Linked Life Data

7489516

Source:http://linkedlifedata.com/resource/pubmed/id/7489516

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
6
pubmed:dateCreated
1996-1-4
pubmed:abstractText
To increase our understanding of the dynamics and complexities of the RNA folding process, and therewith to improve our ability to predict RNA secondary structure by computational means, we have examined the foldings of a large number of phylogenetically and structurally diverse 16S and 16S-like rRNAs and compared these results with their comparatively derived secondary structures. Our initial goals are to establish the range of prediction success for this class of rRNAs, and to begin comparing and contrasting the foldings of these RNAs. We focus here on structural features that are predicted with confidence as well as those that are poorly predicted. Whereas the large set of Archaeal and (eu)Bacterial 16S rRNAs all fold well (69% and 55% respectively), some as high as 80%, many Eucarya and mitochondrial 16S rRNAs are poorly predicted (approximately 30%), with a few of these predicted as low as 10-20%. In general, base pairs interacting over a short distance and, in particular, those closing hairpin loops, are predicted significantly better than long-range base pairs and those closing multistem loops and bulges. The prediction success of hairpin loops varies, however, with their size and context. Analysis of some of the RNAs that do not fold well suggests that the composition of some hairpin loops (e.g., tetraloops) and the higher frequency of noncanonical pairs in their comparatively derived structures might contribute to these lower success rates. Eucarya and mitochondrial rRNAs reveal further novel tetraloop motifs, URRG/A and CRRG, that interchange with known stable tetraloop in the procaryotes.
pubmed:grant
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Aug
pubmed:issn
1355-8382
pubmed:author
pubmed:issnType
Print
pubmed:volume
1
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
559-74
pubmed:dateRevised
2011-8-16
pubmed:meshHeading
pubmed:year
1995
pubmed:articleTitle
A comparison of thermodynamic foldings with comparatively derived structures of 16S and 16S-like rRNAs.
pubmed:affiliation
Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder 80309-0347, USA.
pubmed:publicationType
Journal Article, Comparative Study, Research Support, U.S. Gov't, P.H.S., Research Support, Non-U.S. Gov't