Compact and ordered collapse of randomly generated RNA sequences

Nature Structural and Molecular Biology

Volumn 12, Issue 12, 2005, Pages 1130-1136

  Schultes, Erik A ^a   Spasic, Alexander ^b   Mohanty, Udayan ^b   Bartel, David P ^a  

^a WHITEHEAD INSTITUTE FOR BIOMEDICAL RESEARCH   (United States)

^b BOSTON COLLEGE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MAGNESIUM; RIBOZYME;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL PROCEDURES; CONFORMATION; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RNA ANALYSIS; RNA ISOLATION; RNA SEQUENCE; RNA STRUCTURE;

BASE SEQUENCE; ELECTROPHORESIS, POLYACRYLAMIDE GEL; LEAD; MAGNESIUM; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; OLIGORIBONUCLEOTIDES; RNA; ULTRACENTRIFUGATION;

EID: 28544445024     PISSN: 15459993     EISSN: 15459985     Source Type: Journal    
DOI: 10.1038/nsmb1014     Document Type: Article

References (40)

1. Holley, R.W. et al. Structure of a ribonucleic acid. Science 147, 1462-1465 (1965).
2. Fresco, J.R. From DNA melting profiles to tRNA crystals and RNA chaperones, in RNA Structure and Function (ed. Grunberg-Manago, M.) 1-35 (Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York, USA, 1998).
3. Xia, T. et al. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37, 14719-14735 (1998).
4. Batey, R.T., Rambo, R.P. & Doudna, J.A. Tertiary motifs in RNA structure and folding. Angew. Chem. Int. Edn. Engl. 38, 2326-2343 (1999).
5. Buchmueller, K.L. & Weeks, K.M. Near native structure in an RNA collapsed state. Biochemistry 42, 13869-13878 (2003).
6. Heilman-Miller, S.L., Thirumalai, D. & Woodson, S.A. Role of counterion condensation in folding of the Tetrahymena ribozyme I. Equilibrium stabilization by cations. J. Mol. Biol. 306, 1157-1166 (2001).
7. Heilman-Miller, S.L., Pan, J., Thirumalai, D. & Woodson, S.A. Role of counterion condensation in folding of the Tetrahymena ribozyme II. Counterion-dependence of folding kinetics. J. Mol. Biol. 309, 57-68 (2001).
8. Doty, P., Boedtker, J.R., Fresco, J.R. & Haselkorn, M.L. Secondary structure in ribonucleic acids. Proc. Natl. Acad. Sci. USA 45, 482-499 (1959).
9. Fresco, J.R., Alberts, B.M. & Doty, P. Some molecular details of the secondary structure of ribonucleic acid. Nature 188, 98-101 (1960).
10. Schultes, E.A., Hraber, P.T. & LaBean, T.H. Estimating the contributions of selection and self-organization in RNA secondary structure. J. Mol. Evol. 49, 76-83 (1999).
11. Seffens, W. & Digby, D. mRNAs have greater negative folding free energies than shuffled or codon choice randomized sequences. Nucleic Acids Res. 27, 1578-1584 (1999).
12. Higgs, P.G. RNA secondary structure: Physical and computational aspects. Q. Rev. Biophys. 33, 199-253 (2000).
13. Le, S.Y., Zhang, K.Z. & Maizel, J.V. RNA molecules with structure dependent functions are uniquely folded. Nucleic Acids Res. 30, 3574-3582 (2002).
14. Clote, P., Ferre, F., Kranakis, E. & Krizanc, D. Structural RNA has lower folding energy than random RNA of the same dinucleotide frequency. RNA 11, 578-591 (2005).
15. Shi, H.J. & Moore, P.B. The crystal structure of yeast phenylalanine tRNA at 1.93 angstrom resolution: A classic structure revisited. RNA 6, 1091-1105 (2000).
16. Ferre-D'Amare, A.R., Zhou, K. & Doudna, J.A. Crystal structure of a hepatitis delta virus ribozyme. Nature 395, 567-574 (1998).
17. Cate, J.H. et al. Crystal structure of a group I ribozyme domain: Principles of RNA packing. Science 273, 1678-1685 (1996).
18. Ekland, E.H., Szostak, J.W. & Bartel, D.P. Structurally complex and highly-active RNA ligases derived from random RNA sequences. Science 269, 364-370 (1995).
19. Schultes, E.A. & Bartel, D.P. One sequence, two ribozymes: Implications for the emergence of new ribozyme folds. Science 289, 448-452 (2000).
20. Juneau, K. & Cech, T.R. In vitro selection of RNAs with increased tertiary structure stability. RNA 5, 1119-1129 (1999).
21. Uhlenbeck, O.C. Keeping RNA happy. RNA 1, 4-6 (1995).
22. Lilley, D.M. Analysis of global conformation of branched RNA species using electrophoresis and fluorescence. Methods Enzymol. 317, 368-393 (2000).
23. Philo, J.S. An improved function for fitting sedimentation velocity data for low-molecular-weight solutes. Biophys. J. 72, 435-444 (1997).
24. Phe and the catalytic domain of the B. subtilis RNase P RNA determined by small-angle X-ray scattering. Biochemistry 39, 11107-11113 (2000).
25. Brown, R.S., Dewen, J.C. & Klug, A. Cristallographic and biochemical investigation of the lead(II)-catalyzed hydrolysis of the yeast phenylalanine tRNA. Biochemistry 24, 4785-4801 (1985).
26. Phe. Biochemistry 27, 5771-5777 (1988).
27. Matysiak, M., Wrzesinski, J. & Ciesiolka, J. Sequential folding of the genomic ribozyme of the hepatitis delta virus: Structural analysis of RNA transcription intermediates. J. Mol. Biol. 291, 283-294 (1999).
28. Mathews, D.H., Sabina, J., Zucker, M. & Turner, H. Expanded sequence dependence of thermodynamic parameters provides robust prediction of RNA secondary structure. J. Mol. Biol. 288, 911-940 (1999).
29. Schultes, E.A., LaBean, T.H. & Hraber, P.T. A parameterization of RNA sequence space. Complexity 4, 61-71 (1999).
30. Go, N. Theoretical studies of protein folding. Annu. Rev. Biophys. Bioeng. 12, 183-210 (1983).
31. Nissen, P., Ippolito, J.A., Ban, N., Moore, P.B. & Steitz, T.A. RNA tertiary interactions in the large ribosomal subunit: The A-minor motif. Proc. Natl. Acad. Sci. USA 98, 4899-4903 (2001).
32. Battle, D.J. & Doudna, J.A. Specificity of RNA-RNA helix recognition. Proc. Natl. Acad. Sci. USA 99, 11676-11681 (2002).
33. Hecht, M.H., Das, A., Go, A., Bradley, L.H. & Wei, Y. N. De novo proteins from designed combinatorial libraries. Protein Sci. 13, 1711-1723 (2004).
34. Prijambada, I.D. et al. Solubility of artificial proteins with random sequences. FEBS Lett.382, 21-25 (1996).
35. Davidson, A.R., Liumb, K.J. & Sauer, R.T. Cooperatively folded proteins in random sequence libraries. Nat. Struct. Biol. 2, 856-864 (1995).
36. Davidson, A.R. & Sauer, R.T. Folded proteins occur frequently in libraries of random amino acid sequences. Proc. Natl. Acad. Sci. USA 91, 2146-2150 (1994).
37. Wei, Y.N. & Hecht, M.H. Enzyme-like proteins from an unselected library of designed amino acid sequences. Protein Eng. Des. Sel. 17, 67-75 (2004).
38. Mohanty, U. & McLaughlin, L.W. On the characteristics of migration of oligomeric DNA in polyacrylamide gels and in free solution. Annu. Rev. Phys. Chem. 52, 93-106 (2001).
39. Bloomfield, V., Crothers, D.A. & Tinoco, I. Physical Chemistry of Nucleic Acids (Harper and Row, New York, USA, 1974).
40. Fernandes, M.X., Ortega, A., Lopez Martinez, M.C. & Garcia de la Torre, J. Calculation of hydrodynamic properties of small nucleic acids from their atomic structure. Nucleic Acids Res. 30, 1782-1788 (2002).