Related papers: Polymerization and replication of primordial RNA i…

Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…

Background. Dramatic increases in RNA structural data have made it possible to recognize its conformational preferences much better than a decade ago. This has created an opportunity to use discrete restraint-based conformational sampling…

Long non-coding RNA, microRNA, and messenger RNA enable key regulations of various biological processes through a variety of diverse interaction mechanisms. Identifying the interactions and cross-talk between these heterogeneous RNA classes…

DNA origami is a powerful method to achieve nanoscale folded structures. Despite rapid improvements in folding and purification methods, DNA origami objects are still often produced in small quantities and studied at single molecule scale.…

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…

Recently the physical characterization of a number of biological processes has proven indispensable for a full understanding of natural phenomena. One such example is the mechanical properties of transcription, which have been shown to have…

Non-equilibrium selection pressures were proposed for the formation of oligonucleotides with rich functionalities encoded in their sequences, such as catalysis. Since phase separation was shown to direct various chemical processes, we ask…

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly…

We study DNA adsorption and renaturation in a water-phenol two-phase system, with or without shaking. In very dilute solutions, single-stranded DNA is adsorbed at the interface in a salt-dependent manner. At high salt concentrations the…

Urea, a polar molecule with a large dipole moment, not only destabilizes the folded RNA structures, but can also enhance the folding rates of large ribozymes. Unlike the mechanism of urea-induced unfolding of proteins, which is well…

Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…

RNA molecules are single-stranded analogues of DNA that can fold into various structures which influence their biological function within the cell. RNA structures can be modelled combinatorially in terms of a certain type of graph called an…

Biological sequences encode fundamental instructions for the building blocks of life, in the form of DNA, RNA, and proteins. Modeling these sequences is key to understand disease mechanisms and is an active research area in computational…

The RNA inverse folding problem, a key challenge in RNA design, involves identifying nucleotide sequences that can fold into desired secondary structures, which are critical for ensuring molecular stability and function. The inherent…

The telegraph model is the standard model of stochastic gene expression, which can be solved exactly to obtain the distribution of mature RNA numbers per cell. A modification of this model also leads to an analytical distribution of the…

In many applications of shape analysis, lengths between some landmarks are constrained. For instance, biomolecules often have some bond lengths and some bond angles constrained, and variation occurs only along unconstrained bonds and…

Genetic robustness, the preservation of an optimal phenotype in the face of mutations, is critical to the understanding of evolution as phenotypically expressed genetic variation is the fuel of natural selection. The origin of genetic…

We construct a minimalist model of RNA secondary-structure formation and use it to study the mapping from sequence to structure. There are strong, qualitative differences between two-letter and four or six-letter alphabets. With only two…

Genes with similar transcriptional activation kinetics can display very different temporal mRNA profiles due to differences in transcription time, degradation rate and RNA processing kinetics. Recent studies have shown that a…

The water hydration shell has decisive impact on the structural and functional properties of RNA. Changes of RNA structure upon melting and in biochemical processes are accompanied by a change of hydration patterns, a process which is…