4.8 Article

Scaling Catalytic Contributions of Small Self-Cleaving Ribozymes

Related references

Note: Only part of the references are listed.
Article Chemistry, Physical

Calculations of pKa Values for a Series of Naturally Occurring Modified Nucleobases

Evan L. Jones et al.

Summary: Modified nucleobases play essential structural and biological roles in RNA, but their characteristics are still poorly understood. This study determined the pK(a) values of modified nucleobases using ab initio quantum mechanical calculations, providing insights into their structural and energetic impacts within nucleic acids.

JOURNAL OF PHYSICAL CHEMISTRY A (2022)

Article Biochemistry & Molecular Biology

Structure and mechanism of the methyltransferase ribozyme MTR1

Carolin P. M. Scheitl et al.

Summary: RNA-catalyzed RNA methylation has been found to be part of the catalytic repertoire of ribozymes. The crystal structure of methyltransferase ribozyme MTR1 has been determined, revealing a guanine-binding site similar to natural guanine riboswitches. The structure also suggests the involvement of a protonated cytidine in the methyl transfer reaction. The synergistic effect of 2'-O-methylated ribose residues in the active site accelerates methyl group transfer. These findings suggest that modified nucleotides may have played a role in early RNA catalysis and that metabolite-binding riboswitches resemble inactivated ribozymes.

NATURE CHEMICAL BIOLOGY (2022)

Article Chemistry, Applied

Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism

Natalia Serrano-Aparicio et al.

Summary: This study investigates the reactivity of the pistol ribozyme to clarify its catalytic mechanism and propose a unique mode of action by comparison with other ribozymes. The analysis of different protonation states of the active site reveals that only the canonical system yields reactive conformations. Additionally, changes in the coordination of the Mg2+ ion during simulations offer insights into the enzyme's mechanism.

TOPICS IN CATALYSIS (2022)

Article Chemistry, Multidisciplinary

1-Deazaguanosine-Modified RNA: The Missing Piece for Functional RNA Atomic Mutagenesis

Raphael Bereiter et al.

Summary: We have successfully synthesized 1-deazaguanosine (c(1)G)-modified RNA and demonstrated its potential applications in studying RNA recognition and catalysis. Through thermodynamic analyses, NMR spectroscopy, and X-ray structure analysis, we obtained valuable insights into the base pairing parameters, switching mechanism, backbone interaction, and guanine's critical impact on ribozyme activity.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2022)

Article Biochemistry & Molecular Biology

Towards a comprehensive understanding of RNA deamination: synthesis and properties of xanthosine-modified RNA

Stefan Mair et al.

Summary: This study investigated the biophysical properties and biological effects of X-modified RNA, revealing that X can form distinct wobble geometries with uridine and pair with cytidine in a different manner, affecting the recognition by reverse transcription enzymes. Additionally, the stability differences between pairing modes suggest potential for switching between them, indicating the importance of flexible pairing properties in X-modified RNA.

NUCLEIC ACIDS RESEARCH (2022)

Article Chemistry, Organic

Who stole the proton? Suspect general base guanine found with a smoking gun in the pistol ribozyme

Solen Ekesan et al.

Summary: The pistol ribozyme (Psr) is a recently discovered class of nucleolytic ribozymes that catalyze RNA self-cleavage. This study investigates the mechanism of Psr and proposes different roles for G42 and G40 as general bases. The findings provide new insights and suggest further experimental tests to solve the mystery of proton abstraction in the pistol ribozyme.

ORGANIC & BIOMOLECULAR CHEMISTRY (2022)

Article Biochemistry & Molecular Biology

Biochemical analysis of cleavage and ligation activities of the pistol ribozyme from Paenibacillus polymyxa

Yuliia Lihanova et al.

Summary: The study identified a newly discovered pistol ribozyme with efficient self-cleaving properties and investigated the catalytic role of various metal ions. Additionally, the ligation activity of this ribozyme class was analyzed for the first time, revealing almost complete cleavage at equilibrium.

RNA BIOLOGY (2021)

Review Chemistry, Multidisciplinary

The Varkud Satellite Ribozyme: A Thirty-Year Journey through Biochemistry, Crystallography, and Computation

Saurja DasGupta et al.

Summary: The discovery of catalytic RNAs, or ribozymes, has introduced a new class of enzymes and plays a key role in the RNA World hypothesis. The Varkud satellite (VS) ribozyme, a type of endonucleolytic ribozyme, is structurally complex and has been extensively studied to understand its catalytic mechanism. Through a combination of biochemical, structural, and computational studies, the detailed catalytic mechanism of the VS ribozyme has been revealed, shedding light on the common architectural motifs and catalytic strategies of nucleic acid-based endoribonucleases.

ACCOUNTS OF CHEMICAL RESEARCH (2021)

Article Biochemistry & Molecular Biology

Impact of 3-deazapurine nucleobases on RNA properties

Raphael Bereiter et al.

Summary: The study comprehensively investigates the impact of deazapurine nucleosides on RNA properties, showing that they can significantly decrease thermodynamic stability of base pairing and enhance base pair opening dynamics. The findings by NMR and X-ray crystallography provide a rationale for the reduced pairing strength, marking a major step towards a comprehensive understanding of this important class of nucleoside modifications.

NUCLEIC ACIDS RESEARCH (2021)

Article Chemistry, Multidisciplinary

Crucial Roles of Two Hydrated Mg2+ Ions in Reaction Catalysis of the Pistol Ribozyme

Marianna Teplova et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2020)

Article Chemistry, Multidisciplinary

Molecular dynamics analysis of Mg2+-dependent cleavage of a pistol ribozyme reveals a fail-safe secondary ion for catalysis

Newlyn N. Joseph et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

Small circRNAs with self-cleaving ribozymes are highly expressed in diverse metazoan transcriptomes

Amelia Cervera et al.

NUCLEIC ACIDS RESEARCH (2020)

Review Chemistry, Multidisciplinary

Fundamental studies of functional nucleic acids: aptamers, riboswitches, ribozymes and DNAzymes

Ronald Micura et al.

CHEMICAL SOCIETY REVIEWS (2020)

Article Biochemistry & Molecular Biology

An Ontology for Facilitating Discussion of Catalytic Strategies of RNA-Cleaving Enzymes

Philip C. Bevilacqua et al.

ACS CHEMICAL BIOLOGY (2019)

Article Chemistry, Multidisciplinary

Comparison of the Structures and Mechanisms of the Pistol and Hammerhead Ribozymes

Timothy J. Wilson et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)

Article Biochemistry & Molecular Biology

Complexity in pH-Dependent Ribozyme Kinetics: Dark p&ITK&ITa Shifts and Wavy Rate-pH Profiles

Erica A. Frankel et al.

BIOCHEMISTRY (2018)

Article Chemistry, Multidisciplinary

A Stably Protonated Adenine Nucleotide with a Highly Shifted pKa Value Stabilizes the Tertiary Structure of a GTP-Binding RNA Aptamer

Antje C. Wolter et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Review Cell Biology

Unwinding the twister ribozyme: from structure to mechanism

Jennifer Gebetsberger et al.

WILEY INTERDISCIPLINARY REVIEWS-RNA (2017)

Article Chemistry, Multidisciplinary

Pseudoknot Formation Seeds the Twister Ribozyme Cleavage Reaction Coordinate

Nikola Vusurovic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2017)

Article Multidisciplinary Sciences

Crystal structure of Pistol, a class of self-cleaving ribozyme

Laura A. Nguyen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Article Chemistry, Multidisciplinary

Atom-Specific Mutagenesis Reveals Structural and Catalytic Roles for an Active-Site Adenosine and Hydrated Mg2+ in Pistol Ribozymes

Sandro Neuner et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2017)

Review Biochemistry & Molecular Biology

Structure-based mechanistic insights into catalysis by small self-cleaving ribozymes

Aiming Ren et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2017)

Article Biochemistry & Molecular Biology

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

Erica A. Frankel et al.

BIOCHEMISTRY (2017)

Article Biochemistry & Molecular Biology

Pistol ribozyme adopts a pseudoknot fold facilitating site-specific in-line cleavage

Aiming Ren et al.

NATURE CHEMICAL BIOLOGY (2016)

Article Chemistry, Multidisciplinary

Protonation-Dependent Base Flipping at Neutral pH in the Catalytic Triad of a Self-Splicing Bacterial GroupII Intron

Maria Pechlaner et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Chemistry, Multidisciplinary

A Mini-Twister Variant and Impact of Residues/Cations on the Phosphodiester Cleavage of this Ribozyme Class

Marija Kosutic et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2015)

Article Biochemistry & Molecular Biology

Determination of pKa values for deprotonable nucleobases in short model oligonucleotides

Julio C. Gonzalez-Olvera et al.

BIOPHYSICAL CHEMISTRY (2015)

Article Chemistry, Physical

Prediction of the pKa's of Aqueous Metal Ion+2 Complexes

Virgil E. Jackson et al.

JOURNAL OF PHYSICAL CHEMISTRY A (2015)

Article Biochemistry & Molecular Biology

New classes of self-cleaving ribozymes revealed by comparative genomics analysis

Zasha Weinberg et al.

NATURE CHEMICAL BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Biochemical analysis of pistol self-cleaving ribozymes

Kimberly A. Harris et al.

Review Biochemistry & Molecular Biology

Chemistry and Biology of Self-Cleaving Ribozymes

Randi M. Jimenez et al.

TRENDS IN BIOCHEMICAL SCIENCES (2015)

Review Chemistry, Multidisciplinary

Nucleic Acid Catalysis: Metals, Nucleobases, and Other Cofactors

W. Luke Ward et al.

CHEMICAL REVIEWS (2014)

Review Biochemistry & Molecular Biology

Altered (transition) states: mechanisms of solution and enzyme catalyzed RNA 2′-O-transphosphorylation

Daniel L. Kellerman et al.

CURRENT OPINION IN CHEMICAL BIOLOGY (2014)

Article Biochemistry & Molecular Biology

A widespread self-cleaving ribozyme class is revealed by bioinformatics

Adam Roth et al.

NATURE CHEMICAL BIOLOGY (2014)

Article Multidisciplinary Sciences

In-line alignment and Mg2+ coordination at the cleavage site of the env22 twister ribozyme

Aiming Ren et al.

NATURE COMMUNICATIONS (2014)

Article Chemistry, Multidisciplinary

Intrinsic Acid-Base Properties of a Hexa-2-deoxynucleoside Pentaphosphate, d(ApGpGpCpCpT): Neighboring Effects and Isomeric Equilibria

Alicia Dominguez-Martin et al.

CHEMISTRY-A EUROPEAN JOURNAL (2013)

Review Chemistry, Multidisciplinary

Role of pKa of Nucleobases in the Origins of Chemical Evolution

Ramanarayanan Krishnamurthy

ACCOUNTS OF CHEMICAL RESEARCH (2012)

Article Chemistry, Multidisciplinary

General Acid-Base Catalysis Mediated by Nucleobases in the Hairpin Ribozyme

Stephanie Kath-Schorr et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Review Chemistry, Multidisciplinary

Charged Nucleobases and Their Potential for RNA Catalysis

Jennifer L. Wilcox et al.

ACCOUNTS OF CHEMICAL RESEARCH (2011)

Article Biochemistry & Molecular Biology

Base ionization and ligand binding: how small ribozymes and riboswitches gain a foothold in a protein world

Joseph A. Liberman et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2011)

Article Cell Biology

Small Self-cleaving Ribozymes

Adrian R. Ferre-D'Amare et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2010)

Editorial Material Biotechnology & Applied Microbiology

The amazing world of bacterial structured RNAs

Eric Westhof

GENOME BIOLOGY (2010)

Review Chemistry, Multidisciplinary

Xanthosine 5 '-monophosphate (XMP). Acid-base and metal ion-binding properties of a chameleon-like nucleotide

Helmut Sigel et al.

CHEMICAL SOCIETY REVIEWS (2009)

Article Biochemistry & Molecular Biology

Direct measurement of the ionization state of an essential guanine in the hairpin ribozyme

Lu Liu et al.

NATURE CHEMICAL BIOLOGY (2009)

Review Chemistry, Multidisciplinary

Catalytic strategies of self-cleaving ribozymes

Jesse C. Cochrane et al.

ACCOUNTS OF CHEMICAL RESEARCH (2008)

Article Biochemistry & Molecular Biology

The ionic environment determines ribozyme cleavage rate by modulation of nucleobase pK(a)

M. Duane Smith et al.

Review Chemistry, Multidisciplinary

Alternative roles for metal ions in enzyme catalysis and the implications for ribozyme chemistry

Roland K. O. Sigel et al.

CHEMICAL REVIEWS (2007)

Review Cell Biology

The catalytic diversity of RNAS

MJ Fedor et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Reverse protonation is the key to general acid-base catalysis in enolase

PA Sims et al.

BIOCHEMISTRY (2003)

Article Multidisciplinary Sciences

Transition state stabilization by a catalytic RNA

PB Rupert et al.

SCIENCE (2002)

Article Biochemistry & Molecular Biology

Xanthosine and xanthine - Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems

G Stoychev et al.

EUROPEAN JOURNAL OF BIOCHEMISTRY (2002)

Article Biochemistry & Molecular Biology

Rescue of an abasic hairpin ribozyme by cationic nucleobases: Evidence for a novel mechanism of RNA catalysis

LL Lebruska et al.

CHEMISTRY & BIOLOGY (2002)