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Publication List
1) Mukhopadhyay, S., Deniz, A.A. “Fluorescence from diffusing single molecules illuminates biomolecular
structure and dynamics ”
Online,
Journal of Fluorescence, 2007.
2) Deniz,
A.A., Mukhopadhyay, S., Lemke, E.L. “Single-molecule biophysics: at the
interface of biology, physics and chemistry” J.
Royal Soc. Interface, online.
3) Ferreon,
A.C.M., Deniz, A.A. “a-Synuclein
Multi-State Folding Thermodynamics: Implications for Protein Misfolding and
Aggregation”. Biochemistry,
2007, 46: 4499.
4)
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 (pdf).
5) Tian,
F., Debler, E.W., Millar, D.P., Deniz, A.A., Wilson I.A., Schultz, P.G. “The Effects of Antibodies on
Stilbene Excited-State Energetics”. Angewandte Chemie, 2006, 46:7927.
6)
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: 7682-7687 (pdf).
7) Zhu, P,
Clamme, J-P, Deniz, AA "Fluorescence quenching by TEMPO: a sub-30
Å single molecule ruler" Biophysical Journal, 2005, 89:L37-L39.
8)
Berezhna, S, Schaefer, S, Heintzmann, R, Jahnz, M, Boese, G, Deniz, A,
Schwille, P "New Effects in polynucleotide release from cationic
lipid carriers revealed by confocal imaging, fluorescence correlation
spectroscopy and single particle tracking" Biochimica et Biophysica
Acta 2005, 1669:193.
9) Clamme,
J-P, Deniz, AA “Three-color single-molecule fluorescence resonance
energy transfer” ChemPhysChem, published
online Dec. 13, 2004.
10)
Pljevaljcic, G, Millar, DP, Deniz, AA. “Freely-diffusing single hairpin
ribozymes provide insights into the role of secondary structure and partially
folded states in RNA folding” Biophysical Journal 2004, 87:457.
11) Wang,
L, Xie, J, Deniz, AA, Schultz, PG “Unnatural Amino-Acid Mutagenesis of
Green Fluorescent Protein” J. Org. Chem. 2003, 68:174.
12) Deniz AA, Laurence TA, Dahan M, Chemla DS, Schultz PG,
Weiss S. "Ratiometric single molecule studies of freely diffusing
biomolecules." Annu. Rev. Phys. Chem. 2001, 52:233.
13)
Grunwell JR, Glass JL, Lacoste TD, Deniz AA, Chemla DS, Schultz PG.
"Monitoring the Conformational Fluctuations of DNA Hairpins Using
Single-Pair Fluorescence Resonance Energy Transfer." J. Am. Chem. Soc.
2001, 123:4295.
14) Deniz
AA, Laurence T, Beligere GS, Dahan M, Martin AB, Chemla DS, Dawson PE, Schultz
PG, Weiss S. "Single molecule protein folding: Diffusion Fluorescence
energy transfer studies of the denaturation of Chymotrysin Inhibitor 2."
Proc. Natl. Acad. Sci., USA 2000, 97:5179.
15) Deniz
AA, Dahan M, Grunwell JR, Ha TJ, Faulhaber AE, Chemla DS, Weiss S, Schultz PG.
"Single-pair FRET on freely diffusing molecules: Observation of
Förster distance dependence and subpopulations" Proc. Natl. Acad.
Sci., USA 1999, 96:3670.
16) Dahan
M, Deniz AA, Ha TJ, Chemla DS, Schultz PG, Weiss S. "Ratiometric
measurement and identification of single diffusing molecules." Chemical
Physics, 1999, 247:85.
17) Ha T, Ting AY, Liang
J, Caldwell WB, Deniz AA, Chemla DS, Schultz PG, Weiss S. "Single-molecule
fluorescence spectroscopy of enzyme conformational dynamics and cleavage
mechanism." Proc. Natl. Acad. Sci., USA 1999, 96:893.
18) Ha TJ, Ting AY, Liang
J, Deniz AA, Chemla DS, Schultz PG, Weiss S. "Temporal fluctuations of
fluorescence resonance energy transfer between two dyes conjugated to a single
protein." Chemical Physics, 1999, 247:107.
19) Deniz AA, Peters KS,
Snyder GJ. "Experimental determination of the Antiaromaticity of
Cyclobutadiene" Science, 1999, 286:1119.
20) Lipson M, Deniz AA,
Peters KS "The sub-picosecond dynamics of diphenylmethylchloride ion pairs
and radical pairs." Chem. Phys. Lett. 1998, 288:781.
21) Lipson M, Deniz AA,
Peters KS "Nature of the Potential Energy Surfaces for the SN1 reaction :
A Picosecond Kinetic Study of Photoinduced Homolysis and Heterolysis for
Diphenylmethylchlorides" J. Am. Chem. Soc., 1996, 118:2992.
22) Lipson M, Deniz AA,
Peters KS "Picosecond Kinetic Study of the Dynamics for Photoinduced
Homolysis and Heterolysis of Diphenylmethylchlorides" J. Phys. Chem.,
1996, 100:3580.
23) Deniz AA, Li B, Peters
KS "Role of polarization caging in the SN1 reaction of diphenylmethyl
chloride - A Picosecond Kinetic Study" J. Phys. Chem., 1995, 99:12209.
Last modified August 16, 2007. Please e-mail
comments/corrections to Deniz Lab Webpage
Administrator.