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Human flap endonuclease 1 (FEN1) and related structure-specific 5'nucleases precisely identify and incise aberrant DNA structures during replication, repair and recombination to avoid genomic instability. Yet, it is unclear how the 5'nuclease mechanisms of DNA distortion and protein ordering robustly mediate efficient and accurate substrate recognition and catalytic selectivity. Here, single-molecule sub-millisecond and millisecond analyses of FEN1 reveal a protein-DNA induced-fit mechanism that efficiently verifies substrate and suppresses off-target cleavage. FEN1 sculpts DNA with diffusion-limited kinetics to test DNA substrate. This DNA distortion mutually 'locks' protein and DNA conformation and enables substrate verification with extreme precision. Strikingly, FEN1 never misses cleavage of its cognate substrate while blocking probable formation of catalytically competent interactions with noncognate substrates and fostering their pre-incision dissociation. These findings establish FEN1 has practically perfect precision and that separate control of induced-fit substrate recognition sets up the catalytic selectivity of the nuclease active site for genome stability.

Understanding the dynamic behavior of polymeric fluids in porous media is essential for vast geoscience applications, particularly enhanced oil recovery and polymer-enhanced soil washing, to clean up soil contamination. During the past decades, the behavior of polymeric fluids in microscopic space has only been investigated using ensemble-averaged experimental methods in which a bulk phase behavior of the fluids characterizes flow mechanisms. Multiple flow mechanisms have been proposed based on ensemble-averaged data; however, microscale characterization of the interactions between polymers and solid surfaces and the mechanisms governing polymer retention and permeability reduction as well as the reversibility of polymer retention are lacking, resulting in a limited understanding of the flow mechanisms. Here we report direct visualization and multi-scale characterization of the dynamic behavior of polymer molecules in a representative porous medium by integrating microfluidics with single-molecule imaging. We demonstrate that the polymers' adsorption, entrapment and hydrodynamic retention contribute to their overall retention in porous media. Our study illustrates how microfluidics can help in understanding the dynamic behavior of polymers, their interactions with the solid/fluid interface and their effects on flow properties. Additionally, it demonstrates the role of microfluidic platforms in providing a more representative and accurate model for polymer retention and permeability reduction in porous media. The obtained insights encourage the development of improved models that better capture the behavior of complex fluids in confined environments and have significant implications for a wide range of applications in geoscience, materials science, and rheology. [ABSTRACT FROM AUTHOR]

Experimental and theoretical techniques were combined to investigate the behavior and dynamics of a polymer-dye molecule system. Findings revealed that single molecule spectroscopy, an experimental technique proves to be a method of choice to investigate the various conformations of a dye molecule and their interactions with the surrounding polymer matrix.

Single-molecule fluorescence spectroscopy is performed on a number of multi-peryleneimide substituted polyphenylene dendrimers for the purpose of investigating the parameters, which influence the efficiency of the dendrimers as single-photon sources at room temperature. Analysis of fluorescence intensity, lifetime, and interphoton arrival time distribution revealed that all measured first-generation dendrimers behave as single-photon emitters.

The photophysical properties of a new water-soluble fluorescent dye are investigated. Hydrophilic substituents in the bay region are attached for this purpose.

The directional Forster resonance energy transfer (FRET) process that takes place in single molecules of a first (T1P4) and a second (T2P8) generation of a perylenemonoimide (P)-terrylenediimide (T)-based dendrimer in which the chromophores are separated by rigid polyphenylene arms is studied using a single-molecule spectroscopy. Simultaneous emission from donor and acceptor chromophore is observed when high excitation powers are applied on either single T1P4 or T1P8 molecules.

Dynamic fluorescence anisotropy of Sulforhodamine 101 (SR101) and excitation energy transfer from SR101 to Acid Blue 1 (AB1) at water/carbon tetrachloride (C[Cl.sub.4]) and water/1,2-dichloroethane (DCE) interfaces were studied by using time-resolved total-internal-reflection (TIR) fluorometry. A magic-angle dependence of the TIR fluorescence dynamic anisotropy revealed that rotational reorientation of SR101 at the water/C[Cl.sub.4] interface was restricted in the two-dimensional plane of the interface, while that at the water/DCE interface took place rather freely, similar to reorientation in an isotropic medium. Furthermore, the structural dimension derived from the excitation energy transfer dynamics measurements at the water/C[Cl.sub.4] or water/DCE interface was 1.93 or 2.48, respectively. These results indicated that the water/C[Cl.sub.4] interface was sharp with respect to the molecular size of SR101 ([approximately] 10 [Angstrom]), while the water/DCE interface was relatively rough compared to the water/C[Cl.sub.4] interface. Structural dimension analysis of excitation energy transfer dynamics between dye molecules adsorbed on the water/oil interface measured under the TIR conditions was shown to be a potential means to estimate roughness/thickness of the interface at a molecular level. The present results were also compared with those predicted from molecular dynamics simulations.

The fluorescence dynamics of Rhodamine B (RhB) and excitation energy transfer from RhB to Malachite Green (MG) in cation-exchange resin particles were studied with special reference to elucidating effects of the cross-linking density of the resin on the fluorescence dynamics. In the cation-exchange resin, the fluorescence lifetime and rotational relaxation time of RhB were very slow compared to those determined in an aqueous solution, suggesting strong binding of the dye to the ion-exchange group of the resin. Therefore, the spatial distribution characteristics of the dye in the resin particle was used as a measure for that of the ion-exchange group. The apparent structural dimension determined by the fractal dimension analysis of energy-transfer quenching of RhB by MG, representing the distribution characteristics of the dye in the resin, was smaller than Euclidean dimension (3) and decreased from 2.8 to 2.6 with decrease in the cross-linking density of the resin from 8 to 2%. The origin of the fractal-like distribution of the dye and, thus, that of the ion-exchange group was discussed.