Peker Milas

Precipitate–Coacervate Transformation in Polyelectrolyte–Mixed Micelle Systems

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 Ts. In sharp contrast, the critical temperature for L-L coacervation Tφ, 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 (Zcomplex = Zpolymer + nZmicelle). 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 Ts on micelle charge, Y.

Inexpensive electronics and software for photon statistics and correlation spectroscopy

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.

Single-molecule-sensitive fluorescence resonance energy transfer in freely-diffusing attoliter droplets

Fluorescence resonance energy transfer (FRET) from individual, dye-labeled RNA molecules confined in freely-diffusing attoliter-volume aqueous droplets is carefully compared to FRET from unconfined RNA in solution. The use of freely-diffusing droplets is a remarkably simple and high-throughput technique that facilitates a substantial increase in signal-to-noise for single-molecular-pair FRET measurements. We show that there can be dramatic differences between FRET in solution and in droplets, which we attribute primarily to an altered pH in the confining environment. We also demonstrate that a sufficient concentration of a non-ionic surfactant mitigates this effect and restores FRET to its neutral-pH solution value. At low surfactant levels, even accounting for pH, we observe differences between the distribution of FRET values in solution and in droplets which remain unexplained. Our results will facilitate the use of nanoemulsion droplets as attoliter volume reactors for use in biophysical and biochemical assays, and also in applications such as protein crystallization or nanoparticle synthesis, where careful attention to the pH of the confined phase is required.Fluorescence resonance energy transfer (FRET) from individual, dye-labeled RNA molecules confined in freely-diffusing attoliter-volume aqueous droplets is carefully compared to FRET from unconfined RNA in solution. The use of freely-diffusing droplets is a remarkably simple and high-throughput technique that facilitates a substantial increase in signal-to-noise for single-molecular-pair FRET measurements. We show that there can be dramatic differences between FRET in solution and in droplets, which we attribute primarily to an altered pH in the confining environment. We also demonstrate that a sufficient concentration of a non-ionic surfactant mitigates this effect and restores FRET to its neutral-pH solution value. At low surfactant levels, even accounting for pH, we observe differences between the distribution of FRET values in solution and in droplets which remain unexplained. Our results will facilitate the use of nanoemulsion droplets as attoliter volume reactors for use in biophysical and biochemical assays, and also in applications such as protein crystallization or nanoparticle synthesis, where careful attention to the pH of the confined phase is required.

Observation of a Change in Twist of an RNA Kissing Complex Using the Angular Dependence of Fluorescence Resonance Energy Transfer

Single-molecular-pair FRET is often used to study distance fluctuations of single molecules. It is harder to capture angular changes using FRET, because rotational motion of the dyes tends to wash out the angular sensitivity. Using a dye labeling scheme that minimizes the rotational motion of the dyes with respect to the RNA, we use spFRET to measure a change in twist angle of an RNA kissing complex upon protein binding. The model system studied here, R1inv-R2inv, is derived from the RNA I-RNA II complex in E. coli. RNA II is a primer for replication of the ColE1 plasmid; its function is modulated by interaction with RNA I. Rop protein is known to stabilize the bent R1inv-R2inv kissing complex against dissociation. The effect, if any, of Rop protein on the conformation of the kissing complex is not known. The eight minimized-energy NMR structures reported for R1inv-R2inv show a small difference in end-to-end distances and much larger difference in twist and bend angles. Our spFRET measurement showed an increase in average FRET upon Rop protein binding. With modeling, this increase could be attributed to a change in twist, but not bend or distance. The model used an MD simulation to calculate dye trajectories, and a direct integration of the resulting trajectories to predict FRET. The observed change in FRET is consistent with a decrease in the twist angle of the complex. We propose that Rop has a higher affinity for, and therefore serves to stabilize, these less stable (untwisted) conformations.

MD Simulations and FRET Studies of Dye-Labeled RNA

Fluorescence resonance energy transfer (FRET) is a powerful technique for understanding the structural transformations of RNA, DNA and proteins. With a few notable exceptions, the contribution of fluorophore and linker dynamics to these FRET measurements has not generally been investigated. Towards a better understanding of FRET on dye-labeled RNA, we present molecular dynamic (MD) simulations of 16mer double-stranded RNA with cyanine dyes attached at either the 3’ or 5’ ends with a 3 carbon linker. Water is included explicitly, and both dyes are in the ground state configuration. Differences in these two labeling strategies are discussed. We compare our simulations to data taken both on surface-attached and droplet-confined molecules. The effect of relative dye orientation and distance fluctuations due to the flexible linker are explicitly investigated.