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

Ruth Nussinov | Zendy; Ignacio Tinoco | Zendy; Ann B. Jacobson | Zendy

Open Access

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

Author(s) -

Ruth Nussinov,

Ignacio Tinoco,

Ann B. Jacobson

Publication year - 1982

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/10.1.341

Subject(s) - biology , folding (dsp implementation) , protein secondary structure , rna , nucleic acid secondary structure , nucleotide , energy (signal processing) , nucleic acid structure , biophysics , genetics , computational biology , gene , physics , biochemistry , quantum mechanics , electrical engineering , engineering

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 secondary structure calculations on 2600 nucleotides in a single computer run.

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