All Stories

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

    Article • Proceedings of the National Academy of Sciences, November 2021, Proceedings of the National Academy of Sciences

    Professor Nils G Walter

  2. A translational riboswitch coordinates nascent transcription–translation coupling

    Article • Proceedings of the National Academy of Sciences, April 2021, Proceedings of the National Academy of Sciences

    Professor Nils G Walter

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

    Article • RNA Biology, October 2018, Taylor & Francis

    Professor Nils G Walter

  4. Reactive Conformation of the Active Site in the Hairpin Ribozyme Achieved by Molecular Dynamics Simulations with ε/ζ Force Field Reparametrizations

    Article • The Journal of Physical Chemistry, March 2015, American Chemical Society (ACS)

    Professor Nils G Walter

  5. The role of an active site Mg2+in HDV ribozyme self-cleavage: insights from QM/MM calculations

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Professor Nils G Walter

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

    Article • Physical Chemistry Chemical Physics, January 2015, Royal Society of Chemistry

    Professor Nils G Walter

  7. Mechanical Modulation of Enzyme Activity by Rationally Designed DNA Tweezers: From the Ensemble to the Single-Molecule Level

    Article • Biophysical Journal, January 2015, Elsevier

    Professor Nils G Walter

  8. Native Purification and Labeling of RNA for Single Molecule Fluorescence Studies

    Article • October 2014, Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Archives of Toxicology, September 2014, Springer Science + Business Media

    Professor Nils G Walter

  10. DNA–Cholesterol Barges as Programmable Membrane-Exploring Agents

    Article • ACS Nano, June 2014, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • Nature Nanotechnology, May 2014, Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Methods, May 2014, Elsevier

    Professor Nils G Walter

  13. Terbium(III) Footprinting as a Probe of RNA Structure and Metal Binding Sites

    Article • March 2014, Wiley

    Professor Nils G Walter

  14. Introduction to Single Molecule Imaging and Mechanics: Seeing and Touching Molecules One at a Time

    Article • Chemical Reviews, March 2014, American Chemical Society (ACS)

    Professor Nils G Walter

  15. Single Molecule Fluorescence Approaches Shed Light on Intracellular RNAs

    Article • Chemical Reviews, March 2014, American Chemical Society (ACS)

    Professor Nils G Walter

  16. Single‐molecule enzymology à la Michaelis–Menten

    Article • FEBS Journal, January 2014, Wiley

    Professor Nils G Walter

  17. Riboswitch Structure and Dynamics by smFRET Microscopy

    Article • January 2014, Elsevier

    Professor Nils G Walter

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

    Article • Nature Structural & Molecular Biology, November 2013, Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Nature Communications, September 2013, Springer Science + Business Media

    Professor Nils G Walter

  20. Editorial for “Non-coding RNA methods”

    Article • Methods, September 2013, Elsevier

    Professor Nils G Walter

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

    Article • Methods, September 2013, Elsevier

    Professor Nils G Walter

  22. Introductory editorial:Biopolymerscelebrates 50 years of nucleic acids research

    Article • Biopolymers, July 2013, Wiley

    Professor Nils G Walter

  23. Multifactorial Modulation of Binding and Dissociation Kinetics on Two-Dimensional DNA Nanostructures

    Article • Nano Letters, June 2013, American Chemical Society (ACS)

    Professor Nils G Walter

  24. Paclitaxel-Conjugated PAMAM Dendrimers Adversely Affect Microtubule Structure through Two Independent Modes of Action

    Article • Biomacromolecules, March 2013, American Chemical Society (ACS)

    Professor Nils G Walter, Dr Seok Ki Choi

  25. Super-Resolution Fingerprinting Detects Chemical Reactions and Idiosyncrasies of Single DNA Pegboards

    Article • Nano Letters, February 2013, American Chemical Society (ACS)

    Professor Nils G Walter

  26. Hidden Markov Modeling in Single-Molecule Biophysics

    Article • January 2013, Springer Science + Business Media

    Professor Nils G Walter

  27. Single-Molecule Fluorescence Resonance Energy Transfer

    Article • January 2013, Springer Science + Business Media

    Professor Nils G Walter

  28. The Most Recent, Catalytically Fit HDV Ribozyme Exhibits Minimal Global and Small-Scale Conformational Change upon Cleavage

    Article • Biophysical Journal, January 2013, Elsevier

    Professor Nils G Walter

  29. Investigating the Role of an Extended Hydrogen Bonding Network within the Hairpin Ribozyme Active Site

    Article • Biophysical Journal, January 2013, Elsevier

    Professor Nils G Walter

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

    Article • EMBO Reports, June 2012, EMBO

    Professor Nils G Walter

  31. The Development of Methods for the Site-Specific Fluorescent Labeling of Spliceosomal Proteins for use in Single-Molecule Studies

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nils G Walter

  32. Single Molecule FRET Characterization of Pre-mRNA Splicing: Substrate Dynamics during Recognition and Catalysis

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nils G Walter

  33. Structure-Function Relationships Within the Hepatitis Delta Virus Ribozyme

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nils G Walter

  34. Taxol-Conjugated Pamam Dendrimers Utilize Three Modes of Action on Microtubule Structure

    Article • Biophysical Journal, January 2012, Elsevier

    Professor Nils G Walter

  35. QM/MM Studies of Hairpin Ribozyme Self-Cleavage Suggest the Feasibility of Multiple Competing Reaction Mechanisms

    Article • The Journal of Physical Chemistry, December 2011, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • Wiley Interdisciplinary Reviews Nanomedicine and Nanobiotechnology, November 2011, Wiley

    Professor Nils G Walter

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

    Article • PLoS ONE, May 2011, PLOS

    Professor Nils G Walter

  38. Metal Ions: Supporting Actors in the Playbook of Small Ribozymes

    Article • April 2011, Royal Society of Chemistry

    Professor Nils G Walter

  39. Viral RNAi Suppressor Reversibly Binds siRNA to Outcompete Dicer and RISC via Multiple Turnover

    Article • Journal of Molecular Biology, April 2011, Elsevier

    Professor Nils G Walter

  40. Cooperative and Directional Folding of the preQ 1 Riboswitch Aptamer Domain

    Article • Journal of the American Chemical Society, March 2011, American Chemical Society (ACS)

    Professor Nils G Walter

  41. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA

    Article • Biopolymers, March 2011, Wiley

    Professor Nils G Walter

  42. Structural Landmarks of the Hepatitis Delta Virus (HDV) Ribozyme

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nils G Walter

  43. Imaging an Expanding Molecular Robot World Using Super-Accuracy Single-Molecule Fluorescence Microscopy

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nils G Walter

  44. Developing a Synthetic Mimic of Promoter Searching by RNA Polymerase

    Article • Biophysical Journal, February 2011, Elsevier

    Professor Nils G Walter

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

    Article • Physical Chemistry Chemical Physics, January 2011, Royal Society of Chemistry

    Professor Nils G Walter

  46. Flexible casting of modular self-aligning microfluidic assembly blocks

    Article • Lab on a Chip, January 2011, Royal Society of Chemistry

    Professor Nils G Walter

  47. Motor myosin V caught on video: Foot stomping in biology

    Article • Biopolymers, December 2010, Wiley

    Professor Nils G Walter

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

    Article • PLoS ONE, September 2010, PLOS

    Professor Nils G Walter

  49. Protonation States of the Key Active Site Residues and Structural Dynamics of the glmS Riboswitch As Revealed by Molecular Dynamics

    Article • The Journal of Physical Chemistry, July 2010, American Chemical Society (ACS)

    Professor Nils G Walter

  50. A Divalent Cation Stabilizes the Active Conformation of the B. subtilis RNase P·Pre-tRNA Complex: A Role for an Inner-Sphere Metal Ion in RNase P

    Article • Journal of Molecular Biology, July 2010, Elsevier

    Professor Nils G Walter

  51. Extensive Molecular Dynamics Simulations Showing That Canonical G8 and Protonated A38H + Forms Are Most Consistent with Crystal Structures of Hairpin Ribozyme

    Article • The Journal of Physical Chemistry, May 2010, American Chemical Society (ACS)

    Professor Nils G Walter

  52. Molecular robots guided by prescriptive landscapes

    Article • Nature, May 2010, Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Nature Structural & Molecular Biology, March 2010, Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Accounts of Chemical Research, January 2010, American Chemical Society (ACS)

    Professor Nils G Walter

  55. Preface

    Article • January 2010, Elsevier

    Professor Nils G Walter

  56. Analysis of Complex Single-Molecule FRET Time Trajectories

    Article • January 2010, Elsevier

    Professor Nils G Walter

  57. Preface

    Article • January 2010, Elsevier

    Professor Nils G Walter

  58. A Bird's Eye View

    Article • January 2010, Elsevier

    Professor Nils G Walter

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

    Article • Biophysical Journal, January 2010, Elsevier

    Professor Nils G Walter

  60. Real-Time Super-Resolution Tracking of Single Deoxyribozyme Based Molecular Robots

    Article • Biophysical Journal, January 2010, Elsevier

    Professor Nils G Walter

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

    Article • Methods, October 2009, Elsevier

    Professor Nils G Walter

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

    Article • Methods, October 2009, Elsevier

    Professor Nils G Walter

  63. RNA Chaperones Stimulate Formation and Yield of the U3 snoRNA–Pre-rRNA Duplexes Needed for Eukaryotic Ribosome Biogenesis

    Article • Journal of Molecular Biology, July 2009, Elsevier

    Professor Nils G Walter

  64. Non-Protein Coding RNAs

    Article • January 2009

    Professor Nils G Walter

  65. Single Molecule Detection, Analysis, and Manipulation

    Article • December 2008, Wiley

    Professor Nils G Walter

  66. Assay for Glucosamine 6-Phosphate Using a Ligand-Activated Ribozyme with Fluorescence Resonance Energy Transfer or CE-Laser-Induced Fluorescence Detection

    Article • Analytical Chemistry, November 2008, American Chemical Society (ACS)

    Professor Nils G Walter

  67. Single VS Ribozyme Molecules Reveal Dynamic and Hierarchical Folding Toward Catalysis

    Article • Journal of Molecular Biology, October 2008, Elsevier

    Professor Nils G Walter

  68. General Base Catalysis for Cleavage by the Active-Site Cytosine of the Hepatitis Delta Virus Ribozyme: QM/MM Calculations Establish Chemical Feasibility

    Article • The Journal of Physical Chemistry, September 2008, American Chemical Society (ACS)

    Professor Nils G Walter

  69. RNA dynamics: it is about time

    Article • Current Opinion in Structural Biology, June 2008, Elsevier

    Professor Nils G Walter

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

    Article • Nature Methods, June 2008, Nature

    Professor Nils G Walter

  71. The Interdisciplinary Biophysics Graduate Program at the University of Michigan

    Article • Biopolymers, January 2008, Wiley

    Professor Nils G Walter

  72. Ribozyme Catalysis Revisited: Is Water Involved?

    Article • Molecular Cell, December 2007, Elsevier

    Professor Nils G Walter

  73. Structural Modeling of Sequence Specificity by an Autoantibody against Single-Stranded DNA †

    Article • Biochemistry, June 2007, American Chemical Society (ACS)

    Professor Nils G Walter

  74. Future of biomedical sciences: Single molecule microscopy

    Article • Biopolymers, January 2007, Wiley

    Professor Nils G Walter

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

    Article • Biological Chemistry, January 2007, De Gruyter

    Professor Nils G Walter

  76. Focus on function: Single molecule RNA enzymology

    Article • Biopolymers, January 2007, Wiley

    Professor Nils G Walter

  77. Molecular dynamics simulations of RNA: Anin silico single molecule approach

    Article • Biopolymers, January 2007, Wiley

    Professor Nils G Walter

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

    Article • Biopolymers, January 2007, Wiley

    Professor Nils G Walter

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

    Article • Biopolymers, January 2007, Wiley

    Professor Nils G Walter

  80. Cations and Hydration in Catalytic RNA: Molecular Dynamics of the Hepatitis Delta Virus Ribozyme

    Article • Biophysical Journal, July 2006, Elsevier

    Prof. Bohdan Schneider, Professor Nils G Walter

  81. Catalytic Core Structure of the trans-Acting HDV Ribozyme Is Subtly Influenced by Sequence Variation Outside the Core †

    Article • Biochemistry, June 2006, American Chemical Society (ACS)

    Professor Nils G Walter

  82. Mg2+-Induced Compaction of Single RNA Molecules Monitored by Tethered Particle Microscopy

    Article • Biophysical Journal, May 2006, Elsevier

    Professor Nils G Walter

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

    Article • Nature Chemical Biology, February 2006, Springer Science + Business Media

    Professor Nils G Walter

  84. Single Molecule Fluorescence Control for Nanotechnology

    Article • Journal of Nanoscience and Nanotechnology, December 2005, American Scientific Publishers

    Professor Nils G Walter

  85. The 5‘ Leader of Precursor tRNA Asp Bound to the Bacillus subtilis RNase P Holoenzyme Has an Extended Conformation †

    Article • Biochemistry, December 2005, American Chemical Society (ACS)

    Professor Nils G Walter

  86. Structural Dynamics of Precursor and Product of the RNA Enzyme from the Hepatitis Delta Virus as Revealed by Molecular Dynamics Simulations

    Article • Journal of Molecular Biology, August 2005, Elsevier

    Professor Nils G Walter

  87. Dynamics Inherent in Helix 27 from Escherichia coli 16S Ribosomal RNA †

    Article • Biochemistry, November 2004, American Chemical Society (ACS)

    Professor Nils G Walter

  88. Terbium-mediated Footprinting Probes a Catalytic Conformational Switch in the Antigenomic Hepatitis Delta Virus Ribozyme

    Article • Journal of Molecular Biology, August 2004, Elsevier

    Professor Nils G Walter

  89. Magnesium Dependence of the Amplified Conformational Switch in the Trans-Acting Hepatitis Delta Virus Ribozyme †

    Article • Biochemistry, July 2004, American Chemical Society (ACS)

    Professor Nils G Walter

  90. Significant Kinetic Solvent Isotope Effects in Folding of the Catalytic RNA from the Hepatitis Delta Virus

    Article • Journal of the American Chemical Society, November 2003, American Chemical Society (ACS)

    Professor Nils G Walter

  91. RNA Degradation in Cell Extracts:  Real-Time Monitoring by Fluorescence Resonance Energy Transfer

    Article • Journal of the American Chemical Society, November 2003, American Chemical Society (ACS)

    Professor Nils G Walter

  92. Diffusely Bound Mg 2+ Ions Slightly Reorient Stems I and II of the Hammerhead Ribozyme To Increase the Probability of Formation of the Catalytic Core †

    Article • Biochemistry, August 2003, American Chemical Society (ACS)

    Professor Nils G Walter

  93. Trans-Acting Hepatitis Delta Virus Ribozyme:  Catalytic Core and Global Structure Are Dependent on the 5‘ Substrate Sequence†

    Article • Biochemistry, July 2003, American Chemical Society (ACS)

    Professor Nils G Walter

  94. Probing RNA Structure and Metal-Binding Sites Using Terbium(III) Footprinting

    Article • June 2003, Wiley

    Professor Nils G Walter

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

    Article • December 2002, Wiley

    Professor Nils G Walter

  96. Local Conformational Changes in the Catalytic Core of the Trans-Acting Hepatitis Delta Virus Ribozyme Accompany Catalysis †

    Article • Biochemistry, October 2002, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • RNA, October 2002, Cold Spring Harbor Laboratory Press

    Professor Nils G Walter

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

    Article • Biopolymers, January 2002, Wiley

    Professor Nils G Walter

  99. Reaction Pathway of the Trans-Acting Hepatitis Delta Virus Ribozyme:  A Conformational Change Accompanies Catalysis †

    Article • Biochemistry, January 2002, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • Biopolymers, January 2002, Wiley

    Professor Nils G Walter

  101. Structural Dynamics of Catalytic RNA Highlighted by Fluorescence Resonance Energy Transfer

    Article • Methods, September 2001, Elsevier

    Professor Nils G Walter

  102. Capillary electrophoresis of RNA in dilute and semidilute polymer solutions

    Article • Electrophoresis, July 2001, Wiley

    Professor Nils G Walter

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

    Article • RNA, June 2001, Cold Spring Harbor Laboratory Press

    Professor Nils G Walter

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

    Article • Journal of Molecular Biology, March 2001, Elsevier

    Professor Nils G Walter

  105. A Base Change in the Catalytic Core of the Hairpin Ribozyme Perturbs Function but Not Domain Docking †

    Article • Biochemistry, February 2001, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • Journal of Molecular Biology, May 2000, Elsevier

    Professor Nils G Walter

  107. [25] Fluorescence assays to study structure, dynamics, and function of RNA and RNA-ligand complexes

    Article • January 2000, Elsevier

    Professor Nils G Walter

  108. Structural Basis for the Guanosine Requirement of the Hairpin Ribozyme †

    Article • Biochemistry, December 1999, American Chemical Society (ACS)

    Professor Nils G Walter

  109. Global Structure and Flexibility of Hairpin Ribozymes with Extended Terminal Helices

    Article • Journal of Molecular Biology, June 1999, Elsevier

    Professor Nils G Walter

  110. On-line polymerase chain reaction (PCR) monitoring

    Article • Journal of Biochemical and Biophysical Methods, November 1998, Elsevier

    Professor Nils G Walter

  111. The Solvent-Protected Core of the Hairpin Ribozyme−Substrate Complex †

    Article • Biochemistry, October 1998, American Chemical Society (ACS)

    Professor Nils G Walter

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

    Article • Chemistry & Biology, October 1998, Elsevier

    Professor Nils G Walter

  113. The hairpin ribozyme: structure, assembly and catalysis

    Article • Current Opinion in Chemical Biology, April 1998, Elsevier

    Professor Nils G Walter

  114. The hairpin ribozyme: structure, assembly and catalysis

    Article • Current Opinion in Chemical Biology, February 1998, Elsevier

    Professor Nils G Walter

  115. Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qβ replicase efficiently binds small RNAs by recognizing pyrimidine residues 1 1Edited by I. Tinoco

    Article • Journal of Molecular Biology, October 1997, Elsevier

    Professor Nils G Walter

  116. Quantitative Hybridization Kinetics of DNA Probes to RNA in Solution Followed by Diffusional Fluorescence Correlation Analysis †

    Article • Biochemistry, January 1996, American Chemical Society (ACS)

    Professor Nils G Walter

  117. Modelling Viral Evolutionin VitroUsing exo−Klenow Polymerase: Continuous Selection of Strand Displacement Amplified DNA that Binds an Oligodeoxynucleotide to Form a Triple-helix

    Article • Journal of Molecular Biology, December 1995, Elsevier

    Professor Nils G Walter

  118. Fluorescent Energy Transfer Readout of an Aptazyme-Based Biosensor

    Article • Springer Science + Business Media

    Professor Nils G Walter

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

    Article • Springer Science + Business Media

    Professor Nils G Walter

  120. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites

    Article • Wiley

    Professor Nils G Walter