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Nils G. Walter - Publications

Affiliations: 
Chemistry University of Michigan, Ann Arbor, Ann Arbor, MI 
Area:
structure-function relationships in non-coding (nc)RNAs using single molecule tools and then utilize them for biomedical, bioanalytical and nanotechnological applications
Website:
https://www.chem.lsa.umich.edu/chem/faculty/facultyDetail.php?Uniqname=nwalter

152 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Pitchiaya S, Mourao MDA, Jalihal AP, Xiao L, Jiang X, Chinnaiyan AM, Schnell S, Walter NG. Dynamic Recruitment of Single RNAs to Processing Bodies Depends on RNA Functionality. Molecular Cell. PMID 30952514 DOI: 10.1016/j.molcel.2019.03.001  0.6
2019 Jalihal AP, Lund PE, Walter NG. Coming Together: RNAs and Proteins Assemble under the Single-Molecule Fluorescence Microscope. Cold Spring Harbor Perspectives in Biology. 11. PMID 30936188 DOI: 10.1101/cshperspect.a032441  0.4
2018 Michelini F, Jalihal AP, Francia S, Meers C, Neeb ZT, Rossiello F, Gioia U, Aguado J, Jones-Weinert C, Luke B, Biamonti G, Nowacki M, Storici F, Carninci P, Walter NG, et al. From "Cellular" RNA to "Smart" RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chemical Reviews. PMID 29600857 DOI: 10.1021/acs.chemrev.7b00487  0.4
2018 Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Gil-Ley A, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews. PMID 29297679 DOI: 10.1021/acs.chemrev.7b00427  0.68
2017 Michelini F, Pitchiaya S, Vitelli V, Sharma S, Gioia U, Pessina F, Cabrini M, Wang Y, Capozzo I, Iannelli F, Matti V, Francia S, Shivashankar GV, Walter NG, d'Adda di Fagagna F. Damage-induced lncRNAs control the DNA damage response through interaction with DDRNAs at individual double-strand breaks. Nature Cell Biology. 19: 1400-1411. PMID 29180822 DOI: 10.1038/ncb3643  0.6
2017 Daher M, Widom JR, Tay W, Walter NG. Soft interactions with model crowders and non-canonical interactions with cellular proteins stabilize RNA folding. Journal of Molecular Biology. PMID 29128594 DOI: 10.1016/j.jmb.2017.10.030  0.36
2017 Daher M, Mustoe AM, Morriss-Andrews A, Brooks Iii CL, Walter NG. Tuning RNA folding and function through rational design of junction topology. Nucleic Acids Research. 45: 9706-9715. PMID 28934478 DOI: 10.1093/nar/gkx614  0.36
2017 Pitchiaya S, Heinicke LA, Park JI, Cameron EL, Walter NG. Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution. Cell Reports. 19: 630-642. PMID 28423324 DOI: 10.1016/j.celrep.2017.03.075  0.6
2016 Custer TC, Walter NG. In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines. Protein Science : a Publication of the Protein Society. PMID 28028853 DOI: 10.1002/pro.3108  0.6
2016 Tsekouras K, Custer TC, Jashnsaz H, Walter NG, Pressé S. A Novel Method to Accurately Locate and Count Large Numbers of Steps by Photobleaching. Molecular Biology of the Cell. PMID 27654946 DOI: 10.1091/mbc.E16-06-0404  0.6
2016 Shankar S, Pitchiaya S, Malik R, Kothari V, Hosono Y, Yocum AK, Gundlapalli H, White Y, Firestone A, Cao X, Dhanasekaran SM, Stuckey JA, Bollag G, Shannon K, Walter NG, et al. KRAS Engages AGO2 to Enhance Cellular Transformation. Cell Reports. PMID 26854235 DOI: 10.1016/j.celrep.2016.01.034  0.6
2016 Dhakal S, Adendorff MR, Liu M, Yan H, Bathe M, Walter NG. Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale. PMID 26788713 DOI: 10.1039/c5nr07263h  1
2016 Rinaldi AJ, Lund PE, Blanco MR, Walter NG. The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nature Communications. 7: 8976. PMID 26781350 DOI: 10.1038/ncomms9976  1
2015 Suddala KC, Wang J, Hou Q, Walter NG. Mg2+ Shifts Ligand-Mediated Folding of a Riboswitch from Induced-Fit to Conformational Selection. Journal of the American Chemical Society. PMID 26471732 DOI: 10.1021/jacs.5b09740  1
2015 Blanco MR, Martin JS, Kahlscheuer ML, Krishnan R, Abelson J, Laederach A, Walter NG. Single Molecule Cluster Analysis dissects splicing pathway conformational dynamics. Nature Methods. 12: 1077-84. PMID 26414013 DOI: 10.1038/nmeth.3602  1
2015 Mallik L, Dhakal S, Nichols J, Mahoney J, Dosey AM, Jiang S, Sunahara RK, Skiniotis G, Walter NG. Electron Microscopic Visualization of Protein Assemblies on Flattened DNA Origami. Acs Nano. PMID 26149412 DOI: 10.1021/acsnano.5b01841  1
2015 Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M, Mathews DH, Spitale RC, Walter NG, Wedekind JE. Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 26106162 DOI: 10.1073/pnas.1503955112  1
2015 Johnson-Buck A, Su X, Giraldez MD, Zhao M, Tewari M, Walter NG. Kinetic fingerprinting to identify and count single nucleic acids. Nature Biotechnology. PMID 26098451 DOI: 10.1038/nbt.3246  1
2015 Kahlscheuer ML, Widom J, Walter NG. Single-Molecule Pull-Down FRET to Dissect the Mechanisms of Biomolecular Machines. Methods in Enzymology. 558: 539-70. PMID 26068753 DOI: 10.1016/bs.mie.2015.01.009  1
2015 Dubecký M, Walter NG, Šponer J, Otyepka M, Banáš P. Chemical feasibility of the general Acid/Base mechanism of glmS ribozyme self-cleavage. Biopolymers. PMID 25858644 DOI: 10.1002/bip.22657  1
2015 Walter NG. Going viral: riding the RNA wave to discovery. Rna (New York, N.Y.). 21: 756-7. PMID 25780223 DOI: 10.1261/rna.049403.114  1
2015 Mlýnský V, Kührová P, Zgarbová M, Jure?ka P, Walter NG, Otyepka M, Šponer J, Banáš P. Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with ε/ζ force field reparametrizations. The Journal of Physical Chemistry. B. 119: 4220-9. PMID 25692537 DOI: 10.1021/jp512069n  1
2015 Sripathi KN, Banáš P, Réblová K, Šponer J, Otyepka M, Walter NG. Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Physical Chemistry Chemical Physics : Pccp. 17: 5887-900. PMID 25631765 DOI: 10.1039/c4cp05083e  1
2015 Nyati S, Schinske-Sebolt K, Pitchiaya S, Chekhovskiy K, Chator A, Chaudhry N, Dosch J, Van Dort ME, Varambally S, Kumar-Sinha C, Nyati MK, Ray D, Walter NG, Yu H, Ross BD, et al. The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-β signaling. Science Signaling. 8: ra1. PMID 25564677 DOI: 10.1126/scisignal.2005379  1
2015 Bartke RM, Cameron EL, Cristie-David AS, Custer TC, Denies MS, Daher M, Dhakal S, Ghosh S, Heinicke LA, Hoff JD, Hou Q, Kahlscheuer ML, Karslake J, Krieger AG, Li J, ... ... Walter NG, et al. Meeting report: SMART timing-principles of single molecule techniques course at the University of Michigan 2014. Biopolymers. 103: 296-302. PMID 25546606 DOI: 10.1002/bip.22603  1
2015 Mlýnský V, Walter NG, Šponer J, Otyepka M, Banáš P. The role of an active site Mg(2+) in HDV ribozyme self-cleavage: insights from QM/MM calculations. Physical Chemistry Chemical Physics : Pccp. 17: 670-9. PMID 25412464 DOI: 10.1039/c4cp03857f  1
2015 Rinaldi AJ, Suddala KC, Walter NG. Native purification and labeling of RNA for single molecule fluorescence studies. Methods in Molecular Biology (Clifton, N.J.). 1240: 63-95. PMID 25352138 DOI: 10.1007/978-1-4939-1896-6_6  1
2014 Suddala KC, Walter NG. Riboswitch structure and dynamics by smFRET microscopy. Methods in Enzymology. 549: 343-73. PMID 25432756 DOI: 10.1016/B978-0-12-801122-5.00015-5  1
2014 Widom JR, Dhakal S, Heinicke LA, Walter NG. Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Archives of Toxicology. 88: 1965-85. PMID 25212907 DOI: 10.1007/s00204-014-1357-9  1
2014 Fu J, Yang YR, Johnson-Buck A, Liu M, Liu Y, Walter NG, Woodbury NW, Yan H. Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nature Nanotechnology. 9: 531-6. PMID 24859813 DOI: 10.1038/nnano.2014.100  1
2014 Sripathi KN, Tay WW, Banáš P, Otyepka M, Šponer J, Walter NG. Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. Rna (New York, N.Y.). 20: 1112-28. PMID 24854621 DOI: 10.1261/rna.044982.114  1
2014 Johnson-Buck A, Jiang S, Yan H, Walter NG. DNA-cholesterol barges as programmable membrane-exploring agents. Acs Nano. 8: 5641-9. PMID 24833515 DOI: 10.1021/nn500108k  1
2014 Walter NG, Bustamante C. Introduction to single molecule imaging and mechanics: seeing and touching molecules one at a time. Chemical Reviews. 114: 3069-71. PMID 24666198 DOI: 10.1021/cr500059w  1
2014 Johnson-Buck A, Walter NG. Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy. Methods (San Diego, Calif.). 67: 177-84. PMID 24602840 DOI: 10.1016/j.ymeth.2014.02.032  1
2014 Pitchiaya S, Heinicke LA, Custer TC, Walter NG. Single molecule fluorescence approaches shed light on intracellular RNAs. Chemical Reviews. 114: 3224-65. PMID 24417544 DOI: 10.1021/cr400496q  1
2014 Grima R, Walter NG, Schnell S. Single-molecule enzymology à la Michaelis-Menten. The Febs Journal. 281: 518-30. PMID 24289171 DOI: 10.1111/febs.12663  1
2013 Krishnan R, Blanco MR, Kahlscheuer ML, Abelson J, Guthrie C, Walter NG. Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nature Structural & Molecular Biology. 20: 1450-7. PMID 24240612 DOI: 10.1038/nsmb.2704  1
2013 Walter NG. Editorial for "non-coding RNA methods". Methods (San Diego, Calif.). 63: 93-4. PMID 24119771 DOI: 10.1016/j.ymeth.2013.09.008  1
2013 Ma J, Liu Z, Michelotti N, Pitchiaya S, Veerapaneni R, Androsavich JR, Walter NG, Yang W. High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nature Communications. 4: 2414. PMID 24008311 DOI: 10.1038/ncomms3414  1
2013 Suddala KC, Rinaldi AJ, Feng J, Mustoe AM, Eichhorn CD, Liberman JA, Wedekind JE, Al-Hashimi HM, Brooks CL, Walter NG. Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Research. 41: 10462-75. PMID 24003028 DOI: 10.1093/nar/gkt798  1
2013 Breslauer KJ, Case DA, Walter NG, Woodson SA. Biopolymers celebrates 50 years of nucleic acids research. Biopolymers. 99: 909. PMID 23893377 DOI: 10.1002/bip.22358  1
2013 Pitchiaya S, Krishnan V, Custer TC, Walter NG. Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting. Methods (San Diego, Calif.). 63: 188-99. PMID 23820309 DOI: 10.1016/j.ymeth.2013.05.028  1
2013 Johnson-Buck A, Nangreave J, Jiang S, Yan H, Walter NG. Multifactorial modulation of binding and dissociation kinetics on two-dimensional DNA nanostructures. Nano Letters. 13: 2754-9. PMID 23701430 DOI: 10.1021/nl400976s  1
2013 Todd GC, Walter NG. Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing. Rna (New York, N.Y.). 19: 685-700. PMID 23492219 DOI: 10.1261/rna.037291.112  1
2013 Cline EN, Li MH, Choi SK, Herbstman JF, Kaul N, Meyhöfer E, Skiniotis G, Baker JR, Larson RG, Walter NG. Paclitaxel-conjugated PAMAM dendrimers adversely affect microtubule structure through two independent modes of action. Biomacromolecules. 14: 654-64. PMID 23391096 DOI: 10.1021/bm301719b  1
2013 Johnson-Buck A, Nangreave J, Kim DN, Bathe M, Yan H, Walter NG. Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Letters. 13: 728-33. PMID 23356935 DOI: 10.1021/nl304415b  1
2012 Androsavich JR, Chau BN, Bhat B, Linsley PS, Walter NG. Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. Rna (New York, N.Y.). 18: 1510-26. PMID 22740638 DOI: 10.1261/rna.033308.112  1
2012 Pitchiaya S, Androsavich JR, Walter NG. Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. Embo Reports. 13: 709-15. PMID 22688967 DOI: 10.1038/embor.2012.85  1
2012 Michelotti N, Johnson-Buck A, Manzo AJ, Walter NG. Beyond DNA origami: the unfolding prospects of nucleic acid nanotechnology. Wiley Interdisciplinary Reviews. Nanomedicine and Nanobiotechnology. 4: 139-52. PMID 22131292 DOI: 10.1002/wnan.170  1
2012 Eichhorn CD, Feng J, Suddala KC, Walter NG, Brooks CL, Al-Hashimi HM. Unraveling the structural complexity in a single-stranded RNA tail: implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Research. 40: 1345-55. PMID 22009676 DOI: 10.1093/nar/gkr833  1
2012 Šponer J, Otyepka M, Banáš P, Réblová K, Walter NG. Chapter 6: Molecular dynamics simulations of RNA molecules Rsc Biomolecular Sciences. 129-155.  1
2011 Sobhy MA, Elshenawy MM, Takahashi M, Whitman BH, Walter NG, Hamdan SM. Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics. The Review of Scientific Instruments. 82: 113702. PMID 22128979 DOI: 10.1063/1.3657153  1
2011 Mlýnský V, Banáš P, Walter NG, Šponer J, Otyepka M. QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. The Journal of Physical Chemistry. B. 115: 13911-24. PMID 22014231 DOI: 10.1021/jp206963g  1
2011 Johnson-Buck AE, McDowell SE, Walter NG. Metal ions: supporting actors in the playbook of small ribozymes. Metal Ions in Life Sciences. 9: 175-96. PMID 22010272  1
2011 Hoerter JA, Krishnan V, Lionberger TA, Walter NG. siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract. Plos One. 6: e20359. PMID 21647381 DOI: 10.1371/journal.pone.0020359  1
2011 Marek MS, Johnson-Buck A, Walter NG. The shape-shifting quasispecies of RNA: one sequence, many functional folds. Physical Chemistry Chemical Physics : Pccp. 13: 11524-37. PMID 21603685 DOI: 10.1039/c1cp20576e  1
2011 Spano MN, Walter NG. Solution structure of an alternate conformation of helix27 from Escherichia coli16S rRNA. Biopolymers. 95: 653-68. PMID 21442607 DOI: 10.1002/bip.21626  1
2011 Langelier SM, Livak-Dahl E, Manzo AJ, Johnson BN, Walter NG, Burns MA. Flexible casting of modular self-aligning microfluidic assembly blocks. Lab On a Chip. 11: 1679-87. PMID 21412522 DOI: 10.1039/c0lc00517g  1
2011 Feng J, Walter NG, Brooks CL. Cooperative and directional folding of the preQ1 riboswitch aptamer domain. Journal of the American Chemical Society. 133: 4196-9. PMID 21375305 DOI: 10.1021/ja110411m  1
2011 Rawlings RA, Krishnan V, Walter NG. Viral RNAi suppressor reversibly binds siRNA to outcompete Dicer and RISC via multiple turnover. Journal of Molecular Biology. 408: 262-76. PMID 21354178 DOI: 10.1016/j.jmb.2011.02.038  1
2011 Walter NG. Motor myosin V caught on video: foot stomping in biology. Biopolymers. 95: v. PMID 21140530 DOI: 10.1002/bip.21569  1
2010 McDowell SE, Jun JM, Walter NG. Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. Rna (New York, N.Y.). 16: 2414-26. PMID 20921269 DOI: 10.1261/rna.1829110  1
2010 Pereira MJ, Behera V, Walter NG. Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity. Plos One. 5: e12953. PMID 20886091 DOI: 10.1371/journal.pone.0012953  1
2010 Michelotti N, de Silva C, Johnson-Buck AE, Manzo AJ, Walter NG. A bird's eye view tracking slow nanometer-scale movements of single molecular nano-assemblies. Methods in Enzymology. 475: 121-48. PMID 20627156 DOI: 10.1016/S0076-6879(10)75006-0  1
2010 Blanco M, Walter NG. Analysis of complex single-molecule FRET time trajectories. Methods in Enzymology. 472: 153-78. PMID 20580964 DOI: 10.1016/S0076-6879(10)72011-5  1
2010 Walter NG. Single molecule tools: fluorescence based approaches, part A. Preface. Methods in Enzymology. 472: xxi-xxii. PMID 20580955 DOI: 10.1016/S0076-6879(10)72028-0  1
2010 Banás P, Walter NG, Sponer J, Otyepka M. Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. The Journal of Physical Chemistry. B. 114: 8701-12. PMID 20536206 DOI: 10.1021/jp9109699  1
2010 Lund K, Manzo AJ, Dabby N, Michelotti N, Johnson-Buck A, Nangreave J, Taylor S, Pei R, Stojanovic MN, Walter NG, Winfree E, Yan H. Molecular robots guided by prescriptive landscapes. Nature. 465: 206-10. PMID 20463735 DOI: 10.1038/nature09012  1
2010 Hsieh J, Koutmou KS, Rueda D, Koutmos M, Walter NG, Fierke CA. 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. Journal of Molecular Biology. 400: 38-51. PMID 20434461 DOI: 10.1016/j.jmb.2010.04.050  1
2010 Mlýnský V, Banás P, Hollas D, Réblová K, Walter NG, Sponer J, Otyepka M. Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. The Journal of Physical Chemistry. B. 114: 6642-52. PMID 20420375 DOI: 10.1021/jp1001258  1
2010 Abelson J, Blanco M, Ditzler MA, Fuller F, Aravamudhan P, Wood M, Villa T, Ryan DE, Pleiss JA, Maeder C, Guthrie C, Walter NG. Conformational dynamics of single pre-mRNA molecules during in vitro splicing. Nature Structural & Molecular Biology. 17: 504-12. PMID 20305654 DOI: 10.1038/nsmb.1767  1
2010 Ditzler MA, Otyepka M, Sponer J, Walter NG. Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in. Accounts of Chemical Research. 43: 40-7. PMID 19754142 DOI: 10.1021/ar900093g  1
2009 Walter NG. The blessing and curse of RNA dynamics: past, present, and future. Methods (San Diego, Calif.). 49: 85-6. PMID 19782935 DOI: 10.1016/j.ymeth.2009.09.002  1
2009 Kuszak AJ, Pitchiaya S, Anand JP, Mosberg HI, Walter NG, Sunahara RK. Purification and functional reconstitution of monomeric mu-opioid receptors: allosteric modulation of agonist binding by Gi2. The Journal of Biological Chemistry. 284: 26732-41. PMID 19542234 DOI: 10.1074/jbc.M109.026922  1
2009 Gérczei T, Shah BN, Manzo AJ, Walter NG, Correll CC. RNA chaperones stimulate formation and yield of the U3 snoRNA-Pre-rRNA duplexes needed for eukaryotic ribosome biogenesis. Journal of Molecular Biology. 390: 991-1006. PMID 19482034 DOI: 10.1016/j.jmb.2009.05.072  1
2009 Banás P, Jurecka P, Walter NG, Sponer J, Otyepka M. Theoretical studies of RNA catalysis: hybrid QM/MM methods and their comparison with MD and QM. Methods (San Diego, Calif.). 49: 202-16. PMID 19398008 DOI: 10.1016/j.ymeth.2009.04.007  1
2009 Ditzler MA, Sponer J, Walter NG. Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. Rna (New York, N.Y.). 15: 560-75. PMID 19223444 DOI: 10.1261/rna.1416709  1
2009 de Silva C, Walter NG. Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. Rna (New York, N.Y.). 15: 76-84. PMID 19029309 DOI: 10.1261/rna.1346609  1
2008 Ditzler MA, Rueda D, Mo J, Håkansson K, Walter NG. A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Research. 36: 7088-99. PMID 18988629 DOI: 10.1093/nar/gkn871  1
2008 Furchak JR, Yang P, Jennings C, Walter NG, Kennedy RT. Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection. Analytical Chemistry. 80: 8195-201. PMID 18842060 DOI: 10.1021/ac801410k  1
2008 Banás P, Rulísek L, Hánosová V, Svozil D, Walter NG, Sponer J, Otyepka M. General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. The Journal of Physical Chemistry. B. 112: 11177-87. PMID 18686993 DOI: 10.1021/jp802592z  1
2008 Pereira MJ, Nikolova EN, Hiley SL, Jaikaran D, Collins RA, Walter NG. Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. Journal of Molecular Biology. 382: 496-509. PMID 18656481 DOI: 10.1016/j.jmb.2008.07.020  1
2008 Al-Hashimi HM, Walter NG. RNA dynamics: it is about time. Current Opinion in Structural Biology. 18: 321-9. PMID 18547802 DOI: 10.1016/j.sbi.2008.04.004  1
2008 Walter NG, Huang CY, Manzo AJ, Sobhy MA. Do-it-yourself guide: how to use the modern single-molecule toolkit. Nature Methods. 5: 475-89. PMID 18511916 DOI: 10.1038/nmeth.1215  1
2008 Gafni A, Walter NG. Program review. The Interdisciplinary Biophysics Graduate Program at the University of Michigan. Biopolymers. 89: 256-61. PMID 18293398 DOI: 10.1002/bip.20931  1
2008 Walter NG. Research commentary in brief Biopolymers. 89: iv. DOI: 10.1002/bip.21090  1
2008 Harris DA, Walter NG. Terbium(III) Footprinting as a Probe of RNA Structure and Metal-binding Sites Handbook of Rna Biochemistry. 205-213. DOI: 10.1002/9783527619504.ch12  1
2007 Walter NG. Ribozyme catalysis revisited: is water involved? Molecular Cell. 28: 923-9. PMID 18158891 DOI: 10.1016/j.molcel.2007.12.001  1
2007 Hoerter JA, Walter NG. Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum. Rna (New York, N.Y.). 13: 1887-93. PMID 17804643 DOI: 10.1261/rna.602307  1
2007 Ditzler MA, Alemán EA, Rueda D, Walter NG. Focus on function: single molecule RNA enzymology. Biopolymers. 87: 302-16. PMID 17685395 DOI: 10.1002/bip.20819  1
2007 Tinsley RA, Walter NG. Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme. Biological Chemistry. 388: 705-15. PMID 17570823 DOI: 10.1515/BC.2007.088  1
2007 Bobeck MJ, Rueda D, Walter NG, Glick GD. Structural modeling of sequence specificity by an autoantibody against single-stranded DNA. Biochemistry. 46: 6753-65. PMID 17503778 DOI: 10.1021/bi700212s  1
2007 Liu S, Bokinsky G, Walter NG, Zhuang X. Dissecting the multistep reaction pathway of an RNA enzyme by single-molecule kinetic "fingerprinting". Proceedings of the National Academy of Sciences of the United States of America. 104: 12634-9. PMID 17496145 DOI: 10.1073/pnas.0610597104  1
2007 Sefcikova J, Krasovska MV, Sponer J, Walter NG. The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Research. 35: 1933-46. PMID 17337436 DOI: 10.1093/nar/gkl1104  1
2007 Tinsley RA, Furchak JR, Walter NG. Trans-acting glmS catalytic riboswitch: locked and loaded. Rna (New York, N.Y.). 13: 468-77. PMID 17283212 DOI: 10.1261/rna.341807  1
2007 Sefcikova J, Krasovska MV, Spacková N, Sponer J, Walter NG. Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers. 85: 392-406. PMID 17253610 DOI: 10.1002/bip.20693  1
2007 Walter NG. Future of biomedical sciences: single molecule microscopy. Biopolymers. 85: 103-5. PMID 17111397 DOI: 10.1002/bip.20633  1
2007 Walter NG, Meiners JC, Meyhofer E, Neubig RR, Sunahara RK, Perkins NC, Steel DG, Swanson JA. Under the microscope: single molecule symposium at the University of Michigan, 2006. Biopolymers. 85: 106-14. PMID 17080420 DOI: 10.1002/bip.20621  1
2007 McDowell SE, Spacková N, Sponer J, Walter NG. Molecular dynamics simulations of RNA: an in silico single molecule approach. Biopolymers. 85: 169-84. PMID 17080418 DOI: 10.1002/bip.20620  1
2006 Rhodes MM, Réblová K, Sponer J, Walter NG. Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 103: 13380-5. PMID 16938834 DOI: 10.1073/pnas.0605090103  1
2006 Rueda D, Walter NG. Fluorescent energy transfer readout of an aptazyme-based biosensor. Methods in Molecular Biology (Clifton, N.J.). 335: 289-310. PMID 16785635 DOI: 10.1385/1-59745-069-3:289  1
2006 Gondert ME, Tinsley RA, Rueda D, Walter NG. Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core. Biochemistry. 45: 7563-73. PMID 16768452 DOI: 10.1021/bi052116j  1
2006 Krasovska MV, Sefcikova J, Réblová K, Schneider B, Walter NG, Sponer J. Cations and hydration in catalytic RNA: molecular dynamics of the hepatitis delta virus ribozyme. Biophysical Journal. 91: 626-38. PMID 16617077 DOI: 10.1529/biophysj.105.079368  1
2006 Newby Lambert M, Vöcker E, Blumberg S, Redemann S, Gajraj A, Meiners JC, Walter NG. Mg2+-induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophysical Journal. 90: 3672-85. PMID 16500956 DOI: 10.1529/biophysj.105.067793  1
2006 Tinsley RA, Walter NG. Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. Rna (New York, N.Y.). 12: 522-9. PMID 16431979 DOI: 10.1261/rna.2165806  1
2006 Walter NG. Michaelis-Menten is dead, long live Michaelis-Menten! Nature Chemical Biology. 2: 66-7. PMID 16421583 DOI: 10.1038/nchembio0206-66  1
2005 Rueda D, Walter NG. Single molecule fluorescence control for nanotechnology. Journal of Nanoscience and Nanotechnology. 5: 1990-2000. PMID 16430133 DOI: 10.1166/jnn.2005.505  1
2005 Rueda D, Hsieh J, Day-Storms JJ, Fierke CA, Walter NG. The 5' leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry. 44: 16130-9. PMID 16331973 DOI: 10.1021/bi0519093  1
2005 Lambert MN, Hoerter JA, Pereira MJ, Walter NG. Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA. Rna (New York, N.Y.). 11: 1688-700. PMID 16244134 DOI: 10.1261/rna.2940705  1
2005 Krasovska MV, Sefcikova J, Spacková N, Sponer J, Walter NG. Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. Journal of Molecular Biology. 351: 731-48. PMID 16045932 DOI: 10.1016/j.jmb.2005.06.016  1
2004 Hoerter JA, Lambert MN, Pereira MJ, Walter NG. Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA. Biochemistry. 43: 14624-36. PMID 15544333 DOI: 10.1021/bi048533y  1
2004 Harris DA, Tinsley RA, Walter NG. Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme. Journal of Molecular Biology. 341: 389-403. PMID 15276831 DOI: 10.1016/j.jmb.2004.05.074  1
2004 Tinsley RA, Harris DA, Walter NG. Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme. Biochemistry. 43: 8935-45. PMID 15248751 DOI: 10.1021/bi049471e  1
2004 Rueda D, Bokinsky G, Rhodes MM, Rust MJ, Zhuang X, Walter NG. Single-molecule enzymology of RNA: essential functional groups impact catalysis from a distance. Proceedings of the National Academy of Sciences of the United States of America. 101: 10066-71. PMID 15218105 DOI: 10.1073/pnas.0403575101  1
2003 Harris DA, Walter NG. Probing RNA structure and metal-binding sites using terbium(III) footprinting. Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 6.8. PMID 18428913 DOI: 10.1002/0471142700.nc0608s13  1
2003 Walter NG. Probing RNA structural dynamics and function by fluorescence resonance energy transfer (FRET). Current Protocols in Nucleic Acid Chemistry / Edited by Serge L. Beaucage ... [Et Al.]. Unit 11.10. PMID 18428904 DOI: 10.1002/0471142700.nc1110s11  1
2003 Uhler SA, Cai D, Man Y, Figge C, Walter NG. RNA degradation in cell extracts: real-time monitoring by fluorescence resonance energy transfer. Journal of the American Chemical Society. 125: 14230-1. PMID 14624543 DOI: 10.1021/ja036854b  1
2003 Tinsley RA, Harris DA, Walter NG. Significant kinetic solvent isotope effects in folding of the catalytic RNA from the hepatitis delta virus. Journal of the American Chemical Society. 125: 13972-3. PMID 14611229 DOI: 10.1021/ja037870b  1
2003 Rueda D, Wick K, McDowell SE, Walter NG. Diffusely bound Mg2+ ions slightly reorient stems I and II of the hammerhead ribozyme to increase the probability of formation of the catalytic core. Biochemistry. 42: 9924-36. PMID 12924941 DOI: 10.1021/bi0347757  1
2003 Bokinsky G, Rueda D, Misra VK, Rhodes MM, Gordus A, Babcock HP, Walter NG, Zhuang X. Single-molecule transition-state analysis of RNA folding. Proceedings of the National Academy of Sciences of the United States of America. 100: 9302-7. PMID 12869691 DOI: 10.1073/pnas.1133280100  1
2003 Jeong S, Sefcikova J, Tinsley RA, Rueda D, Walter NG. Trans-acting hepatitis delta virus ribozyme: catalytic core and global structure are dependent on the 5' substrate sequence. Biochemistry. 42: 7727-40. PMID 12820882 DOI: 10.1021/bi034627g  1
2002 Sekella PT, Rueda D, Walter NG. A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. Rna (New York, N.Y.). 8: 1242-52. PMID 12403463 DOI: 10.1017/S1355838202028066  1
2002 Walter NG, Engelke DR. Ribozymes: catalytic RNAs that cut things, make things, and do odd and useful jobs. Biologist (London, England). 49: 199-203. PMID 12391409  1
2002 Harris DA, Rueda D, Walter NG. Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry. 41: 12051-61. PMID 12356305 DOI: 10.1021/bi026101m  1
2002 Zhuang X, Kim H, Pereira MJ, Babcock HP, Walter NG, Chu S. Correlating structural dynamics and function in single ribozyme molecules. Science (New York, N.Y.). 296: 1473-6. PMID 12029135 DOI: 10.1126/science.1069013  1
2002 Pereira MJ, Harris DA, Rueda D, Walter NG. Reaction pathway of the trans-acting hepatitis delta virus ribozyme: a conformational change accompanies catalysis. Biochemistry. 41: 730-40. PMID 11790094 DOI: 10.1021/bi011963t  1
2001 Walter NG, Harris DA, Pereira MJ, Rueda D. In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs. Biopolymers. 61: 224-42. PMID 11987183 DOI: 10.1002/bip.10144  1
2001 Walter NG. Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer. Methods (San Diego, Calif.). 25: 19-30. PMID 11558994 DOI: 10.1006/meth.2001.1212  1
2001 Todorov TI, de Carmejane O, Walter NG, Morris MD. Capillary electrophoresis of RNA in dilute and semidilute polymer solutions. Electrophoresis. 22: 2442-7. PMID 11519948 DOI: 10.1002/1522-2683(200107)22:12<2442::AID-ELPS2442>3.0.CO;2-9  1
2001 Fay MJ, Walter NG, Burke JM. Identification of cis-acting elements involved in 3′-end formation of Saccharomyces cerevisiae 18S rRNA Rna. 7: 896-903. PMID 11421364 DOI: 10.1017/S1355838201010196  1
2001 Fay MJ, Walter NG, Burke JM. Imaging of single hairpin ribozymes in solution by atomic force microscopy. Rna (New York, N.Y.). 7: 887-95. PMID 11421363  1
2001 Walter NG, Chan PA, Hampel KJ, Millar DP, Burke JM. A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking. Biochemistry. 40: 2580-7. PMID 11327881 DOI: 10.1021/bi001609f  1
2001 Pinard R, Lambert D, Heckman JE, Esteban JA, Gundlach CW, Hampel KJ, Glick GD, Walter NG, Major F, Burke JM. The hairpin ribozyme substrate binding-domain: a highly constrained D-shaped conformation. Journal of Molecular Biology. 307: 51-65. PMID 11243803 DOI: 10.1006/jmbi.2000.4472  1
2000 Walter NG, Burke JM. Fluorescence assays to study structure, dynamics, and function of RNA and RNA-ligand complexes. Methods in Enzymology. 317: 409-40. PMID 10829293  1
2000 Walter NG, Yang N, Burke JM. Probing non-selective cation binding in the hairpin ribozyme with Tb(III). Journal of Molecular Biology. 298: 539-55. PMID 10772868 DOI: 10.1006/jmbi.2000.3691  1
1999 Pinard R, Lambert D, Walter NG, Heckman JE, Major F, Burke JM. Structural basis for the guanosine requirement of the hairpin ribozyme. Biochemistry. 38: 16035-9. PMID 10587425 DOI: 10.1021/bi992024s  1
1999 Porschke D, Burke JM, Walter NG. Global structure and flexibility of hairpin ribozymes with extended terminal helices. Journal of Molecular Biology. 289: 799-813. PMID 10369762 DOI: 10.1006/jmbi.1999.2777  1
1999 Walter NG, Burke JM, Millar DP. Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nature Structural Biology. 6: 544-9. PMID 10360357 DOI: 10.1038/9316  1
1998 Ederhof T, Walter NG, Schober A. On-line polymerase chain reaction (PCR) monitoring. Journal of Biochemical and Biophysical Methods. 37: 99-104. PMID 9870184 DOI: 10.1016/S0165-022X(98)00011-6  1
1998 Murray JB, Seyhan AA, Walter NG, Burke JM, Scott WG. The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chemistry & Biology. 5: 587-95. PMID 9818150  1
1998 Hampel KJ, Walter NG, Burke JM. The solvent-protected core of the hairpin ribozyme-substrate complex. Biochemistry. 37: 14672-82. PMID 9778342 DOI: 10.1021/bi981083n  1
1998 Walter NG, Burke JM. The hairpin ribozyme: structure, assembly and catalysis Current Opinion in Chemical Biology. 2: 303. PMID 9667943  1
1998 Walter NG, Burke JM. The hairpin ribozyme: structure, assembly and catalysis. Current Opinion in Chemical Biology. 2: 24-30. PMID 9667918  1
1998 Esteban JA, Walter NG, Kotzorek G, Heckman JE, Burke JM. Structural basis for heterogeneous kinetics: reengineering the hairpin ribozyme. Proceedings of the National Academy of Sciences of the United States of America. 95: 6091-6. PMID 9600922 DOI: 10.1073/pnas.95.11.6091  1
1998 Walter NG, Hampel KJ, Brown KM, Burke JM. Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. The Embo Journal. 17: 2378-91. PMID 9545249 DOI: 10.1093/emboj/17.8.2378  1
1997 Preuss R, Dapprich J, Walter NG. Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qbeta replicase efficiently binds small RNAs by recognizing pyrimidine residues. Journal of Molecular Biology. 273: 600-13. PMID 9356249 DOI: 10.1006/jmbi.1997.1343  1
1997 Walter NG, Burke JM. Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. Rna (New York, N.Y.). 3: 392-404. PMID 9085846  1
1996 Walter NG, Schwille P, Eigen M. Fluorescence correlation analysis of probe diffusion simplifies quantitative pathogen detection by PCR. Proceedings of the National Academy of Sciences of the United States of America. 93: 12805-10. PMID 8917500 DOI: 10.1073/pnas.93.23.12805  1
1996 Schwille P, Oehlenschläger F, Walter NG. Quantitative hybridization kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation analysis. Biochemistry. 35: 10182-93. PMID 8756483 DOI: 10.1021/bi960517g  1
1995 Schober A, Walter NG, Tangen U, Strunk G, Ederhof T, Dapprich J, Eigen M. Multichannel PCR and serial transfer machine as a future tool in evolutionary biotechnology. Biotechniques. 18: 652-61. PMID 7598900  1
1995 Walter NG. 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. Journal of Molecular Biology. 254: 856-68. PMID 7500356 DOI: 10.1006/jmbi.1995.0661  1
1994 Walter NG, Strunk G. Strand displacement amplification as an in vitro model for rolling-circle replication: deletion formation and evolution during serial transfer. Proceedings of the National Academy of Sciences of the United States of America. 91: 7937-41. PMID 8058737 DOI: 10.1073/pnas.91.17.7937  1
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