N. Walter

发表

Correlating Structural Dynamics and Function in Single Ribozyme Molecules

X. Zhuang, S. Chu, H. Babcock, 2002, Science.

Single-molecule transition-state analysis of RNA folding

A. Gordus, X. Zhuang, H. Babcock, 2003, Proceedings of the National Academy of Sciences of the United States of America.

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

J. Šponer, N. Walter, M. Ditzler, 2009, Accounts of chemical research.

Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme.

N. Walter, Chamaree de Silva, 2008, RNA.

RNA dynamics: it is about time.

H. Al‐Hashimi, N. Walter, 2008, Current opinion in structural biology.

The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts

Nils G. Walter, N. Walter, A. J. Rinaldi, 2016, Nature Communications.

Single molecule fluorescence approaches shed light on intracellular RNAs.

Nils G Walter, N. Walter, Thomas C. Custer, 2014, Chemical reviews.

Biological Pathway Specificity in the Cell—Does Molecular Diversity Matter?

N. Walter, Nils G. Walter, 2019, BioEssays : news and reviews in molecular, cellular and developmental biology.

Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat

Hao Yan, William M. Shih, Nils G. Walter, 2018, Nature Nanotechnology.

Following the messenger: Recent innovations in live cell single molecule fluorescence imaging

Ameya P. Jalihal, N. Walter, Andreas Schmidt, 2020, Wiley interdisciplinary reviews. RNA.

RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview

Richard A. Cunha, J. Šponer, Sandro Bottaro, 2018, Chemical reviews.

DNA-cholesterol barges as programmable membrane-exploring agents.

Hao Yan, Shuoxing Jiang, Alexander Johnson-Buck, 2014, ACS nano.

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm.

Hao Yan, Yan Liu, Alexander Johnson-Buck, 2014, Nature nanotechnology.

Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis.

Hao Yan, M. Bathe, N. Walter, 2016, Nanoscale.

Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami.

Joseph Nichols, Georgios Skiniotis, Shuoxing Jiang, 2015, ACS nano.

Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy.

Alexander Johnson-Buck, Nils G Walter, N. Walter, 2014, Methods.

Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology.

Anthony J. Manzo, Nicole Michelotti, Alexander Johnson-Buck, 2012, Wiley interdisciplinary reviews. Nanomedicine and nanobiotechnology.

Do-it-yourself guide: how to use the modern single-molecule toolkit

Anthony J. Manzo, Anthony J Manzo, Nils G Walter, 2008, Nature Methods.

Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope.

Ameya P. Jalihal, N. Walter, P. E. Lund, 2019, Cold Spring Harbor perspectives in biology.

Molecular dynamics simulations of RNA: an in silico single molecule approach.

Nils G Walter, J. Šponer, N. Špačková, 2007, Biopolymers.

Life under the Microscope: Single-Molecule Fluorescence Highlights the RNA World.

N. Walter, Sujay Ray, J. Widom, 2018, Chemical reviews.

Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting.

N. Walter, Thomas C. Custer, Sethuramasundaram Pitchiaya, 2013, Methods.

Riboswitch structure and dynamics by smFRET microscopy.

N. Walter, K. C. Suddala, K. Suddala, 2014, Methods in enzymology.

Double-Stranded RNA Interacts With Toll-Like Receptor 3 in Driving the Acute Inflammatory Response Following Lung Contusion

M. V. Suresh, N. Walter, S. Kunkel, 2016, Critical care medicine.

Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch

C. Brooks, H. Al‐Hashimi, N. Walter, 2011, Nucleic acids research.

Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

Asaminew H. Aytenfisu, D. Mathews, J. Wedekind, 2015, Proceedings of the National Academy of Sciences.

In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines

N. Walter, Thomas C. Custer, 2017, Protein science : a publication of the Protein Society.

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting

S. Pressé, N. Walter, Yamuna Krishnan, 2019, Angewandte Chemie.

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting.

S. Pressé, N. Walter, Yamuna Krishnan, 2019, Angewandte Chemie.

EIGHTEEN Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines

N. Walter, Matthew L. Kahlscheuer, J. Widom, 2015 .

Significant kinetic solvent isotope effects in folding of the catalytic RNA from the hepatitis delta virus.

N. Walter, D. Harris, Rebecca A Tinsley, 2003, Journal of the American Chemical Society.

Structural basis for control of bacterial RNA polymerase pausing by a riboswitch and its ligand

J. Porta, A. Frank, N. Walter, 2021, Nature Structural & Molecular Biology.

Tracking Single DNA Nanodevices in Hierarchically Meso-Macroporous Antimony-Doped Tin Oxide Demonstrates Finite Confinement.

Hao Yan, N. Walter, Minghui Liu, 2017, Langmuir : the ACS journal of surfaces and colloids.

Precise tuning of bacterial translation initiation by non-equilibrium 5′-UTR unfolding observed in single mRNAs

N. Walter, Sujay Ray, Surajit Chatterjee, 2021, Nucleic acids research.

Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple turnover.

Renata A Rawlings, N. Walter, V. Krishnan, 2011, Journal of molecular biology.

Dynamic recruitment of single RNAs to processing bodies depends on RNA functionality

Márcio A. Mourão, Ameya P. Jalihal, A. Chinnaiyan, 2018, bioRxiv.

Highly sensitive protein detection by aptamer-based single-molecule kinetic fingerprinting.

N. Walter, Alexander Johnson-Buck, T. Chatterjee, 2022, Biosensors & bioelectronics.

Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics

A. Laederach, Joshua S. Martin, N. Walter, 2015, Nature Methods.

Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qbeta replicase efficiently binds small RNAs by recognizing pyrimidine residues.

N. Walter, J. Dapprich, R. Preuss, 1997, Journal of molecular biology.

Single Molecule Cluster Analysis Identifies Signature Dynamic Conformations along the Splicing Pathway

A. Laederach, Joshua S. Martin, N. Walter, 2016 .

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

Hao Yan, Alexander Johnson-Buck, Minghui Liu, 2016, Nature Communications.

Multifactorial modulation of binding and dissociation kinetics on two-dimensional DNA nanostructures.

Hao Yan, Shuoxing Jiang, Jeanette Nangreave, 2013, Nano letters.

Assembly of multienzyme complexes on DNA nanostructures

Hao Yan, Minghui Liu, Jinglin Fu, 2016, Nature Protocols.

Tuning RNA folding and function through rational design of junction topology

Charles L. Brooks III, N. Walter, A. Morriss-Andrews, 2017, Nucleic acids research.

Protein unties the pseudoknot: S1-mediated unfolding of RNA higher order structure

N. Walter, P. E. Lund, Surajit Chatterjee, 2019, Nucleic acids research.

Probing Transient Riboswitch Structures via Single Molecule Accessibility Analysis.

N. Walter, Andreas Schmidt, Robb S. Welty, 2023, Methods in molecular biology.

RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer.

Dawen Cai, N. Walter, Yunfang Man, 2003, Journal of the American Chemical Society.

FRETtranslator: translating FRET traces into RNA structural pathways

P. Stadler, I. Hofacker, J. Gorodkin, 2016, 1610.00340.

Spontaneous confinement of mRNA at RNP granule interfaces

N. Walter, Andreas Schmidt, Umar Khan, 2022, bioRxiv.

Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

N. Walter, Laurie A. Heinicke, Soma Dhakal, 2014, Archives of Toxicology.

A bio-hybrid DNA rotor/stator nanoengine that moves along predefined tracks

Julián Valero, Michael Famulok, Nils G. Walter, 2018, Nature Nanotechnology.

The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations.

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Physical chemistry chemical physics : PCCP.

Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme.

K. Réblová, J. Šponer, N. Walter, 2010, The journal of physical chemistry. B.

Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme.

K. Réblová, J. Šponer, B. Schneider, 2006, Biophysical journal.

Local-to-global signal transduction at the core of the Mn2+ sensing riboswitch

J. Šponer, N. Walter, P. Banáš, 2019, bioRxiv.

Chemical feasibility of the general acid/base mechanism of glmS ribozyme self‐cleavage

Michal Otyepka, Pavel Banáš, Jiří Šponer, 2015, Biopolymers.

Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations.

J. Šponer, N. Walter, M. Otyepka, 2015, The journal of physical chemistry. B.

Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.

K. Réblová, J. Šponer, N. Walter, 2015, Physical chemistry chemical physics : PCCP.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

J. Šponer, N. Walter, M. Otyepka, 2014, RNA.

Single Molecule Detection, Analysis, and Manipulation

N. Walter, 2008 .

Future of biomedical sciences: single molecule microscopy.

N. Walter, 2007, Biopolymers.

The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field.

Emil F. Khisamutdinov, Lydia M. Contreras, N. Walter, 2021, ACS nano.

Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM.

J. Šponer, N. Walter, M. Otyepka, 2009, Methods.

Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance.

Michael J Rust, X. Zhuang, N. Walter, 2004, Proceedings of the National Academy of Sciences of the United States of America.

In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs.

M. J. Pereira, N. Walter, D. Rueda, 2001, Biopolymers.

The solvent-protected core of the hairpin ribozyme-substrate complex.

N. Walter, John M. Burke, K. Hampel, 1998, Biochemistry.

The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone.

W. Scott, J. Murray, N. Walter, 1998, Chemistry & biology.

Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme.

N. Walter, J. Esteban, J. Heckman, 1998, Proceedings of the National Academy of Sciences of the United States of America.

Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer

N. Walter, J. Burke, Kirk M Brown, 1998, The EMBO journal.

Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates.

N. Walter, John M. Burke, 1997, RNA.

Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme.

Nils G Walter, J. Šponer, N. Walter, 2009, RNA.

Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”

X. Zhuang, N. Walter, Gregory Bokinsky, 2007, Proceedings of the National Academy of Sciences.

A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking.

N. Walter, D. Millar, John M. Burke, 2001, Biochemistry.

Structural basis for the guanosine requirement of the hairpin ribozyme.

F. Major, N. Walter, J. Heckman, 1999, Biochemistry.

Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction

N. Walter, D. Millar, J. Burke, 1999, Nature Structural Biology.

Probing RNA Structural Dynamics and Function by Fluorescence Resonance Energy Transfer (FRET)

N. Walter, 2002, Current Protocols in Nucleic Acid Chemistry.

Imaging of single hairpin ribozymes in solution by atomic force microscopy.

M. J. Fay, N. Walter, John M. Burke, 2001, RNA.

Global structure and flexibility of hairpin ribozymes with extended terminal helices.

N. Walter, John M. Burke, D. Porschke, 1999, Journal of molecular biology.

FIFTEEN Riboswitch Structure and Dynamics by smFRET Microscopy

N. Walter, K. Suddala, 2014 .

Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation.

N. Walter, Rebecca A Tinsley, 2006, RNA.

The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation.

C. Fierke, N. Walter, D. Rueda, 2005, Biochemistry.

Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA.

M. J. Pereira, N. Walter, John A. H. Hoerter, 2004, Biochemistry.

A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage.

N. Walter, D. Rueda, Phillip Sekella, 2002, RNA.

Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer.

N. Walter, Nils G. Walter, 2001, Methods.

The hairpin ribozyme substrate binding-domain: a highly constrained D-shaped conformation.

F. Major, N. Walter, G. Glick, 2001, Journal of molecular biology.

Probing non-selective cation binding in the hairpin ribozyme with Tb(III).

N. Walter, John M. Burke, N. Yang, 2000, Journal of molecular biology.

Fluorescence assays to study structure, dynamics, and function of RNA and RNA-ligand complexes.

N. Walter, John M. Burke, 2000, Methods in enzymology.

Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy.

N. Walter, S. Blumberg, J. Meiners, 2006, Biophysical journal.

Quantitative hybridization kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation analysis.

P. Schwille, N. Walter, P Schwille, 1996, Biochemistry.

Intracellular single molecule microscopy reveals time and mRNA dependent microRNA assembly

N. Walter, J. Androsavich, S. Pitchiaya, 2012 .

The shape-shifting quasispecies of RNA: one sequence, many functional folds.

Alexander Johnson-Buck, Nils G Walter, N. Walter, 2011, Physical chemistry chemical physics : PCCP.

Flexible casting of modular self-aligning microfluidic assembly blocks.

Brian N. Johnson, Anthony J. Manzo, Mark A Burns, 2011, Lab on a chip.

Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

G. Shivashankar, N. Walter, Sheetal Sharma, 2017, Nature Cell Biology.

Attomolar Sensitivity in Single Biomarker Counting upon Aqueous Two-Phase Surface Enrichment.

M. Tewari, N. Walter, E. Sandford, 2022, ACS sensors.

Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution.

N. Walter, Laurie A. Heinicke, S. Pitchiaya, 2017, Cell reports.

The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling

Hongtao Yu, Alnawaz Rehemtulla, Nils G. Walter, 2015, Science Signaling.

Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver.

P. Linsley, N. Walter, B. Bhat, 2012, RNA.

From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond.

Ameya P. Jalihal, G. Biamonti, Piero Carninci, 2018, Chemical reviews.

KRAS Engages AGO2 to Enhance Cellular Transformation.

S. Dhanasekaran, A. Chinnaiyan, Xuhong Cao, 2016, Cell reports.

Fluorescence correlation analysis of probe diffusion simplifies quantitative pathogen detection by PCR.

M. Eigen, P. Schwille, N. Walter, 1996, Proceedings of the National Academy of Sciences of the United States of America.

Cytoplasmic TDP43 Binds microRNAs: New Disease Targets in Amyotrophic Lateral Sclerosis

N. Walter, J. Hur, E. Feldman, 2020, Frontiers in Cellular Neuroscience.

Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome.

N. Walter, M. Blanco, C. Rohlman, 2016, Methods in enzymology.

Super-resolution imaging identifies PARP1 and the Ku complex acting as DNA double-strand break sensors

Shih-Hsun Chen, N. Walter, Xiaochun Yu, 2018, Nucleic acids research.

Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly

N. Walter, J. Androsavich, S. Pitchiaya, 2012, EMBO reports.

Dynamic Recruitment of S ingle RNAs to Processing Bodies Depends on RNA Functionality Graphical

Márcio A. Mourão, Ameya P. Jalihal, A. Chinnaiyan, 2019 .

Soft Interactions with Model Crowders and Non-canonical Interactions with Cellular Proteins Stabilize RNA Folding.

N. Walter, J. Widom, May Daher, 2017, Journal of molecular biology.

Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme.

N. Walter, D. Harris, Rebecca A Tinsley, 2004, Journal of molecular biology.

High-resolution three-dimensional mapping of mRNA export through the nuclear pore

N. Walter, Weidong Yang, Jiong Ma, 2013, Nature Communications.

Dynamic competition between a ligand and transcription factor NusA governs riboswitch-mediated transcription regulation

N. Walter, R. Yadav, Adrien Chauvier, 2021, Proceedings of the National Academy of Sciences.

An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch

N. Walter, R. Yadav, J. Widom, 2022, Nature Communications.

An anionic ligand snap-locks a long-range interaction in a magnesium-folded riboswitch

N. Walter, R. Yadav, J. Widom, 2021, Nature communications.

A novel method to accurately locate and count large numbers of steps by photobleaching

Hossein Jashnsaz, Steve Pressé, Nils G. Walter, 2016, Molecular biology of the cell.

Direct Kinetic Fingerprinting for High-Accuracy Single-Molecule Counting of Diverse Disease Biomarkers.

M. Tewari, N. Walter, S. Mandal, 2020, Accounts of chemical research.

Direct kinetic fingerprinting and digital counting of single protein molecules

M. Tewari, N. Walter, E. Sandford, 2020, Proceedings of the National Academy of Sciences.

Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors.

N. Walter, Yongzhong Qian, J. Qiu, 2019, Analytical chemistry.

Ultraspecific and Amplification-Free Quantification of Mutant DNA by Single-Molecule Kinetic Fingerprinting.

M. Tewari, N. Walter, P. E. Lund, 2018, Journal of the American Chemical Society.

Kinetic fingerprinting to identify and count single nucleic acids

Muneesh Tewari, Alexander Johnson-Buck, Nils G Walter, 2015, Nature Biotechnology.

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

C. Guthrie, N. Walter, M. Ditzler, 2010, Nature Structural &Molecular Biology.

Single-Molecule Tracking of Nanorobots on Pseudo-One-Dimensional DNA Origami Tracks

Anthony J. Manzo, Hao Yan, E. Winfree, 2010 .

Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing

C. Guthrie, N. Walter, M. Blanco, 2013, Nature Structural &Molecular Biology.

Multivalent proteins rapidly and reversibly phase-separate upon osmotic cell volume change

Ameya P. Jalihal, A. Chinnaiyan, Xia Jiang, 2019, bioRxiv.

Regulating DNA Self-Assembly Dynamics with Controlled Nucleation.

Hao Yan, Yan Liu, Shuoxing Jiang, 2021, ACS nano.

ICLES Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks

G. Shivashankar, N. Walter, Sheetal Sharma, 2017 .

Hyperosmotic phase separation: Condensates beyond inclusions, granules and organelles

Ameya P. Jalihal, N. Walter, Andreas Schmidt, 2020, The Journal of biological chemistry.

Resolving Subcellular miR NA Trafficking and Turnover at Single-Molecule Resolution Graphical

N. Walter, Laurie A. Heinicke, S. Pitchiaya, 2017 .

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

C. Brooks, R. L. Hayes, N. Walter, 2018, bioRxiv.

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

C. Brooks, R. L. Hayes, N. Walter, 2018, bioRxiv.

Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics

N. Walter, Sujay Ray, Adrien Chauvier, 2018, RNA biology.

Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.

Nils G Walter, N. Walter, Krishna C Suddala, 2015, Journal of the American Chemical Society.

Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure

J. Wedekind, C. Brooks, H. Al‐Hashimi, 2013, Nucleic acids research.

Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing.

N. Walter, Gabrielle C. Todd, 2013, RNA.

Cooperative and directional folding of the preQ1 riboswitch aptamer domain.

Jun Feng, Nils G Walter, C. Brooks, 2011, Journal of the American Chemical Society.

Provided for Non-commercial Research and Educational Use Only. Not for Reproduction, Distribution or Commercial Use. Analysis of Complex Single-molecule Fret Time Trajectories Author's Personal Copy

Nils G Walter, N. Walter, M. Blanco, 2022 .

Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis.

Shawna L. Hiley, M. J. Pereira, N. Walter, 2008, Journal of molecular biology.

Trapped water molecules are essential to structural dynamics and function of a ribozyme

K. Réblová, J. Šponer, N. Walter, 2006, Proceedings of the National Academy of Sciences.

Probing RNA structure and interaction dynamics at the single molecule level.

N. Walter, J. Cabello-Villegas, Adrien Chauvier, 2019, Methods.

Automatic classification and segmentation of single-molecule fluorescence time traces with deep learning

Leyou Zhang, Alexander Johnson-Buck, Nils G Walter, 2020, Nature Communications.

Transcriptional Riboswitches Integrate Timescales for Bacterial Gene Expression Control

N. Walter, Catherine E. Scull, Shiba S Dandpat, 2021, Frontiers in Molecular Biosciences.

Single‐molecule enzymology à la Michaelis–Menten

Ramon Grima, Santiago Schnell, Nils G Walter, 2013, The FEBS journal.

Integrative and Comparative Biology

N. Walter, C. Grillo, M. Holford, 2022 .

From Flatland to Jupiter: Searching for Rules of Interaction Across Biological Scales.

N. Walter, C. Grillo, M. Holford, 2021, Integrative and comparative biology.

A translational riboswitch coordinates nascent transcription–translation coupling

N. Walter, I. Artsimovitch, Surajit Chatterjee, 2021, Proceedings of the National Academy of Sciences.

Hierarchical mechanism of amino acid sensing by the T-box riboswitch

N. Walter, E. Nikonowicz, J. Cabello-Villegas, 2018, Nature Communications.

Ultraspecific analyte detection by direct kinetic fingerprinting of single molecules.

M. Tewari, N. Walter, Alexander Johnson-Buck, 2020, Trends in analytical chemistry : TRAC.

Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards.

Hao Yan, M. Bathe, N. Walter, 2013, Nano letters.

Molecular robots guided by prescriptive landscapes

Erik Winfree, Hao Yan, Milan N. Stojanovic, 2010, Nature.

RNA chaperones stimulate formation and yield of the U3 snoRNA-Pre-rRNA duplexes needed for eukaryotic ribosome biogenesis.

Anthony J. Manzo, N. Walter, C. C. Correll, 2009, Journal of molecular biology.

Spliceosomal DEAH-Box ATPases Remodel Pre-mRNA to Activate Alternative Splice Sites

N. Walter, M. Blanco, Jonathan P Staley, 2016, Cell.

Focus on function: single molecule RNA enzymology.

N. Walter, D. Rueda, M. Ditzler, 2007, Biopolymers.

Purification and functional reconstitution of monomeric mu-opioid receptors: allosteric modulation of agonist binding by Gi2.

Adam J Kuszak, Nils G Walter, R. Sunahara, 2009, The Journal of biological chemistry.

Capillary electrophoresis of RNA in dilute and semidilute polymer solutions

M. Morris, N. Walter, O. de Carmejane, 2001, Electrophoresis.

Native purification and labeling of RNA for single molecule fluorescence studies.

N. Walter, A. J. Rinaldi, K. Suddala, 2015, Methods in molecular biology.

Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations.

N. Walter, S. E. McDowell, J. M. Jun., 2010, RNA.

A rugged free energy landscape separates multiple functional RNA folds throughout denaturation

N. Walter, D. Rueda, M. Ditzler, 2008, Nucleic acids research.

Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core.

N. Walter, D. Rueda, Rebecca A Tinsley, 2006, Biochemistry.

The Small Ribozymes: Common and Diverse Features Observed through the FRET Lens.

N. Walter, Shiamalee Perumal, 2009, Springer series in biophysics.

Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme

N. Walter, Rebecca A Tinsley, 2007, Biological chemistry.

Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core.

N. Walter, D. Rueda, S. E. McDowell, 2003, Biochemistry.

Editorial for "non-coding RNA methods".

N. Walter, 2013, Methods.

Versatile transcription control based on reversible dCas9 binding

N. Walter, J. Widom, C. Rohlman, 2019, RNA.

Rapid kinetic fingerprinting of single nucleic acid molecules by a FRET-based dynamic nanosensor.

M. Tewari, N. Walter, S. Mandal, 2021, Biosensors & bioelectronics.

Rapid Kinetic Fingerprinting of Single Nucleic Acid Molecules by a FRET-based Dynamic Nanosensor

M. Tewari, N. Walter, S. Mandal, 2021, bioRxiv.

A guide to nucleic acid detection by single-molecule kinetic fingerprinting.

M. Tewari, N. Walter, Jieming Li, 2019, Methods.

Under the microscope: single molecule symposium at the University of Michigan, 2006.

R. Neubig, N. Perkins, J. Swanson, 2007, Biopolymers.

Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme.

Nils G Walter, J. Šponer, N. Špačková, 2007, Biopolymers.

The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis

Nils G. Walter, Jiří Šponer, J. Šponer, 2007, Nucleic acids research.

Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA.

M. J. Pereira, N. Walter, John A. H. Hoerter, 2005, RNA.

Introduction to single molecule imaging and mechanics: seeing and touching molecules one at a time.

Carlos Bustamante, Nils G Walter, C. Bustamante, 2014, Chemical reviews.

Purification and Functional Reconstitution of Monomeric

R. Sunahara, N. Walter, H. Mosberg, 2009 .

Paclitaxel-conjugated PAMAM dendrimers adversely affect microtubule structure through two independent modes of action.

Jeffrey F. Herbstman, R. Larson, G. Skiniotis, 2013, Biomacromolecules.

A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies.

Anthony J. Manzo, Nicole Michelotti, Anthony J Manzo, 2010, Methods in enzymology.

Single bacterial resolvases first exploit, then constrain intrinsic dynamics of the Holliday junction to direct recombination

N. Walter, Nibedita Pal, Sujay Ray, 2021, Nucleic acids research.

Microsoft Word-Ray_et_al_NAR_SI_2ndRevision_Final

N. Walter, Nibedita Pal, Sujay Ray, 2021 .

A bacterial resolvase first exploits, then constrains intrinsic dynamics of the Holliday junction to direct recombination

N. Walter, Nibedita Pal, Sujay Ray, 2019, bioRxiv.

Nondenaturing Purification of Co-Transcriptionally Folded RNA Avoids Common Folding Heterogeneity

M. J. Pereira, N. Walter, Vivek Behera, 2010, PloS one.

Dynamic superresolution by Bayesian nonparametric image processing

Ameya P. Jalihal, S. Pressé, N. Walter, 2023, bioRxiv.

Scribble Subcellular Localization Modulates Recruitment of Distinct YES1 Conformations to Regulate YAP Phosphorylation

N. Walter, J. Nandakumar, Dongyu Zhao, 2020 .

Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching.

Elizabeth C. Duran, N. Walter, Aaron T. Blanchard, 2022, Nano letters.

A guide to accelerated direct digital counting of single nucleic acid molecules by FRET-based intramolecular kinetic fingerprinting.

N. Walter, S. Mandal, Alexander Johnson-Buck, 2021, Methods.

Ribozyme catalysis revisited: is water involved?

N. Walter, 2007, Molecular cell.

Structural modeling of sequence specificity by an autoantibody against single-stranded DNA.

N. Walter, D. Rueda, G. Glick, 2007, Biochemistry.

Modelling viral evolution in vitro using exo- Klenow polymerase: continuous selection of strand displacement amplified DNA that binds an oligodeoxynucleotide to form a triple-helix.

N. Walter, 1995, Journal of molecular biology.

Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum.

N. Walter, John A. H. Hoerter, 2007, RNA.

General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility.

J. Šponer, N. Walter, M. Otyepka, 2008, The journal of physical chemistry. B.

Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics.

S. Hamdan, N. Walter, M. A. Sobhy, 2011, The Review of scientific instruments.

Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics.

J. Šponer, N. Walter, M. Otyepka, 2010, The journal of physical chemistry. B.

Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection.

N. Walter, R. Kennedy, Peilin Yang, 2008, Analytical Chemistry.

Trans-acting glmS catalytic riboswitch: locked and loaded.

N. Walter, Rebecca A Tinsley, Jennifer R W Furchak, 2007, RNA.

QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms.

J. Šponer, N. Walter, M. Otyepka, 2011, The journal of physical chemistry. B.

Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations.

J. Šponer, N. Špačková, N. Walter, 2005, Journal of molecular biology.

Purification and Functional Reconstitution of Monomeric μ-Opioid Receptors

R. Sunahara, N. Walter, H. Mosberg, 2009, Journal of Biological Chemistry.

Purification and Functional Reconstitution of Monomeric-Opioid Receptors ALLOSTERIC MODULATION OF AGONIST BINDING BY Gi 2 *

R. Sunahara, N. Walter, H. Mosberg, 2009 .

Michaelis-Menten is dead, long live Michaelis-Menten!

Nils G Walter, N. Walter, 2006, Nature chemical biology.

Ribozymes: catalytic RNAs that cut things, make things, and do odd and useful jobs.

D. Engelke, N. Walter, 2002, Biologist.

Fluorescent energy transfer readout of an aptazyme-based biosensor.

N. Walter, D. Rueda, 2006, Methods in molecular biology.

Non-protein coding RNAs

R. Batey, N. Walter, S. Woodson, 2009 .

Super-resolution, particle tracking, multiparameter, and force based methods

Nils G. Walter, N. Walter, 2010 .

Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis.

M. J. Pereira, N. Walter, D. Rueda, 2002, Biochemistry.

BNP-Track: A framework for superresolved tracking

Ameya P. Jalihal, S. Pressé, N. Walter, 2023, bioRxiv.

Dynamic superresolution by Bayesian nonparametric image processing

Ameya P. Jalihal, S. Pressé, N. Walter, 2023 .

Utilizing functional cell‐free extracts to dissect ribonucleoprotein complex biology at single‐molecule resolution

Ameya P. Jalihal, N. Walter, Andreas Schmidt, 2023, Wiley interdisciplinary reviews. RNA.

Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme.

N. Walter, D. Harris, Rebecca A Tinsley, 2004, Biochemistry.

Meeting report: SMART timing--principles of single molecule techniques course at the University of Michigan 2014.

N. Walter, Thomas C. Custer, P. E. Lund, 2015, Biopolymers.

siRNA-Like Double-Stranded RNAs Are Specifically Protected Against Degradation in Human Cell Extract

N. Walter, Troy A. Lionberger, V. Krishnan, 2011, PloS one.

Metal ions: supporting actors in the playbook of small ribozymes.

N. Walter, Alexander Johnson-Buck, S. E. McDowell, 2011, Metal ions in life sciences.

Motor myosin V caught on video: foot stomping in biology.

N. Walter, 2011, Biopolymers.

Riboswitches as therapeutic targets: promise of a new era of antibiotics

N. Walter, Sujay Ray, Emily Ellinger, 2023, Expert opinion on therapeutic targets.

Single molecule fluorescence control for nanotechnology.

N. Walter, D. Rueda, 2005, Journal of nanoscience and nanotechnology.

Local-to-global signal transduction at the core of a Mn2+ sensing riboswitch

J. Šponer, N. Walter, P. Banáš, 2019, Nature Communications.

Cholesterol Barges as Programmable Membrane-Exploring Agents

Nils G. Walter, Shuoxing Jiang, Alexander Johnson-Buck, 2014 .

DNACholesterol Barges as Programmable Membrane-Exploring

Shuoxing Jiang, N. Walter, Hao Yan, 2014 .

A divalent cation stabilizes the active conformation of the B. subtilis RNase P x pre-tRNA complex: a role for an inner-sphere metal ion in RNase P.

C. Fierke, N. Walter, D. Rueda, 2010, Journal of molecular biology.

The hairpin ribozyme: structure, assembly and catalysis

N. Walter, John M. Burke, Walter, 1998, Current opinion in chemical biology.

High-resolution three-dimensional mapping of mRNA export through the nuclear pore

N. Walter, Weidong Yang, Jiong Ma, 2013, Nature Communications.

Quantitative Mapping of Endosomal DNA Processing by Single Molecule Counting.

S. Pressé, N. Walter, Yamuna Krishnan, 2019, Angewandte Chemie.

The blessing and curse of RNA dynamics: past, present, and future.

N. Walter, 2009, Methods.

Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update

N. Walter, Laurie A. Heinicke, Soma Dhakal, 2014, Archives of Toxicology.

Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion

Hao Yan, Yan Liu, N. Walter, 2016, Nature Communications.

DNA-cholesterol barges as programmable membrane-exploring agents.

Hao Yan, Shuoxing Jiang, N. Walter, 2014, ACS nano.

Using Single-Molecule FRET to Evaluate DNA Nanodevices at Work.

N. Walter, Nibedita Pal, 2023, Methods in molecular biology.

Mg(2+) shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection.

N. Walter, K. Suddala, Jiarui Wang, 2015, Journal of the American Chemical Society.

Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence.

N. Walter, D. Rueda, Sohee Jeong, 2003, Biochemistry.

Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines.

N. Walter, Matthew L. Kahlscheuer, J. Widom, 2015, Methods in enzymology.

Putting Humpty-Dumpty Together: Clustering the Functional Dynamics of Single Biomolecular Machines Such as the Spliceosome.

N. Walter, M. Blanco, C. Rohlman, 2016, Methods in enzymology.

Probing RNA structure and interaction dynamics at the single molecule level.

N. Walter, J. Cabello-Villegas, Adrien Chauvier, 2019, Methods.

Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver.

P. Linsley, N. Walter, B. Bhat, 2012, RNA.

Kinetics coming into focus: single-molecule microscopy of riboswitch dynamics

N. Walter, Sujay Ray, Adrien Chauvier, 2018, RNA biology.

Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

Asaminew H. Aytenfisu, D. Mathews, J. Wedekind, 2015, Proceedings of the National Academy of Sciences.

Single-Molecule Kinetic Fingerprinting for the Ultrasensitive Detection of Small Molecules with Aptasensors.

N. Walter, Yongzhong Qian, Xin Su, 2018, Analytical chemistry.

Conformational dynamics of single pre-mRNA molecules during in vitro splicing

C. Guthrie, N. Walter, M. Ditzler, 2010, Nature Structural &Molecular Biology.