Role of monovalent counterions in the ultrafast dynamics of DNA

This paper examines the contribution of counterion motion to the electric-field dynamics in the interior of DNA. The electric field is measured by a coumarin fluorophore that is synthetically incorporated into an oligonucleotide, where it replaces a native base pair. The DNA is a 17-base-pair oligomer with no A- or G-tracts. Time-resolved Stokes-shift measurements on the coumarin are made from 40 ps to 40 ns with each of the alkali ions and or one of several tetraalkylammonium ions as the DNA counterion. With the possible exception of rubidium, there are no indications of site-specific binding of the counterions. For sodium and other ions with a smaller hydrodynamic radius, the dynamics are identical and are fit to a power law. For larger ions, there is a progressive increase in the rate of shifting after 1 ns. This effect correlates with the hydrodynamic radius of the counterion. The lack of change in the spectral shape of the emission shows that neither the broadly distributed power-law relaxation nor the extra nanosecond dynamics are due to heterogeneity in the relaxation rates of different helices.     

Sodium-ion binding to DNA: detection by ultrafast time-resolved stokes-shift spectroscopy

The nature of the counterion is shown to have a pronounced effect on the apparent dynamic polarity in the interior of DNA. Time-resolved Stokes-shift measurements in the 80 ps to 40 ns time range were made on a polarity-sensitive fluorophore (coumarin 102) that replaces a base pair in an oligonucleotide. With sodium counterions, the emission spectrum narrows with time, whereas with tetrabutylammonium counterions, it does not. Our interpretation is that a subpopulation of helices have sodium cations bound in a fashion that slows the normal dynamics.     

Power-law solvation dynamics in DNA over six decades in time

Time-resolved Stokes shifts in a dye-containing oligonucleotide have been observed over the entire time range from 40 fs to 40 ns. The dynamics fit to a power law with a small exponent of 0.15. Similar relaxation has been seen in proteins but has not been anticipated in DNA. Distinct relaxation components due to specific subcomponents of the system, bulk water, bound water, counterions, backbone, bases, and so on, are not found. The various subcomponents may be so strongly coupled that their motions cannot be treated separately.     

Similarity of the relaxation modulus of polydisperse polymers

A similarity rule due to Markovitz is used for the correlation of the relaxation modulus for different polymeric materials. This rule has long been employed implicitly in the empirical shifting rules for the reduction to common curves of viscoelastic data measured on the same polymer over a range of temperatures and concentrations. It is shown here for the rubbery regime of polydisperse polymers that when relaxation moduli are scaled with the steady-state compliance and the time with the mean relaxation time, data for a variety of amorphous polymeric materials tend to plot on a common curve. This suggests that the dimensionless rubber modulus is, to first order, a common function of dimensionless time for materials which include whole polymers and polymer solutions, the effects of temperature and concentration being automatically incorporated into the two scaling parameters. For materials with sufficient polydispersity the correlation appears to be valid over a wide range of the available experimental data. These amorphous materials appear to share only one feature, flexible molecules with broadly distributed molecular weights. For narrowly dispersed polymers the modulus in the terminal zone is also correlated according to the above rule, but the influence of other parameters appears as the transition to the glassy regime is approached. An additional application of the similarity rule allows the relaxation modulus computed from molecular dynamics simulations of idealized polymers to be compared with experimental moduli for real materials even though the characteristic times for these systems differ by more than ten orders of magnitude.     

The dynamics of the B-A transition of natural DNA double helices

The dynamics of the B-A transition of DNA double helices with different GC contents and various chain lengths has been characterized by an electric field pulse technique. The field-induced B-A reaction is separated from orientation effects using the magic angle technique. Amplitudes reflecting the B-A reaction are observed selectively in the limited range of ethanol contents, where CD spectra demonstrate the B-A transition. The maximum amplitude appears at 1-2% higher ethanol content than the center of the B-A transition observed by CD because electric field pulses induce a relatively large perturbation from the A- toward the B-form. The relaxation curves measured after pulse termination reflect a spectrum of up to three relaxation processes. For DNA's with approximately 50% GC, the main part of the amplitude ( approximately 75%) is associated with time constants of approximately 2 micros, and another major component appears with time constants of 50-100 micros. These relaxation effects have been observed for DNA samples with 859, 2629, 7160, and 48501 bp. The time constant associated with the main amplitude increases with decreasing GC content from approximately 2 micros at 50% GC to approximately 3 mus at 41% GC and approximately 10 micros at 0% GC at the center of the B-A transition. Model calculations on the kinetics of cooperative linear Ising lattices predict the appearance of a distinct maximum of the mean relaxation time at the center of the transition. The absence of such maximum in our experimental data indicates a low cooperativity of the B-A transition with a nucleation parameter of approximately 0.1. The rate of the B-A transition is lower by approximately 3 orders of magnitude than that predicted by molecular dynamics simulations.     

Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove

The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.     

Edge excitation red shift and energy migration in quinine bisulphate dication

Photoinduced excited state dynamical processes in quinine sulphate dication (QSD) have been studied over a wide range of solute concentrations using steady state and nanosecond time-resolved fluorescence spectroscopic techniques. The edge excitation red shift (EERS) of emission maximum, emission wavelength dependence of fluorescence lifetimes and the time dependence of emission maximum are known to occur due to the solvent relaxation process. With increase in solute concentration, the emission spectrum shifts towards the lower frequencies accompanied with decrease in fluorescence intensity, however, absorption spectrum remains unchanged. A decrease in EERS, fluorescence lifetimes, time dependent fluorescence Stokes shift (TDFSS), fluorescence polarization and the solvent relaxation time (τ_r) is observed with the increase in solute concentration. The process of energy migration among the QSD ions along with solvent relaxation has been found responsible for the above experimental findings.     

Electric field-induced translocation of single-stranded DNA through a polarized carbon nanotube membrane

Molecular dynamics simulations based on a novel polarizable nanotube model were performed to study the dynamics in translocation of a single-stranded deoxyribonucleic acid oligonucleotide through a polarized carbon nanotube membrane by an applied electric field. The study revealed a nonlinear dependence of translocation velocity and an inverse quadratic dependence of translocation time on the electric field strength, as well as a threshold electric field below which the translocation process becomes impossible. The translocation rate was found to be pore-size dependent. The polarizable nanotube model developed for this study provides a useful platform for investigating the dynamics of a range of bionanosystems.     

Relaxation dynamics in glycerol-water mixtures: I. Glycerol-rich mixtures

We discuss the relaxation dynamics of glycerol-water mixtures, as studied by dielectric spectroscopy in the frequency range from 1 Hz to 250 MHz and at temperatures between 173 and 323 K. The experimental results obtained for the glycerol-rich mixtures suggest that the main dielectric relaxation process, as well as the so-called high-frequency "excess wing" (EW) and dc conductivity, follow the same temperature dependence. This result indicates that all of these processes are induced by the same molecular origin. A new phenomenological function is proposed to describe the whole dielectric spectrum in the covered frequency range, and some possible mechanisms of dielectric behaviors through the dc conductivity, the main relaxation process, and the EW are discussed.     

Heterogeneous dynamics and dynamic heterogeneities at the glass transition probed with single molecule spectroscopy

We studied the temperature dependence of the structural relaxation in poly(vinyl acetate) near the glass transition temperature with single molecule spectroscopy from Tg-1 K to Tg+12 K. The temperature dependence of the observed relaxation times matches results from bulk experiments; the observed relaxation times are, however, 80-fold slower than those from bulk experiments at the same temperature. We attribute this factor to the size of the probe molecule. The individual relaxation times of the single molecule environments are distributed normally on a logarithmic time scale, confirming that the dynamics in poly(vinyl acetate) is heterogeneous. The width of the distribution of individual relaxation times is essentially independent of temperature. The observed full width at half maximum (FWHM) on a logarithmic time axis is approximately 0.7, corresponding to a factor of about 5-fold, significantly narrower than the dielectric spectrum of the same material with a FWHM of about 2.0 on a logarithmic time axis, corresponding to a factor of about 100-fold. We explain this narrow width as the effect of temporal averaging of single molecule fluorescence signals over numerous environments due to a limited lifetime of the probed heterogeneities, indicating that heterogeneities are dynamic. We determine a loose upper limit for the ratio of the structural relaxation time to the lifetime of the heterogeneities (the rate memory parameter) of Q<80 for the range of investigated temperatures.     

Polarization relaxation in an ionic liquid confined between electrified walls

The response of a room temperature molten salt to an external electric field when it is confined to a nanoslit is studied by molecular dynamics simulations. The fluid is confined between two parallel and oppositely charged walls, emulating two electrified solid-liquid interfaces. Attention is focused on structural, electrostatic, and dynamical properties, which are compared with those of the nonpolarized fluid. It is found that the relaxation of the electrostatic potential, after switching the electric field off, occurs in two stages. A first, subpicosecond process accounts for 80% of the decay and is followed by a second subdiffusive process with a time constant of 8 ps. Diffusion is not involved in the relaxation, which is mostly driven by small anion translations. The relaxation of the polarization in the confined system is discussed in terms of the spectrum of charge density fluctuations in the bulk.     

Early Time Solvation Dynamics Probed by Spectrally Resolved Degenerate Pump-Probe Spectroscopy

The dynamic role of solvent in influencing the rates of physico-chemical processes (for example, polar solvation and electron transfer) has been extensively studied using time-resolved fluorescence spectroscopy. Here we study ultrafast excited state relaxation dynamics of three different fluorescent probes (DNTTCI, IR-140 and IR-144) in two polar solvents, ethanol and ethylene glycol, using spectrally resolved degenerate pump-probe spectroscopy. We discuss how time-resolved emission spectra can be directly used for constructing relaxation correlation function, obviating spectral reconstruction and estimation of time-zero spectrum in non-polar solvents. We show that depending on the specific probe used, the relaxation dynamics is governed either by intramolecular vibrational relaxation (for IR140) or by intermolecular solvation (for DNTTCI) or by both (for IR144). We further show (using DNTTCI as a probe) that major differences in solvation by ethanol and ethylene glycol is contributed by early time (<1 ps) dynamics.     

The protein "glass" transition and the role of the solvent

Hydrated proteins undergo a change in their dynamical properties in the neighborhood of a temperature. The change of dynamics has been likened to glass transition of glass-forming substances because similar properties were found. However, a complete understanding of the conformation fluctuations of hydrated proteins and their relation to the dynamics of the solvent is still not available, possibly due to the protein molecules being more complex than ordinary glass-formers. For this reason, we turn our attention to the experimental findings of the dynamics of mixtures of water with simpler glass-formers (small molecules and polymers). Two major relaxation processes have been observed in these aqueous mixtures. One is the structural alpha-relaxation of the hydrophilic glass-former hydrogen bonded to the water, which is responsible for glass transition. The other one is the local secondary beta-relaxation of water in the mixture. Remarkably, these two relaxation processes in aqueous mixtures have analogues in hydrated proteins with the same properties. The conformation fluctuations of the protein and the relaxation of the solvent in hydrated proteins behave like the alpha-relaxation of the hydrophilic glass-former hydrogen bonded to the water and the beta-relaxation of water in other aqueous mixtures, respectively. At low temperatures, the Arrhenius activation energy of the relaxation time of the solvent in a hydrated protein is almost the same as that of the beta-relaxation of water in the glassy states of aqueous mixtures. The Arrhenius T-dependence of the solvent relaxation times no longer holds at temperatures that exceed the "glass" transition temperature of the hydrated protein, defined as the temperature at which the conformation relaxation time is very long. This behavior of the solvent in hydrated proteins is similar to that found in the beta-relaxation of water in aqueous mixtures when crossing the glass transition temperature of the mixture (Capaccioli, S.; Ngai, K. L.; Shinyashiki, N. J. Phys. Chem. B 2007, 111, 8197). Furthermore, the same dynamics were found in mixtures of two van der Waals glass-formers, which are even simpler systems than aqueous mixtures because of the absence of hydrogen bonding. The experimental data of these ideal mixtures of van der Waals glass-formers have been given a satisfactory theoretical explanation. Since the properties of hydrated proteins, aqueous mixtures, and the mixtures of van der Waals liquids are similar, we transfer the theoretical understanding gained in the study of the last system sequentially to the two other increasingly more complex systems.     

On the molecular interpretation of the dielectric relaxation of nematic liquid crystals

This paper presents the results of studies of the dielectric relaxation of nematic 6CHBT obtained for different values of the angle between the directions of the macroscopic orientation of the sample (director n) and the probing electric field E. Analysis of the evolution of the relaxation spectrum from epsilon*(omega) (E n) to epsilon*(omega) (E n) allows one to explain the hitherto existing inconsistency in the molecular interpretation of the spectra. A model of the molecular dynamics in the oriented nematics is proposed.     

Auger recombination dynamics in clusters

Electronic relaxation dynamics following interband excitation from the 6s to the 6p band in mass selected clusters are measured through femtosecond time-resolved photoelectron imaging (TRPEI). This interband transition is pumped at 4.65 eV and probed at 1.55 eV. Auger decay of occurs on a timescale of 490 ± 100 fs, and a similar time constant is seen for the transient excited state population created by the pump pulse. These time constants are an order of magnitude faster than those seen in previous experiments in which the lone p-electron in was excited within the p-band. The results presented here imply that substantial relaxation of either electrons in the p-band or the hole in the s-band takes place prior to Auger emission, with electron–electron scattering playing a key role in the fast observed dynamics.     

Wash-free magnetic oligonucleotide probes-based NMR sensor for detecting the Hg ion

An easily applied and sensitive sensor for the detection of heavy metal ion residues based entirely on magnetic nanoparticle and oligonucleotide was developed. The tool is established on the relaxation of magnetic nanoparticles with different dispersion states. The target analyte, Hg ions, induce the aggregation of the MNP oligonucleotide probes. Accordingly, the light produced by the magnetic relaxation image and the transverse relaxation time (T(2)) all change due to the effect of the aggregation. The limit of qualitative detection of the sensor is 0.15 ppt. The recoveries from test samples range between 97.1-101.8%. Using the nuclear resonance instrument, the method is a high throughput and sensitive sensor.     

Exciton dynamics of GaSe nanoparticle aggregates

Time-resolved and static spectroscopic results on GaSe nanoparticle aggregates are presented to elucidate the exciton relaxation and diffusion dynamics. These results are obtained in room-temperature TOP/TOPO solutions at various concentrations. The aggregate absorption spectra are interpreted in terms of electrostatic coupling and covalent interactions between particles. The spectra at various concentrations may then be interpreted in terms of aggregate distributions calculated from a simple equilibrium model. These distributions are used to interpret concentration-dependent emission anisotropy kinetics and time-dependent emission spectral shifts. The emission spectra are reconstructed from the static emission spectra and decay kinetics obtained at a range of wavelengths. The results indicate that the aggregate z axis persistence length is about 9 particles. The results also show that the one-dimensional exciton diffusion coefficient is excitation wavelength dependent and has a value of about 2 x 10(-5) cm(2)/s following 406 nm excitation. Although exciton diffusion results in very little energy relaxation, subsequent hopping of trapped electron/hole pairs occurs by a Forster mechanism and strongly red shifts the emission spectrum.