Publications

If you want to download a pdf file, please review the copyright notes of the respective journal.

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



2014:
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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. Nature Nanotechnology 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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. 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. Full text in pdf format.

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. Full text in pdf format. Supplementary Information in pdf format.

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. Full text in pdf format. Supplementary Information in pdf format.

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. Full text in pdf format.

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

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplementary Information in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplementary Information in pdf format.

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. Full text in pdf format. Supplementary Information in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Full supplement in pdf format. Listed under "top downloads" on the EMBO reports website.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format.

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. Full text in pdf format. Supplement in pdf format.

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. Full text in pdf format.

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

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. subtilis RNase P-pre-tRNA complex: A role for an inner-sphere metal ion in RNase P. J. Mol. Biol. 400, p. 38-51. Full text in pdf format.

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. Full text in pdf format.

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

90. Walter, N.G. (2010) Preface. Methods Enzymol. 472, p. xxi-xxii. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format. See reference on the cover. Highlighted in Nature News and Views. For more highlights, please see "In the News" link on the left.

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. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on March 21, 2010. See also Science and Technology of C&E News on March 21, 2011. For more highlights, please see "In The News" link on your left.

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.Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. 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. Full text in pdf format.

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. Full text in pdf format.

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/. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format.

73. Al-Hashimi, H.M. and Walter, N.G. (2008) RNA dynamics: it is about time. Curr. Opin. Struct. Biol. 18, p. 321-329. Full text in pdf format. Editorial comments in Curr. Opin. Struct. Biol. 18, p. 279-281.

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. Full text in pdf format. 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. Full text in pdf format.

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

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

59. Walter, N.G. (2007) Future of biomedical sciences: Single molecule microscopy. Biopolymers  85, p. 103-105. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on August 21, 2006. For more highlights please see "In The News" link on your left.

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. Full text in pdf format. Supplement in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Sch?n, and E. Westhof, eds.), Wiley-VCH Verlag, Weinheim. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format. Highlighted as UM News Release on June 29, 2004. For more highlights please see "In The News" link on your left.

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. Full text in pdf format. Supplement in pdf format.

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. USA 125, p. 13972-13973. Full text in pdf format. Supplement in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Highlighted in Science Concentrates of C&E News on July 21, 2003, see in pdf format. For more highlights please see "In The News" link on your left.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format. Supplement in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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. Full text in pdf format.

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 15, p. 926-931. Full text in pdf format.



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Biochemistry
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Nature
Proc. Natl. Acad. Sci USA
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