The dynamics of the electric fields in the interior of DNA are measured by using oligonucleotides in which a native base pair is replaced by a dye molecule (coumarin 102) whose emission spectrum is sensitive to the local electric field. Time-resolved measurements of the emission spectrum have been extended to a six decade time range (40 fs to 40 ns) by combining results from time-correlated photon counting, fluorescence up-conversion and transient absorption. Recent results showed that when the reporter is placed in the center of the oligonucleotide, the dynamics are very broadly distributed over this entire time range and do not show specific time constants associated with individual processes [J. Am. Chem. Soc. 2005, 127, 7270]. This paper examines an oligonucleotide with the reporter near its end. The broadly distributed relaxation seen before remains with little attenuation. In addition, a new relaxation with a well defined relaxation time of 5 ps appears. This process is assigned to the rapid component of "fraying" at the end of the helix.

Time-resolved Stokes-shift experiments measure the dynamics of biomolecules and of the perturbed solvent near them on subnanosecond time scales, but molecular dynamics simulations are needed to provide a clear interpretation of the results. Here we show that simulations using standard methods quantitatively reproduce the main features of TRSS experiments in DNA and provide a molecular assignment for the dynamics. The simulations reproduce the magnitude and unusual power-law dynamics of the Stokes shift seen in recent experiments [D. Andreatta, et al., J. Am. Chem. Soc. 127, 7270 (2005)]. A polarization model is introduced to eliminate cross correlations between the different components contributing to the signal. Using this model, well-defined contributions of the DNA, water and counterion to the experimental signal are extracted. Water is found to have the largest contribution and to be responsible for the power-law dynamics. The counterions have a smaller, but non-negligible contribution with a time constant of 220 ps. The contribution to the signal of the DNA itself is minor and fits a 30 ps stretched exponential. Both time-averaged and dynamic distributions are calculated. They show a small subset of ions with a different coupling, but no other evidence of substates or dynamic heterogeneity.

Fluorescence correlation spectroscopy (FCS) is an ideal tool for measuring molecular diffusion and size under extremely dilute conditions. However, the power of FCS has not been utilized to its best to measure diffusion and size parameters of complex chemical systems. Here, we apply FCS to measure the size, and, most importantly, the size distribution and polydispersity of a supramolecular nanostructure (i.e., microemulsion droplets, MEDs) in dilute solution. It is shown how the refractive index mismatch of a solution can be corrected in FCS to obtain accurate size parameters of particles, bypassing the optical matching problem of light scattering techniques that are used often for particle-size measurements. We studied the MEDs of 13 different W(0) values from 2 to 50 prepared in a ternary mixture of water, sodium bis(2-ethylhexyl) sulfosuccinate (AOT), and isooctane, with sulforhodamine-B as a fluorescent marker. We find that, near the optical matching point of MEDs, the dynamic light scattering (DLS) measurements underestimate the droplet sizes while FCS estimates the accurate ones. A Gaussian distribution model (GDM) and a maximum-entropy-based FCS data fitting model (MEMFCS) are used to analyze the fluorescence correlation curves that unfold Gaussian-type size distributions of MEDs in solution. We find the droplet size varies linearly with W(0) up to ~20, but beyond this W(0) value, the size variation deviates from this linearity. To explain nonlinear variation of droplet size for W(0) values beyond ~20, we invoke a model (the coated-droplet model) that incorporates the size polydispersity of the droplets.

Even though nanostructures of various shapes and sizes can be controlled by microemulsions, there is substantial difficulty in understanding their growth mechanism. The evolution of nanostructures from the time of mixing of reactants to their final stage is a heterogeneous process involving a variety of intermediates. To obtain a deeper insight into these kinetic steps, we studied the slow growth kinetics (extending over eight days) of iron oxalate nanorods inside the polar core of water-in-oil microemulsion droplets made of cetyltrimethylammonium bromide/1-butanol/isooctane. Fluorescence correlation spectroscopy (FCS), dynamic light scattering (DLS), and transmission electron microscopy (TEM) have been employed to monitor the nanostructure growth at (near) the single-droplet level and in an ensemble. Analyzing FCS data with suitable kinetic model we obtain transient dimer lifetime (28 μs) and the droplet fusion rates (and fusion tendency) on each day as the reaction proceeds. The droplet fusion rate is found to directly control the nanorod growth in microemulsion solution and attains its maximum value (3.55 × 10(4) s(-1)) on day 6, when long nanorods are found in TEM data, implying that more and more reactants are fed into the growing system at this stage. Combining FCS, DLS, and TEM results, we find three distinct periods in the entire growth process: a long nucleation-dominant nanoparticle growth period which forms nanoparticles of critical (average) size of ∼53 nm, followed by a short period where isotropic nanoparticles switch to anisotropic growth to form nanorods, and finally elongation of nanorods and growth (and shrinking) of nanoparticles.

Time-resolved fluorescence Stokes shift dynamics of a fluorescent probe, 4',6-diamidino-2-phenylindole (DAPI), inside the minor groove of the DNA is measured over five decades in time spans from 100 fs to 10 ns. Two different techniques, fluorescence up-conversion and time correlated single photon counting, are combined to obtain the time-resolved emission spectra of DAPI in DNA over the entire five decades in time. Having the dynamics of groove-bound DAPI in DNA measured over such a broad time window, we are able to convincingly compare our data to earlier time-resolved fluorescence results of a base-stacked probe that replaces a DNA base pair. Results show that the dynamics measured with either the groove-bound or the base-stacked probe are similar in the time span of 100 fs to approximately 100 ps but differ substantially from approximately 100 ps to 10 ns. Our present data also help to reconcile the previously reported molecular dynamics simulation results and provide important clues that the groove-bound water molecules inside DNA are mainly responsible for the slow dynamics seen in native DNA.

G-quadruplex DNA (GqDNA) structures act as promising anticancer targets for small-molecules (ligands). Solvation dynamics of a ligand (DAPI: 4',6-diamidino-2-phenylindole) inside antiparallel-GqDNA is studied through direct comparison of time-resolved experiments to molecular dynamics (MD) simulation. Dynamic Stokes shifts of DAPI in GqDNA prepared in H2O buffer and D2O are compared to find the effect of water on ligand solvation. Experimental dynamics (in H2O) is then directly compared with the dynamics computed from 65 ns simulation on the same DAPI-GqDNA complex. Ligand solvation follows power-law relaxation (summed with fast exponential relaxation) from ~100 fs to 10 ns. Simulation results show relaxation below ~5 ps is dominated by water motion, while both water and DNA contribute comparably to dictate long-time power-law dynamics. Ion contribution is, however, found to be negligible. Simulation results also suggest that anomalous solvation dynamics may have origin in subdiffusive motion of perturbed water near GqDNA.

The fluorescence anisotropy decay of two dyes merocyanine 540 and oxazine 1 has been studied in a polymer−surfactant aggregate containing poly(vinylpyrrolidone) (PVP) and sodium dodecyl sulfate (SDS). The results are analyzed in terms of the necklace model of the polymer−surfactant aggregate. The rotational motion of the probe is assumed to involve “wobbling-in-cone” along with translational motion along the micellar surface. It is observed that the presence of the polymer chains around the spherical SDS micelles causes significant retardation of both the wobbling motion as well as the translational motion of the two dyes. As a result, the wobbling and translational diffusion of the dyes in the PVP−SDS aggregate are slower than those in SDS micelle.

Time-resolved fluorescence Stokes shifts (TRFSS) of 4',6-diamidino-2-phenylindole (DAPI) inside the minor groove of DNA are measured in the presence of three different monovalent counterions: sodium (Na(+)), rubidium (Rb(+)), and tetrabutylammonium (TBA(+)). Fluorescence up-conversion and time-correlated single photon counting are combined to obtain the time-resolved emission spectra (TRES) of DAPI in DNA from 100 fs to 10 ns. Time-resolved Stokes shift data suggest that groove-bound DAPI can not sense the counterion dynamics because the ions are displaced by DAPI far from the probe-site. However, when these results are compared to the earlier base-stacked coumarin data, the same ions are found to affect the nanosecond dynamics significantly. This suggests that the ions come close to the probe-site, such that they can affect the dynamics when measured by base-stacked coumarin. These results support previous molecular dynamics (MD) simulation data of groove-bound and base-stacked probes inside DNA.