Publications

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Links to the respective years of publications:
2017 2016 2015  2014  2013  2012  2011  2010  2009 2008  2007  2006  2005  2004  2003  2002  2001  2000  1999  1998  1997  1996  1995  1994  1993

2017

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163. Daher, M., Li, X., Mustoe, A.M., Morriss-Andrews, A.,Brooks III, C.L., and Walter, N.G. (2017) Tuning RNA folding and function through rational design of junction topology. Nucleic Acids Res. 45, 9706–9715. Full text (with supplement) in pdf format.

162. Mieritz, D., Li, X., Volosin, A., Liu, M.,Yan, H., Walter, N.G., and Seo, D. (2017) Tracking Single DNA Nanodevices in Hierarchically MesoMacroporous Antimony-Doped Tin Oxide Demonstrates Finite Confinement. Langmuir 33, 6410-6418. Full text (with supplement) in pdf format.

161. Custer, T.C. and Walter, N.G. (2017) In vitro labeling strategies for in cellulo fluorescence microscopy of single ribonucleoprotein machines. Protein Sci 26, 1363-1379. Full text (with supplement) in pdf format.

160. Pitchiaya, S., Heinicke, L.A., Park, J.A., Cameron, E.L., Walter, N.G. (2017) Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution. Cell Rep. 19, 630–642. Full text (with supplement) in pdf format.

2016

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159. Tsekouras, K., Custer, T.C., Jashnsaz, H., Walter, N.G. and Pressé, S. (2016) A novel method to accurately locate and count large numbers of steps by photobleaching. Mol. Biol. Cell 27, 3601-3615. Full text in pdf format.

158. Rohlman, C.E., Blanco, M.R. and Walter N.G. (2016) Putting Humpty–Dumpty together: clustering the functional dynamics of single biomolecular machines such as the spliceosome. Methods Enzymol. 581, 257-283. Full text in pdf format.

157. Suresh, M.V., Thomas, B., Machado-Aranda, D., Dolgachev, V.A., Ramakrishnan, S.K., Talarico, N., Cavassani, K., Sherman, M.A., Hemmila, M.R., Kunkel, S.L., Walter, N.G., Hogaboam, C.M. and Raghavendran, K. (2016) Double-stranded RNA interacts with toll-like receptor 3 in driving the acute inflammatory response following lung contusion. Crit. Care Med. 44, e1054-e1066. Full text in pdf format.

156. Fu, J., Yang, Y.R., Dhakal, S., Zhao, Z., Liu, M., Zhang, T., Walter, N.G. and Yan, H. (2016) Assembly of multienzyme complexes on DNA nanostructures. Nat. Protoc. 11, 2243-2273. Full text in pdf format.

155. Walter, N.G. (2016) Introductory Editorial: Special section on single-molecule and super-resolution microscopy of biopolymers. Biopolymers 105, 669. Full text in pdf format.

154. Semlow, D.R., Blanco, M.R., Walter, N.G. and Staley, J. (2016) Spliceosomal DEAH-box ATPases remodel pre-mRNA to activate alternative splice sites. Cell 164, 985-998.  Full text in pdf format.

153. Zhao, Z., Fu, J., Dhakal, S., Johnson-Buck, A., Liu, M., Zhang, T., Woodbury, N.W., Liu, Y., Walter, N.G. and Yan, H. (2016) Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. Nat. Commun. 7, 1–8. Full text in pdf format. Supplementary Information in pdf format.

152. Shankar, S., Pitchiaya, S., Malik, R., Kothari, V., Hosono, Y., Yocum, A.K., Gundlapalli, H., White, Y., Firestone, A., Cao, X., Dhanasekaran, S.M., Stuckey, J.A., Bollag, G., Shannon, K., Walter, N.G., Kumar-Sinha, C. and Chinnaiyan, A.M. (2016) KRAS engages AGO2 to enhance cellular transformation. Cell Rep. 14, 1448–1461. Full text and Supplementary Information in pdf format.

151. Dhakal, S., Adendorff, M.R., Liu, M., Yan, H., Bathe, M. and Walter, N.G. (2016) Rational design of DNA-actuated enzyme nanoreactors guided by single molecule analysis. Nanoscale 8, 3125–3137. Full text in pdf format. Supplementary Information in pdf format. Please click here to access supplementary movies.

150. Rinaldi, A.J., Lund, P.E., Blanco, M.R. and Walter, N.G. (2016) The Shine-Dalgarno sequence of riboswitch-regulated single mRNAs shows ligand-dependent accessibility bursts. Nat. Commun. 7, 8976. Full text in pdf format. Supplementary Information in pdf format.

2015

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149. Suddala, K.C., Wang, J., Hou, Q., and Walter, N.G. (2015) Mg2+ shifts ligand-mediated folding of a riboswitch from induced-fit to conformational selection. J. Am. Chem. Soc. 137, p. 14075−14083. Full text in pdf format. Supplementary Information in pdf format. See Spotlights on recent JACS publications.

148. Blanco, M.R., Martin, J.S., Kahlscheuer, M.L., Krishnan, R., Abelson, J., Laederach, A. and Walter, N.G. (2015) Single molecule cluster analysis dissects splicing pathway conformational dynamics. Nature Methods 12, p. 1077-1086. Full text in pdf format. Supplementary Information in pdf format.

147. Mallik, L., Dhakal, S., Nichols, J., Mahoney, J., Dosey, A.M., Jiang, S., Sunahara, R.K., Skiniotis, G. and Walter, N.G. (2015) Electron microscopic visualization of protein assemblies on flattened DNA origami. ACS Nano 9, p. 7133-7141. Full text in pdf format. Supplementary Information in pdf format.

146. Dubecký, M., Walter N.G., Šponer, J., Otyepka, M. and Banáš, P. (2015) Chemical feasibility of the general base/acid mechanism of glmS ribozyme self-cleavage. Biopolymers 103, p. 550-562. Full text in pdf format. Supplementary Information in pdf format.

145. Johnson-Buck, A., Su, X., Giraldez, M.D., Zhao, M., Tewari, M. and Walter, N.G. (2015) Kinetic fingerprinting to identify and count single nucleic acids. Nat. Biotechnol. 33, p. 730-732. Full text in pdf format. Supplementary Information in pdf format.

144. Liberman, J.A., Suddala, K.C., Aytenfisu, A.H., Chan, D., Belashov, I.A., SalimM., Mathews, D.H., Spitale, R.C., Walter, N.G. and Wedekind, J.E. (2015) Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics. Proc. Natl. Acad. Sci. USA 112, p. E3485-E3494. Full text and Supplementary Information in pdf format.

143. Kahlscheuer, M.L., Widom, J.R. and Walter, N.G. (2015) Single-Molecule Pull-down FRET (SiMPull-FRET) to dissect the mechanisms of biomolecular machines. Methods Enzymol. 558, p. 539-570. Full text in pdf format.

142. Mlynsky, V., Kuhrova, P., Zgarbova, M., Jurecka, P., Walter N.G., Otyepka, M., Sponer, J. and Banas, P. (2015). Reactive conformation of the active site in the hairpin ribozyme achieved by molecular dynamics simulations with epsilon/zeta force field reparameterizations. J. Phys. Chem. B 119, p. 4220-4229. Full text in pdf format.

141. Walter, N.G. (2015). Going viral: riding the RNA wave to discovery. RNA 21, p. 756-757. Full text in pdf format.

140. Bartke, R.M., Cameron, E.L., Cristie-David, A.S., Custer, T.C., Denies, M.S., Daher, M., Dhakal, S., Ghosh, S., Heinicke, L.A., Hoff, J.D., Hou, Q., Kahlscheuer, M.L., Karslake, J., Krieger, A.G., Li, J., Li, X., Lund, P.E., Vo, N.N., Park, J., Pitchiaya, S., Rai, V., Smith, D.J., Suddala, K.C., Wang, J., Widom, J.R. and Walter, N.G. (2015). Meeting report: SMART timing-principles of single molecule techniques course at the University of Michigan 2014. Biopolymers 103, p. 296-302. Full text in pdf format.

139. Sripathi, K.N., Banas, P., Reblova, K., Sponer, J., Otyepka, M., and Walter, N.G. (2015). Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics. Phys. Chem. Chem. Phys. 17, p. 5887-5900. Full text in pdf format.

138. Nyati, S., Schinske-Sebolt, K., Pitchiaya, S., Chekhovskiy, K., Chator, A., Chaudhry, N., Dosch, J., Van Dort, M.E., Varambally, S., Kumar-Sinha, C., Nyati, M.K., Ray, D., Walter, N.G., Yu, H., Ross, B.D. and Rehemtulla, A. (2015). The kinase activity of the Ser/Thr kinase BUB1 promotes TGF-b signaling. Sci. Signal. 8, ra1, p. 1-11. Full text in pdf format. Supplementary Information in pdf format.

137. Mlynsky, V., Walter, N.G., Sponer, J., Otyepka, M. and Banas, P. (2015). The role of an active site Mg2+ in HDV ribozyme self-cleavage: insights from QM/MM calculations. Phys. Chem. Chem. Phys. 17, p. 670-679. Full text in pdf format.

136. Rinaldi, A.J., Suddala, K.C. and Walter, N.G. (2015). Native purification and labeling of RNA for single molecule fluorescence studies. Methods Mol. Biol. 1240, p. 63-95. Full text in pdf format.

2014

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135. Pitchiaya, S., Androsavich, J.R. and Walter, N.G. (2014). Super-accuracy and super-resolution fluorescence microscopy based on single molecule detection. In Imaging Life: Chapter 9, pp. 228-259 (G. C. Howard, W. E. Brown, and M. Auer, eds.), Oxford University Press, New York. Full text in pdf format.

134. Suddala, K.C. and Walter, N.G. (2014). Riboswitch structure and dynamics by smFRET microscopy. Methods Enzymol. 549, p. 343-373. Full text in pdf format.

133. Widom, J.R., Dhakal, S., Heinicke, L.A. and Walter, N.G. (2014). Single-molecule tools for enzymology, structural biology, systems biology and nanotechnology: an update. Arch. Toxicol. 88, p. 1965-1985. Full text in pdf format.

132. Fu, J., Yang, Y.R., Johnson-Buck, A., Liu, M., Liu, Y., Walter, N.G., Woodbury, N.W. and Yan, H. (2014). Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm. Nat. Nanotechnol. 9, p. 531-536. Full text in pdf format. Supplementary Information in pdf format. Access the recommendation on F1000Prime

131. Johnson-Buck, A., Jiang, S., Yan, H. and Walter, N.G. (2014). DNA-cholesterol barges as programmable membrane-exploring agents. ACS Nano 8, p. 5641-5649. Full text in pdf format. Supplementary Information in pdf format.

130. Sripathi, K.N., Tay, W.W., Banas, P., Otyepka, M., Sponer, J. and Walter, N.G. (2014). Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape. RNA 20, p. 1112-1128. pdf

129. Johnson-Buck, A. and Walter, N.G. (2014). Discovering anomalous hybridization kinetics on DNA nanostructures using single-molecule fluorescence microscopy. Methods 67, p. 177–184. pdf

128. Harris, D.A., Todd, G.C. and Walter, N.G. (2014). Terbium(III) footprinting as a probe of RNA structure and metal binding sites. In Handbook of RNA Biochemistry: Second, Completely Revised and Enlarged Edition, Part II, pp. 255-268 (R.K. Hartmann, A. Bindereif, A. Schon, and E. Westhof, eds.), Wiley-VCH Verlag, Weinheim. pdf

127. Walter, N.G. and Bustamante, C.J. (2014). Introduction to single molecule imaging and mechanics: seeing and touching molecules one at a time. Chem. Rev. 114, p. 3069−3071. pdf

126. Pitchiaya, S., Heinicke, L.A., Custer, T.C. and Walter, N.G. (2014). Single molecule fluorescence approaches shed light on intracellular RNAs. Chem. Rev. 114, p. 3224-3265. pdf  Access the recommendation on F1000Prime

125. Grima, R., Walter, N.G. and Schnell, S. (2014). Single-molecule enzymology a la Michaelis-Menten. FEBS Journal. 281, p. 518-530. pdf

 2013

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124. Suddala, K.C., Rinaldi, A.J., Feng, J., Mustoe, A.M., Eichhorn, C.D., Liberman, J.A., Wedekind, J.E., Al-Hashimi, H.M., Brooks III, C.L. and Walter, N.G. (2013). Single transcriptional and translational preQ1 riboswitches adopt similar pre-folded ensembles that follow distinct folding pathways into the same ligand-bound structure. Nucleic Acids Res. 41, p. 10462-10475. pdf. Supplementary Information

123. Krishnan, R., Blanco, M.R., Kahlscheuer, M.L., Abelson, J., Guthrie, C. and Walter, N.G. (2013). Biased Brownian ratcheting leads to pre-mRNA remodeling and capture prior to first-step splicing. Nat. Struct. Mol. Biol. 20, p. 1450-1459. pdf. Supplementary Information

122. Pitchiaya, S., Krishnan, V., Custer, T.C. and Walter, N.G. (2013). Dissecting non-coding RNA mechanisms in cellulo by Single-molecule High-Resolution Localization and Counting. Methods. 63, p. 188-199. pdf

121. Walter, N.G. (2013). The bright future of (non-coding) RNAs: methods light the way. Methods. 63, p. 93-94. pdf

120. Breslauer, K.J., Case, D.A., Walter, N.G. and Woodson, S.A. (2013). Biopolymers celebrates 50 years of nucleic acids research. Biopolymers. 99, p. 909. PDF

119. Ma, J., Liu, Z., Michelotti, N., Pitchiaya, S., Veerapaneni, R., Androsavich, J.R., Walter, N.G. and Yang, W. (2013). High-resolution three-dimensional mapping of mRNA export through the nuclear pore. Nat. Commun. 4: 2414, doi: 10.1038/ncomms3414. pdf

118. Johnson-Buck, A., Nangreave, J., Jiang, S., Yan, H. and Walter, N.G. (2013). Multifactorial modulation of binding and dissociation kinetics on two-dimensional DNA nanostructures. Nano Lett. 13, p. 2754-2759. pdf. Supplementary Information

117. Todd, G.C. and Walter, N.G. (2013). Secondary structure of bacteriophage T4 gene 60 mRNA: implications for translational bypassing. RNA. 19, p. 685-700. pdf

116. Cline, E.N., Li, M., Choi, S.K., Herbstman, J.F., Kaul, N., Meyhofer, E., Skiniotis, G., Baker, J.R., Larson, R.G. and Walter, N.G. (2013). Paclitaxel-conjugated PAMAM dendrimers adversely affect microtubule structure through two independent modes of action. Biomacromolecules. 14, p. 654-664. pdf. Supplementary Information

115. Johnson-Buck, A., Nangreave, J., Kim, D., Bathe, M., Yan, H., and Walter, N.G. (2013) Super-resolution fingerprinting detects chemical reactions and idiosyncrasies of single DNA pegboards. Nano Lett. 13, p. 728-733. pdf. Supplementary Information

2012

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114. Sponer, J., Otyepka, M., Banas, P., Reblova, K. and Walter N.G. (2012). Molecular dynamics simulations of RNA molecules. Chapter 6 in Innovations in Biomolecular Modeling and Simulations, Vol. 2 (Ed. T. Schlick) RSC. PDF

113. Blanco, M.R., Johnson-Buck, A.E. and Walter, N.G. (2012). Hidden Markov modeling. In G.C.K. Roberts (ed.), Encyclopedia of Biophysics, pp. 971-975 (Ed. G. Roberts), Springer. PDF

112. Johnson-Buck, A.E., Blanco, M.R. and Walter, N.G. (2012). Single-molecule fluorescence resonance energy transfer. In G.C.K. Roberts (ed.), Encyclopedia of Biophysics, pp. 2329-2335 (Ed. G. Roberts), Springer. PDF

111. Androsavich, J.R., Chau, B.N., Bhat, B., Linsley, P.S. and Walter, N.G. (2012) Disease-linked microRNA-21 exhibits drastically reduced mRNA binding and silencing activity in healthy mouse liver. RNA. 18, p. 1510-1526. PDF

110. Pitchiaya, S., Androsavich, J.R., and Walter, N.G. (2012) Intracellular single molecule microscopy reveals two kinetically distinct pathways for microRNA assembly. EMBO reports 13, p. 709-715. PDF. Full supplement

109. Michelotti, N., Johnson-Buck, A., Manzo, A.J., M. and Walter, N.G. (2012) Beyond DNA origami: The unfolding prospects of nucleic acid nanotechnology. WIREs: Nanomed Nanobiotechnol. 4, p. 139-152. doi: 10.1002/wnan.170. PDF

108. Eichhorn, C.D., Feng, J., Suddala, K.C., Walter, N.G., Brooks III, C.L. and Al-Hashimi, H.M. (2012) Unraveling the structural complexity in a single stranded RNA tail: Implications for efficient ligand binding in the prequeuosine riboswitch. Nucleic Acids Res. 40, p. 1345-1355. PDF

2011

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107. Sobhy, M.A., Eishenawy, M.M., Takahashi, M., Whitman, B.H., Walter, N.G., Hamdan,S.M. (2011) Versatile single-molecule multi-color excitation and detection fluorescence setup for studying biomolecular dynamics. Rev. Sci. Instrum. 82, p. 113702. PDF

106. Mlynsky, V., Banas, P., Walter, N.G., Sponer, J., Otyepka, M. (2011) QM/MM studies of hairpin ribozyme self-cleavage suggest the feasibility of multiple competing reaction mechanisms. J. Phys. Chem. B 115, p. 13911-13924. PDF

105. Spano, M.N. and Walter, N.G. (2011) Solution structure of an alternate conformation of Helix 27 from Escherichia Coli 16S rRNA. Biopolymers 95, p. 653-668. PDF

104. Marek, M.S., Johnson-Buck, A. and Walter, N.G. (2011) The shape-shifting quasispecies of RNA: one sequence, many functional folds. Phys. Chem. Chem. Phys. 13, p. 11524-11537. PDF

103. Hoerter, J.A.H., Krishnan, V., Lionberger, T.A. and Walter, N.G. (2011) siRNA-like double-stranded RNAs are specifically protected against degradation in human cell extract. PLoS ONE 6, e20359. PDF

102. Johnson-Buck, A.E., McDowell, S.E. and Walter, N.G. (2011) Metal ions: Supporting actors in the playbook of small ribozymes. Met. Ions Life Sci. 9, p. 175-196. PDF

101. Langelier, S.M., Livak-Dahl, E., Manzo, A.J., Johnson, B.N., Walter, N.G., Burns, M.A. (2011) Flexible casting of modular self-aligning microfluidic assembly blocks. Lab Chip 11, p. 1679-1687. PDF. Supplement

100. Rawlings, R.A., Krishnan, V., Walter, N.G. (2011) Viral RNAi suppressor reversibly binds siRNA to outcompete dicer and RISC via multiple turnover.J. Mol. Biol. 408, p. 262-276. PDF. Supplement

99. Feng, J., Walter, N.G., Brooks, C.L. III. (2011) Cooperative and directional folding of the preQ1 riboswitch aptamer domain. J. Am. Chem. Soc. 133, p. 4196-4199. PDF

98. Walter, N.G. (2011) Motor myosin V caught on video: Foot stomping in biology. Biopolymers 95, V. PDF

2010

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97. McDowell, S.E., Jun, J.M., and Walter, N.G. (2010) Long-range tertiary interactions in single hammerhead ribozymes bias motional sampling toward catalytically active conformations. RNA 16, p. 2414-2426. PDF

96. Pereira, M.J.B., Behera, V. and Walter, N.G. (2010) Nondenaturing purification of co-transcriptionally folded RNA avoids common folding heterogeneity. PLoS ONE 5, e12953. PDF

95. Michelotti, N., de Silva, C., Johnson-Buck, A.E., Manzo, A.J., Walter, N.G. (2010) A bird’s eye view: tracking slow nanometer-scale movements of single molecular nano-assemblies. Methods Enzymol. 475, p. 121-148. PDF

94. Banas, P., Walter, N.G., Sponer, J. and Otyepka, M. (2010) Protonation states of the key active site residues and structural dynamics of the glmS riboswitch as revealed by molecular dynamics. J. Phys. Chem. B 114, p. 8701-8712. PDF

93. Hsieh, J., Koutmou, K.s., Rueda, D., Koutmos, M., Walter, N.G., Fierke, C.A. (2010) A divalent cation stabilizes the active conformation of the B. subtilisRNase P-pre-tRNA complex: A role for an inner-sphere metal ion in RNase P. J. Mol. Biol. 400, p. 38-51. PDF

92. Mlynsky, V., Banas, P., Hollas, D., Reblova, K., Walter, N.G., Sponer, J., and Otyepka, M. (2010) Extensive molecular dynamics simulations showing that canonical G8 and protonated A38H+ forms are most consistent with crystal structures of hairpin ribozyme. J. Phys. Chem. B 114, p. 6642-6652. PDF

91. Blanco, M., Walter, N.G. (2010) Analysis of complex single-molecule FRET time trajectories. Methods Enzymol. 472, p. 154-176. PDF

90. Walter, N.G. (2010) Preface. Methods Enzymol. 472, p. xxi-xxii. PDF

89. Lund, K., Manzo, A.J., Dabby, N., Michelotti, N., Johnson-Buck, A., Nangreave, J., Taylor, S., Pei, Stojanovic, M.N., Walter, N.G., Winfree, E., and Yan, H. (2010) Molecular robots guided by prescriptive landscapes. Nature 465, p. 206-210. PDF. Supplement. See reference on the cover. Highlighted in Nature News and Views.

88. Abelson, J., Blanco, M., Ditzler, M.A., Fuller, F., Aravamudhan, P., Wood, M., Villa, T., Ryan, D.E., Pleiss, J.A., Maeder, C., Guthrie, C. and Walter, N.G. (2010) Conformational dynamics of single pre-mRNA molecules in spliceosome assembly. Nat. Struct. Mol. Biol. 17, p. 504-512. PDF. Supplement. Highlighted as UM News Release on March 21, 2010. See also Science and Technology of C&E News on March 21, 2011.

87. Ditzler, M.A., Otyepka, M., Sponer, J. and Walter, N.G. (2010) Molecular dynamics and quantum mechanics of RNA: Conformational and chemical change we can believe in. Acc. Chem. Res. 40, p.40-47. PDF

2009

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86. Walter, N.G. (2009) The blessing and curse of RNA dynamics: past, present, and future. Methods  49, p.85-86. PDF

85. Banas, P., Jurecka, P., Walter, N.G., Sponer, J., and Otyepka, M. (2009) Theoretical studies of RNA catalysis: Hybrid QM/MM methods and their comparison with MD and QM. Methods  49, p.202-216. PDF

84. Kuszak, A., Pitchiaya, S., Anand, J.P., Mosberg, H.I., Walter, N.G., and Sunahara, R.K. (2009) Purification and functional reconstitution of monomeric Mu-Opioid receptors. Journal of Biological Chemistry vol. 284, number 39, p.26732-26741. Full text in pdf format. Supplement in pdf format.

83. Gerczei, T., Shah, B.N., Manzo, A.J., Walter, N.G., and Correll, C.C. (2009) RNA chaperones stimulate formation and yield of the U3 snoRNA-pre-rRNA duplexes needed for eukaryotic ribosome biogenesis. J. Mol. Biol. 390, p. 991-1006. Full text in pdf format. Supplement in pdf format.

82. Ditzler, M.A., Sponer, J., and Walter, N.G. (2009) Molecular dynamics suggest multifunctionality of an adenine imino group in acid-base catalysis of the hairpin ribozyme. RNA 15, p. 560-575.  PDF. Supplement in pdf format.

81. de Silva, C. and Walter, N.G. (2009) Leakage and slow allostery limit performance of single drug-sensing aptazyme molecules based on the hammerhead ribozyme. RNA 15, p. 76-84. PDF

80. Walter, N.G. and Perumal, S. (2009) The small ribozymes: Common and diverse features observed through the FRET lens. In: Non-Protein Coding RNAs, p. 103-127 (N.G. Walter, S.A. Woodson and R.T. Batey, eds.), Springer Series in Biophysics volume 13, Springer Publishers, Berlin. PDF

2008

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79. Walter, N.G. (2008) Single molecule detection, analysis, and manipulation. Encycl. Anal. Chem.   DOI 10.1002/9780470027318.a0213m.pub2, John Wiley & Sons, Ltd., online at http://www.mrw.interscience.wiley.com/eac/. PDF

78. Ditzler, M.A., Rueda, D., Mo, J., Hakansson, K., and Walter, N.G. (2008) A rugged free energy landscape separates multiple functional RNA folds throughout denaturation. Nucleic Acids Res. 36, p. 7088-7099. Full text in pdf format. Highlighted in Science and Technology of C&E News on March 1, 2010, see in pdf format. For more highlights, please see “In the News”.

77. Walter, N.G. (2008) Resolving the pivotal role of argonaut proteins in RNAi. Biopolymers 89, p. IV. PDF

76. Furchak, J.R.W., Yang, P., Jennings, C., Walter, N.G., and Kennedy, R.T. (2008) Assay for glucosamine 6-phosphate using a ligand-activated ribozyme with fluorescence resonance energy transfer or CE-laser-induced fluorescence detection. Anal. Chem. 80, p. 8195-8201. PDF

75. Banas, P., Rulisek, L., Hanosova, V., Svozil, D., Walter, N.G., Sponer, J., and Otyepka, M. (2008) General base catalysis for cleavage by the active-site cytosine of the hepatitis delta virus ribozyme: QM/MM calculations establish chemical feasibility. J. Phys. Chem. B 112, p. 11177-11187. PDF

74. Pereira, M.J.B., Nikolova, E.N., Hiley, S.L, Jaikaran, D., Collins, R.A., and Walter, N.G. (2008) Single VS ribozyme molecules reveal dynamic and hierarchical folding toward catalysis. J. Mol. Biol. 382, p. 496-509. PDF.  Supplemental Information.

73. Al-Hashimi, H.M. and Walter, N.G. (2008) RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, p. 321-329. PDF

72. Walter, N.G., Huang, C.-Y., Manzo, A.J., and Sobhy, M.A. (2008) Do-it-yourself guide: How to use the modern single-molecule toolkit. Nat. Methods 5, p. 475-489. PDF. Editorial Comments in Nat. Methods 5, p. 457.

71. Gafni, A. and Walter, N.G. (2008) Program review: The interdisciplinary biophysics graduate program at the University of Michigan. Biopolymers 89, p. 256-261. PDF

2007

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70. Walter, N.G. (2007) Ribozyme catalysis revisited: Is water involved? Mol. Cell 28, p. 923-929. PDF

69. Ditzler, M.A., Aleman, E.A., Rueda, D., and Walter, N.G. (2007) Focus on function: Single molecule RNA enzymology. Biopolymers 87, p. 302-316. PDF

68. Hoerter, J.A.H. and Walter, N.G. (2007) Chemical modification resolves the asymmetry of siRNA strand degradation in human blood serum. RNA 13, p. 1887-1893. PDF

67. Liu, S., Bokinsky, G., Walter, N.G., and Zhuang, X. (2007) Dissecting the multi-step reaction pathway of an RNA enzyme by single-molecule kinetic “fingerprinting”. Proc. Natl. Acad. Sci. USA 104, p. 12634-12639. PDF

66. Tinsley, R.A. and Walter, N.G. (2007) Long-range impact of peripheral joining elements on structure and function of the hepatitis delta virus ribozyme.Biol. Chem. 388, p. 705-715. PDF

65. Bobeck, M.J., Rueda, D., Walter, N.G., and Glick, G.D. (2007) Structural modeling of sequence specificity by an autoantibody against single-stranded DNA Biochemistry 46, p. 6753-6765. PDF

64. Sefcikova, J, Krasovska, M.V., Sponer, J., and Walter, N.G. (2007) The genomic HDV ribozyme utilizes a previously unnoticed U-turn motif to accomplish fast site-specific catalysis. Nucleic Acids Res.  35, p. 1933-1946. PDF

63. Tinsley, R.A., Furchak, J.R.W., and Walter, N.G. (2007) Trans-acting glmS catalytic riboswitch: Locked and loaded. RNA 13, p. 468-477. PDF

62. Sefcikova, J., Krasovska, M.V., Spackova, N., Sponer, J., and Walter, N.G. (2007) Impact of an extruded nucleotide on cleavage activity and dynamic catalytic core conformation of the hepatitis delta virus ribozyme. Biopolymers  85, p. 392-406. PDF

61. McDowell, S.E., Spackova, N., Sponer, J., and Walter, N.G. (2007) Molecular dynamics simulations of RNA: An in silico single molecule approach. Biopolymers  85, p. 169-184. PDF

60. Walter, N.G., Meiners, J-C, Meyhofer, E., Neubig, R.R., Sunahara, R.K., Perkins, N.C., Steel, D.G., and Swanson, J.A. (2007) Under the microscope: Single molecule symposium at the University of Michigan, 2006. Biopolymers  85, p. 106-114. PDF

59. Walter, N.G. (2007) Future of biomedical sciences: Single molecule microscopy. Biopolymers  85, p. 103-105. PDF

2006

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58. Rhodes, M.M., Reblova, K., Sponer, J., and Walter, N.G. (2006) Trapped water molecules are essential to structural dynamics and function of a ribozyme. Proc. Natl. Acad. Sci. USA  103, p. 13381-13385. PDF. Supplement.

57. Krasovska, M.V., Sefcikova, J., Reblova, K., Schneider, B., Walter, N.G., and Sponer, J. (2006) Cations and hydration in catalytic RNA: Molecular dynamics of the hepatitis delta virus ribozyme. Biophys. J.  91, p. 626-638. PDF. Supplement.

56. Gondert, M.E., Tinsley, R.A., Rueda, D., and Walter, N.G. (2006) Catalytic core structure of the trans-acting HDV ribozyme is subtly influenced by sequence variation outside the core. Biochemistry  45, p. 7563-7573. PDF

55. Lambert, M.N., Vocker, E., Blumberg S., Redemann, S., Gajraj, A., Meiners, J., and Walter, N.G. (2006) Mg2+ induced compaction of single RNA molecules monitored by tethered particle microscopy. Biophys. J.  90, p. 3672-3685. PDF

54. Tinsley, R.A. and Walter, N.G. (2006) Pyrrolo-C as a fluorescent probe for monitoring RNA secondary structure formation. RNA  12, p. 522-529. PDF

53. Rueda, D. and Walter, N.G. (2006) Fluorescent energy transfer readout of an aptazyme-based biosensor. Methods in Mol. Biol.  335, p. 289-310. PDF

52. Walter, N.G. (2006) Michaelis-Menten is dead, long live Michaelis-Menten! Nature Chem. Biol.  2, p. 66-67. PDF

2005

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51. Rueda, D. and Walter, N.G. (2005) Single molecule fluorescence control for nanotechnology. J. Nanosci. Nanotechnol.  5, p. 1990-2000. PDF

50. Rueda, D., Hsieh, J., Day-Storms, J.J., Fierke, C.A., and Walter N.G. (2005) The 5′ leader of precursor tRNAAsp bound to the Bacillus subtilis RNase P holoenzyme has an extended conformation. Biochemistry  44, p. 16130-16139. PDF

49. Lambert, M.N., Hoerter, J.A.H., Pereira M.J.B., and Walter, N.G. (2005) Solution probing of metal ion binding by helix 27 from Escherichia coli 16S rRNA. RNA  11, p. 1688-1700. PDF

48. Krasovska, M.V., Sefcikova, J., Spackova, N., Sponer, J., and Walter, N.G. (2005) Structural dynamics of precursor and product of the RNA enzyme from the hepatitis delta virus as revealed by molecular dynamics simulations. J. Mol. Biol.  351, p. 731-748. PDF

47. Harris, D.A. and Walter, N.G. (2005) Terbium(III) footprinting as a probe of RNA structure and metal-binding sites. In:  Handbook of RNA Biochemistry, p. 205-213 (A. Bindereif, R. Hartmann, A. Schön, and E. Westhof, eds.), Wiley-VCH Verlag, Weinheim. PDF

2004

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46. Hoerter, J.A.H., Lambert, M.N., Pereira M.J.B., and Walter, N.G. (2004) Dynamics inherent in helix 27 from Escherichia coli 16S ribosomal RNA.Biochemistry  43, p. 14624-14636. PDF

45. Harris, D.A., Tinsley, R.A., and Walter, N.G. (2004) Terbium-mediated footprinting probes a catalytic conformational switch in the antigenomic hepatitis delta virus ribozyme. J. Mol. Biol.  341, p. 389-403. PDF

44. Tinsley, R.A., Harris, D.A., and Walter, N.G. (2004) Magnesium dependence of the amplified conformational switch in the trans-acting hepatitis delta virus ribozyme. Biochemistry 43, p. 8935-8945. PDF

43. Rueda, D., Bokinsky, G., Rhodes, M.M., Rust, M.J., Zhuang X., and Walter, N.G. (2004) Single-molecule enzymology of RNA: Essential functional groups impact catalysis from a distance. Proc. Natl. Acad. Sci. USA 101, p. 10066-10071. PDF. Supplement.

2003

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42. Uhler, S.A., Cai, D., Man, Y., Figge, C., and Walter, N.G. (2003) RNA degradation in cell extracts: Real-time monitoring by fluorescence resonance energy transfer. J. Am. Chem. Soc. USA 125, p. 14230-14321. PDF. Supplement.

41. Tinsley, R.T., Harris, D.A., and Walter, N.G. (2003) Significant kinetic solvent isotope effects in folding of the catalytic RNA from the hepatitis delta virus. J. Am. Chem. Soc. 125, p. 13972-13973. PDF. Supplement.

40. Rueda, D., Wick, K., McDowell, S.E., and Walter, N.G. (2003) 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, p. 9924-9936. PDF

39. Bokinsky, G., Rueda, D., Misra, V.K., Rhodes, M.M., Gordus, A., Babcock, H.P., Walter, N.G., and Zhuang, X. (2003) Single-molecule transition-state analysis of RNA folding. Proc. Natl. Acad. Sci. USA 100, p. 9302-9307. PDF. Highlighted in Science Concentrates of C&E News on July 21, 2003, see in PDF format. For more highlights please see “In The News

38. Harris, D.A., and Walter, N.G. (2003) Probing RNA structure and metal-binding sites using terbium(III) footprinting. Curr. Protocols in Nucleic Acid Chem. Chapter 6.8 pp. 6.8.1-6.8.8. PDF

37. Jeong, S., Sefcikova, J., Tinsley, R.A., Rueda, D., and Walter, N.G. (2003) Trans-acting hepatitis delta virus ribozyme: Catalytic core and gobal structure are dependent on the 5′ substrate sequence. Biochemistry 42, p. 7727-7740. PDF

36. Walter, N.G. (2003) Probing RNA structural dynamics and function by fluorescence resonance energy transfer. Curr. Protocols Nucleic Acid Chem. Chapter 11.10, pp. 11.10.1-11.10.23. PDF

2002

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35. Walter, N.G., and Engelke, D.R. (2002) Ribozymes: Catalytic RNAs that cut things, make things, and do odd and useful jobs. The Biologist 49, p. 199-203. PDF

34. Sekella, P.T, Rueda, D., and Walter, N.G. (2002) A biosensor for theophylline based on fluorescence detection of ligand-induced hammerhead ribozyme cleavage. RNA 8, p. 1242-1252. PDF

33. Harris, D.A., Rueda, D., and Walter, N.G. (2002) Local conformational changes in the catalytic core of the trans-acting hepatitis delta virus ribozyme accompany catalysis. Biochemistry 41, p. 12051-12061. PDF

32. Zhuang, X., Kim, H., Pereira, M.J.B., Babcock, H.P., Walter, N.G., and Chu, S. (2002) Correlating structural dynamics and function in single ribozyme molecules. Science 296, p. 1473-1476. PDF. Supplement.

31. Walter, N.G., Harris, D.A., Pereira, M.J.B., and Rueda, D. (2002) In the fluorescent spotlight: global and local conformational changes of small catalytic RNAs. Biopolymers 61, p. 224-241. PDF

30. Pereira, M.J.B., Harris, D.A., Rueda, D., and Walter, N.G. (2002) Reaction pathway of the trans-acting hepatitis delta virus ribozyme: A conformational change accompanies catalysis. Biochemistry 41, p. 730-740. PDF

2001

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29. Walter, N.G. (2001) Structural dynamics of catalytic RNA highlighted by fluorescence resonance energy transfer. Methods 25, p. 19-30. PDF

28. Todorov, T.I., Carmejane, O., Walter, N.G., and Morris, M.D. (2001) Capillary electrophoresis of RNA in dilute and semi-dilute polymer solutions.Electrophoresis 22,p. 2442-2447. PDF

27. Michael J. Fay, Walter, N.G., and Burke, J.M. (2001) Imaging of single hairpin ribozymes in solution by atomic force microscopy. RNA 7, p. 887-895. PDF

26. Walter, N.G., Chan, P.A., Hampel, K.J., Millar, D.P., and Burke, J.M. (2001) A base change in the catalytic core of the hairpin ribozyme perturbs function but not domain docking. Biochemistry 40, p. 2580-2587. PDF

25. Pinard, R., Lambert, D., Heckman, J.E., Esteban, J.A., Gundlach, C.W., Hampel, K.J., Heckman, J.E., Glick, G.D., Walter, N.G., Major, F., and Burke, J.M. (2001) The hairpin ribozyme substrate binding-domain: A highly constrained D-shaped conformation. J. Mol. Biol. 307, p. 51-65. PDF

2000

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24. Walter, N.G., Yang, N., and Burke, J.M. (2000) Probing non-selective cation binding in the hairpin ribozyme with Tb(III). J. Mol. Biol. 298, p. 539-555. PDF

23. Walter, N.G., and Burke, J.M. (2000) Fluorescence assays to study structure, dynamics, and function in RNA and RNA-ligand complexes. Methods Enzymol. 317, p. 409-440. PDF

1999

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22. Pinard, R., Lambert, D., Walter, N.G., Heckman, J.E., Major, F., and Burke, J.M. (1999) Structural basis for the guanosine requirement of the hairpin ribozyme. Biochemistry 38, p. 16035-16039. PDF

21. Porschke, D., Burke, J.M., and Walter, N.G. (1999) Global structure and flexibility of hairpin ribozymes with extended terminal helices. J. Mol. Biol. 289, p.799-813. PDF

20. Walter, N.G., Burke, J.M., and Millar, D.P. (1999) Stability of hairpin ribozyme tertiary structure is governed by the interdomain junction. Nat. Struct. Biol. 6, p. 544-549. PDF

1998

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19. Ederhof, T., Walter, N.G., and Schober A. (1998) On-line polymerase chain reaction (PCR) monitoring. J. Biochem. Biophys. Meth. 37, p.99-104. PDF

18. Hampel, K.J., Walter, N.G., and Burke, J.M. (1998) The solvent-protected core of the hairpin ribozyme-substrate complex. Biochemistry 37, p.14672-14682. PDF

17. Murray, J.B., Seyhan, A.A., Walter, N.G., Burke, J.M., and Scott, W.G. (1998) The hammerhead, hairpin and VS ribozymes are catalytically proficient in monovalent cations alone. Chem. Biol. 5, p. 587-595. PDF

16. Esteban, J.A., Walter, N.G., Kotzorek, G., Heckman, J.E., and Burke, J.M. (1998) Structural basis for heterogeneous kinetics: Reengineering the hairpin ribozyme. Proc. Natl. Acad. Sci. USA 95, p.6091-6095. PDF

15. Walter, N.G., Hampel, K.J., Brown, K.M., and Burke, J.M. (1998) Tertiary structure formation in the hairpin ribozyme monitored by fluorescence resonance energy transfer. EMBO J. 17, p. 2378-2391. PDF

14. Walter, N.G. and Burke, J.M. (1998) The hairpin ribozyme: structure, assembly and catalysis. Curr. Opin. Chem. Biol. 2, p. 24-30. PDF

1997

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13. Preuss, R., Dapprich, J., and Walter, N.G. (1997) Probing RNA-protein interactions using pyrene-labeled oligodeoxynucleotides: Qb replicase efficiently binds replicable RNAs by recognizing pyrimidine residues. J. Mol. Biol. 273, p.600-613. PDF

12. Walter, N.G., Albinson, E., and Burke, J.M. (1997) Probing structure formation in the hairpin ribozyme using fluorescent substrate analogs. Nucleic Acids Symp. Ser. 36, p. 175-177.

11. Dapprich, J., Walter, N.G., Salingue, F., and Staerk, H. (1997) Base-dependent pyrene fluorescence used for in-solution detection of nucleic acids. In Proceedings of the 4th International Conference on Methods and Applications of Fluorescence Spectroscopy (D. Birch and J. Miller, eds.). J. Fluorescence 7, p. 87S-89S.

10. Walter, N.G., and Burke, J.M. (1997) Real-time monitoring of hairpin ribozyme kinetics through base-specific quenching of fluorescein-labeled substrates. RNA 3, p. 392-404. PDF

1996

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9. Walter, N.G., Schwille, P., and Eigen, M. (1996) Fluorescence correlation analysis of probe diffusion simplifies quantitative pathogen detection by PCR.Proc. Natl. Acad. Sci. USA 93, p. 12805-12810. PDF

8. Schwille, P., Oehlenschlaeger, F., and Walter, N.G. (1996) Quantitative hybridization kinetics of DNA probes to RNA in solution followed by diffusional fluorescence correlation spectroscopy. Biochemistry 35, p.10182-10193. PDF

1995

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7. Walter, N.G. (1995) 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. J. Mol. Biol.  254, p. 856-868. PDF

6. Walter, N. (1995) Untersuchung molekularer in vitro-Evolution mit Hilfe nicht-radioaktiver Detektion von Nukleinsaeuren. Cuvillier Verlag, Goettingen. 

5. Schober, A., Walter, N.G., Tangen, U., Strunk, G., Ederhof, T., Dapprich J., and Eigen, M. (1995) A multichannel PCR and serial transfer machine as a future tool in evolutionary biotechnology. Biotechniques 18, p.652-660. PDF

1994

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4. Walter, N.G., and Steiner, C. (1994) Screening for polymerase activities by fast quantification of chemiluminescent dot blot membranes using a filter adapter in a photon counting microplate luminometer. In Bioluminescence and Chemiluminescence: Fundamentals and Applied Aspects. (A. Campbell, L. Kricka and P. Stanley, eds.), John Wiley & Sons, Chichester pp. 83-86. PDF

3. Walter, N.G., and Strunk, G. (1994) Strand displacement amplification as an in vitro model for rolling-circle replication: Deletion formation and evolution during serial transfer. Proc. Natl. Acad. Sci. USA 91, p.7937-7941. PDF

2. Walter, N.G., and Steiner, C. (1994) Fast quantification of chemiluminescent dot blot membranes using a filter adapter in a microplate luminometer: Application to polymerase activity assays. J. Biolum. Chemilum. 9, 302.

1993

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1. Walter, N., and Steiner, C. (1993) Fast chemiluminescent measurement of T7 RNA polymerase activity based on photon counting technology. Biotechniques 12, p.926-931. PDF

Copyright Notes:
Biochemistry
JACS
Science
Nature
Proc. Natl. Acad. Sci USA
J. Mol. Biol.