Demystifying PIFE: The Photophysics Behind the Protein-Induced Fluorescence Enhancement Phenomenon in Cy3.

Protein-induced fluorescence enhancement (PIFE) is a term used to describe the increase in fluorescence intensity observed when a protein binds to a nucleic acid in the proximity of a fluorescent probe. PIFE using the single-molecule dye Cy3 is gaining popularity as an approach to investigate the dynamics of proteins that interact with nucleic acids. In this work, we used complexes of DNA and Klenow fragment and a combination of time-resolved fluorescence and transient spectroscopy techniques to elucidate the photophysical mechanism that leads to protein-enhanced fluorescence emission of Cy3 when in close proximity to a protein (PIFE).

Thermodynamics and mechanism of protonated cysteine decomposition: a guided ion beam and computational study.

A quantitative molecular description of the decomposition of protonated cysteine, H(+)Cys, is provided by studying the kinetic energy dependence of threshold collision-induced dissociation (CID) with Xe using a guided ion beam tandem mass spectrometer (GIBMS). Primary dissociation channels are deamidation (yielding both NH3 loss and NH4(+) formation) and (H2O + CO) loss reactions, followed by an additional six subsequent decompositions. Analysis of the kinetic energy-dependent CID cross sections provides the 0 K barriers for six different reactions after accounting for unimolecular decay rates, internal energy of reactant ions, multiple ion-molecule collisions, and competition among the decay channels.

Photophysical and dynamical properties of doubly linked Cy3-DNA constructs.

Photophysical measurements are reported for Cy3-DNA constructs in which both Cy3 nitrogen atoms are attached to the DNA backbone by short linkers. While this linking was thought to rigidify the orientation of the dye and hinder cis-isomerization, the relatively low fluorescence quantum yield and the presence of a short component in the time-resolved fluorescence decay of the dye indicated that cis-isomerization remained possible. Fluorescence correlation spectroscopy and transient absorption experiments showed that photoisomerization occurred with high efficiency.

Photophysical processes in single molecule organic fluorescent probes.

The use of organic fluorescent probes in biochemical and biophysical applications of single molecule spectroscopy and fluorescence microscopy techniques continues to increase. As single molecule measurements become more quantitative and new developments in super-resolution imaging allow researchers to image biological materials with unprecedented resolution, it is becoming increasingly important to understand how the properties of the probes influence the signals measured in these experiments. In this review, we focus on the photochemical and photophysical processes of organic fluorophores that affect the properties of fluorescence emission.

Photobleaching and blinking of TAMRA induced by Mn(2+).

Blinking and bleaching: Coordination of Mn(2+) to DNA induces intersystem crossing, causing fluctuations in the fluorescence intensity and accelerated photobleaching.

pH-dependent spectral properties of para-aminobenzoic acid and its derivatives.

The local environment dictates the structural and functional properties of many important chemical and biological systems. The impact of pH on the photophysical properties of a series of para-aminobenzoic acids is examined using a combination of experimental spectroscopy and quantum chemical calculations. Following photoexcitation, PABA derivatives may undergo an intramolecular charge transfer (ICT) resulting in the formation of a zwitterionic species.

An experimental and theoretical study of alkali metal cation interactions with cysteine.

The interactions of alkali metal cations (M(+) = Li(+), Na(+), K(+), Rb(+)) with the amino acid cysteine (Cys) are examined in detail. Experimentally, bond energies are determined using threshold collision-induced dissociation of the M(+)(Cys) complexes with xenon in a guided ion beam mass spectrometer. Analyses of the energy dependent cross sections provide 0 K bond energies of 2.