The polycation/anionic-nonionic mixed micelle, poly(diallyldimethylammonium chloride)-sodium dodecyl sulfate/Triton X-100 (PDADMAC-SDS/TX100), is a model polyelectrolyte-colloid system in that the micellar mole fraction of SDS (Y) controls the micelle surface charge density, thus modulating the polyelectrolyte-colloid interaction. The exquisite temperature dependence of this system provides an important additional variable, controlling both liquid-liquid (L-L) and liquid-solid (L-S) phase separation, both of which are driven by the entropy of small ion release. In order to elucidate these transitions, we applied high-precision turbidimetry (±0.1 %), isothermal titration calorimetry, and epifluorescence microscopy which demonstrates preservation of micelle structure under all conditions. The L-S region at large Y including precipitation displays a remarkable linear, inverse Y-dependence of the L-S transition temperature T. In sharp contrast, the critical temperature for L-L coacervation T, shows nearly symmetrical effects of positive and negative deviations in Y from the point of soluble complex neutrality, which is controlled in solution by the micelle charge and the number of micelles bound per polymer chain n (Z = Z + nZ). In solid-like states, n no longer signifies the number of micelles bound per polymer chain, since the proximity of micelles inverts the host-guest relationship with each micelle binding multiple PE chains. This intimate binding goes hand-in-hand with the entropy of release of micelle-localized charge-compensating ions whose concentration depends on Y. These ions need not be released in L-L coacervation, but during L-S transition their displacement by PE accounts for the inverse dependence of T on micelle charge, Y.

Cyanine dyes are widely used to study the folding and structural transformations of nucleic acids using fluorescence resonance energy transfer (FRET). The extent to which FRET can be used to extract inter- and intramolecular distances has been the subject of considerable debate in the literature; the contribution of dye and linker dynamics to the observed FRET signal is particularly troublesome. We used molecular dynamics (MD) simulations to study the dynamics of the indocarbocyanine dyes Cy3 and Cy5 attached variously to the 3' or 5' terminal bases of a 16-base-pair RNA duplex. We then used Monte Carlo modeling of dye photophysics to predict the results of single-molecule-sensitive FRET measurements of these same molecules. Our results show that the average value of FRET depends on both the terminal base and the linker position. In particular, 3' attached dyes typically explore a wide region of configuration space, and the relative orientation factor, κ(2), has a distribution that approaches that of free-rotators. This is in contrast to 5' attached dyes, which spend a significant fraction of their time in one or more configurations that are effectively stacked on the ends of the RNA duplex. The presence of distinct dye configurations for 5' attached dyes is consistent with observations, made by others, of multiple fluorescence lifetimes of Cy3 on nucleic acids. Although FRET is frequently used as a molecular "ruler" to measure intramolecular distances, the unambiguous measurement of distances typically relies on the assumption that the rotational degrees of freedom of the dyes can be averaged out and that the donor lifetime in the absence of the acceptor is a constant. We demonstrate that even for the relatively free 3' attached dyes, the correlation time of κ(2) is still too long to justify the use of a free-rotation approximation. We further explore the consequences of multiple donor lifetimes on the predicted value of FRET.

Single-molecule-sensitive microscopy and spectroscopy are transforming biophysics and materials science laboratories. Techniques such as fluorescence correlation spectroscopy (FCS) and single-molecule sensitive fluorescence resonance energy transfer (FRET) are now commonly available in research laboratories but are as yet infrequently available in teaching laboratories. We describe inexpensive electronics and open-source software that bridges this gap, making state-of-the-art research capabilities accessible to undergraduates interested in biophysics. We include a discussion of the intensity correlation function relevant to FCS and how it can be determined from photon arrival times. We demonstrate the system with a measurement of the hydrodynamic radius of a protein using FCS that is suitable for the undergraduate teaching laboratory. The FPGA-based electronics, which are easy to construct, are suitable for more advanced measurements as well, and several applications are described. As implemented, the system has 8 ns timing resolution, can control up to four laser sources, and can collect information from as many as four photon-counting detectors.

The decay dynamics of BODIPY dye molecules embedded in porous silicon nanostructures produced by electrochemical etching of a silicon wafer in an HF solution are investigated using a confocal fluorescence lifetime imaging technique. Time-resolved experiments show that there is an efficient energy-transfer mechanism between BODIPY and porous silicon. It is observed that such an energy-transfer efficiency strongly depends on the thickness of the silicon dioxide layer covering the porous silicon. Silicon nanostructures are oxidized over time in air. As oxidation increases, the energy-transfer rate decreases. This change in energy-transfer rate seems to obey the NSET mechanism, which allows us to obtain a three-dimensional topographic map of the developed oxide layer on the rough and complicated surface of a porous silicon nanostructure.

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