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Philip Bevilacqua

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Hepatitis Delta Virus

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Thermodynamics

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TOP 3
Chun Kit Kwok; Madeline E Sherlock; Philip C Bevilacqua
Effect of loop sequence and loop length on the intrinsic fluorescence of g-quadruplexes.
Chun Kit Kwok; Madeline E Sherlock; Sarah M Assmann; Yiliang Ding; Philip C Bevilacqua
A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation.
Chun Kit Kwok; Madeline E Sherlock; Philip C Bevilacqua
Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes.

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All Publications

2013: Chun Kit Kwok; Madeline E Sherlock; Philip C Bevilacqua
Effect of loop sequence and loop length on the intrinsic fluorescence of g-quadruplexes.
Biochemistry 2013;52(18):3019-21.
2013: Chun Kit Kwok; Madeline E Sherlock; Sarah M Assmann; Yiliang Ding; Philip C Bevilacqua
A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation.
Analytical biochemistry 2013;435(2):181-6.
2013: Chun Kit Kwok; Madeline E Sherlock; Philip C Bevilacqua
Decrease in RNA folding cooperativity by deliberate population of intermediates in RNA G-quadruplexes.
Angewandte Chemie (International ed. in English) 2013;52(2):683-6.
2013: Subba Rao Nallagatla; SURESH SHARMA; Linda L Spremulli; Craig E Cameron; Saikat Kumar B Ghosh; Christie N Jones; Philip C Bevilacqua
Native tertiary structure and nucleoside modifications suppress tRNA's intrinsic ability to activate the innate immune sensor PKR.
PloS one 2013;8(3):e57905.
2012: Sunita Patel; Lois Pollack; Joshua E Sokoloski; Joshua M Blose; Philip C Bevilacqua
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 2012;51(46):9312-22.
2012: Christopher A Strulson; Christine D Keating; Rosalynn C Molden; Philip C Bevilacqua
RNA catalysis through compartmentalization.
Nature chemistry 2012;4(11):941-6.
2012: Philip C Bevilacqua; Peter C Breen; Pallavi Thaplyal
Prospecting for aptamers in the human genome.
Chemistry & biology 2012;19(10):1218-20.
2012: Melissa A Mullen; Sarah M Assmann; Philip C Bevilacqua
Toward a digital gene response: RNA G-quadruplexes with fewer quartets fold with higher cooperativity.
Journal of the American Chemical Society 2012;134(2):812-5.
2012: Durga M Chadalavada; Nathan A Siegfried; Jennifer L Wilcox; Andrea L Cerrone-Szakal; Philip C Bevilacqua
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.) 2012;848():21-40.
2011: Narayanan Veeraraghavan; Philip C Bevilacqua; Abir Ganguly; Barbara L Golden; Sharon Hammes-Schiffer
Mechanistic strategies in the HDV ribozyme: chelated and diffuse metal ion interactions and active site protonation.
The journal of physical chemistry. B 2011;115(25):8346-57.
2011: Narayanan Veeraraghavan; Abir Ganguly; Jui-Hui Chen; Philip C Bevilacqua; Sharon Hammes-Schiffer; Barbara L Golden
Metal binding motif in the active site of the HDV ribozyme binds divalent and monovalent ions.
Biochemistry 2011;50(13):2672-82.
2011: Subba Rao Nallagatla; Rebecca Toroney; Philip C Bevilacqua
Regulation of innate immunity through RNA structure and the protein kinase PKR.
Current opinion in structural biology 2011;21(1):119-27.
2010: Melissa A Mullen; Kalee J Olson; Paul Dallaire; François Major; Sarah M Assmann; Philip C Bevilacqua
RNA G-Quadruplexes in the model plant species Arabidopsis thaliana: prevalence and possible functional roles.
Nucleic acids research 2010;38(22):8149-63.
2010: Narayanan Veeraraghavan; Philip C Bevilacqua; Sharon Hammes-Schiffer
Long-distance communication in the HDV ribozyme: insights from molecular dynamics and experiments.
Journal of molecular biology 2010;402(1):278-91.
2010: Jui-Hui Chen; Rieko Yajima; Durga M Chadalavada; Elaine Chase; Philip C Bevilacqua; Barbara L Golden
A 1.9 A crystal structure of the HDV ribozyme precleavage suggests both Lewis acid and general acid mechanisms contribute to phosphodiester cleavage.
Biochemistry 2010;49(31):6508-18.
2010: Rebecca Toroney; Subba Rao Nallagatla; Joshua A Boyer; Craig E Cameron; Philip C Bevilacqua
Regulation of PKR by HCV IRES RNA: importance of domain II and NS5A.
Journal of molecular biology 2010;400(3):393-412.
2010: Durga M Chadalavada; Elizabeth A Gratton; Philip C Bevilacqua
The human HDV-like CPEB3 ribozyme is intrinsically fast-reacting.
Biochemistry 2010;49(25):5321-30.
2010: Nathan A Siegfried; Ryszard Kierzek; Philip C Bevilacqua
Role of unsatisfied hydrogen bond acceptors in RNA energetics and specificity.
Journal of the American Chemical Society 2010;132(15):5342-4.
2010: Nathan A Siegfried; Bernie O'Hare; Philip C Bevilacqua
Driving forces for nucleic acid pK(a) shifting in an A(+).C wobble: effects of helix position, temperature, and ionic strength.
Biochemistry 2010;49(15):3225-36.
2009: Bo Gong; Jui-Hui Chen; Philip C Bevilacqua; Barbara L Golden; Paul R Carey
Competition between Co(NH(3)(6)3+ and inner sphere Mg2+ ions in the HDV ribozyme.
Biochemistry 2009;48(50):11961-70.
2009: Rebecca Toroney; Philip C Bevilacqua
PKR and the ribosome compete for mRNA.
Nature chemical biology 2009;5(12):873-4.
2009: Bo Gong; Jui-Hui Chen; Rieko Yajima; Yuanyuan Chen; Elaine Chase; Durga M Chadalavada; Barbara L Golden; Paul R Carey; Philip C Bevilacqua
Raman crystallography of RNA.
Methods (San Diego, Calif.) 2009;49(2):101-11.
2009: Joshua M Blose; Kenneth P Lloyd; Philip C Bevilacqua
Portability of the GN(R)A hairpin loop motif between RNA and DNA.
Biochemistry 2009;48(37):8787-94.
2009: Laurie A Heinicke; C Jason Wong; Jeffrey Lary; Subba Rao Nallagatla; Amy M. Diegelman; Xiaofeng Zheng; James L Cole; Philip C Bevilacqua
RNA dimerization promotes PKR dimerization and activation.
Journal of molecular biology 2009;390(2):319-38.
2009: Joshua M Blose; David Proctor; Narayanan Veeraraghavan; Vinod K Misra; Philip C Bevilacqua
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 2009;131(24):8474-84.
2009: Durga M Chadalavada; Philip C Bevilacqua
Analyzing RNA and DNA folding using temperature gradient gel electrophoresis (TGGE) with application to in vitro selections.
Methods in enzymology 2009;468():389-408.
2009: Nathan A Siegfried; Philip C Bevilacqua
Thinking inside the box: designing, implementing, and interpreting thermodynamic cycles to dissect cooperativity in RNA and DNA folding.
Methods in enzymology 2009;455():365-93.
2008: Andrea L Cerrone-Szakal; Durga M Chadalavada; Barbara L Golden; Philip C Bevilacqua
Mechanistic characterization of the HDV genomic ribozyme: the cleavage site base pair plays a structural role in facilitating catalysis.
RNA (New York, N.Y.) 2008;14(9):1746-60.
2008: Bo Gong; Yuanyuan Chen; Eric L Christian; Jui-Hui Chen; Elaine Chase; Durga M Chadalavada; Rieko Yajima; Barbara L Golden; Philip C Bevilacqua; Paul R Carey
Detection of innersphere interactions between magnesium hydrate and the phosphate backbone of the HDV ribozyme using Raman crystallography.
Journal of the American Chemical Society 2008;130(30):9670-2.
2008: Subba Rao Nallagatla; Rebecca Toroney; Philip C Bevilacqua
A brilliant disguise for self RNA: 5'-end and internal modifications of primary transcripts suppress elements of innate immunity.
RNA biology 2008;5(3):140-4.
2008: Subba Rao Nallagatla; Philip C Bevilacqua
Nucleoside modifications modulate activation of the protein kinase PKR in an RNA structure-specific manner.
RNA (New York, N.Y.) 2008;14(6):1201-13.
2008: Philip C Bevilacqua; Joshua M Blose
Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.
Annual review of physical chemistry 2008;59():79-103.
2007: Durga M Chadalavada; Andrea L Cerrone-Szakal; Philip C Bevilacqua
Wild-type is the optimal sequence of the HDV ribozyme under cotranscriptional conditions.
RNA (New York, N.Y.) 2007;13(12):2189-201.
2007: Subba Rao Nallagatla; Jungwook Hwang; Rebecca Toroney; Xiaofeng Zheng; Craig E Cameron; Philip C Bevilacqua
5'-triphosphate-dependent activation of PKR by RNAs with short stem-loops.
Science (New York, N.Y.) 2007;318(5855):1455-8.
2007: Adam P McGraw; Philip C Bevilacqua; Paul Babitzke
TRAP-5' stem loop interaction increases the efficiency of transcription termination in the Bacillus subtilis trpEDCFBA operon leader region.
RNA (New York, N.Y.) 2007;13(11):2020-33.
2007: Bo Gong; Jui-Hui Chen; Elaine Chase; Durga M Chadalavada; Rieko Yajima; Barbara L Golden; Philip C Bevilacqua; Paul R Carey
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 2007;129(43):13335-42.
2007: Philip C Bevilacqua; John SantaLucia
The biophysics of RNA.
ACS chemical biology 2007;2(7):440-4.
2007: Joshua M Blose; Scott K Silverman; Philip C Bevilacqua
A simple molecular model for thermophilic adaptation of functional nucleic acids.
Biochemistry 2007;46(14):4232-40.
2007: Shu-ichi Nakano; Philip C Bevilacqua
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 2007;46(11):3001-12.
2007: Philip C Bevilacqua; Andrea L Cerrone-Szakal; Nathan A Siegfried
Insight into the functional versatility of RNA through model-making with applications to data fitting.
Quarterly reviews of biophysics 2007;40(1):55-85.
2007: Nathan A Siegfried; Shana Metzger; Philip C Bevilacqua
Folding cooperativity in RNA and DNA is dependent on position in the helix.
Biochemistry 2007;46(1):172-81.
2007: Rieko Yajima; David Proctor; Ryszard Kierzek; Elzbieta Kierzek; Philip C Bevilacqua
A conformationally restricted guanosine analog reveals the catalytic relevance of three structures of an RNA enzyme.
Chemistry & biology 2007;14(1):23-30.
2006: Philip C Bevilacqua; Rieko Yajima
Nucleobase catalysis in ribozyme mechanism.
Current opinion in chemical biology 2006;10(5):455-64.
2006: Hairong Ma; David Proctor; Elzbieta Kierzek; Ryszard Kierzek; Philip C Bevilacqua; Martin Gruebele
Exploring the energy landscape of a small RNA hairpin.
Journal of the American Chemical Society 2006;128(5):1523-30.
2005: Philip C Bevilacqua; Trevor S Brown; Durga M Chadalavada; Juliette T J Lecomte; Ellen M Moody; Shu-ichi Nakano
Linkage between proton binding and folding in RNA: implications for RNA catalysis.
Biochemical Society transactions 2005;33(Pt 3):466-70.
2005: Trevor S Brown; Philip C Bevilacqua
Method for assigning double-stranded RNA structures.
BioTechniques 2005;38(3):368, 370, 372.
2005: Ellen M Moody; Juliette T J Lecomte; Philip C Bevilacqua
Linkage between proton binding and folding in RNA: a thermodynamic framework and its experimental application for investigating pKa shifting.
RNA (New York, N.Y.) 2005;11(2):157-72.
2004: Bin Tian; Philip C Bevilacqua; Amy M. Diegelman; Michael B Mathews
The double-stranded-RNA-binding motif: interference and much more.
Nature reviews. Molecular cell biology 2004;5(12):1013-23.
2004: Tracy L Paxon; Trevor S Brown; Hsiao-Yu Nancy Lin; Sam J Brancato; Elizabeth S Roddy; Philip C Bevilacqua; Andrew G Ewing
Continuous monitoring of enzyme reactions on a microchip: application to catalytic RNA self-cleavage.
Analytical chemistry 2004;76(23):6921-7.
2004: Xiaofeng Zheng; Philip C Bevilacqua
Activation of the protein kinase PKR by short double-stranded RNAs with single-stranded tails.
RNA (New York, N.Y.) 2004;10(12):1934-45.
2004: David Proctor; Hairong Ma; Elzbieta Kierzek; Ryszard Kierzek; Martin Gruebele; Philip C Bevilacqua
Folding thermodynamics and kinetics of YNMG RNA hairpins: specific incorporation of 8-bromoguanosine leads to stabilization by enhancement of the folding rate.
Biochemistry 2004;43(44):14004-14.
2004: Ellen M Moody; Trevor S Brown; Philip C Bevilacqua
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 2004;126(33):10200-1.
2004: Trevor S Brown; Durga M Chadalavada; Philip C Bevilacqua
Design of a highly reactive HDV ribozyme sequence uncovers facilitation of RNA folding by alternative pairings and physiological ionic strength.
Journal of molecular biology 2004;341(3):695-712.
2004: Ellen M Moody; Philip C Bevilacqua
Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop.
Journal of the American Chemical Society 2004;126(31):9570-7.
2004: Ellen M Moody; Jessica C Feerrar; Philip C Bevilacqua
Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart.
Biochemistry 2004;43(25):7992-8.
2004: Philip C Bevilacqua; Trevor S Brown; Shu-ichi Nakano; Rieko Yajima
Catalytic roles for proton transfer and protonation in ribozymes.
Biopolymers 2004;73(1):90-109.
2003: Ellen M Moody; Philip C Bevilacqua
Folding of a stable DNA motif involves a highly cooperative network of interactions.
Journal of the American Chemical Society 2003;125(52):16285-93.
2003: Janell E Schaak; Paul Babitzke; Philip C Bevilacqua
Phylogenetic conservation of RNA secondary and tertiary structure in the trpEDCFBA operon leader transcript in Bacillus.
RNA (New York, N.Y.) 2003;9(12):1502-15.
2003: Janell E Schaak; Helen Yakhnin; Philip C Bevilacqua; Paul Babitzke
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 2003;332(3):555-74.
2003: Shu-ichi Nakano; Andrea L Cerrone; Philip C Bevilacqua
Mechanistic characterization of the HDV genomic ribozyme: classifying the catalytic and structural metal ion sites within a multichannel reaction mechanism.
Biochemistry 2003;42(10):2982-94.
2003: David Proctor; Elzbieta Kierzek; Ryszard Kierzek; Philip C Bevilacqua
Restricting the conformational heterogeneity of RNA by specific incorporation of 8-bromoguanosine.
Journal of the American Chemical Society 2003;125(9):2390-1.
2003: Philip C Bevilacqua
Mechanistic considerations for general acid-base catalysis by RNA: revisiting the mechanism of the hairpin ribozyme.
Biochemistry 2003;42(8):2259-65.
2003: Ellen M Moody; Philip C Bevilacqua
Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs.
Journal of the American Chemical Society 2003;125(8):2032-3.
2003: Paul Babitzke; Janell E Schaak; Alexander V Yakhnin; Philip C Bevilacqua
Role of RNA structure in transcription attenuation in Bacillus subtilis: the trpEDCFBA operon as a model system.
Methods in enzymology 2003;371():392-404.
2002: Mariko Nakano; Ellen M Moody; Jing Liang; Philip C Bevilacqua
Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc).
Biochemistry 2002;41(48):14281-92.
2002: Amy M. Diegelman; Philip C Bevilacqua
A mechanistic framework for co-transcriptional folding of the HDV genomic ribozyme in the presence of downstream sequence.
Journal of molecular biology 2002;324(1):1-16.
2002: David Proctor; Janell E Schaak; Joanne M Bevilacqua; Christopher J Falzone; Philip C Bevilacqua
Isolation and characterization of a family of stable RNA tetraloops with the motif YNMG that participate in tertiary interactions.
Biochemistry 2002;41(40):12062-75.
2002: Philip C Bevilacqua; Douglas H Turner
Use of fluorescence spectroscopy to elucidate RNA folding pathways.
Current protocols in nucleic acid chemistry / edited by Serge L. Beaucage ... [et al.] 2002;Chapter 11():Unit 11.8.
2002: Philip C Bevilacqua
Battle for the bulge: directing small molecules to DNA and RNA defects.
Chemistry & biology 2002;9(8):854-5.
2002: Durga M Chadalavada; Susan E Senchak; Philip C Bevilacqua
The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots.
Journal of molecular biology 2002;317(4):559-75.
2001: Shu-ichi Nakano; Philip C Bevilacqua
Proton inventory of the genomic HDV ribozyme in Mg(2+)-containing solutions.
Journal of the American Chemical Society 2001;123(45):11333-4.
2001: Shu-ichi Nakano; David Proctor; Philip C Bevilacqua
Mechanistic characterization of the HDV genomic ribozyme: assessing the catalytic and structural contributions of divalent metal ions within a multichannel reaction mechanism.
Biochemistry 2001;40(40):12022-38.
2001: Xiaofeng Zheng; Philip C Bevilacqua
Efficient construction of long DNA duplexes with internal non-Watson-Crick motifs and modifications.
Nucleic acids research 2001;29(2):E6.
2000: Xiaofeng Zheng; Philip C Bevilacqua
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 2000;97(26):14162-7.
2000: Durga M Chadalavada; S M Knudsen; Shu-ichi Nakano; Philip C Bevilacqua
A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme.
Journal of molecular biology 2000;301(2):349-67.
2000: Shu-ichi Nakano; Durga M Chadalavada; Philip C Bevilacqua
General acid-base catalysis in the mechanism of a hepatitis delta virus ribozyme.
Science (New York, N.Y.) 2000;287(5457):1493-7.
1999: Z Shu; Philip C Bevilacqua
Isolation and characterization of thermodynamically stable and unstable RNA hairpins from a triloop combinatorial library.
Biochemistry 1999;38(46):15369-79.
1999: Jamie J Arnold; Saikat Kumar B Ghosh; Philip C Bevilacqua; Craig E Cameron
Single-nucleotide resolution of RNA strands in the presence of their RNA complements.
BioTechniques 1999;27(3):450-2, 454, 456.
1998: J M Bevilacqua; Philip C Bevilacqua
Thermodynamic analysis of an RNA combinatorial library contained in a short hairpin.
Biochemistry 1998;37(45):15877-84.