Theory for RNA Folding, Stretching, and Melting Including Loops and Salt

Theory for RNA folding, stretching, and melting including loops and salt.

Secondary structure formation of nucleic acids strongly depends on salt concentration and temperature. We develop a theory for RNA folding that correctly accounts for sequence effects, the entropic contributions associated with loop formation, and salt effects. Using an iterative expression for the partition function that neglects pseudoknots, we calculate folding free energies and minimum free...

RNA Folding and Large N Matrix Theory

We formulate the RNA folding problem as an N ×N matrix field theory. This matrix formalism allows us to give a systematic classification of the terms in the partition function according to their topological character. The theory is set up in such a way that the limit N →∞ yields the so-called secondary structure (Hartree theory). Tertiary structure and pseudo-knots are obtained by calculating t...

Stretching Folding Instablility and Nanoemulsion

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

The Kinefold web server provides a web interface for stochastic folding simulations of nucleic acids on second to minute molecular time scales. Renaturation or co-transcriptional folding paths are simulated at the level of helix formation and dissociation in agreement with the seminal experimental results. Pseudoknots and topologically 'entangled' helices (i.e. knots) are efficiently predicted ...

Stretching and folding in finite time.

Complex flows mix efficiently, and this process can be understood by considering the stretching and folding of material volumes. Although many metrics have been devised to characterize stretching, fewer are able to capture folding in a quantitative way in spatiotemporally variable flows. Here, we extend our previous methods based on the finite-time curving of fluid-element trajectories to nonze...