The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry

Relative Strength of Noncovalent Interactions and Covalent Backbone Bonds in Gaseous RNA–Peptide Complexes

(2019) Jovana Vušurović et al.   ANALYTICAL CHEMISTRY

Conformations and N-glycosidic bond stabilities of sodium cationized 2′-deoxycytidine and cytidine: Solution conformation of [Cyd + Na] + is preserved upon ESI

(2018) Y. Zhu et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Adenine protonation enables cyclic-di-GMP binding to cyclic-GAMP sensing riboswitches

(2018) Heiko Keller et al.   RNA

Protonation of Nucleobases in Single- and Double-Stranded DNA

(2018) Julio C. González-Olvera et al.   CHEMBIOCHEM

Cellular Small Molecules Contribute to Twister Ribozyme Catalysis

(2018) Kyle J. Messina et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Submicrometer Nanospray Emitters Provide New Insights into the Mechanism of Cation Adduction to Anionic Oligonucleotides

(2018) Thomas Kenderdine et al.   ANALYTICAL CHEMISTRY

N3 and O2 Protonated Conformers of the Cytosine Mononucleotides Coexist in the Gas Phase

(2017) R. R. Wu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

IRMPD Action Spectroscopy, ER-CID Experiments, and Theoretical Studies of Sodium Cationized Thymidine and 5-Methyluridine: Kinetic Trapping During the ESI Desolvation Process Preserves the Solution Structure of [Thd+Na]+

(2017) Y. Zhu et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry

(2017) Heidelinde Glasner et al.   NUCLEIC ACIDS RESEARCH

The intrinsic basicity of the phosphate backbone exceeds that of uracil and thymine residues: protonation of the phosphate moiety is preferred over the nucleobase for pdThd and pUrd

(2017) R. R. Wu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Effects of sodium cationization versus protonation on the conformations and N-glycosidic bond stabilities of sodium cationized Urd and dUrd: solution conformation of [Urd+Na]+ is preserved upon ESI

(2017) Y. Zhu et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Interactions of Protonated Guanidine and Guanidine Derivatives with Multiply Deprotonated RNA Probed by Electrospray Ionization and Collisionally Activated Dissociation

(2017) Jovana Vušurović et al.   ChemistryOpen

Compaction of Duplex Nucleic Acids upon Native Electrospray Mass Spectrometry

(2017) Massimiliano Porrini et al.   ACS Central Science

Native Top-Down Mass Spectrometry of TAR RNA in Complexes with a Wild-Type tat Peptide for Binding Site Mapping

(2016) Eva-Maria Schneeberger et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2016) Antje C. Wolter et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Facile synthesis of a 3-deazaadenosine phosphoramidite for RNA solid-phase synthesis

(2016) Elisabeth Mairhofer et al.   Beilstein Journal of Organic Chemistry

Molecular Dynamics Study of Twister Ribozyme: Role of Mg2+ Ions and the Hydrogen-Bonding Network in the Active Site

(2016) Melek N. Ucisik et al.   BIOCHEMISTRY

O2 Protonation Controls Threshold Behavior for N-Glycosidic Bond Cleavage of Protonated Cytosine Nucleosides

(2016) R. R. Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

N3 Protonation Induces Base Rotation of 2′-Deoxyadenosine-5′-monophosphate and Adenosine-5′-monophosphate

(2016) R. R. Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

The Novel Chemical Mechanism of the Twister Ribozyme

(2016) Timothy J. Wilson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ribozyme Catalysis with a Twist: Active State of the Twister Ribozyme in Solution Predicted from Molecular Simulation

(2016) Colin S. Gaines et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Many Activities, One Structure: Functional Plasticity of Ribozyme Folds

(2016) Matthew Lau et al.   MOLECULES

Crystal structure of a poly(rA) staggered zipper at acidic pH: evidence that adenine N1 protonation mediates parallel double helix formation

(2016) Michael L. Gleghorn et al.   NUCLEIC ACIDS RESEARCH

Unwinding the twister ribozyme: from structure to mechanism

(2016) Jennifer Gebetsberger et al.   Wiley Interdisciplinary Reviews-RNA

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

(2015) Maria Pechlaner et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

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

(2015) Marija Košutić et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Gas-Phase Conformations and Energetics of Protonated 2′-Deoxyadenosine and Adenosine: IRMPD Action Spectroscopy and Theoretical Studies

(2015) R. R. Wu et al.   JOURNAL OF PHYSICAL CHEMISTRY B

On the mechanism of RNA phosphodiester backbone cleavage in the absence of solvent

(2015) C. Riml et al.   NUCLEIC ACIDS RESEARCH

Nucleotide modifications within bacterial messenger RNAs regulate their translation and are able to rewire the genetic code

(2015) Thomas Philipp Hoernes et al.   NUCLEIC ACIDS RESEARCH

Chemistry and Biology of Self-Cleaving Ribozymes

(2015) Randi M. Jimenez et al.   TRENDS IN BIOCHEMICAL SCIENCES

Nucleic Acid Catalysis: Metals, Nucleobases, and Other Cofactors

(2014) W. Luke Ward et al.   CHEMICAL REVIEWS

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

(2014) Daniel L Kellerman et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Characterization of nucleic acids by tandem mass spectrometry - The second decade (2004-2013): From DNA to RNA and modified sequences

(2014) Stefan Schürch   MASS SPECTROMETRY REVIEWS

Feasibility of occurrence of different types of protonated base pairs in RNA: a quantum chemical study

(2014) Antarip Halder et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

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

(2014) Aiming Ren et al.   Nature Communications

A Simple Fluorescence Method for pKa Determination in RNA and DNA Reveals Highly Shifted pKa’s

(2013) Jennifer L. Wilcox et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Characterization of Modified RNA by Top-Down Mass Spectrometry

(2012) Monika Taucher et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

A Transition-State Interaction Shifts Nucleobase Ionization toward Neutrality To Facilitate Small Ribozyme Catalysis

(2012) Joseph A. Liberman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Charged Nucleobases and Their Potential for RNA Catalysis

(2011) Jennifer L. Wilcox et al.   ACCOUNTS OF CHEMICAL RESEARCH

Understanding the Acid-Base Properties of Adenosine: The Intrinsic Basicities of N1, N3 and N7

(2011) Larisa E. Kapinos  et al.   CHEMISTRY-A EUROPEAN JOURNAL

IR Spectroscopy of Isolated Neutral and Protonated Adenine and 9-Methyladenine

(2011) Gydo C. P. van Zundert et al.   CHEMPHYSCHEM

Noncanonical Hydrogen Bonding in Nucleic Acids. Benchmark Evaluation of Key Base–Phosphate Interactions in Folded RNA Molecules Using Quantum-Chemical Calculations and Molecular Dynamics Simulations

(2011) Marie Zgarbová et al.   JOURNAL OF PHYSICAL CHEMISTRY A

A Novel 9.4 Tesla FTICR Mass Spectrometer with Improved Sensitivity, Mass Resolution, and Mass Range

(2011) Nathan K. Kaiser et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Identification, localization, and relative quantitation of pseudouridine in RNA by tandem mass spectrometry of hydrolysis products

(2010) Monika Taucher et al.   INTERNATIONAL JOURNAL OF MASS SPECTROMETRY

Top-down mass spectrometry for sequencing of larger (up to 61 nt) RNA by CAD and EDD

(2010) Monika Taucher et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

The Many Pathways of RNA Degradation

(2009) Jonathan Houseley et al.   CELL

Gas-Phase Thermochemical Properties of the Damaged BaseO6-Methylguanine versus Adenine and Guanine

(2009) Anna Zhachkina et al.   JOURNAL OF ORGANIC CHEMISTRY

Minimizing base loss and internal fragmentation in collisionally activated dissociation of multiply deprotonated RNA

(2009) Monika Taucher et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Classification and energetics of the base-phosphate interactions in RNA

(2009) Craig L. Zirbel et al.   NUCLEIC ACIDS RESEARCH

Calculation of pKaValues of Nucleobases and the Guanine Oxidation Products Guanidinohydantoin and Spiroiminodihydantoin using Density Functional Theory and a Polarizable Continuum Model

(2008) Vincenzo Verdolino et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Fluorine Substituted Adenosines As Probes of Nucleobase Protonation in Functional RNAs

(2008) Ian T. Suydam et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Ion Trap Collision-Induced Dissociation of Multiply Deprotonated RNA: c/y-Ions versus (a-B)/w-Ions

(2008) T HUANG et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Stepwise evolution of protein native structure with electrospray into the gas phase, 10-12 to 102 s

(2008) K. Breuker et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA