
Ion specificity and related Hofmeister effects, ubiquitous in aqueous systems, can have spectacular consequences in hydrated clays, where ion-specific nanoscale surface forces can determine large scale cohesive, swelling and shrinkage…
Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological…
Proteins' fuzziness are features for communicating changes in cell signaling instigated by binding with secondary messengers, such as calcium ions, associated with the coordination of muscle contraction, neurotransmitter release, and gene…
The effect of polyvalent molecular cations, such as spermine, on the condensation of DNA into very well-defined toroidal shapes have been well studied and understood. However, a great effort has been made trying to obtain similar condensed…
The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming non-specific…
As a consequence of the rugged landscape of RNA molecules their folding is described by the kinetic partitioning mechanism according to which only a small fraction ($\phi_F$) reaches the folded state while the remaining fraction of…
Mode-coupling theory provides a unified description of the rotational and translational dynamics of polyatomic ions. These molecular ions are distinct from usual models of ion diffusion, such as K+ , Cl- etc., and also different from…