Base-pair ambiguity and the kinetics of RNA folding
نویسندگان
چکیده
منابع مشابه
RNA hairpin-folding kinetics.
Based on the complete ensemble of hairpin conformations, a statistical mechanical model that combines the eigenvalue solutions of the rate matrix and the free-energy landscapes has been able to predict the temperature-dependent folding rate, kinetic intermediates, and folding pathways for hairpin-forming RNA sequences. At temperatures higher than a "glass transition" temperature, T(g), the eige...
متن کاملKinetics of Folding of Proteins and RNA
The assembly of biological molecules, most notably globular proteins1 and RNA,2,3 into unique threedimensional structures with well-defined topology is a complex and fascinating phenomenon in molecular biology. There are two aspects to the problem of folding of proteins and RNA. The first is the prediction of the three-dimensional structure of the folded state from the one-dimensional primary s...
متن کاملBiphasic folding kinetics of RNA pseudoknots and telomerase RNA activity.
Using a combined master equation and kinetic cluster approach, we investigate RNA pseudoknot folding and unfolding kinetics. The energetic parameters are computed from a recently developed Vfold model for RNA secondary structure and pseudoknot folding thermodynamics. The folding kinetics theory is based on the complete conformational ensemble, including all the native-like and non-native states...
متن کاملRNA folding: conformational statistics, folding kinetics, and ion electrostatics.
RNA folding is a remarkably complex problem that involves ion-mediated electrostatic interaction, conformational entropy, base pairing and stacking, and noncanonical interactions. During the past decade, results from a variety of experimental and theoretical studies pointed to (a) the potential ion correlation effect in Mg2+-RNA interactions, (b) the rugged energy landscapes and multistate RNA ...
متن کاملFast, Approximate Kinetics of RNA Folding
In this article, we introduce the software suite Hermes, which provides fast, novel algorithms for RNA secondary structure kinetics. Using the fast Fourier transform to efficiently compute the Boltzmann probability that a secondary structure S of a given RNA sequence has base pair distance x (resp. y) from reference structure A (resp. B), Hermes computes the exact kinetics of folding from A to ...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: BMC Bioinformatics
سال: 2019
ISSN: 1471-2105
DOI: 10.1186/s12859-019-3303-6