Department of Chemistry

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2012 - 20203

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Author: search.filters.author.Patra, SatyajitSubject: search.filters.subject.Molecules

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    Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides
    (ACS, 2020-03) Patra, Satyajit
    Zero-mode waveguide (ZMW) nano-apertures milled in metal films were proposed to improve the Förster resonance energy transfer (FRET) efficiency and enable single-molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in a homogeneous medium. However, the earlier ZMW demonstrations were limited to the Atto 550–Atto 647N fluorophore pair, asking the question whether the FRET enhancement observation was an artifact related to this specific set of fluorescent dyes. Here, we use Alexa Fluor 546 and Alexa Fluor 647 to investigate single-molecule FRET at large donor–acceptor separations exceeding 10 nm inside ZMWs. These Alexa fluorescent dyes feature a markedly different chemical structure, surface charge, and hydrophobicity as compared to their Atto counterparts. Our single molecule data on Alexa 546–Alexa 647 demonstrate enhanced FRET efficiencies at large separations exceeding 10 nm, extending the spatial range available for FRET and confirming the earlier conclusions. By showing that the FRET enhancement inside a ZMW does not depend on the set of fluorescent dyes, this report is an important step to establish the relevance of ZMWs to extend the sensitivity and detection range of FRET, while preserving its ability to work on regular fluorescent dye pairs.
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    Deep Ultraviolet Plasmonic Enhancement of Single Protein Autofluorescence in Zero-Mode Waveguides
    (ACS, 2019-09) Patra, Satyajit
    Single molecule detection provides detailed information about molecular structures and functions but it generally requires the presence of a fluorescent marker which can interfere with the activity of the target molecule or complicate the sample production. Detecting a single protein with its natural UV autofluorescence is an attractive approach to avoid all the issues related to fluorescence labeling. However, the UV autofluorescence signal from a single protein is generally extremely weak. Here, we use aluminum plasmonics to enhance the tryptophan autofluorescence emission of single proteins in the UV range. Zero-mode waveguide nanoapertures enable the observation of the UV fluorescence of single label-free β-galactosidase proteins with increased brightness, microsecond transit times, and operation at micromolar concentrations. We demonstrate quantitative measurements of the local concentration, diffusion coefficient, and hydrodynamic radius of the label-free protein over a broad range of zero-mode waveguide diameters. Although the plasmonic fluorescence enhancement has generated a tremendous interest in the visible and near-infrared parts of the spectrum, this work pushes further the limits of plasmonic-enhanced single molecule detection into the UV range and constitutes a major step forward in our ability to interrogate single proteins in their native state at physiological concentrations.
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    Microheterogeneity of Some Imidazolium Ionic Liquids As Revealed by Fluorescence Correlation Spectroscopy and Lifetime Studies
    (ACS, 2012-10) Patra, Satyajit
    The microscopic structure and dynamics of the room temperature ionic liquids (RTILs) that are responsible for some of the peculiar properties of this class of solvents continue to intrigue the researchers and stimulate new investigations. Herein, we use the fluorescence correlation spectroscopy (FCS) technique to study the diffusion of some probe molecules in RTILs, the results of which, when combined with those obtained from fluorescence lifetime studies, provide insights into the microscopic structural details of this class of novel solvents. Experiments performed with three charged and neutral probe molecules in five carefully selected 1-alkyl-3-methylimidazolium ionic liquids reveal that unlike in conventional solvents these probes exhibit a bimodal diffusion behavior in RTILs thus indicating the presence of two distinct environments. It is found that the contribution of the slow component of the diffusion increases with increasing alkyl chain length of the cation. Not only are these results supported by the biexponential decay behavior of the fluorescence intensity of the systems, but the individual values of the lifetime components and their weight allow determination of the nature of the two major environments. In essence, the results point to the potential of the two combined techniques in unraveling some of the complex features of the ionic liquids.