Apical Loop-Internal Loop RNA Pseudoknots
نویسندگان
چکیده
منابع مشابه
Predicting 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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The TAR hairpin of the HIV-1 RNA genome is indispensable for trans-activation of the viral promoter and virus replication. The TAR structure has been studied extensively, but most attention has been directed at the three-nucleotide bulge that constitutes the binding site of the viral Tat protein. In contrast, the conformational properties of the apical loop have remained elusive. We performed b...
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The essential splicing factor Prp24 contains four RNA Recognition Motif (RRM) domains, and functions to anneal U6 and U4 RNAs during spliceosome assembly. Here, we report the structure and characterization of the C-terminal RRM4. This domain adopts a novel non-canonical RRM fold with two additional flanking α-helices that occlude its β-sheet face, forming an occluded RRM (oRRM) domain. The flan...
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ژورنال
عنوان ژورنال: Journal of Biological Chemistry
سال: 2008
ISSN: 0021-9258
DOI: 10.1074/jbc.m802829200