Models for pairing of IS10 encoded antisense RNAs in vivo

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Antisense regulation of IS10 transposase synthesis is mediated by a small RNA molecule, RNA-OUT which is complementary to the 5' region of the IS10 transposase mRNA, RNA-IN. Pairing between the two species in vivo prevents initiation of RNA-IN translation by steric occlusion of the ribosome binding site. The goal of this work is to develop a mathematical basis for antisense repression in vivo. Thus, by modeling antisense pairing as a bimolecular reaction in vivo, I have developed equations which relate the degree of translation inhibition to a relative pairing rate constant, k, and the in vivo RNA-OUT concentration. Using the methodology developed here, an analysis of mutations in the first three 5' bases of RNA-IN reveals a semi-logarithmic relationship between k and ΔG, the estimated change in the free energy of pairing. Such correlations are not observed for mutations at other positions, implicating only the first three 5' bases of RNA-IN in the formation of a pairing nucleus with RNA-OUT. Finally, an analysis of mutations that affect antisense action at a post-nucleation step has been undertaken here and a specific model for how these mutations may affect antisense pairing is discussed.

Original languageEnglish
Pages (from-to)431-439
Number of pages9
JournalJournal of Theoretical Biology
Volume186
Issue number4
DOIs
StatePublished - Jun 21 1997
Externally publishedYes

Fingerprint

antisense RNA
Antisense RNA
RNA
Pairing
Mutation
mutation
Model
translation (genetics)
Rate Constant
Nucleation
Occlusion
Messenger RNA
Nucleus
Free Energy
Logarithmic
Binding sites
ribosomes
Ribosomes
Molecules
Synthesis

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Models for pairing of IS10 encoded antisense RNAs in vivo. / Jain, Chaitanya.

In: Journal of Theoretical Biology, Vol. 186, No. 4, 21.06.1997, p. 431-439.

Research output: Contribution to journalArticle

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