An approximation of loop free energy values of RNA H-pseudoknots
نویسندگان
چکیده
منابع مشابه
An Algorithm for RNA Pseudoknots
An RNA molecule is a heteropolymer, consisting of four types of nucleotides—uracil (U), adenine (A), guanine (G) and cytosine (C)—which are linked into a chain by phosphate bonds. The nucleotides then form saturating hydrogen bonds with one another, with A bonding to U and C bonding to G. These bonds cause the RNA to fold up into a stable, three dimensional structure. The structure is further s...
متن کاملFluorescence Competition Assay Measurements of Free Energy Changes for RNA Pseudoknots†
RNA pseudoknots have important functions, and thermodynamic stability is a key to predicting pseudoknots in RNA sequences and to understanding their functions. Traditional methods, such as UV melting and differential scanning calorimetry, for measuring RNA thermodynamics are restricted to temperature ranges around the melting temperature for a pseudoknot. Here, we report RNA pseudoknot free ene...
متن کاملPredicting loop-helix tertiary structural contacts in RNA pseudoknots.
Tertiary interactions between loops and helical stems play critical roles in the biological function of many RNA pseudoknots. However, quantitative predictions for RNA tertiary interactions remain elusive. Here we report a statistical mechanical model for the prediction of noncanonical loop-stem base-pairing interactions in RNA pseudoknots. Central to the model is the evaluation of the conforma...
متن کاملAn Iterated loop matching approach to the prediction of RNA secondary structures with pseudoknots
MOTIVATION Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to its difficulty in modeling. Although, several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On the other hand, comparative methods are more reliable, but are often done in an ad hoc manner and...
متن کاملAn Iterative Loop Matching Approach to the Prediction of RNA Secondary Structures with Pseudoknots
Motivation: Pseudoknots have generally been excluded from the prediction of RNA secondary structures due to the difficulty in modeling and complexity in computing. Although several dynamic programming algorithms exist for the prediction of pseudoknots using thermodynamic approaches, they are neither reliable nor efficient. On the other hand, comparative methods are more reliable, but are often ...
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ژورنال
عنوان ژورنال: RNA
سال: 1999
ISSN: 1355-8382
DOI: 10.1017/s135583829998189x