Chapter 13 Thinking Inside the Box. Designing, Implementing, and Interpreting Thermodynamic Cycles to Dissect Cooperativity in RNA and DNA Folding

Methods in Enzymology

Volumn 455, Issue A, 2009, Pages 365-393

  Siegfried, Nathan A ^a   Bevilacqua, Philip C ^a  

^a PENNSYLVANIA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; NUCLEIC ACID; RNA;

BIOCHEMISTRY; COMPUTER PROGRAM; DEVELOPMENT; ENERGY; EXPERIMENTAL DESIGN; MELTING POINT; MOLECULAR INTERACTION; MOLECULE; MUTANT; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; REVIEW; THERMODYNAMICS; ULTRAVIOLET RADIATION; WASTE; ANIMAL; ARTICLE; CHEMISTRY; CONFORMATION; DNA DENATURATION; RADIATION EXPOSURE;

ANIMALS; DNA; NUCLEIC ACID CONFORMATION; NUCLEIC ACID DENATURATION; RNA; THERMODYNAMICS;

EID: 61849123673     PISSN: 00766879     EISSN: None     Source Type: Book Series    
DOI: 10.1016/S0076-6879(08)04213-4     Document Type: Review

References (49)

1. Antao V.P., Lai S.Y., and Tinoco Jr. I. A thermodynamic study of unusually stable RNA and DNA hairpins. Nucleic Acids Res. 19 (1991) 5901-5905
2. Bevilacqua P.C., and Blose J.M. Structures, kinetics, thermodynamics, and biological functions of RNA hairpins. Annu. Rev. Phys. Chem. 59 (2007) 79-103
3. Bevilacqua P.C., Brown T.S., Chadalavada D., Parente A.D., and Yajima R. Kinetic analysis of ribozyme cleavage (2003), Oxford University Press, Oxford
4. Bevilacqua P.C., Brown T.S., Nakano S., and Yajima R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers 73 (2004) 90-109
5. Bevilacqua P.C., and Turner D.H. Comparison of binding of mixed ribose-deoxyribose analogues of CUCU to a ribozyme and to GGAGAA by equilibrium dialysis: Evidence for ribozyme specific interactions with 2′ OH groups. Biochemistry 30 (1991) 10632-10640
6. Borer P.N. In: Fasman G.D. (Ed). Handbook of biochemistry and molecular biology: Nucleic acids Vol. 1 (1975), CRC Press, Cleveland, OH 589
7. Cantor C.R., and Schimmel P.R. Biophysical chemistry, part II: Techniques for the study of biological structure and function (1980), W. H. Freeman, San Francisco, CA
8. Carter P.J., Winter G., Wilkinson A.J., and Fersht A.R. The use of double mutants to detect structural changes in the active site of the tyrosyl-tRNA synthetase (Bacillus stearothermophilus). Cell 38 (1984) 835-840
9. Cavaluzzi M.J., and Borer P.N. Revised UV extinction coefficients for nucleoside-5′-monophosphates and unpaired DNA and RNA. Nucleic Acids Res. 32 (2004) e13
10. Chadalavada D.M., Senchak S.E., and Bevilacqua P.C. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. J. Mol. Biol. 317 (2002) 559-575
11. Di Cera E. Site-specific thermodynamics: Understanding cooperativity in molecular recognition. Chem. Rev. 98 (1998) 1563-1592
12. Dill K.A., and Bromberg S. Molecular driving forces: Statistical thermodynamics in chemistry and biology (2003), Garland Science, New York
13. Draper D.E., Bukhman Y.V., and Gluick T.C. Thermal Methods for the Analysis of RNA Folding Pathways. In: Beaucage S.L., Bergstrom D.E., Glick G.D., and Jones R.A. (Eds). Current Protocols in Nucleic Acid Chemistry (2000), John Wiley & Sons, New York 11.13.11-11.13.13
14. Duarte C.M., and Pyle A.M. Stepping through an RNA structure: A novel approach to conformational analysis. J. Mol. Biol. 284 (1998) 1465-1478
15. Fresco J.R., Klotz L.C., and Richards E.G. A new spectroscopic approach to the determination of helical secondary structure in ribonucleic acids. Cold Spring Harb. Symp. Quant. Biol. 28 (1963) 83-90
16. Gluick T.C., and Draper D.E. Thermodynamics of folding a pseudoknotted mRNA fragment. J. Mol. Biol. 241 (1994) 246-262
17. Gluick T.C., Wills N.M., Gesteland R.F., and Draper D.E. Folding of an mRNA pseudoknot required for stop codon readthrough: Effects of mono- and divalent ions on stability. Biochemistry 36 (1997) 16173-16186
18. Good N.E., Winget G.D., Winter W., Connolly T.N., Izawa S., and Singh R.M. Hydrogen ion buffers for biological research. Biochemistry 5 (1966) 467-477
19. Gray D.M., and Ratliff R.L. Circular dichroism evidence for G-U and G-T base pairing in poly[r(G-U)] and poly[d(G-T)]. Biopolymers 16 (1977) 1331-1342
20. Herschlag D., and Cech T.R. Catalysis of RNA cleavage by the Tetrahymena thermophila ribozyme. 1. Kinetic description of the reaction of an RNA substrate complementary to the active site. Biochemistry 29 (1990) 10159-10171
21. Hirao I., Kawai G., Yoshizawa S., Nishimura Y., Ishido Y., Watanabe K., and Miura K. Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: An extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res. 22 (1994) 576-582
22. Kahn J.D., Yun E., and Crothers D.M. Detection of localized DNA flexibility. Nature 368 (1994) 163-166
23. Kebbekus P., Draper D.E., and Hagerman P. Persistence length of RNA. Biochemistry 34 (1995) 4354-4357
24. Klostermeier D., and Millar D.P. Energetics of hydrogen bond networks in RNA: Hydrogen bonds surrounding G+1 and U42 are the major determinants for the tertiary structure stability of the hairpin ribozyme. Biochemistry 41 (2002) 14095-14102
25. Lu Y., Weers B., and Stellwagen N.C. DNA persistence length revisited. Biopolymers 61 (2001) 261-275
26. Mathews D.H., Sabina J., Zuker M., and Turner D.H. Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J. Mol. Biol. 288 (1999) 911-940
27. Misra V.K., and Draper D.E. The linkage between magnesium binding and RNA folding. J. Mol. Biol. 317 (2002) 507-521
28. Misra V.K., Shiman R., and Draper D.E. A thermodynamic framework for the magnesium-dependent folding of RNA. Biopolymers 69 (2003) 118-136
29. Moody E.M., and Bevilacqua P.C. Folding of a stable DNA motif involves a highly cooperative network of interactions. J. Am. Chem. Soc. 125 (2003) 16285-16293
30. Moody E.M., and Bevilacqua P.C. Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop. J. Am. Chem. Soc. 126 (2004) 9570-9577
31. Moody E.M., Feerrar J.C., and Bevilacqua P.C. Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry 43 (2004) 7992-7998
32. Moody E.M., Lecomte J.T., and Bevilacqua P.C. Linkage between proton binding and folding in RNA: A thermodynamic framework and its experimental application for investigating pKa shifting. RNA 11 (2005) 157-172
33. Murthy V.L., Srinivasan R., Draper D.E., and Rose G.D. A complete conformational map for RNA. J. Mol. Biol. 291 (1999) 313-327
34. Nakano S., Cerrone A.L., and Bevilacqua P.C. Mechanistic characterization of the HDV genomic ribozyme: Classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry 42 (2003) 2982-2994
35. Proctor D.J., Kierzek E., Kierzek R., and Bevilacqua P.C. Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. J. Am. Chem. Soc. 125 (2003) 2390-2391
36. Proctor D.J., Schaak J.E., Bevilacqua J.M., Falzone C.J., and Bevilacqua P.C. Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. Biochemistry 41 (2002) 12062-12075
37. Puglisi J.D., and Tinoco Jr. I. Absorbance melting curves of RNA. Methods Enzymol. 180 (1989) 304-325
38. Richards E.G. In: Fasman G.D. (Ed). Handbook of biochemistry and molecular biology: Nucleic acids Vol. 1 (1975), CRC Press, Cleveland, OH 597
39. SantaLucia Jr. J. A unified view of polymer, dumbbell, and oligonucleotide DNA nearest- neighbor thermodynamics. Proc. Natl. Acad. Sci. USA 95 (1998) 1460-1465
40. SantaLucia Jr. J., Kierzek R., and Turner D.H. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science 256 (1992) 217-219
41. Sattin B.D., Zhao W., Travers K., Chu S., and Herschlag D. Direct measurement of tertiary contact cooperativity in RNA folding. J. Am. Chem. Soc. 23 (2008) 23
42. Schaak J.E., Yakhnin H., Bevilacqua P.C., and Babitzke P. A Mg2+-dependent RNA tertiary structure forms in the Bacillus subtilis trp operon leader transcript and appears to interfere with trpE translation control by inhibiting TRAP binding. J. Mol. Biol. 332 (2003) 555-574
43. Serra M.J., and Turner D.H. Predicting thermodynamic properties of RNA. Methods Enzymol. 259 (1995) 242-261
44. Siegfried N.A., Metzger S.L., and Bevilacqua P.C. Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry 46 (2007) 172-181
45. Silverman S.K., and Cech T.R. Energetics and cooperativity of tertiary hydrogen bonds in RNA structure. Biochemistry 38 (1999) 8691-8702
46. Turner D.H. Conformational changes. In: Bloomfield V.A., Crothers D.M., and Tinoco Jr. I. (Eds). Nucleic acids: Structure, properties, and functions (2000), University Science Books, Sausalito, California 259-334
47. Xia T., SantaLucia Jr. J., Burkard M.E., Kierzek R., Schroeder S.J., Jiao X., Cox C., and Turner D.H. Thermodynamic parameters for an expanded nearest-neighbor model for formation of RNA duplexes with Watson-Crick base pairs. Biochemistry 37 (1998) 14719-14735
48. Yu Q., Kandegedara A., Xu Y., and Rorabacher D.B. Avoiding interferences from Good's buffers: A contiguous series of noncomplexing tertiary amine buffers covering the entire range of pH 3-11. Anal. Biochem. 253 (1997) 50-56
49. Zaug A.J., Grosshans C.A., and Cech T.R. Sequence-specific endoribonuclease activity of the Tetrahymena ribozyme: Enhanced cleavage of certain oligonucleotide substrates that form mismatched ribozyme-substrate complexes. Biochemistry 27 (1988) 8924-8931