ArticleNucleic acids research1997
Inferring the conformation of RNA base pairs and triples from patterns of sequence variation.
Article in Nucleic acids research, 1997. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- An innate twist between Crick's wobble and Watson-Crick base pairs.RNA (New York, N.Y.) · 2013Review
- Article
- Predicting and modeling RNA architecture.Cold Spring Harbor perspectives in biology · 2011Review
- Structural characterization of naturally occurring RNA single mismatches.Nucleic acids research · 2011Article
- Saturation mutagenesis of a +1 programmed frameshift-inducing mRNA sequence derived from a yeast retrotransposon.RNA (New York, N.Y.) · 2007Article
- CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.Nucleic acids research · 2006Article
- The non-Watson-Crick base pairs and their associated isostericity matrices.Nucleic acids research · 2002Article
- Comparative analysis of more than 3000 sequences reveals the existence of two pseudoknots in area V4 of eukaryotic small subunit ribosomal RNA.Nucleic acids research · 2000Article
- Coupled nucleotide covariations reveal dynamic RNA interaction patterns.RNA (New York, N.Y.) · 2000Review
- Identity and geometry of a base triple in 16S rRNA determined by comparative sequence analysis and molecular modeling.RNA (New York, N.Y.) · 1999Article
- Molecular dynamics simulations of solvated yeast tRNA(Asp).Biophysical journal · 1999Article
- Conformational specificity of non-canonical base pairs and higher order structures in nucleic acids: crystal structure database analysis.Journal of computer-aided molecular designArticle
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The success of comparative analysis in resolving RNA secondary structure and numerous tertiary interactions relies on the presence of base covariations. Although the majority of base covariations in aligned sequences is associated to Watson-Crick base pairs, many involve non-canonical or restricted base pair exchanges (e.g. only G:C/A:U), reflecting more specific structural constraints. We have developed a computer program that determines potential base pairing conformations for a given set of paired nucleotides in a sequence alignment. This program (ISOPAIR) assumes that the base pair conformation is maintained through sequence variation without significantly affecting the path of the sugar-phosphate backbone. ISOPAIR identifies such 'isomorphic' structures for any set of input base pair or base triple sequences. The program was applied to base pairs and triples with known structures and sequence exchanges. In several instances, isomorphic structures were correctly identified with ISOPAIR. Thus, ISOPAIR is useful when assessing non-canonical base pair conformations in comparative analysis. ISOPAIR applications are limited to those cases where unusual base pair exchanges indeed reflect a non-canonical conformation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.