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Deniz Lab Single Molecule Biophysics

Selected Publications

Pubmed search for Deniz Lab publications.

Ferreon, A.C.M., Ferreon, J.C., Wright, P.E., Deniz, A.A. “Modulation of Allostery by Protein Intrinsic DisorderNature, 2013, 498:390. (Featured/Highlighted in Nature News and Views)

Gambin, Y., Vandelinder, V., Ferreon, A.C.M., Lemke, E.L., Groisman, A., Deniz, A.A. "Visualizing a one-way protein encounter complex by ultrafast single-molecule mixing” Nature Methods, 2011, 8:239. (Featured/Highlighted in TSRI News and Views, Nature Methods News and Views, Physics Today, ACS Chemical Biology, PSI-Nature Structural Biology Knowledgebase, Genetic Engineering and Biotechnology, Chemistry and Industry)

Tyagi N.K., Fenton W.A., Deniz A.A., Horwich A.L. “Double mutant MBP refolds at same rate in free solution as inside the GroEL/GroES chaperonin chamber when aggregation in free solution is prevented” FEBS Lett. 2011, 585:1969.

Ferreon, A.C.M., Deniz, A.A. “Protein folding at single molecule resolution” BBA Proteins and Proteomics, 2011, 1814:1021. (Part of Special issue on protein dynamics. Issue Cover Figure from our review)

Ferreon, A.C.M., Moran, C.R., Ferreon, J.C., Deniz A.A. “Alteration of the α-synuclein Folding Landscape by a Mutation Related to Parkinson’s Disease” Angew. Chem. Int. Ed. Eng., 2010, 49:3469. (Highlighted as a Very Important Paper (VIP) by Angewandte Chemie)

Ferreon, A.C.M., Moran, C.R., Gambin, Y., Deniz, A.A. “Single-molecule fluorescence studies of intrinsically disordered proteins”, Methods in Enzymology, 2010, 472:179

Gambin, Y., Simonnet, C., VanDelinder, V., Deniz, A.A., Groisman, A. “Ultrafast microfluidic mixer with three-dimensional flow focusing for studies of biochemical kinetics” Lab on a Chip, 2010, 10:598.

Gambin, Y., Deniz, A.A. “Multicolor single-molecule FRET to explore protein folding and binding” Molecular BioSystems, 2010, 6:1540. (Part of an Emerging Investigators Issue on work at the Chemical and Systems Biology Interfaces)

Gambin, Y., Schug, A., Lemke, E.A., Lavinder, J.J., Ferreon, A.C., Magliery, T.J., Onuchic, J.N., Deniz, A.A. “Direct single-molecule observation of a protein living in two opposed native structures.” Proc. Natl. Acad. Sci. USA. 2009, 106:10153. (Featured on TSRI News and Views; Among Top 10 most-viewed articles on the Faculty of 1000 Biology, Oct. 2009)

Lemke, E.A., Gambin, Y., Vandelinder, V., Brustad, E.M., Liu, H-W., Schultz, P.G., Groisman, A. and Deniz, A.A. “Microfluidic device for Single-Molecule Fluorescence Experiments with high Photostability.” J. Amer. Chem. Soc.2009, 131:13610. (Highlighted in Lab on a Chip)

Ferreon, A., Gambin, Y., Lemke, E.L., Deniz, A.A. “Interplay of α-synuclein binding and conformational switching probed by single molecule fluorescence.” Proc. Natl. Acad. Sci. USA. 2009, 106:5645. (Featured on TSRI News and Views, on the NIGMS/NIH website under Featured Areas/Single Molecule Detection & Manipulation, and mentioned as recent paper of interest in the May 2009 Biophysical Society Newsletter)

Vandelinder, V., Ferreon, A.C.M., Gambin, Y., Deniz, A.A., Goisman, A. “ High-Resolution temperature-concentration diagram of α-synuclein conformation obtained from a single Förster Resonance Energy transfer image in a microfluidic device.” Analytical Chemistry, 2009, 81:6929.

Berezhna SY, Supekova L, Sever MJ, Schultz PG, Deniz A.A. “Dual regulation of hepatitis C viral RNA by cellular RNAi requires partitioning of Ago2 to lipid droplets and P-bodies” RNA, 2011, 17:1831.

Brustad, E.M., Lemke, E.A., Schultz, P.G., Deniz, A.A. “ A General and Efficient Method for the Site-Specific Dual-Labeling of Proteins for Single Molecule Fluorescence Resonance Energy Transfer” Journal of the American Chemical Society, 2008, 130:17664.

Wang, H., Duennwald, M.L., Roberts, B.E., Rozeboom, L.M., Zhang, Y.L., Steele, A.D., Krishnan, R., Su, L.J., Griffin, D., Mukhopadhyay, S., Hennessy, E.J., Weigele, P., Blanchard, B.J., King, J., Deniz, A.A., Buchwald, S.L., Ingram, V.M., Lindquist, S., and Shorter, J. “ Direct and Selective Elimination of Specific Prions and Amyloids by 4,5-Dianilinophthalimide and Analogs.” Proc. Natl. Acad. Sci. USA. 2008, 105:7159.

Mukhopadhyay, S., Krishnan, R., Lemke, E.L., Lindquist, S., Deniz, A.A. “A natively unfolded yeast prion monomer adopts an ensemble of compact and fluctuating structures”. Proc. Natl. Acad. Sci. USA 2007, 104:2649. (Featured on TSRI News and Views)

Deniz, A.A., Lemke, E.L., Mukhopadhyay, S. “Single-Molecule Biophysics: At the Interface of Biology, Physics and Chemistry” J. Royal Soc. Interface, 2008, 5:15. (Remains among most-read articles at the JRSI website).

Ferreon, A.C.M., Deniz, A.A. “a-Synuclein Multi-State Folding Thermodynamics: Implications for Protein Misfolding and Aggregation”. Biochemistry 2007, 46:4499.

Mukhopadhyay, S., Deniz, A. A. “Fluorescence from diffusing single molecules illuminates biomolecular structure and dynamics” J. Fluorescence 2007, 17:775.

Berezhna, S.Y., Supekova, L., Supek, F., Schultz, P.G., Deniz, A.A. “siRNA in human cells selectively localizes to target RNA sites”Proc. Natl. Acad. Sci., USA, 2006, 103: 7682.

Zhu, P., Clamme, J-P., Deniz, A.A. "Fluorescence quenching by TEMPO: a sub-30 Å single molecule ruler" Biophysical Journal 2005, 89:L37.

Clamme, J-P., Deniz, A.A. “Three-Color Single-Molecule Fluorescence Resonance Energy transfer” ChemPhysChem 2005, 6:74.

Pljevaljcic, G., Millar, D.P., Deniz, A.A. “Freely diffusing single hairpin ribozymes provide insights into the role of secondary structure and unfolded states in RNA folding” Biophys. J. 2004, 87:457-467.

Deniz, A.A., Laurence, T.A., Dahan, M., Chemla, D.S., Schultz, P.G. and Weiss S. “Ratiometric single molecule studies of freely diffusing biomolecules.” Annu. Rev. Phys. Chem. 2001, 52:233.

Deniz, A.A., Laurence, T., Beligere, G.S., Dahan, M., Martin, A.B., Chemla, D.S., Dawson, P.E., Schultz, P.G. and Weiss, S. “Single molecule protein folding: Diffusion Fluorescence energy transfer studies of the denaturation of Chymotrysin Inhibitor 2.” Proc. Natl. Acad. Sci. 2000, 97:5179.

Deniz, A.A., Dahan, M., Grunwell, J.R., Ha, T.J., Faulhaber, A.E., Chemla, D.S., Weiss, S. and Schultz, P,G. “Single-pair FRET on freely diffusing molecules: Observation of Förster distance dependence and subpopulations” Proc. Natl. Acad. Sci. 1999, 96:3670.

Ha, T., Ting, A.Y., Liang, J., Caldwell, W.B., Deniz, A.A., Chemla, D.S., Schultz, P.G., Weiss, S. "Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism." Proc. Natl. Acad. Sci., USA 1999, 96:893.

Deniz, A.A., Peters, K.S. and Snyder, GJ. “Experimental determination of the Antiaromaticity of Cyclobutadiene” Science, 1999, 286:1119. PMID: 10550042

Lipson, M., Deniz, A.A., Peters, K.S. "The sub-picosecond dynamics of diphenylmethylchloride ion pairs and radical pairs." Chem. Phys. Lett. 1998, 288:781.

Deniz, A.A., Li, B., Peters, K.S. “Role of polarization caging in the SN1 reaction of diphenylmethyl chloride - A Picosecond Kinetic Study” J. Phys. Chem., 1995, 99:12209.