Philip C Bevilacqua: search on Z-Library

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1

Minor-Groove Recognition of Double-Stranded RNA by the Double-Stranded RNA-Binding Domain from the RNA-Activated Protein Kinase PKR †

Bevilacqua, Philip C., Cech, Thomas R.

Journal:

Year:

1996

Language:

english

File:

PDF, 669 KB

english, 1996

2

Mechanistic Considerations for General Acid−Base Catalysis by RNA: Revisiting the Mechanism of the Hairpin Ribozyme †

Bevilacqua, Philip C.

Journal:

Year:

2003

Language:

english

File:

PDF, 93 KB

english, 2003

3

The Biophysics of RNA

Bevilacqua, Philip C., SantaLucia, John

Journal:

ACS Chemical Biology

Year:

2007

Language:

english

File:

PDF, 346 KB

english, 2007

4

Discriminating Self and Non-Self by RNA: Roles for RNA Structure, Misfolding, and Modification in Regulating the Innate Immune Sensor PKR

Hull, Chelsea M., Bevilacqua, Philip C.

Journal:

Accounts of Chemical Research

Year:

2016

Language:

english

File:

PDF, 1.61 MB

english, 2016

5

Bridging the gap between in vitro and in vivo RNA folding

Leamy, Kathleen A., Assmann, Sarah M., Mathews, David H., Bevilacqua, Philip C.

Journal:

Quarterly Reviews of Biophysics

Year:

2016

Language:

english

File:

PDF, 713 KB

english, 2016

6

Assessing Risk of Disease Progression and Pharmacological Management of Autosomal Dominant Polycystic Kidney Disease

Soroka, Steven, Alam, Ahsan, Bevilacqua, Micheli, Girard, Louis-Philippe, Komenda, Paul, Loertscher, Rolf, McFarlane, Philip, Pandeya, Sanjaya, Tam, Paul, Bichet, Daniel G.

Journal:

Canadian Journal of Kidney Health and Disease

Year:

2017

File:

PDF, 1.73 MB

2017

7

StructureFold2: Bringing chemical probing data into the computational fold of RNA structural analysis

Tack, David C., Tang, Yin, Ritchey, Laura E., Assmann, Sarah M., Bevilacqua, Philip C.

Journal:

Year:

2018

Language:

english

File:

PDF, 448 KB

english, 2018

8

Template-directed RNA polymerization and enhanced ribozyme catalysis inside membraneless compartments formed by coacervates

Poudyal, Raghav R., Guth-Metzler, Rebecca M., Veenis, Andrew J., Frankel, Erica A., Keating, Christine D., Bevilacqua, Philip C.

Journal:

Nature Communications

Year:

2019

Language:

english

File:

PDF, 2.21 MB

english, 2019

9

Catalytic roles for proton transfer and protonation in ribozymes

Philip C. Bevilacqua, Trevor S. Brown, Shu-ichi Nakano, Rieko Yajima

Journal:

Year:

2004

Language:

english

File:

PDF, 291 KB

english, 2004

10

Editorial: Mechanism of catalytic RNA

Philip C. Bevilacqua

Journal:

Year:

2004

Language:

english

File:

PDF, 34 KB

english, 2004

11

Nucleobase catalysis in ribozyme mechanism

Philip C Bevilacqua, Rieko Yajima

Journal:

Current Opinion in Chemical Biology

Year:

2006

Language:

english

File:

PDF, 341 KB

english, 2006

12

Editorial overview: exploring the vast dynamic range of RNA dynamics

Philip C Bevilacqua, Rick Russell

Journal:

Current Opinion in Chemical Biology

Year:

2008

Language:

english

File:

PDF, 100 KB

english, 2008

13

A Conformationally Restricted Guanosine Analog Reveals the Catalytic Relevance of Three Structures of an RNA Enzyme

Rieko Yajima, David J. Proctor, Ryszard Kierzek, Elzbieta Kierzek, Philip C. Bevilacqua

Journal:

Chemistry & Biology

Year:

2007

Language:

english

File:

PDF, 399 KB

english, 2007

14

Battle for the Bulge: Directing Small Molecules to DNA and RNA Defects

Philip C Bevilacqua

Journal:

Chemistry & Biology

Year:

2002

Language:

english

File:

PDF, 29 KB

english, 2002

15

PKR and the ribosome compete for mRNA

Toroney, Rebecca, Bevilacqua, Philip C

Journal:

Nature Chemical Biology

Year:

2009

Language:

english

File:

PDF, 313 KB

english, 2009

16

The double-stranded-RNA-binding motif: interference and much more

Tian, Bin, Bevilacqua, Philip C., Diegelman-Parente, Amy, Mathews, Michael B.

Journal:

Nature Reviews Molecular Cell Biology

Year:

2004

Language:

english

File:

PDF, 241 KB

english, 2004

17

Regulation of innate immunity through RNA structure and the protein kinase PKR

Subba Rao Nallagatla, Rebecca Toroney, Philip C Bevilacqua

Journal:

Current Opinion in Structural Biology

Year:

2011

Language:

english

File:

PDF, 513 KB

english, 2011

18

RNA catalysis through compartmentalization

Strulson, Christopher A., Molden, Rosalynn C., Keating, Christine D., Bevilacqua, Philip C.

Journal:

Nature Chemistry

Year:

2012

Language:

english

File:

PDF, 1.83 MB

english, 2012

19

A role for upstream RNA structure in facilitating the catalytic fold of the genomic hepatitis delta virus ribozyme

Durga M. Chadalavada, Scott M. Knudsen, Shu-ichi Nakano, Philip C. Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2000

Language:

english

File:

PDF, 611 KB

english, 2000

20

The folding pathway of the genomic hepatitis delta virus ribozyme is dominated by slow folding of the pseudoknots

Durga M Chadalavada, Susan E Senchak, Philip C Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 330 KB

english, 2002

21

Design of a Highly Reactive HDV Ribozyme Sequence Uncovers Facilitation of RNA Folding by Alternative Pairings and Physiological Ionic Strength

Trevor S. Brown, Durga M. Chadalavada, Philip C. Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2004

Language:

english

File:

PDF, 785 KB

english, 2004

22

RNA Dimerization Promotes PKR Dimerization and Activation

Laurie A. Heinicke, C. Jason Wong, Jeffrey Lary, Subba Rao Nallagatla, Amy Diegelman-Parente, Xiaofeng Zheng, James L. Cole, Philip C. Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2009

Language:

english

File:

PDF, 2.70 MB

english, 2009

23

Regulation of PKR by HCV IRES RNA: Importance of Domain II and NS5A

Rebecca Toroney, Subba Rao Nallagatla, Joshua A. Boyer, Craig E. Cameron, Philip C. Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 2.25 MB

english, 2010

24

Long-Distance Communication in the HDV Ribozyme: Insights from Molecular Dynamics and Experiments

Narayanan Veeraraghavan, Philip C. Bevilacqua, Sharon Hammes-Schiffer

Journal:

Journal of Molecular Biology

Year:

2010

Language:

english

File:

PDF, 1.61 MB

english, 2010

25

Raman crystallography of RNA

Bo Gong, Jui-Hui Chen, Rieko Yajima, Yuanyuan Chen, Elaine Chase, Durga M. Chadalavada, Barbara L. Golden, Paul R. Carey, Philip C. Bevilacqua

Journal:

Year:

2009

Language:

english

File:

PDF, 527 KB

english, 2009

26

A Mechanistic Framework for Co-transcriptional Folding of the HDV Genomic Ribozyme in the Presence of Downstream Sequence

Amy Diegelman-Parente, Philip C Bevilacqua

Journal:

Journal of Molecular Biology

Year:

2002

Language:

english

File:

PDF, 1.57 MB

english, 2002

27

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

Janell E. Schaak, Helen Yakhnin, Philip C. Bevilacqua, Paul Babitzke

Journal:

Journal of Molecular Biology

Year:

2003

Language:

english

File:

PDF, 2.05 MB

english, 2003

28

Prospecting for Aptamers in the Human Genome

Philip C. Bevilacqua, Peter C. Breen, Pallavi Thaplyal

Journal:

Chemistry & Biology

Year:

2012

Language:

english

File:

PDF, 193 KB

english, 2012

29

Decrease in RNA Folding Cooperativity by Deliberate Population of Intermediates in RNA G-Quadruplexes

Kwok, Chun Kit, Sherlock, Madeline E., Bevilacqua, Philip C.

Journal:

Angewandte Chemie

Year:

2013

Language:

english

File:

PDF, 747 KB

english, 2013

30

Decrease in RNA Folding Cooperativity by Deliberate Population of Intermediates in RNA G-Quadruplexes

Kwok, Chun Kit, Sherlock, Madeline E., Bevilacqua, Philip C.

Journal:

Angewandte Chemie International Edition

Year:

2013

Language:

english

File:

PDF, 772 KB

english, 2013

31

Regulation of PKR By Viral RNAS

Wong, C. Jason, Heinicke, Laurie A., Launer-Felty, Katherine, Lary, Jeffrey W., Conn, Graeme L., Bevilacqua, Philip C., Cole, James L.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 43 KB

english, 2010

32

Possible seasonal variability of mesospheric water vapor

Bevilacqua, R. M., Wilson, William J., Ricketts, William B., Schwartz, Philip R., Howard, R. J.

Journal:

Geophysical Research Letters

Year:

1985

Language:

english

File:

PDF, 279 KB

english, 1985

33

The variability of carbon monoxide in the terrestrial mesosphere as determined from ground-based observations of the J = 1 → 0 emission line

Bevilacqua, Richard M., Stark, Antony A., Schwartz, Philip R.

Journal:

Journal of Geophysical Research

Year:

1985

Language:

english

File:

PDF, 595 KB

english, 1985

34

Measurements of mesospheric water vapor in 1984 and 1985: Results and implications for middle atmospheric transport

Bevilacqua, Richard M., Wilson, William J., Schwartz, Philip R.

Journal:

Journal of Geophysical Research

Year:

1987

Language:

english

File:

PDF, 822 KB

english, 1987

35

5'-Amino pyrene provides a sensitive, nonperturbing fluorescent probe of RNA secondary and tertiary structure formation

Kierzek, Ryszard, Li, Yi, Turner, Douglas H., Bevilacqua, Philip C.

Journal:

Journal of the American Chemical Society

Year:

1993

Language:

english

File:

PDF, 1.06 MB

english, 1993

36

A hybridization-based approach for quantitative and low-bias single-stranded DNA ligation

Kwok, Chun Kit, Ding, Yiliang, Sherlock, Madeline E., Assmann, Sarah M., Bevilacqua, Philip C.

Journal:

Analytical Biochemistry

Year:

2013

Language:

english

File:

PDF, 553 KB

english, 2013

37

Thermodynamics of Ligand Binding to a Heterogeneous RNA Population in the Malachite Green Aptamer

Sokoloski, Joshua E., Dombrowski, Sarah E., Bevilacqua, Philip C.

Journal:

Year:

2012

Language:

english

File:

PDF, 1.90 MB

english, 2012

38

Effect of Loop Sequence and Loop Length on the Intrinsic Fluorescence of G-Quadruplexes

Kwok, Chun Kit, Sherlock, Madeline E., Bevilacqua, Philip C.

Journal:

Year:

2013

Language:

english

File:

PDF, 519 KB

english, 2013

39

Isolation and Characterization of a Family of Stable RNA Tetraloops with the Motif YNMG That Participate in Tertiary Interactions †

Proctor, David J., Schaak, Janell E., Bevilacqua, Joanne M., Falzone, Christopher J., Bevilacqua, Philip C.

Journal:

Year:

2002

Language:

english

File:

PDF, 289 KB

english, 2002

40

A Simple Fluorescence Method for p K a Determination in RNA and DNA Reveals Highly Shifted p K a ’s

Wilcox, Jennifer L., Bevilacqua, Philip C.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 777 KB

english, 2013

41

Structures, Kinetics, Thermodynamics, and Biological Functions of RNA Hairpins

Bevilacqua, Philip C., Blose, Joshua M.

Journal:

Annual Review of Physical Chemistry

Year:

2008

Language:

english

File:

PDF, 275 KB

english, 2008

42

Identification of the Catalytic Mg 2+ Ion in the Hepatitis Delta Virus Ribozyme

Chen, Ji, Ganguly, Abir, Miswan, Zulaika, Hammes-Schiffer, Sharon, Bevilacqua, Philip C., Golden, Barbara L.

Journal:

Year:

2013

Language:

english

File:

PDF, 2.63 MB

english, 2013

43

Driving Forces for Nucleic Acid p K a Shifting in an A + ·C Wobble: Effects of Helix Position, Temperature, and Ionic Strength

Siegfried, Nathan A., O’Hare, Bernie, Bevilacqua, Philip C.

Journal:

Year:

2010

Language:

english

File:

PDF, 1.58 MB

english, 2010

44

Thio Effects and an Unconventional Metal Ion Rescue in the Genomic Hepatitis Delta Virus Ribozyme

Thaplyal, Pallavi, Ganguly, Abir, Golden, Barbara L., Hammes-Schiffer, Sharon, Bevilacqua, Philip C.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.49 MB

english, 2013

45

Charged Nucleobases and Their Potential for RNA Catalysis

Wilcox, Jennifer L., Ahluwalia, Amarpreet K., Bevilacqua, Philip C.

Journal:

Accounts of Chemical Research

Year:

2011

Language:

english

File:

PDF, 2.24 MB

english, 2011

46

p K a Shifting in Double-Stranded RNA Is Highly Dependent upon Nearest Neighbors and Bulge Positioning

Wilcox, Jennifer L., Bevilacqua, Philip C.

Journal:

Year:

2013

Language:

english

File:

PDF, 1.35 MB

english, 2013

47

In vivo genome-wide profiling of RNA secondary structure reveals novel regulatory features

Ding, Yiliang, Tang, Yin, Kwok, Chun Kit, Zhang, Yu, Bevilacqua, Philip C., Assmann, Sarah M.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.84 MB

english, 2013

48

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

Tubbs, Jason D., Condon, David E., Kennedy, Scott D., Hauser, Melanie, Bevilacqua, Philip C., Turner, Douglas H.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.05 MB

english, 2013

49

Contribution of the Closing Base Pair to Exceptional Stability in RNA Tetraloops: Roles for Molecular Mimicry and Electrostatic Factors

Blose, Joshua M., Proctor, David J., Veeraraghavan, Narayanan, Misra, Vinod K., Bevilacqua, Philip C.

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 4.05 MB

english, 2009

50

Determination of in vivo RNA structure in low-abundance transcripts

Kwok, Chun Kit, Ding, Yiliang, Tang, Yin, Assmann, Sarah M., Bevilacqua, Philip C

Journal:

Nature Communications

Year:

2013

Language:

english

File:

PDF, 6.29 MB

english, 2013

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