1,119 research outputs found
Salt Effects on the Thermodynamics of a Frameshifting RNA Pseudoknot under Tension
Because of the potential link between -1 programmed ribosomal frameshifting
and response of a pseudoknot (PK) RNA to force, a number of single molecule
pulling experiments have been performed on PKs to decipher the mechanism of
programmed ribosomal frameshifting. Motivated in part by these experiments, we
performed simulations using a coarse-grained model of RNA to describe the
response of a PK over a range of mechanical forces (s) and monovalent salt
concentrations (s). The coarse-grained simulations quantitatively reproduce
the multistep thermal melting observed in experiments, thus validating our
model. The free energy changes obtained in simulations are in excellent
agreement with experiments. By varying and , we calculated the phase
diagram that shows a sequence of structural transitions, populating distinct
intermediate states. As and are changed, the stem-loop tertiary
interactions rupture first, followed by unfolding of the -end
hairpin (). Finally, the
-end hairpin unravels, producing an extended state
(). A theoretical analysis of the phase
boundaries shows that the critical force for rupture scales as with for
() transition. This relation is used to
obtain the preferential ion-RNA interaction coefficient, which can be
quantitatively measured in single-molecule experiments, as done previously for
DNA hairpins. A by-product of our work is the suggestion that the frameshift
efficiency is likely determined by the stability of the -end
hairpin that the ribosome first encounters during translation.Comment: Final draft accepted in Journal of Molecular Biology, 16 pages
including Supporting Informatio
A Seeded Genetic Algorithm for RNA Secondary Structural Prediction with Pseudoknots
This work explores a new approach in using genetic algorithm to predict RNA secondary structures with pseudoknots. Since only a small portion of most RNA structures is comprised of pseudoknots, the majority of structural elements from an optimal pseudoknot-free structure are likely to be part of the true structure. Thus seeding the genetic algorithm with optimal pseudoknot-free structures will more likely lead it to the true structure than a randomly generated population. The genetic algorithm uses the known energy models with an additional augmentation to allow complex pseudoknots. The nearest-neighbor energy model is used in conjunction with Turner’s thermodynamic parameters for pseudoknot-free structures, and the H-type pseudoknot energy estimation for simple pseudoknots. Testing with known pseudoknot sequences from PseudoBase shows that it out performs some of the current popular algorithms
Prediction of RNA pseudoknots by Monte Carlo simulations
In this paper we consider the problem of RNA folding with pseudoknots. We use
a graphical representation in which the secondary structures are described by
planar diagrams. Pseudoknots are identified as non-planar diagrams. We analyze
the non-planar topologies of RNA structures and propose a classification of RNA
pseudoknots according to the minimal genus of the surface on which the RNA
structure can be embedded. This classification provides a simple and natural
way to tackle the problem of RNA folding prediction in presence of pseudoknots.
Based on that approach, we describe a Monte Carlo algorithm for the prediction
of pseudoknots in an RNA molecule.Comment: 22 pages, 14 figure
TT2NE: A novel algorithm to predict RNA secondary structures with pseudoknots
We present TT2NE, a new algorithm to predict RNA secondary structures with
pseudoknots. The method is based on a classification of RNA structures
according to their topological genus. TT2NE guarantees to find the minimum free
energy structure irrespectively of pseudoknot topology. This unique proficiency
is obtained at the expense of the maximum length of sequence that can be
treated but comparison with state-of-the-art algorithms shows that TT2NE is a
very powerful tool within its limits. Analysis of TT2NE's wrong predictions
sheds light on the need to study how sterical constraints limit the range of
pseudoknotted structures that can be formed from a given sequence. An
implementation of TT2NE on a public server can be found at
http://ipht.cea.fr/rna/tt2ne.php
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