Predicting common foldings of homologous RNAs.

Le SY; Zuker M

Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario.

J Biomol Struct Dyn 8: 1027-44 (1991)

Abstract
A new approach is proposed for determining common RNA secondary structures within a set of homologous RNAs. The approach is a combination of phylogenetic and thermodynamic methods which is based on the prediction of optimal and suboptimal secondary structures, topological similarity searches and phylogenetic comparative analysis. The optimal and suboptimal RNA secondary structures are predicted by energy minimization. Structural comparison of the predicted RNA secondary structures is used to find conserved structures that are topologically similar in all these homologous RNAs. The validity of the conserved structural elements found is then checked by phylogenetic comparison of the sequences. This procedure is used to predict common structures of ribonuclease P (RNAase P) RNAs.

Mesh Headings

Algorithms

Bacteria

Base Sequence

Computer Simulation

Endoribonucleases*

Molecular Sequence Data

Nucleic Acid Conformation

Phylogeny

RNA*

RNA, Bacterial

RNA, Catalytic*

Sequence Homology, Nucleic Acid

Thermodynamics

Unique Identifier: 91345773

Chemical Identifiers (Names)

EC 3.1.- (Endoribonucleases)

EC 3.1.26.5 (ribonuclease P)

9010-74-6 (RNA, Bacterial)