Philip C. Bevilacqua - Publications

Affiliations: 
Chemistry Pennsylvania State University, State College, PA, United States 
Area:
RNA Folding and Catalysis
Website:
http://www.chem.psu.edu/directory/pcb5

166 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2020 Tack DC, Su Z, Yu Y, Bevilacqua PC, Assmann SM. Tissue-specific changes in the RNA structurome mediate salinity response in . Rna (New York, N.Y.). PMID 31937672 DOI: 10.1261/rna.072850.119  0.48
2019 Waldron JA, Tack DC, Ritchey LE, Gillen SL, Wilczynska A, Turro E, Bevilacqua PC, Assmann SM, Bushell M, Le Quesne J. mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity. Genome Biology. 20: 300. PMID 31888698 DOI: 10.1186/s13059-019-1901-2  0.48
2019 Messina KJ, Kierzek R, Tracey MA, Bevilacqua PC. Small Molecule Rescue and Glycosidic Conformational Analysis of the Twister Ribozyme. Biochemistry. PMID 31742390 DOI: 10.1021/acs.biochem.9b00742  0.68
2019 Leamy KA, Yamagami R, Yennawar NH, Bevilacqua PC. Single-nucleotide control of tRNA folding cooperativity under near-cellular conditions. Proceedings of the National Academy of Sciences of the United States of America. PMID 31666318 DOI: 10.1073/pnas.1913418116  0.72
2019 Mitchell D, Assmann SM, Bevilacqua PC. Probing RNA structure in vivo. Current Opinion in Structural Biology. 59: 151-158. PMID 31521910 DOI: 10.1016/j.sbi.2019.07.008  0.48
2019 Yamagami R, Huang R, Bevilacqua PC. Cellular Concentrations of Nucleotide Diphosphate-Chelated Magnesium Ions Accelerate Catalysis by RNA and DNA Enzymes. Biochemistry. PMID 31512860 DOI: 10.1021/acs.biochem.9b00578  0.72
2019 Messina KJ, Bevilacqua PC. Correction to "Cellular Small Molecules Contribute to Twister Ribozyme Catalysis". Journal of the American Chemical Society. PMID 31184145 DOI: 10.1021/jacs.9b05662  0.36
2019 Poudyal RR, Keating CD, Bevilacqua PC. Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates. Acs Chemical Biology. PMID 31181897 DOI: 10.1021/acschembio.9b00205  0.64
2019 Bevilacqua PC, Harris ME, Piccirilli JA, Gaines C, Ganguly A, Kostenbader K, Ekesan Ş, York DM. An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes. Acs Chemical Biology. PMID 31095369 DOI: 10.1021/acschembio.9b00202  0.6
2019 Ritchey LE, Su Z, Assmann SM, Bevilacqua PC. In Vivo Genome-Wide RNA Structure Probing with Structure-seq. Methods in Molecular Biology (Clifton, N.J.). 1933: 305-341. PMID 30945195 DOI: 10.1007/978-1-4939-9045-0_20  0.48
2019 Poudyal RR, Guth-Metzler RM, Veenis AJ, Frankel EA, Keating CD, Bevilacqua PC. Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates. Nature Communications. 10: 490. PMID 30700721 DOI: 10.1038/s41467-019-08353-4  0.64
2018 Yamagami R, Kayedkhordeh M, Mathews DH, Bevilacqua PC. Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study. Nucleic Acids Research. PMID 30462314 DOI: 10.1093/nar/gky1118  0.72
2018 Su Z, Tang Y, Ritchey LE, Tack DC, Zhu M, Bevilacqua PC, Assmann SM. Genome-wide RNA structurome reprogramming by acute heat shock globally regulates mRNA abundance. Proceedings of the National Academy of Sciences of the United States of America. PMID 30413617 DOI: 10.1073/pnas.1807988115  0.48
2018 Mitchell D, Renda AJ, Douds CA, Babitzke P, Assmann SM, Bevilacqua PC. In vivo RNA structural probing of uracil and guanine base pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). Rna (New York, N.Y.). PMID 30341176 DOI: 10.1261/rna.067868.118  0.48
2018 Bevilacqua PC, Assmann SM. Technique Development for Probing RNA Structure In Vivo and Genome-Wide. Cold Spring Harbor Perspectives in Biology. 10. PMID 30275275 DOI: 10.1101/cshperspect.a032250  0.48
2018 Messina KJ, Bevilacqua PC. Cellular Small Molecules Contribute to Twister Ribozyme Catalysis. Journal of the American Chemical Society. 140: 10578-10582. PMID 30102530 DOI: 10.1021/jacs.8b06065  0.36
2018 Yamagami R, Bingaman JL, Frankel EA, Bevilacqua PC. Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis. Nature Communications. 9: 2149. PMID 29858572 DOI: 10.1038/s41467-018-04415-1  0.72
2018 Leamy KA, Yennawar NH, Bevilacqua PC. Molecular Mechanism for Folding Cooperativity of Functional RNAs in Living Organisms. Biochemistry. PMID 29733204 DOI: 10.1021/acs.biochem.8b00345  0.36
2018 Poudyal RR, Pir Cakmak F, Keating CD, Bevilacqua PC. Physical Principles and Extant Biology Reveal Roles for RNA-Containing Membraneless Compartments in Origins of Life Chemistry. Biochemistry. PMID 29560725 DOI: 10.1021/acs.biochem.8b00081  0.64
2018 Bevilacqua PC, Assmann SM. RNA structure: A LASER-focused view into cells. Nature Chemical Biology. 14: 200-201. PMID 29443973 DOI: 10.1038/nchembio.2570  0.48
2018 Tack DC, Tang Y, Ritchey LE, Assmann SM, Bevilacqua PC. StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis. Methods (San Diego, Calif.). PMID 29410279 DOI: 10.1016/j.ymeth.2018.01.018  0.48
2017 Frankel EA, Bevilacqua PC. Complexity in pH-Dependent Ribozyme Kinetics: Dark pKa Shifts and Wavy Rate-pH Profiles. Biochemistry. PMID 29271644 DOI: 10.1021/acs.biochem.7b00784  0.64
2017 Spasic A, Assmann SM, Bevilacqua PC, Mathews DH. Modeling RNA secondary structure folding ensembles using SHAPE mapping data. Nucleic Acids Research. PMID 29177466 DOI: 10.1093/nar/gkx1057  0.72
2017 Mitchell D, Ritchey LE, Park H, Babitzke P, Assmann SM, Bevilacqua PC. Glyoxals as In Vivo RNA Structural Probes of Guanine Base Pairing. Rna (New York, N.Y.). PMID 29030489 DOI: 10.1261/rna.064014.117  0.48
2017 Bingaman JL, Gonzalez IY, Wang B, Bevilacqua PC. Activation of the glmS Ribozyme Nucleophile via Overdetermined Hydrogen Bonding. Biochemistry. PMID 28787138 DOI: 10.1021/acs.biochem.7b00662  0.36
2017 Leamy KA, Yennawar NH, Bevilacqua PC. Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization. Biochemistry. PMID 28657303 DOI: 10.1021/acs.biochem.7b00325  0.36
2017 Ritchey LE, Su Z, Tang Y, Tack DC, Assmann SM, Bevilacqua PC. Structure-seq2: sensitive and accurate genome-wide profiling of RNA structure in vivo. Nucleic Acids Research. PMID 28637286 DOI: 10.1093/nar/gkx533  0.48
2017 Frankel EA, Strulson CA, Keating CD, Bevilacqua PC. Cooperative Interactions in the Hammerhead Ribozyme Drive pKa Shifting of G12 and Its Stacked Base C17. Biochemistry. PMID 28485924 DOI: 10.1021/acs.biochem.7b00174  0.64
2017 Bingaman JL, Messina KJ, Bevilacqua PC. Probing fast ribozyme reactions under biological conditions with rapid quench-flow kinetics. Methods (San Diego, Calif.). PMID 28315484 DOI: 10.1016/j.ymeth.2017.03.011  0.36
2017 Bingaman JL, Zhang S, Stevens DR, Yennawar NH, Hammes-Schiffer S, Bevilacqua PC. The GlcN6P cofactor plays multiple catalytic roles in the glmS ribozyme. Nature Chemical Biology. PMID 28192411 DOI: 10.1038/nchembio.2300  1
2016 Bingaman JL, Frankel EA, Hull CM, Leamy KA, Messina KJ, Mitchell D, Park H, Ritchey LE, Babitzke P, Bevilacqua PC. Eliminating blurry bands in gels with a simple cost-effective repair to the gel cassette. Rna (New York, N.Y.). 22: 1929-1930. PMID 27852929 DOI: 10.1261/rna.059303.116  0.68
2016 Zhang S, Stevens DR, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S. Assessing the Potential Effects of Active Site Mg(2+) Ions in the glmS Ribozyme-Cofactor Complex. The Journal of Physical Chemistry Letters. 3984-3988. PMID 27677922 DOI: 10.1021/acs.jpclett.6b01854  1
2016 Leamy KA, Assmann SM, Mathews DH, Bevilacqua PC. Bridging the gap between in vitro and in vivo RNA folding. Quarterly Reviews of Biophysics. 49: e10. PMID 27658939 DOI: 10.1017/S003358351600007X  0.72
2016 Bevilacqua PC, Ritchey LE, Su Z, Assmann SM. Genome-Wide Analysis of RNA Secondary Structure. Annual Review of Genetics. PMID 27648642 DOI: 10.1146/annurev-genet-120215-035034  0.48
2016 Ucisik MN, Bevilacqua PC, Hammes-Schiffer S. Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+ Ions and Hydrogen-Bonding Network in Active Site. Biochemistry. PMID 27295275 DOI: 10.1021/acs.biochem.6b00203  1
2016 Hull CM, Bevilacqua PC. Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR. Accounts of Chemical Research. PMID 27269119 DOI: 10.1021/acs.accounts.6b00151  0.68
2016 Sherlock ME, Rumble CA, Kwok CK, Breffke J, Maroncelli M, Bevilacqua PC. Steady-State and Time-Resolved Studies into the Origin of the Intrinsic Fluorescence of G-Quadruplexes. The Journal of Physical Chemistry. B. PMID 27267433 DOI: 10.1021/acs.jpcb.6b03790  1
2016 Hull CM, Anmangandla A, Bevilacqua PC. Bacterial Riboswitches and Ribozymes Potently Activate the Human Innate Immune Sensor PKR. Acs Chemical Biology. PMID 27011290 DOI: 10.1021/acschembio.6b00081  0.68
2016 Frankel EA, Bevilacqua PC, Keating CD. Polyamine/Nucleotide Coacervates Provide Strong Compartmentalization of Mg2+, Nucleotides, and RNA. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 26844692 DOI: 10.1021/acs.langmuir.5b04462  1
2016 Yennawar NH, Fecko JA, Showalter SA, Bevilacqua PC. A High-Throughput Biological Calorimetry Core: Steps to Startup, Run, and Maintain a Multiuser Facility. Methods in Enzymology. 567: 435-60. PMID 26794364 DOI: 10.1016/bs.mie.2015.07.024  1
2015 Crenshaw E, Leung BP, Kwok CK, Sharoni M, Olson K, Sebastian NP, Ansaloni S, Schweitzer-Stenner R, Akins MR, Bevilacqua PC, Saunders AJ. Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex. Plos One. 10: e0143160. PMID 26618502 DOI: 10.1371/journal.pone.0143160  1
2015 Tang Y, Assmann SM, Bevilacqua PC. Protein Structure is Related to RNA Structural Reactivity in vivo. Journal of Molecular Biology. PMID 26598238 DOI: 10.1016/j.jmb.2015.11.012  1
2015 Ding Y, Kwok CK, Tang Y, Bevilacqua PC, Assmann SM. Genome-wide profiling of in vivo RNA structure at single-nucleotide resolution using structure-seq. Nature Protocols. 10: 1050-66. PMID 26086407 DOI: 10.1038/nprot.2015.064  1
2015 Hull CM, Bevilacqua PC. Mechanistic Analysis of Activation of the Innate Immune Sensor PKR by Bacterial RNA. Journal of Molecular Biology. PMID 26026708 DOI: 10.1016/j.jmb.2015.05.018  1
2015 Tang Y, Bouvier E, Kwok CK, Ding Y, Nekrutenko A, Bevilacqua PC, Assmann SM. StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo. Bioinformatics (Oxford, England). PMID 25886980 DOI: 10.1093/bioinformatics/btv213  1
2015 Thaplyal P, Ganguly A, Hammes-Schiffer S, Bevilacqua PC. Inverse thio effects in the hepatitis delta virus ribozyme reveal that the reaction pathway is controlled by metal ion charge density. Biochemistry. 54: 2160-75. PMID 25799319 DOI: 10.1021/acs.biochem.5b00190  1
2015 Kwok CK, Tang Y, Assmann SM, Bevilacqua PC. The RNA structurome: transcriptome-wide structure probing with next-generation sequencing. Trends in Biochemical Sciences. 40: 221-32. PMID 25797096 DOI: 10.1016/j.tibs.2015.02.005  1
2015 Kwok CK, Ding Y, Shahid S, Assmann SM, Bevilacqua PC. A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation. The Biochemical Journal. 467: 91-102. PMID 25793418 DOI: 10.1042/BJ20141063  1
2015 Bevilacqua PC. The wonder of RNA: a personal reflection of the last 20 years. Rna (New York, N.Y.). 21: 515-6. PMID 25780120 DOI: 10.1261/rna.050401.115  1
2015 Zhang S, Ganguly A, Goyal P, Bingaman JL, Bevilacqua PC, Hammes-Schiffer S. Role of the active site guanine in the glmS ribozyme self-cleavage mechanism: quantum mechanical/molecular mechanical free energy simulations. Journal of the American Chemical Society. 137: 784-98. PMID 25526516 DOI: 10.1021/ja510387y  1
2014 Thaplyal P, Bevilacqua PC. Experimental approaches for measuring pKa's in RNA and DNA. Methods in Enzymology. 549: 189-219. PMID 25432750 DOI: 10.1016/B978-0-12-801122-5.00009-X  1
2014 Dewey DC, Strulson CA, Cacace DN, Bevilacqua PC, Keating CD. Bioreactor droplets from liposome-stabilized all-aqueous emulsions. Nature Communications. 5: 4670. PMID 25140538 DOI: 10.1038/ncomms5670  1
2014 Strulson CA, Boyer JA, Whitman EE, Bevilacqua PC. Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions. Rna (New York, N.Y.). 20: 331-47. PMID 24442612 DOI: 10.1261/rna.042747.113  1
2014 Ganguly A, Thaplyal P, Rosta E, Bevilacqua PC, Hammes-Schiffer S. Quantum mechanical/molecular mechanical free energy simulations of the self-cleavage reaction in the hepatitis delta virus ribozyme. Journal of the American Chemical Society. 136: 1483-96. PMID 24383543 DOI: 10.1021/ja4104217  1
2014 Ding Y, Tang Y, Kwok CK, Zhang Y, Bevilacqua PC, Assmann SM. In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features. Nature. 505: 696-700. PMID 24270811 DOI: 10.1038/nature12756  1
2013 Kwok CK, Ding Y, Tang Y, Assmann SM, Bevilacqua PC. Determination of in vivo RNA structure in low-abundance transcripts. Nature Communications. 4: 2971. PMID 24336128 DOI: 10.1038/ncomms3971  1
2013 Strulson CA, Yennawar NH, Rambo RP, Bevilacqua PC. Molecular crowding favors reactivity of a human ribozyme under physiological ionic conditions. Biochemistry. 52: 8187-97. PMID 24187989 DOI: 10.1021/bi400816s  1
2013 Wilcox JL, Bevilacqua PC. pKa shifting in double-stranded RNA is highly dependent upon nearest neighbors and bulge positioning. Biochemistry. 52: 7470-6. PMID 24099082 DOI: 10.1021/bi400768q  1
2013 Thaplyal P, Ganguly A, Golden BL, Hammes-Schiffer S, Bevilacqua PC. Thio effects and an unconventional metal ion rescue in the genomic hepatitis delta virus ribozyme. Biochemistry. 52: 6499-514. PMID 24001219 DOI: 10.1021/bi4000673  1
2013 Kwok CK, Sherlock ME, Bevilacqua PC. Effect of loop sequence and loop length on the intrinsic fluorescence of G-quadruplexes. Biochemistry. 52: 3019-21. PMID 23621657 DOI: 10.1021/bi400139e  1
2013 Nallagatla SR, Jones CN, Ghosh SK, Sharma SD, Cameron CE, Spremulli LL, Bevilacqua PC. Native tertiary structure and nucleoside modifications suppress tRNA's intrinsic ability to activate the innate immune sensor PKR. Plos One. 8: e57905. PMID 23483938 DOI: 10.1371/journal.pone.0057905  1
2013 Wilcox JL, Bevilacqua PC. A simple fluorescence method for pK(a) determination in RNA and DNA reveals highly shifted pK(a)'s. Journal of the American Chemical Society. 135: 7390-3. PMID 23432144 DOI: 10.1021/ja3125299  1
2013 Kwok CK, Ding Y, Sherlock ME, Assmann SM, Bevilacqua PC. A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation. Analytical Biochemistry. 435: 181-6. PMID 23399535 DOI: 10.1016/j.ab.2013.01.008  1
2013 Chen J, Ganguly A, Miswan Z, Hammes-Schiffer S, Bevilacqua PC, Golden BL. Identification of the catalytic Mg²⁺ ion in the hepatitis delta virus ribozyme. Biochemistry. 52: 557-67. PMID 23311293 DOI: 10.1021/bi3013092  1
2013 Tubbs JD, Condon DE, Kennedy SD, Hauser M, Bevilacqua PC, Turner DH. The nuclear magnetic resonance of CCCC RNA reveals a right-handed helix, and revised parameters for AMBER force field torsions improve structural predictions from molecular dynamics. Biochemistry. 52: 996-1010. PMID 23286901 DOI: 10.1021/bi3010347  1
2013 Kwok CK, Sherlock ME, Bevilacqua PC. Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes. Angewandte Chemie (International Ed. in English). 52: 683-6. PMID 23166020 DOI: 10.1002/anie.201206475  1
2012 Patel S, Blose JM, Sokoloski JE, Pollack L, Bevilacqua PC. Specificity of the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR for double-stranded RNA: insights from thermodynamics and small-angle X-ray scattering. Biochemistry. 51: 9312-22. PMID 23140277 DOI: 10.1021/bi300935p  1
2012 Heinicke LA, Bevilacqua PC. Activation of PKR by RNA misfolding: HDV ribozyme dimers activate PKR. Rna (New York, N.Y.). 18: 2157-65. PMID 23105000 DOI: 10.1261/rna.034744.112  1
2012 Bevilacqua PC, Breen PC, Thaplyal P. Prospecting for aptamers in the human genome. Chemistry & Biology. 19: 1218-20. PMID 23102215 DOI: 10.1016/j.chembiol.2012.10.001  1
2012 Strulson CA, Molden RC, Keating CD, Bevilacqua PC. RNA catalysis through compartmentalization. Nature Chemistry. 4: 941-6. PMID 23089870 DOI: 10.1038/nchem.1466  1
2012 Toroney R, Hull CM, Sokoloski JE, Bevilacqua PC. Mechanistic characterization of the 5'-triphosphate-dependent activation of PKR: lack of 5'-end nucleobase specificity, evidence for a distinct triphosphate binding site, and a critical role for the dsRBD. Rna (New York, N.Y.). 18: 1862-74. PMID 22912486 DOI: 10.1261/rna.034520.112  1
2012 Sokoloski JE, Bevilacqua PC. Analysis of RNA folding and ligand binding by conventional and high-throughput calorimetry. Methods in Molecular Biology (Clifton, N.J.). 905: 145-74. PMID 22736003 DOI: 10.1007/978-1-61779-949-5_10  1
2012 Chadalavada DM, Cerrone-Szakal AL, Wilcox JL, Siegfried NA, Bevilacqua PC. Mechanistic analysis of the hepatitis delta virus (HDV) ribozyme: methods for RNA preparation, structure mapping, solvent isotope effects, and co-transcriptional cleavage. Methods in Molecular Biology (Clifton, N.J.). 848: 21-40. PMID 22315061 DOI: 10.1007/978-1-61779-545-9_3  1
2012 Mullen MA, Assmann SM, Bevilacqua PC. Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity. Journal of the American Chemical Society. 134: 812-5. PMID 22239732 DOI: 10.1021/ja2096255  1
2012 Sokoloski JE, Dombrowski SE, Bevilacqua PC. Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer. Biochemistry. 51: 565-72. PMID 22192051 DOI: 10.1021/bi201642p  1
2011 Ganguly A, Bevilacqua PC, Hammes-Schiffer S. Quantum Mechanical/Molecular Mechanical Study of the HDV Ribozyme: Impact of the Catalytic Metal Ion on the Mechanism. The Journal of Physical Chemistry Letters. 2: 2906-2911. PMID 22163069 DOI: 10.1021/jz2013215  1
2011 Sokoloski JE, Godfrey SA, Dombrowski SE, Bevilacqua PC. Prevalence of syn nucleobases in the active sites of functional RNAs. Rna (New York, N.Y.). 17: 1775-87. PMID 21873463 DOI: 10.1261/rna.2759911  1
2011 Wilcox JL, Ahluwalia AK, Bevilacqua PC. Charged nucleobases and their potential for RNA catalysis. Accounts of Chemical Research. 44: 1270-9. PMID 21732619 DOI: 10.1021/ar2000452  1
2011 Veeraraghavan N, Ganguly A, Golden BL, Bevilacqua PC, Hammes-Schiffer S. Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation. The Journal of Physical Chemistry. B. 115: 8346-57. PMID 21644800 DOI: 10.1021/jp203202e  1
2011 Heinicke LA, Nallagatla SR, Hull CM, Bevilacqua PC. RNA helical imperfections regulate activation of the protein kinase PKR: effects of bulge position, size, and geometry. Rna (New York, N.Y.). 17: 957-66. PMID 21460237 DOI: 10.1261/rna.2636911  1
2011 Veeraraghavan N, Ganguly A, Chen JH, Bevilacqua PC, Hammes-Schiffer S, Golden BL. Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions. Biochemistry. 50: 2672-82. PMID 21348498 DOI: 10.1021/bi2000164  1
2011 Nallagatla SR, Toroney R, Bevilacqua PC. Regulation of innate immunity through RNA structure and the protein kinase PKR. Current Opinion in Structural Biology. 21: 119-27. PMID 21145228 DOI: 10.1016/j.sbi.2010.11.003  1
2010 Mullen MA, Olson KJ, Dallaire P, Major F, Assmann SM, Bevilacqua PC. RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles. Nucleic Acids Research. 38: 8149-63. PMID 20860998 DOI: 10.1093/nar/gkq804  1
2010 Chen JH, Yajima R, Chadalavada DM, Chase E, Bevilacqua PC, Golden BL. A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage. Biochemistry. 49: 6508-18. PMID 20677830 DOI: 10.1021/bi100670p  1
2010 Veeraraghavan N, Bevilacqua PC, Hammes-Schiffer S. Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments. Journal of Molecular Biology. 402: 278-91. PMID 20643139 DOI: 10.1016/j.jmb.2010.07.025  1
2010 Chadalavada DM, Gratton EA, Bevilacqua PC. The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting. Biochemistry. 49: 5321-30. PMID 20524672 DOI: 10.1021/bi100434c  1
2010 Anderson BR, Muramatsu H, Nallagatla SR, Bevilacqua PC, Sansing LH, Weissman D, Karikó K. Incorporation of pseudouridine into mRNA enhances translation by diminishing PKR activation. Nucleic Acids Research. 38: 5884-92. PMID 20457754 DOI: 10.1093/nar/gkq347  1
2010 Toroney R, Nallagatla SR, Boyer JA, Cameron CE, Bevilacqua PC. Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A. Journal of Molecular Biology. 400: 393-412. PMID 20447405 DOI: 10.1016/j.jmb.2010.04.059  1
2010 Siegfried NA, Kierzek R, Bevilacqua PC. Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity. Journal of the American Chemical Society. 132: 5342-4. PMID 20345162 DOI: 10.1021/ja9107726  1
2010 Siegfried NA, O'Hare B, Bevilacqua PC. Driving forces for nucleic acid pK(a) shifting in an A(+).C wobble: effects of helix position, temperature, and ionic strength. Biochemistry. 49: 3225-36. PMID 20337429 DOI: 10.1021/bi901920g  1
2009 Chadalavada DM, Bevilacqua PC. Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections. Methods in Enzymology. 468: 389-408. PMID 20946779 DOI: 10.1016/S0076-6879(09)68018-6  1
2009 Toroney R, Bevilacqua PC. PKR and the ribosome compete for mRNA. Nature Chemical Biology. 5: 873-4. PMID 19915532 DOI: 10.1038/nchembio.262  1
2009 Gong B, Chen JH, Bevilacqua PC, Golden BL, Carey PR. Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme. Biochemistry. 48: 11961-70. PMID 19888753 DOI: 10.1021/bi901091v  1
2009 Blose JM, Lloyd KP, Bevilacqua PC. Portability of the GN(R)A hairpin loop motif between RNA and DNA. Biochemistry. 48: 8787-94. PMID 19681609 DOI: 10.1021/bi901038s  1
2009 Blose JM, Proctor DJ, Veeraraghavan N, Misra VK, Bevilacqua PC. Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. Journal of the American Chemical Society. 131: 8474-84. PMID 19476351 DOI: 10.1021/ja900065e  1
2009 Heinicke LA, Wong CJ, Lary J, Nallagatla SR, Diegelman-Parente A, Zheng X, Cole JL, Bevilacqua PC. RNA dimerization promotes PKR dimerization and activation. Journal of Molecular Biology. 390: 319-38. PMID 19445956 DOI: 10.1016/j.jmb.2009.05.005  1
2009 Gong B, Chen JH, Yajima R, Chen Y, Chase E, Chadalavada DM, Golden BL, Carey PR, Bevilacqua PC. Raman crystallography of RNA. Methods (San Diego, Calif.). 49: 101-11. PMID 19409996 DOI: 10.1016/j.ymeth.2009.04.016  1
2009 Siegfried NA, Bevilacqua PC. Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding. Methods in Enzymology. 455: 365-93. PMID 19289213 DOI: 10.1016/S0076-6879(08)04213-4  1
2009 Chen JH, Gong B, Bevilacqua PC, Carey PR, Golden BL. A catalytic metal ion interacts with the cleavage Site G.U wobble in the HDV ribozyme. Biochemistry. 48: 1498-507. PMID 19178151 DOI: 10.1021/bi8020108  1
2009 McGraw AP, Mokdad A, Major F, Bevilacqua PC, Babitzke P. Molecular basis of TRAP-5'SL RNA interaction in the Bacillus subtilis trp operon transcription attenuation mechanism. Rna (New York, N.Y.). 15: 55-66. PMID 19033375 DOI: 10.1261/rna.1314409  1
2008 Bevilacqua PC, Russell R. Editorial overview: exploring the vast dynamic range of RNA dynamics. Current Opinion in Chemical Biology. 12: 601-3. PMID 19013256 DOI: 10.1016/j.cbpa.2008.10.006  1
2008 Cerrone-Szakal AL, Siegfried NA, Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: solvent isotope effects and proton inventories in the absence of divalent metal ions support C75 as the general acid. Journal of the American Chemical Society. 130: 14504-20. PMID 18842044 DOI: 10.1021/ja801816k  1
2008 Nallagatla SR, Toroney R, Bevilacqua PC. A brilliant disguise for self RNA: 5'-end and internal modifications of primary transcripts suppress elements of innate immunity. Rna Biology. 5: 140-4. PMID 18769134  1
2008 Cerrone-Szakal AL, Chadalavada DM, Golden BL, Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis. Rna (New York, N.Y.). 14: 1746-60. PMID 18658121 DOI: 10.1261/rna.1140308  1
2008 Gong B, Chen Y, Christian EL, Chen JH, Chase E, Chadalavada DM, Yajima R, Golden BL, Bevilacqua PC, Carey PR. Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography. Journal of the American Chemical Society. 130: 9670-2. PMID 18593125 DOI: 10.1021/ja801861s  1
2008 Nallagatla SR, Bevilacqua PC. Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner. Rna (New York, N.Y.). 14: 1201-13. PMID 18426922 DOI: 10.1261/rna.1007408  1
2008 Bevilacqua PC, Blose JM. Structures, kinetics, thermodynamics, and biological functions of RNA hairpins. Annual Review of Physical Chemistry. 59: 79-103. PMID 17937599 DOI: 10.1146/annurev.physchem.59.032607.093743  1
2007 Nallagatla SR, Hwang J, Toroney R, Zheng X, Cameron CE, Bevilacqua PC. 5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops. Science (New York, N.Y.). 318: 1455-8. PMID 18048689 DOI: 10.1126/science.1147347  1
2007 Chadalavada DM, Cerrone-Szakal AL, Bevilacqua PC. Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions. Rna (New York, N.Y.). 13: 2189-201. PMID 17956974 DOI: 10.1261/rna.778107  1
2007 Gong B, Chen JH, Chase E, Chadalavada DM, Yajima R, Golden BL, Bevilacqua PC, Carey PR. Direct measurement of a pK(a) near neutrality for the catalytic cytosine in the genomic HDV ribozyme using Raman crystallography. Journal of the American Chemical Society. 129: 13335-42. PMID 17924627 DOI: 10.1021/ja0743893  1
2007 McGraw AP, Bevilacqua PC, Babitzke P. TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region. Rna (New York, N.Y.). 13: 2020-33. PMID 17881743 DOI: 10.1261/rna.719507  1
2007 Bevilacqua PC, SantaLucia J. The biophysics of RNA. Acs Chemical Biology. 2: 440-4. PMID 17649965 DOI: 10.1021/cb7001363  1
2007 Bevilacqua PC, Cerrone-Szakal AL, Siegfried NA. Insight into the functional versatility of RNA through model-making with applications to data fitting. Quarterly Reviews of Biophysics. 40: 55-85. PMID 17391549 DOI: 10.1017/S0033583507004593  1
2007 Blose JM, Silverman SK, Bevilacqua PC. A simple molecular model for thermophilic adaptation of functional nucleic acids. Biochemistry. 46: 4232-40. PMID 17361991 DOI: 10.1021/bi0620003  1
2007 Nakano S, Bevilacqua PC. 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: 3001-12. PMID 17315949 DOI: 10.1021/bi061732s  1
2007 Yajima R, Proctor DJ, Kierzek R, Kierzek E, Bevilacqua PC. A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme. Chemistry & Biology. 14: 23-30. PMID 17254949 DOI: 10.1016/j.chembiol.2006.11.004  1
2007 Siegfried NA, Metzger SL, Bevilacqua PC. Folding cooperativity in RNA and DNA is dependent on position in the helix. Biochemistry. 46: 172-81. PMID 17198387 DOI: 10.1021/bi061375l  1
2006 Bevilacqua PC, Yajima R. Nucleobase catalysis in ribozyme mechanism. Current Opinion in Chemical Biology. 10: 455-64. PMID 16935552 DOI: 10.1016/j.cbpa.2006.08.014  1
2006 Ma H, Proctor DJ, Kierzek E, Kierzek R, Bevilacqua PC, Gruebele M. Exploring the energy landscape of a small RNA hairpin. Journal of the American Chemical Society. 128: 1523-30. PMID 16448122 DOI: 10.1021/ja0553856  1
2005 Bevilacqua PC, Brown TS, Chadalavada D, Lecomte J, Moody E, Nakano SI. Linkage between proton binding and folding in RNA: implications for RNA catalysis. Biochemical Society Transactions. 33: 466-70. PMID 15916542 DOI: 10.1042/BST0330466  1
2005 Brown TS, Bevilacqua PC. Method for assigning double-stranded RNA structures. Biotechniques. 38: 368, 370, 372. PMID 15786803  1
2005 Moody EM, Lecomte JT, Bevilacqua PC. Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting. Rna (New York, N.Y.). 11: 157-72. PMID 15659356 DOI: 10.1261/rna.7177505  1
2004 Tian B, Bevilacqua PC, Diegelman-Parente A, Mathews MB. The double-stranded-RNA-binding motif: interference and much more. Nature Reviews. Molecular Cell Biology. 5: 1013-23. PMID 15573138 DOI: 10.1038/nrm1528  1
2004 Paxon TL, Brown TS, Lin HY, Brancato SJ, Roddy ES, Bevilacqua PC, Ewing AG. Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage. Analytical Chemistry. 76: 6921-7. PMID 15571342 DOI: 10.1021/ac0491758  1
2004 Zheng X, Bevilacqua PC. Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails. Rna (New York, N.Y.). 10: 1934-45. PMID 15547138 DOI: 10.1261/rna.7150804  1
2004 Proctor DJ, Ma H, Kierzek E, Kierzek R, Gruebele M, Bevilacqua PC. Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate. Biochemistry. 43: 14004-14. PMID 15518549 DOI: 10.1021/bi048213e  1
2004 Moody EM, Brown TS, Bevilacqua PC. Simple method for determining nucleobase pK(a) values by indirect labeling and demonstration of a pK(a) of neutrality in dsDNA. Journal of the American Chemical Society. 126: 10200-1. PMID 15315405 DOI: 10.1021/ja047362h  1
2004 Moody EM, Bevilacqua PC. Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop. Journal of the American Chemical Society. 126: 9570-7. PMID 15291560 DOI: 10.1021/ja048368+  1
2004 Brown TS, Chadalavada DM, Bevilacqua PC. Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength. Journal of Molecular Biology. 341: 695-712. PMID 15288780 DOI: 10.1016/j.jmb.2004.05.071  1
2004 Moody EM, Feerrar JC, Bevilacqua PC. Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart. Biochemistry. 43: 7992-8. PMID 15209494 DOI: 10.1021/bi049350e  1
2004 Bevilacqua PC, Brown TS, Nakano S, Yajima R. Catalytic roles for proton transfer and protonation in ribozymes. Biopolymers. 73: 90-109. PMID 14691943 DOI: 10.1002/bip.10519  1
2004 Bevilacqua PC. Mechanism of catalytic RNA. Biopolymers. 73: 69-70. PMID 14691940 DOI: 10.1002/bip.10522  1
2003 Babitzke P, Schaak J, Yakhnin AV, Bevilacqua PC. Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system. Methods in Enzymology. 371: 392-404. PMID 14712717 DOI: 10.1016/S0076-6879(03)71030-1  1
2003 Moody EM, Bevilacqua PC. Folding of a stable DNA motif involves a highly cooperative network of interactions. Journal of the American Chemical Society. 125: 16285-93. PMID 14692769 DOI: 10.1021/ja038897y  1
2003 Schaak JE, Babitzke P, Bevilacqua PC. Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus. Rna (New York, N.Y.). 9: 1502-15. PMID 14624006 DOI: 10.1261/rna.5149603  1
2003 Schaak JE, Yakhnin H, Bevilacqua PC, 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. Journal of Molecular Biology. 332: 555-74. PMID 12963367 DOI: 10.1016/S0022-2836(03)00969-0  1
2003 Nakano S, Cerrone AL, Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism. Biochemistry. 42: 2982-94. PMID 12627964 DOI: 10.1021/bi026815x  1
2003 Proctor DJ, Kierzek E, Kierzek R, Bevilacqua PC. Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine. Journal of the American Chemical Society. 125: 2390-1. PMID 12603116 DOI: 10.1021/ja029176m  1
2003 Bevilacqua PC. Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme. Biochemistry. 42: 2259-65. PMID 12600192 DOI: 10.1021/bi027273m  1
2003 Moody EM, Bevilacqua PC. Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs. Journal of the American Chemical Society. 125: 2032-3. PMID 12590515 DOI: 10.1021/ja029831q  1
2002 Bevilacqua PC, Turner DH. Use of fluorescence spectroscopy to elucidate RNA folding pathways. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.8. PMID 18428886 DOI: 10.1002/0471142700.nc1108s09  1
2002 Nakano M, Moody EM, Liang J, Bevilacqua PC. 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: 14281-92. PMID 12450393 DOI: 10.1021/bi026479k  1
2002 Diegelman-Parente A, Bevilacqua PC. A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence. Journal of Molecular Biology. 324: 1-16. PMID 12421555 DOI: 10.1016/S0022-2836(02)01027-6  1
2002 Proctor DJ, Schaak JE, Bevilacqua JM, Falzone CJ, Bevilacqua PC. Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions. Biochemistry. 41: 12062-75. PMID 12356306 DOI: 10.1021/bi026201s  1
2002 Bevilacqua PC. Battle for the bulge: directing small molecules to DNA and RNA defects. Chemistry & Biology. 9: 854-5. PMID 12204683 DOI: 10.1016/S1074-5521(02)00197-7  1
2002 Chadalavada DM, Senchak SE, Bevilacqua PC. The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots. Journal of Molecular Biology. 317: 559-75. PMID 11955009 DOI: 10.1006/jmbi.2002.5434  1
2001 Nakano S, Bevilacqua PC. Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions. Journal of the American Chemical Society. 123: 11333-4. PMID 11697993 DOI: 10.1021/ja0166850  1
2001 Nakano S, Proctor DJ, Bevilacqua PC. Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism. Biochemistry. 40: 12022-38. PMID 11580278 DOI: 10.1021/bi011253n  1
2001 Zheng X, Bevilacqua PC. Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications. Nucleic Acids Research. 29: E6. PMID 11139636  1
2000 Zheng X, Bevilacqua PC. Straightening of bulged RNA by the double-stranded RNA-binding domain from the protein kinase PKR. Proceedings of the National Academy of Sciences of the United States of America. 97: 14162-7. PMID 11114159 DOI: 10.1073/pnas.011355798  1
2000 Chadalavada DM, Knudsen SM, Nakano S, Bevilacqua PC. A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme. Journal of Molecular Biology. 301: 349-67. PMID 10926514 DOI: 10.1006/jmbi.2000.3953  1
2000 Nakano S, Chadalavada DM, Bevilacqua PC. General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme. Science (New York, N.Y.). 287: 1493-7. PMID 10688799 DOI: 10.1126/science.287.5457.1493  1
1999 Shu Z, Bevilacqua PC. Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library. Biochemistry. 38: 15369-79. PMID 10563823 DOI: 10.1021/bi991774z  1
1999 Arnold JJ, Ghosh SK, Bevilacqua PC, Cameron CE. Single-nucleotide resolution of RNA strands in the presence of their RNA complements. Biotechniques. 27: 450-2, 454, 456. PMID 10489603  1
1998 Bevilacqua JM, Bevilacqua PC. Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin. Biochemistry. 37: 15877-84. PMID 9843393 DOI: 10.1021/bi981732v  1
1998 Szewczak AA, Podell ER, Bevilacqua PC, Cech TR. Thermodynamic stability of the P4-P6 domain RNA tertiary structure measured by temperature gradient gel electrophoresis. Biochemistry. 37: 11162-70. PMID 9698362 DOI: 10.1021/bi980633e  1
1998 Bevilacqua PC, George CX, Samuel CE, Cech TR. Binding of the protein kinase PKR to RNAs with secondary structure defects: role of the tandem A-G mismatch and noncontiguous helixes. Biochemistry. 37: 6303-16. PMID 9572845 DOI: 10.1021/bi980113j  1
1996 Bevilacqua PC, Cech TR. Minor-groove recognition of double-stranded RNA by the double-stranded RNA-binding domain from the RNA-activated protein kinase PKR. Biochemistry. 35: 9983-94. PMID 8756460 DOI: 10.1021/bi9607259  1
1996 Bevilacqua PC, Sugimoto N, Turner DH. A mechanistic framework for the second step of splicing catalyzed by the Tetrahymena ribozyme. Biochemistry. 35: 648-58. PMID 8555239 DOI: 10.1021/bi951962z  1
1995 Li Y, Bevilacqua PC, Mathews D, Turner DH. Thermodynamic and activation parameters for binding of a pyrene-labeled substrate by the Tetrahymena ribozyme: docking is not diffusion-controlled and is driven by a favorable entropy change. Biochemistry. 34: 14394-9. PMID 7578043 DOI: 10.1021/bi00044a016  1
1994 Bevilacqua PC, Li Y, Turner DH. 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: 11340-8. PMID 7727385  1
1993 Bevilacqua PC, Johnson KA, Turner DH. Cooperative and anticooperative binding to a ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 90: 8357-61. PMID 8397404  1
1993 Kierzek R, Li Y, Turner DH, Bevilacqua PC. 5′-amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation Journal of the American Chemical Society. 115: 4985-4992.  1
1992 Bevilacqua PC, Kierzek R, Johnson KA, Turner DH. Dynamics of ribozyme binding of substrate revealed by fluorescence-detected stopped-flow methods. Science (New York, N.Y.). 258: 1355-8. PMID 1455230  1
1991 Bevilacqua PC, Turner DH. 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: 10632-40. PMID 1931984  1
1989 Sugimoto N, Tomka M, Kierzek R, Bevilacqua PC, Turner DH. 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 Research. 17: 355-71. PMID 2643083 DOI: 10.1093/nar/17.1.355  1
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