IDENTIFICATION OF BASE-TRIPLES IN RNA USING COMPARATIVE SEQUENCE-ANALYSIS

被引：66

作者：

GAUTHERET, D ^{[1
]}

DAMBERGER, SH ^{[1
]}

GUTELL, RR ^{[1
]}

机构：

[1] UNIV COLORADO, DEPT MOLEC CELLULAR & DEV BIOL, BOULDER, CO 80309 USA

来源：

JOURNAL OF MOLECULAR BIOLOGY | 1995年 / 248卷 / 01期

关键词：

RNA STRUCTURE; COMPARATIVE SEQUENCE ANALYSIS; BASE-TRIPLES;

D O I：

10.1006/jmbi.1995.0200

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Comparative sequence analysis has proven to be a very efficient tool for the determination of RNA secondary structure and certain tertiary interactions. However, base-triples, an important RNA structural element, cannot be predicted accurately from sequence data. We show here that the poor base correlations observed at base-triple positions are the result of two factors. (1) Base covariation is not as strictly required in triples as it is in Watson-Crick pairs. (2) Base-triple structures are less conserved among homologous molecules. A particularity of known triple-helical regions is the presence of multiple base correlations that do not reflect direct pairing. We suggest that natural mutations in base-triples create structural changes that require compensatory mutations in adjacent base-pairs and triples to maintain the triple-helix conformation. On the basis of these observations, we devised two new measures of association that significantly enhance the base-triple signal in correlation studies. We evaluated correlations between base-pairs and single stranded bases, and correlations between adjacent base-pairs. Positions that score well in both analyses are the best triple candidates. This procedure correctly identifies triples, or interactions very close to the proposed triples, in type I and type II tRNAs and in the group I intron.

引用

页码：27 / 43

页数：17

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