Small changes in free energy assignments for unpaid bases do not affect predicted secondary structures in single stranded RNA

Ruth Nussinov*, Ignacio Tinoco, Ann B. Jacobson

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

We present extensive calculations of the secondary structure of mRNA which point to its insensitivity to small changes in the free energy assignments of single stranded regions. Truncating the free energies of hairpin loops, bulges, internal loops and multibranched junctions to two significant digits yields structures nearly identical to those generated using three digit values. The results show that one can safely use truncated values in RNA folding calculations. The implementation of these results enabled us to carry out second ary structure calculations on 2600 nucleotides in a single computer run.

Original languageEnglish
Pages (from-to)341-349
Number of pages9
JournalNucleic Acids Research
Volume10
Issue number1
DOIs
StatePublished - 11 Jan 1982
Externally publishedYes

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