Improved free-energy parameters for predictions of RNA duplex stability.

Thermodynamic parameters for prediction of RNA duplex stability are reported. One parameter for duplex initiation and 10 parameters for helix propagation are derived from enthalpy and free-energy changes for helix formation by 45 RNA oligonucleotide duplexes. The oligomer sequences were chosen to maximize reliability of secondary structure predictions. Each of the 10 nearest-neighbor sequences is well-represented among the 45 oligonucleotides, and the sequences were chosen to minimize experimental errors in delta GO at 37 degrees C. These parameters predict melting temperatures of most oligonucleotide duplexes within 5 degrees C. This is about as good as can be expected from the nearest-neighbor model. Free-energy changes for helix propagation at dangling ends, terminal mismatches, and internal G X U mismatches, and free-energy changes for helix initiation at hairpin loops, internal loops, or internal bulges are also tabulated.

[1]  P. Ross,et al.  Heat of the reaction forming the three‐stranded poly (A + 2U) complex , 1965, Biopolymers.

[2]  P. R. Bevington,et al.  Data Reduction and Error Analysis for the Physical Sciences , 1969 .

[3]  R. L. Baldwin,et al.  Helix formation by d(TA) oligomers. II. Analysis of the helix-coli transitions of linear and circular oligomers. , 1970, Journal of molecular biology.

[4]  P. Doty,et al.  Self-complementary oligoribonucleotides: effects of helix defects and guanylic acid-cytidylic acid base pairs. , 1971, Journal of molecular biology.

[5]  I. Tinoco,et al.  Estimation of Secondary Structure in Ribonucleic Acids , 1971, Nature.

[6]  D M Crothers,et al.  Relaxation kinetics of dimer formation by self complementary oligonucleotides. , 1971, Journal of molecular biology.

[7]  D. Crothers,et al.  Free energy of imperfect nucleic acid helices. I. The bulge defect. , 1973, Journal of molecular biology.

[8]  P. Philippsen,et al.  The conformational transitions in yeast tRNAPhe as studied with tRNAPhe fragments. , 1973, European journal of biochemistry.

[9]  N. Kallenbach,et al.  Theory of oligonucleotide stabilization. I. The effect of single‐strand stacking , 1973, Biopolymers.

[10]  D. Crothers,et al.  Free energy of imperfect nucleic acid helices. II. Small hairpin loops. , 1973, Journal of molecular biology.

[11]  D. Crothers,et al.  Free energy of imperfect nucleic acid helices. 3. Small internal loops resulting from mismatches. , 1973, Journal of molecular biology.

[12]  D. Crothers,et al.  Improved estimation of secondary structure in ribonucleic acids. , 1973, Nature: New biology.

[13]  I. Tinoco,et al.  Stability of ribonucleic acid double-stranded helices. , 1974, Journal of molecular biology.

[14]  J. Gangloff,et al.  Conformational transitions in tRNA Asp (brewer's yeast). Thermodynamic, kinetic, and enzymatic measurements on oligonucleotide fragments and the intact molecule. , 1974, Biochemistry.

[15]  I. Tinoco,et al.  Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. , 1975, Journal of molecular biology.

[16]  E. Freire,et al.  Calorimetric determination of the heat capacity changes associated with the conformational transitions of polyriboadenylic acid and polyribouridylic acid , 1977, Biopolymers.

[17]  W. Salser.  Globin mRNA sequences: analysis of base pairing and evolutionary implications. , 1978, Cold Spring Harbor symposia on quantitative biology.

[18]  J. Steitz,et al.  The 3' terminus of 16S rRNA: secondary structure and interaction with ribosomal protein S1. , 1979, Nucleic acids research.

[19]  The effects of base sequence and dangling bases on the stability of short ribonucleic acid duplexes. , 1980, Nucleic acids symposium series.

[20]  C. Cantor,et al.  Biophysical chemistry. Part III, The behavior of biologicalmacromolecules , 1980 .

[21]  Michael Zuker,et al.  Optimal computer folding of large RNA sequences using thermodynamics and auxiliary information , 1981, Nucleic Acids Res..

[22]  D. Turner,et al.  Thermodynamics of (dG--dC)3 double-helix formation in water and deuterium oxide. , 1981, Biochemistry.

[23]  I. Tinoco,et al.  DNA and RNA oligomer thermodynamics: The effect of mismatched bases on double‐helix stability , 1981, Biopolymers.

[24]  Ruth Nussinov,et al.  Small changes in free energy assignments for unpaired bases do not affect predicted secondary structures in single stranded RNA , 1982, Nucleic Acids Res..

[25]  W. P. Rindone,et al.  Computer-aided prediction of RNA secondary structures , 1982, Nucleic Acids Res..

[26]  D. Turner,et al.  Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. , 1983, Biochemistry.

[27]  R. Gutell,et al.  Detailed analysis of the higher-order structure of 16S-like ribosomal ribonucleic acids. , 1983, Microbiological reviews.

[28]  M. Zuker,et al.  Secondary structure of the Tetrahymena ribosomal RNA intervening sequence: structural homology with fungal mitochondrial intervening sequences. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Turner,et al.  Thermodynamic studies of RNA stability. , 1984, Journal of biomolecular structure & dynamics.

[30]  M. Gait,et al.  Oligonucleotide synthesis : a practical approach , 1984 .

[31]  G. Steger,et al.  Conformational transitions in viroids and virusoids: comparison of results from energy minimization algorithm and from experimental data. , 1984, Journal of biomolecular structure & dynamics.

[32]  Manolo Gouy,et al.  An energy model that predicts the correct folding of both the tRNA and the 5S RNA molecules , 1984, Nucleic Acids Res..

[33]  Michael Zuker,et al.  Some simple computational methods to improve the folding of large RNAs , 1984, Nucleic Acids Res..

[34]  D. Turner,et al.  Contributions of dangling end stacking and terminal base-pair formation to the stabilities of XGGCCp, XCCGGp, XGGCCYp, and XCCGGYp helixes. , 1985, Biochemistry.

[35]  D. Turner,et al.  Improved free energies for G.C base-pairs. , 1985, Journal of molecular biology.

[36]  D. Turner,et al.  Solvent effects on the stability of A7U7p. , 1985, Biochemistry.

[37]  D. Turner,et al.  Stability of XGCGCp, GCGCYp, and XGCGCYp helixes: an empirical estimate of the energetics of hydrogen bonds in nucleic acids. , 1986, Biochemistry.

[38]  D. Turner,et al.  Free energy contributions of G.U and other terminal mismatches to helix stability. , 1986, Biochemistry.

[39]  D. Turner,et al.  Energetics of internal GU mismatches in ribooligonucleotide helixes. , 1986, Biochemistry.