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Proc Natl Acad Sci U S A. Jun 1975; 72(6): 2017–2021.
PMCID: PMC432683

Method for predicting RNA secondary structure.


We report a method for predicting the most stable secondary structure of RNA from its primary sequence of nucleotides. The technique consists of a series of three computer programs interfaced to take the nucleotide sequence of any RNA and (a) list all possible helical regions, using modified Watson-Crick base-pairing rules; (b) create all possible secondary structures by forming permutations of compatible helical regions; and (c)evaluate each structure for total free energy of formation from a completely extended chain. A free energy distribution and the base-by-base bonding interactions of each possible structure are catalogued by the system and are readily available for examination. The method has been applied to 62 tRNA sequences. The total free-energy of the predicted most stable structures ranged from -19 to -41 kcal/mole (-22 to -49 kJ/mole). The number of structures created was also highly sequence-dependent and ranged from 200 to 13,000. In nearly all cases the cloverleaf is predicted to be the structure with the lowest free energy of formation.

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  • Gartland WJ, Sueoka N. Two interconvertible forms of tryptophanyl sRNA in E. coli. Proc Natl Acad Sci U S A. 1966 Apr;55(4):948–956. [PMC free article] [PubMed]
  • Fresco JR, Adams A, Ascione R, Henley D, Lindahl T. Tertiary structure in transfer ribonucleic acids. Cold Spring Harb Symp Quant Biol. 1966;31:527–537. [PubMed]
  • Goldberger RF. Autogenous regulation of gene expression. Science. 1974 Mar 1;183(4127):810–816. [PubMed]
  • Pace NR. Structure and synthesis of the ribosomal ribonucleic acid of prokaryotes. Bacteriol Rev. 1973 Dec;37(4):562–603. [PMC free article] [PubMed]
  • Gralla J, Steitz JA, Crothers DM. Direct physical evidence for secondary structure in an isolated fragment of R17 bacteriophage mRNA. Nature. 1974 Mar 15;248(445):204–208. [PubMed]
  • Weissmann C, Billeter MA, Goodman HM, Hindley J, Weber H. Structure and function of phage RNA. Annu Rev Biochem. 1973;42:303–328. [PubMed]
  • FRESCO JR, ALBERTS BM, DOTY P. Some molecular details of the secondary structure of ribonucleic acid. Nature. 1960 Oct 8;188:98–101. [PubMed]
  • Tumanian VG, Sotnikova LE, Kholopov AV. Ob opredelenii vtorichnoi struktury RNK po posledovatel'nosti nukleotidov. Dokl Akad Nauk SSSR. 1966 Feb 21;166(6):1465–1468. [PubMed]
  • Delisi C, Crothers DM. Prediction of RNA secondary structure. Proc Natl Acad Sci U S A. 1971 Nov;68(11):2682–2685. [PMC free article] [PubMed]
  • Tinoco I, Jr, Uhlenbeck OC, Levine MD. Estimation of secondary structure in ribonucleic acids. Nature. 1971 Apr 9;230(5293):362–367. [PubMed]
  • Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. II. Small hairpin loops. J Mol Biol. 1973 Feb 5;73(4):497–511. [PubMed]
  • Cole PE, Yang SK, Crothers DM. Conformational changes of transfer ribonucleic acid. Equilibrium phase diagrams. Biochemistry. 1972 Nov 7;11(23):4358–4368. [PubMed]
  • Crothers DM, Cole PE, Hilbers CW, Shulman RG. The molecular mechanism of thermal unfolding of Escherichia coli formylmethionine transfer RNA. J Mol Biol. 1974 Jul 25;87(1):63–88. [PubMed]
  • Shulman RG, Hilbers CW, Wong YP, Wong KL, Lightfoot DR, Reid BR, Kearns DR. Determination of secondary and tertiary structural features of transfer RNA molecules in solution by nuclear magnetic resonance. Proc Natl Acad Sci U S A. 1973 Jul;70(7):2042–2045. [PMC free article] [PubMed]
  • Robertus JD, Ladner JE, Finch JT, Rhodes D, Brown RS, Clark BF, Klug A. Structure of yeast phenylalanine tRNA at 3 A resolution. Nature. 1974 Aug 16;250(467):546–551. [PubMed]
  • Kim SH, Suddath FL, Quigley GJ, McPherson A, Sussman JL, Wang AH, Seeman NC, Rich A. Three-dimensional tertiary structure of yeast phenylalanine transfer RNA. Science. 1974 Aug 2;185(4149):435–440. [PubMed]
  • Kearns DR, Wong YP. Investigation of the secondary structure of Escherichia coli 5 S RNA by high-resolution nuclear magnetic resonance. J Mol Biol. 1974 Aug 25;87(4):755–774. [PubMed]
  • Kearns DR, Wong YP, Chang SH, Hawkins E. Investigation of the structure of native and denatured conformations of tRNALeu3 by high-resolution nuclear magnetic resonance. Biochemistry. 1974 Nov 5;13(23):4736–4746. [PubMed]
  • Uhlenbeck OC, Borer PN, Dengler B, Tinoco I., Jr Stability of RNA hairpin loops: A 6 -C m -U 6 . J Mol Biol. 1973 Feb 5;73(4):483–496. [PubMed]
  • Gralla J, Crothers DM. Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. J Mol Biol. 1973 Aug 5;78(2):301–319. [PubMed]

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