Crowding Shifts the FMN Recognition Mechanism of Riboswitch Aptamer from Conformational Selection to Induced Fit

An integrated perspective on RNA aptamer ligand-recognition models: clearing muddy waters

(2017) K. McCluskey et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Riboswitch diversity and distribution

(2017) Phillip J. McCown et al.   RNA

Molecular simulations and Markov state modeling reveal the structural diversity and dynamics of a theophylline-binding RNA aptamer in its unbound state

(2017) Becka M. Warfield et al.   PLoS One

tRNA Shifts the G-quadruplex-Hairpin Conformational Equilibrium in RNA towards the Hairpin Conformer

(2016) Ambadas B. Rode et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Emerging applications of riboswitches – from antibacterial targets to molecular tools

(2016) Piotr Machtel et al.   JOURNAL OF APPLIED GENETICS

Conformational Rearrangements of Individual Nucleotides during RNA-Ligand Binding Are Rate-Differentiated

(2016) Marina Frener et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Reducing Ribosome Biosynthesis Promotes Translation during Low Mg 2+ Stress

(2016) Mauricio H. Pontes et al.   MOLECULAR CELL

RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression

(2015) Christian Berens et al.   Biotechnology Journal

Key Tertiary Interactions in FMN Riboswitch Aptamers Required for Ligand Binding

(2015) Ambadas B. Rode et al.   BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN

Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection

(2015) Krishna C. Suddala et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Selective small-molecule inhibition of an RNA structural element

(2015) John A. Howe et al.   NATURE

Automated physics-based design of synthetic riboswitches from diverse RNA aptamers

(2015) Amin Espah Borujeni et al.   NUCLEIC ACIDS RESEARCH

Rapid RNA–ligand interaction analysis through high-information content conformational and stability landscapes

(2015) Nathan J. Baird et al.   Nature Communications

RNA aptamers as genetic control devices: The potential of riboswitches as synthetic elements for regulating gene expression

(2015) Christian Berens et al.   Biotechnology Journal

Tuning Riboswitch-Mediated Gene Regulation by Rational Control of Aptamer Ligand Binding Properties

(2014) Ambadas B. Rode et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Molecular Crowding Accelerates Ribozyme Docking and Catalysis

(2014) Bishnu P. Paudel et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Bacterial Mg2+Homeostasis, Transport, and Virulence

(2013) Eduardo A. Groisman et al.   Annual Review of Genetics

Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

(2013) Shu-ichi Nakano et al.   CHEMICAL REVIEWS

Conformational Selection or Induced Fit? A Critical Appraisal of the Kinetic Mechanism

(2012) Austin D. Vogt et al.   BIOCHEMISTRY

Dehydration from conserved stem regions is fundamental for ligand-dependent conformational transition of the adenine-specific riboswitch

(2012) Vinit Kumar et al.   CHEMICAL COMMUNICATIONS

Molecular sensing by the aptamer domain of the FMN riboswitch: a general model for ligand binding by conformational selection

(2011) Quentin Vicens et al.   NUCLEIC ACIDS RESEARCH

Molecular Crowding Stabilizes Folded RNA Structure by the Excluded Volume Effect

(2010) Duncan Kilburn et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Magnesium-sensing riboswitches in bacteria

(2010) Arati Ramesh et al.   RNA Biology

Idiosyncratically tuned switching behavior of riboswitch aptamer domains revealed by comparative small-angle X-ray scattering analysis

(2010) N. J. Baird et al.   RNA

Facilitation of RNA Enzyme Activity in the Molecular Crowding Media of Cosolutes

(2009) Shu-ichi Nakano et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Coenzyme recognition and gene regulation by a flavin mononucleotide riboswitch

(2009) Alexander Serganov et al.   NATURE