Department of Microbiology, State University of New York at Stony Brook 11794-5222.
J Mol Biol 233: 261-9 (1993)
Abstract
We have predicted the secondary structure of the entire 4217 nucleotide
sequence of the genomic RNA of coliphage Q beta in one computer run
using the computer program MFOLD that computes RNA structures within any
prescribed increment of the computed minimum free energy. The results
are presented in the form of an "energy dot plot" that shows both an
optimal folding as well as the superposition of all base-pairs that can
form in slightly suboptimal foldings. The plot reveals five large,
well-determined, independent structural domains that cover approximately
50% of the viral genome. The predicted structural domains are
consistent with and provide support for five large structural domains
identified previously by quantitative electron microscopy in Q beta RNA.
The dot plot also contains cluttered regions that indicate large
numbers of alternative foldings within or between segments of an RNA
molecule. These reflect the impossibility of accurate structure
prediction and/or the biological reality of more than one folding.
Weaker, long range structures, that are observed by electron microscopy
in two alternate competing conformations, are located in the regions of
the Q beta sequence that correspond to cluttered regions of the dot
plot. The potential biological significance of these secondary
structures is discussed.
Mesh Headings
Unique Identifier: 93389747
Chemical Identifiers (Names)