Publications Ph.D. Theses Honors Theses

Publications

(Undergraduate authors are in bold, blue font.)

69. Nallagatla, S. R., Bevilacqua, P.C. "Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner" RNA (in press). pdf Supporting Info

68. Bevilacqua, P.C., Blose, J.M. "Structures, kinetics, thermodynamics, and biological functions of RNA hairpins." Annu. Rev. Phys. Chem. 59, 79-103 (2008). pdf

67. Bevilacqua, P.C. "Proton transfer in ribozyme catalysis." Ribozymes and RNA Catalysis. D.M. Lilley and F. Eckstein eds. RSC Publishing, Cambridge, UK (2008). Online material

66. Nallagatla, S.R., Hwang, J., Toroney, R., Zheng, X., Cameron, C.E., Bevilacqua. P.C. "5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops." Science 318, 1455-1458 (2007). Abstract and Full-text available from Science Supporting Info: Low Res PDF High Res Figs

65. Gong, B, Chen, J.H., Chase, E., Chadalavada, D.M., Yajima, R., Golden, B.L., Bevilacqua, P.C., Carey, P.R. "Direct measurement of a pKa near neutrality for the catalytic cytosine in the genomic HDV ribozyme by Raman crystallography." J. Am. Chem. Soc. 129, 13335-13342 (2007). pdf Supporting Info

64. McGraw, A.P., Bevilacqua, P.C., Babitzke, P. "TRAP-5' Stem-Loop interaction increases the effect the efficiency of transcription termination in the Bacillus subtillis trpEDCFBA operon leader region by increasing the rate of TRAP binding to the nascent transcript." RNA 13, 2020-2033 (2007). pdf

63. Chadalavada, D.M., Cerrone-Szakal, A.L., Bevilacqua, P.C. "Wild-type is the optimal sequence of the HDV ribozyme under co-transcriptional conditions." RNA 13, 2189-2201 (2007). pdf Supporting Info

62. Bevilacqua, P.C., SantaLucia, J. Jr. "The biophysics of RNA." ACS Chem. Biol. 2, 440-444 (2007). pdf

61. Bevilacqua, P.C., Cerrone-Szakal, AL, Siegfried, N.A. "Insight into the functional diversity of RNA through model-making with applications to data fitting." Q. Rev. Biophys. 40, 55-85 (2007). pdf

60. Blose, J.M., Silverman, SK, Bevilacqua, P.C. "A simple molecular model for thermophilic adaptation of functional nucleic acids." Biochemistry 46, 4232-4240 (2007). pdf Supporting Info

59. Nakano, S., Bevilacqua, P.C. "Mechanistic characterization of the HDV genomic ribozyme: A mutant of the C41 motif provides insight into the positioning and thermodynamic linkage of metal ions and protons." Biochemistry 46, 3001-3012 (2007). Biochemistry 46, 3001-3012 (2007). pdf Supporting Information

58. Yajima, R., Proctor, D.J., Kierzek, R., Kierzek, E., Bevilacqua, P.C. "A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme." Chem. Biol. 14, 23-30 (2007). pdf

57. Siegfried, N.A., Metzger, S.L., Bevilacqua, P.C. "Folding cooperativity in RNA and DNA is dependent on position in the helix." Biochemistry 46, 172-181 (2007). pdf Supporting Info

56. Bove, J., Hord, C.L., Mullen, M.A. "The blossoming of RNA biology: Novel insights from plant systems." RNA 12, 2035-2046 (2006). pdf

55. Bevilacqua, P.C., Yajima, R. "Nucleobase catalysis in ribozyme mechanism." Curr. Opin. Chem. Biol. 10, 455-464 (2006). pdf

54. Ma, H., Proctor, D. J., Kierzek, E., Kierzek, R., Bevilacqua, P. C.* Gruebele, M.*  "Exploring the energy landscape of a small RNA hairpin." J. Am. Chem. Soc. 128, 1523-1530 (2006). (*=corresponding authors) pdf

53. Bevilacqua, P. C., Brown, T. S., Chadalavada, D., Lecomte, J., Moody, E., and Nakano, S.-i. "Linkage between proton binding and folding in RNA: Implications for RNA catalysis." Biochem. Soc. Trans. 33, 466-470 (2005). pdf

52. Brown, T. S., and Bevilacqua, P. C. "Method for assigning double-stranded RNA structures." Biotechniques 38, 368-372 (2005). pdf An overview of the article appears in the front of this issue. pdf

51. Moody, E. M., Lecomte, J. T. J., and Bevilacqua, P. C. "Linkage between proton binding and RNA folding: A thermodynamic framework and its experimental application for investigating pKa shifting." RNA 11, 157-172 (2005). pdf

50. Zheng, X., and Bevilacqua, P. C. "Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails." RNA 10, 1934-1945 (2004). pdf

49. Tian, B., Bevilacqua, P. C., Diegelman-Parente, A., and Mathews, M. B. "The double-stranded RNA binding motif: interference and much more." Nat. Rev. Mol. Cell. Biol. 5, 1013-1023 (2004). pdf

48. Proctor, D. J., Ma, H., Kierzek, E., Kierzek, R., Gruebele, M.,* and Bevilacqua, P. C.* "Folding thermodynamics and kinetics of YNMG RNA hairpins: Specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate." Biochemistry 43, 14004-14014 (2004).(*=corresponding authors) pdf Supporting Info

47. Paxon, T. L., Brown, T. S. Hsiao-yu, N. L. Brancato, S. J., Roddy, E. S., Bevilacqua, P. C., and Ewing, A. G. "Continuous monitoring of enzyme reactions on a microchip: Application to catalytic RNA self-cleavage." Anal. Chem. 76, 6921-6927 (2004). (A 1 page overview of the article appears in the front of this issue.) pdf

46. Moody, E. M.,* Brown, T. S.,* and Bevilacqua, P. C. "Simple method for determining nucleobase pKa values by indirect labeling and demonstration of a pKa of neutrality in dsDNA." J. Am. Chem. Soc. 126, 10200-10201 (2004).(*=equal contributions) pdf  Supporting Info

45. Brown, T. S.,* Chadalavada, D. M.,* and Bevilacqua, P. C. "Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength." J. Mol. Biol. 341, 695-712 (2004). (*=equal contributions) pdf

44. 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, 9570-9577 (2004). pdf

43. Moody, E. M., Feerrar, J. C., and Bevilacqua, P. C. "Evidence that folding of RNA tetraloop hairpin is less cooperative than its DNA counterpart." Biochemistry, 43, 7992-7998 (2004). pdf

42. Bevilacqua, P. C. "Mechanism of catalytic RNA." Biopolymers 73, 69-70 (2004). pdf

41. Bevilacqua, P. C., Brown, T. S., Nakano, S., and Yajima, R. "Catalytic roles for proton transfer and protonation in ribozymes." Biopolymers 73, 90-109 (2004). pdf

40. 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, 16285-16293 (2003). pdf

39. Schaak, J. E., Babitzke, P.,* and Bevilacqua, P. C.* "Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus." RNA9, 1502-1515 (2003). (*=corresponding authors) pdf

38. 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, 555-574 (2003). (*=corresponding authors) pdf

37. Babitzke, P., Schaak, J., Yakhnin, A. V., and Bevilacqua, P. C. "Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system." Methods Enzymol., 371, 392-404 (2003). pdf

36. Bevilacqua, P. C., Brown, T. S., Chadalavada, D. M., Parente, A. D. and Yajima, R. "Kinetic analysis of ribozyme cleavage." In Kinetic Analysis of Macromolecules: A Practical Approach (K. Johnson, ed.) Oxford University Press. Chpt 3, 49-74 (2003). pdf

35. 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, 2982-2994 (2003). pdf

34. Bevilacqua, P. C. "Mechanistic considerations for general acid-base catalysis by RNA: Revisiting the mechanism of thehairpin ribozyme." Biochemistry, 42, 2259-2265 (2003). pdf

33. 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, 2390-2391 (2003). pdf  Supporting Info

32. Moody, E. M., and Bevilacqua, P. C. "Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs." J. Am. Chem. Soc., 125, 2032-2033 (2003). pdf Supporting Info

31. Nakano, M., Moody, E. M., Liang, J., and Bevilacqua, P. C. "Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc)." Biochemistry, 41, 14281-14292 (2002). pdf

30. Diegelman-Parente, A., and Bevilacqua, P. C. "A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence." J. Mol. Biol., 324, 1-16 (2002). pdf

29. Proctor, D. J., Schaak, J. E., Bevilacqua, J. M., Falzone, C. J. and Bevilacqua, P. C. "Isolation and characterization of a family of stable tetraloops with the motif YNMG that participate in tertiary interactions." Biochemistry, 41, 12062-12075 (2002). pdf Supporting Info

28. Bevilacqua, P. C. "Battle for the bulge: Directing natural products to DNA defects." Chem. Biol., 9, 854-855 (2002). pdf

27. Bevilacqua, P.C. and Turner, D.H. "Use of fluorescence spectroscopy to elucidate RNA folding pathways." In Current Protocols in Nucleic Acid Chemistry (S. Beaucage et al., eds.). John Wiley & Sons, New York. 11.8.1-11.8.6 (2002). pdf

26. Chadalavada, D. M., Senchak, S. E., and Bevilacqua, P. C. "The folding pPathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots." J. Mol. Biol., 317, 559-575 (2002). pdf

25. Nakano, S. and Bevilacqua, P. C. "Proton inventory of the genomic HDV ribozyme in Mg2+-containing solutions." J. Am. Chem. Soc., 123, 11333-11334 (2001). pdf

24. Nakano, S., Proctor, D. J., and Bevilacqua, P. C. "Mechanistic characterization of the HDV genomic ribozyme: Assessing the catalytic and structural contributions of divalent metal ions within a multi-channel reaction mechanism." Biochemistry, 40, 12022-12038 (2001). pdf

23. Bevilacqua, P. C. "Making biochemistry required reading." Chemical & Engineering News. 79, 219 (2001). pdf

22. Zheng, X. and Bevilacqua, P. C. "Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications." Nucleic Acids Res.29, E6 (2001). pdf

21. Zheng, X., and Bevilacqua, P. C. "Straightening of bulged RNA by the double-stranded domain from the protein kinase PKR." Proc. Natl. Acad. Sci. USA (Track II) 97, 14162-14167 (2000). pdf

20. Chadalavada, D. M., Knudsen, S. K., Nakano, S., and Bevilacqua, P. C. "A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme." J. Mol. Biol. 301, 349-368 (2000). pdf

19. Nakano, S., Chadalavada, D. M., and Bevilacqua, P. C. "General acid-base catalysis in the mechanism of an HDV ribozyme." Science, 287, 1493-1497 (2000). pdf

18. Bevilacqua, P. C. "Exploring the possibility of an RNA world." Book Review of "The RNA World," 2nd Ed., Gesteland, R. F., Cech, T. R., and Atkins, J. F. Eds. for Nature Struct. Biol., 6, 997 (1999). pdf

17. Shu, Z., and Bevilacqua, P. C. "Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library." Biochemistry, 38, 15369-15379 (1999). pdf

16. Arnold, J. J., Ghosh, S.K.B., Bevilacqua, P. C. and Cameron, C. "Single-nucleotide resolution of RNA strands in the presence of their RNA complements." Biotechniques, 27, 450-456 (1999). pdf

15. Bevilacqua, J. M. and Bevilacqua, P. C. "Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin." Biochemistry, 37, 15877-15884 (1998). pdf

14. Szewczak, A. A., Podell, E., Bevilacqua, P. C., and Cech, T. R. "Thermodynamic stability of the P4-P6 domain RNA tertiary structure measure by temperature gradient gel electrophoresis." Biochemistry 37, 11162-11170 (1998). pdf

13. Bevilacqua, P. C., George, C., Samuel, C. E., and Cech, T. R. "Binding of the protein kinase PKR to RNAs with secondary structure defects: Role of the tandem A-G mismatch and noncontiguous helixes." Biochemistry 37, 6303-6316 (1998). pdf

12. Bevilacqua, P. C. and Cech, T. R. "Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR." Biochemistry 35, 9983-9994 (1996). pdf

11. Turner, D. H., Li, Y., Fountain, M., Profenno, L. and Bevilacqua, P. C. "Dynamics of a group I ribozyme detected by spectroscopic methods." In Nucleic Acids & Molecular Biology, eds Fritz Eckstein & David M. J. Lilley, 10, 19-32 (1996). pdf

10. Bevilacqua, P. C., Sugimoto, N. and Turner, D. H. "A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme." Biochemistry 35, 648-658 (1996). pdf

9. Li, Y., Bevilacqua, P. C., Mathews, D. and Turner, D. H. "Thermodynamic and activation parameters for binding of a pyrene labelled substrate by the Tetrahymena ribozyme: Docking is not diffusion controlled and is driven by a favorable entropy change." Biochemistry 34, 14394-14399 (1995). pdf

8. Bevilacqua, P. C., Li, Y. and Turner, D. H. "Fluorescence-detected stopped flow with a pyrene labeled substrate reveals that guanosine facilitates docking of the 5' cleavage site into a high free energy binding mode in the Tetrahymena ribozyme." Biochemistry 33, 11340-11348 (1994). pdf

7. Cech, T. R., Bevilacqua, P. C., Doudna, J. A., McConnell, T. S., Strobel, S. A., Weinstein, L. B. "Mechanism and structure of a catalytic RNA molecule." In Proceedings of the Robert A. Welch Foundation, 91-110 (1993). pdf

6. Turner, D. H. and Bevilacqua, P. C. "Thermodynamic considerations for evolution by RNA." Invited Chapter in RNA World, Cold Spring Harbor Press, eds Ray Gesteland and John Atkins, 447-464 (1993). pdf

5. Bevilacqua, P. C., Johnson, K. A. and Turner, D. H. "Cooperative and anticooperative binding to a ribozyme." Proc. Natl. Acad. Sci. USA 90, 8357-8361 (1993). pdf

4. Kierzek, R., Li, Y., Turner, D. H. and Bevilacqua, P. C. "5'-Amino pyrene provides a sensitive, non-perturbing fluorescent probe of RNA secondary and tertiary structure formation." J. Am. Chem. Soc. 115, 4985-4992 (1993). pdf

3. Bevilacqua, P. C., Kierzek, R., Johnson, K. A. and Turner, D. H. "Dynamics of ribozyme binding of substrate revealed by fluorescence detected stopped-flow." Science 258, 1355-1358 (1992). pdf

2. 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, 10632-10640 (1991). pdf

1. Sugimoto, N., Tomka, M., Kierzek, R., Bevilacqua, P. C. and Turner, D. H. "Effects of substrate structure on the kinetics of circle opening reactions of the self-splicing intervening sequence from Tetrahymena thermophila: Evidence for substrate and Mg2+ binding interactions." Nucleic Acids Res. 17, 355-371 (1989). pdf
Ph.D. Theses

5. Rieko Yajima, Ph.D. "Insight into Ribozyme Structure and Function Using Conformationally-Restricted RNA: Applications to X-Ray Crystallography" (2006) pdf

4. Trevor S. Brown, Ph.D. "Problem-Oriented Investigation of the pKa of Active-Site Cytosine 75 in the
Hepatitis Delta Virus (HDV) Ribozyme." (2005) pdf

3. Ellen M. Moody, Ph.D. "Stability in Nucleic Acid Hairpins: 1. Molecular Determinants of Cooperativity and 2. Linkage Between Proton Binding and Folding." (2004) pdf

2. David J. Proctor, Ph.D. "Studies of the Molecular Origins of Thermodynamic Stability in RNA Secondary Structure." (2004) pdf

1. Janell E. Schaak, Ph.D. "Understanding the Role of RNA Structure and Stability in the Regulation of the trpEDCFBA Operon in Bacillus." Co-advisor: Paul Babitzke. (2003) pdf
Honors Theses

4. Sherry Yang "Preparation of a Three-Piece HDV Ribozyme Construct for Single Molecule Studies" (2007).

3. Melanie Hauser "Effects of Salt Identity and Concentration on the Thermodynamic Parameters for the RNA Tetraloop Hairpins C4 and U4: Evidence for Three-State Unfolding" (2001).

2. Robert S. Bridges "Towards Ultraspecific Biosensors for Neurotransmitters" Co-advisor: Anne Andrews (2001).

1. Jing Liang "Isolation of Exceptionally Stable DNA Hairpins" (2000).

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