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Technique Development for Probing RNA Structure In Vivo and Genome-Wide

Cold Spring Harbor perspectives in biology, 2018-10, Vol.10 (10), p.a032250

2018

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Genome-Wide Analysis of RNA Secondary Structure

Annual review of genetics, 2016-11, Vol.50 (1), p.235-266

2016

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

Nature communications, 2019-01, Vol.10 (1), p.490-490, Article 490

2019

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Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

Nature communications, 2020-11, Vol.11 (1), p.5949-5949, Article 5949

2020

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Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates

ACS chemical biology, 2019-06, Vol.14 (6), p.1243-1248

2019

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Bioreactor droplets from liposome-stabilized all-aqueous emulsions

Nature communications, 2014-08, Vol.5 (1), p.4670-4670, Article 4670

2014

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Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

Nature communications, 2018-06, Vol.9 (1), p.2149-12, Article 2149

2018

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

Current opinion in structural biology, 2011-02, Vol.21 (1), p.119-127

2011

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A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation

Biochemical journal, 2015-04, Vol.467 (1), p.91-102

2015

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In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells

Nucleic acids research, 2023-11, Vol.51 (20), p.11298

2023

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Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization

Biochemistry (Easton), 2017-07, Vol.56 (27), p.3422-3433

2017

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Determination of in vivo RNA structure in low-abundance transcripts

Nature communications, 2013-12, Vol.4 (1), p.2971-2971, Article 2971

2013

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Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme

Journal of the American Chemical Society, 2014-01, Vol.136 (4), p.1483-1496

2014

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mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

Genome Biology, 2019-12, Vol.20 (1), p.300-23, Article 300

2019

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Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Genome Biology, 2022-04, Vol.23 (1), p.101-101, Article 101

2022

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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, 2015-01, Vol.137 (2), p.784-798

2015

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In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)

RNA (Cambridge), 2019-01, Vol.25 (1), p.147-157

2019

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

Biochemistry (Easton), 2013-05, Vol.52 (18), p.3019-3021

2013

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Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

RNA (Cambridge), 2014-03, Vol.20 (3), p.331-347

2014

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StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo

Bioinformatics, 2015-08, Vol.31 (16), p.2668-2675

2015

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Cooperative Interactions in the Hammerhead Ribozyme Drive pKa Shifting of G12 and Its Stacked Base C17

Biochemistry (Easton), 2017-05, Vol.56 (20), p.2537-2548

2017

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

Biochemistry (Easton), 2003-03, Vol.42 (8), p.2259-2265

Bevilacqua, Philip C

2003

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Structures, kinetics, thermodynamics, and biological functions of RNA hairpins

Annual review of physical chemistry, 2008-01, Vol.59 (1), p.79-103

2008

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Molecular Crowding Favors Reactivity of a Human Ribozyme Under Physiological Ionic Conditions

Biochemistry (Easton), 2013-11, Vol.52 (46), p.8187-8197

2013

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Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex

PloS one, 2015-11, Vol.10 (11), p.e0143160-e0143160

2015

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Technique Development for Probing RNA Structure In Vivo and Genome-Wide

Genome-Wide Analysis of RNA Secondary Structure

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

Prebiotically-relevant low polyion multivalency can improve functionality of membraneless compartments

Polyanion-Assisted Ribozyme Catalysis Inside Complex Coacervates

Bioreactor droplets from liposome-stabilized all-aqueous emulsions

Cellular conditions of weakly chelated magnesium ions strongly promote RNA stability and catalysis

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

A stable RNA G-quadruplex within the 5'-UTR of Arabidopsis thaliana ATR mRNA inhibits translation

In vivo-like nearest neighbor parameters improve prediction of fractional RNA base-pairing in cells

Cooperative RNA Folding under Cellular Conditions Arises From Both Tertiary Structure Stabilization and Secondary Structure Destabilization

Determination of in vivo RNA structure in low-abundance transcripts

Quantum Mechanical/Molecular Mechanical Free Energy Simulations of the Self-Cleavage Reaction in the Hepatitis Delta Virus Ribozyme

mRNA structural elements immediately upstream of the start codon dictate dependence upon eIF4A helicase activity

Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis

Role of the Active Site Guanine in the glmS Ribozyme Self-Cleavage Mechanism: Quantum Mechanical/Molecular Mechanical Free Energy Simulations

In vivo RNA structural probing of uracil and guanine base-pairing by 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC)

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

Molecular crowders and cosolutes promote folding cooperativity of RNA under physiological ionic conditions

StructureFold: genome-wide RNA secondary structure mapping and reconstruction in vivo

Cooperative Interactions in the Hammerhead Ribozyme Drive pKa Shifting of G12 and Its Stacked Base C17

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

Structures, kinetics, thermodynamics, and biological functions of RNA hairpins

Molecular Crowding Favors Reactivity of a Human Ribozyme Under Physiological Ionic Conditions

Amyloid Precursor Protein Translation Is Regulated by a 3'UTR Guanine Quadruplex

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