A periodic table of symmetric tandem mismatches in RNA.

The stabilities and structures of a series of RNA octamers containing symmetric tandem mismatches were studied by UV melting and imino proton NMR. The free energy increments for tandem mismatch formation are found to depend upon both mismatch sequence and adjacent base pairs. The observed sequence dependence of tandem mismatch stability is UGGU > GUUG > GAAG > or = AGGA > UUUU > CAAC > or = CUUC approximately UCCU approximately CCCC approximately ACCA approximately AAAA, and the closing base pair dependence is 5'G3'C > 5'C3'G > 5'U3'A approximately 5'A3'U. These results differ from expectations based on models used in RNA folding algorithms and from the sequence dependence observed for folding of RNA hairpins. Imino proton NMR results indicate the sequence dependence is partially due to hydrogen bonding within mismatches.

[1]  A. E. Walter,et al.  Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[2]  A. E. Walter,et al.  The stability and structure of tandem GA mismatches in RNA depend on closing base pairs. , 1994, Biochemistry.

[3]  A. Pardi,et al.  In situ Probing of Adenine Protonation in RNA by 13C NMR , 1994 .

[4]  A. Lane,et al.  Thermodynamic stability and solution conformation of tandem G.A mismatches in RNA and RNA.DNA hybrid duplexes. , 1994, European journal of biochemistry.

[5]  D. Turner,et al.  Structure of (rGGCGAGCC)2 in solution from NMR and restrained molecular dynamics. , 1993, Biochemistry.

[6]  D. Crothers,et al.  Major groove accessibility of RNA. , 1993, Science.

[7]  A. Pardi,et al.  An efficient procedure for assignment of the proton, carbon and nitrogen resonances in 13C/15N labeled nucleic acids. , 1993, Journal of molecular biology.

[8]  D. Turner,et al.  RNA hairpin loop stability depends on closing base pair. , 1993, Nucleic acids research.

[9]  R. Gutell,et al.  A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993. , 1992, Nucleic acids research.

[10]  S. Chou,et al.  Base pairing geometry in GA mismatches depends entirely on the neighboring sequence. , 1992, Journal of Molecular Biology.

[11]  A. Pardi,et al.  Three-dimensional heteronuclear NMR studies of RNA , 1992, Nature.

[12]  A. E. Walter,et al.  Nearest-neighbor parameters for G.U mismatches: [formula; see text] is destabilizing in the contexts [formula; see text] and [formula; see text] but stabilizing in [formula; see text]. , 1991, Biochemistry.

[13]  D. Turner,et al.  Stabilities of consecutive A.C, C.C, G.G, U.C, and U.U mismatches in RNA internal loops: Evidence for stable hydrogen-bonded U.U and C.C.+ pairs. , 1991, Biochemistry.

[14]  W D Wilson,et al.  Thermodynamics of DNA duplexes with adjacent G.A mismatches. , 1991, Biochemistry.

[15]  D. Turner,et al.  Thermodynamic study of internal loops in oligoribonucleotides: symmetric loops are more stable than asymmetric loops. , 1991, Biochemistry.

[16]  D. Turner,et al.  Functional group substitutions as probes of hydrogen bonding between GA mismatches in RNA internal loops , 1991 .

[17]  D. Turner,et al.  Effects of GA mismatches on the structure and thermodynamics of RNA internal loops. , 1990, Biochemistry.

[18]  D. Turner,et al.  Improved predictions of secondary structures for RNA. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[19]  G. Varani,et al.  Conformation and dynamics of an RNA internal loop. , 1989, Biochemistry.

[20]  C. W. Hilbers,et al.  Effects of base sequence on the loop folding in DNA hairpins. , 1989, Biochemistry.

[21]  D. Turner,et al.  RNA structure prediction. , 1988, Annual review of biophysics and biophysical chemistry.

[22]  C. E. Longfellow,et al.  Polymer-supported RNA synthesis and its application to test the nearest-neighbor model for duplex stability. , 1986, Biochemistry.

[23]  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.

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

[25]  P. J. Hore,et al.  Solvent suppression in Fourier transform nuclear magnetic resonance , 1983 .

[26]  B. Reid,et al.  Nuclear Overhauser assignment of the imino protons of the acceptor helix and the ribothymidine helix in the nuclear magnetic resonance spectrum of Escherichia coli isoleucine transfer ribonucleic acid: evidence for costacked helices in solution. , 1982, Biochemistry.

[27]  P. D. Johnston,et al.  Nuclear magnetic resonance and nuclear Overhauser effect study of yeast phenylalanine transfer ribonucleic acid imino protons. , 1981, Biochemistry.

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

[29]  J. Ninio Prediction of pairing schemes in RNA molecules-loop contributions and energy of wobble and non-wobble pairs. , 1980, Biochimie.

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

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

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