Analysis of Cation-Dependent DNA (G3T1)4 Shape Change Using Fluorescence Correlation Spectroscopy.

In G-rich DNA, it is well known that the form changes from single-strand DNA to G-quadruplex due to cations. In this study, we analyze the diffusion coefficient and fluorescence intensity obtained by fluorescence correlation spectroscopy for short G-rich DNA of the (G3T1)4 sequence labeled as 5-Carboxytetramethylrhodamine (TAMRA) with variation of the K+ ion concentration. At a K+ ion concentration of more than 200 mM, the single-strand DNA was changed to the G-quadruplex. The size of the G-quadruplex decreased to 86% than the size of the single strand DNA at K+ ion concentration of 0 M. The size of the G-quadruplex and the fluorescence intensity of TAMRA attached to the DNA were constant with an increase in the K+ ion concentration between 200 and 800 mM. This means that the size of the DNA and the fluorescence intensity of the TAMRA are not affected by the K+ ion concentration at the G-quadruplex structure because the binding structure of DNA and TAMRA dye leads to stability at a concentration of less than 100 mM K+. Based on our short G-rich DNA results, longer G-rich DNA is analyzed for the diffusion coefficient of the DNA and the fluorescence intensity variation of fluorescence dye attached to the DNA.

Analysis of the Fluorescence Correlation Function of Quantum Rods with Different Lengths.

We built a polarization fluorescence correlation spectroscopy system to analyze the variation of the correlation function in rotational diffusion based on the length of rod-like fluorescent particles. Because the rotational diffusion of particles in liquid depends on the relative polarization states of the laser source and particle fluorescence, we compared the amplitudes of the rotational diffusion using the autocorrelation function in different polarization states. For experiments that depend on the length of the fluorescent particles, we prepared three kinds of quantum rod samples with a width of 6.5 ± 0.5 nm and lengths of 17 ± 3, 40 ± 3, and 46 ± 3 nm. Through the experiment, we obtained the hydrodynamic radii of each particle using the rotational diffusion coefficient: 10.7 ± 0.8, 13.4 ± 0.7, and 14.1 ± 0.4 nm with the length of the particles. All the obtained values for radii are 3 nm larger than the calculated equivalent radii of spheres with the same volume as the rod samples. Through a fraction analysis by polarization state, we confirmed that the ratio of rotational fraction for polarization increases with the aspect ratio of the actual particle.

Investigation of the nanoviscosity effect of a G-quadruplex and single-strand DNA using fluorescence correlation spectroscopy.

Guanine (G)-quadruplexes are of interest because of their presence in the telomere sequence and the oncogene promoter region. Their diffusion and change of structure, especially in high viscosity solutions, are important for understanding their dynamics. G-quadruplexes may have less effective viscosity (nanoviscosity) when they are smaller than the solvent molecules. In this paper, we report the difference in the diffusion dynamics of the G-rich DNA sequences of single-strand DNA (ssDNA) and the G-quadruplex in aqueous, sucrose, and polyethylene glycol (PEG) solutions. From experiments with aqueous and sucrose solutions, we confirm that a simple diffusion model according to the viscosity is appropriate. In the PEG experiments, the nanoviscosity effect is observed according to PEG's molecular weight. In the PEG 200 solution, both the ssDNA and the G-quadruplex possess macroviscosity. In the PEG 10,000 solution, the G-quadruplex possesses nanoviscosity and the ssDNA possesses macroviscosity, whereas, in the PEG 35,000 solution, both ssDNA and the G-quadruplex possess nanoviscosity. The experimental results are consistent with the theoretical predictions.

Viscosity-dependent diffusion of fluorescent particles using fluorescence correlation spectroscopy.

Fluorescent particles show the variety characteristics by the interaction with other particles and solvent. In order to investigate the relationship between the dynamic properties of fluorescent particles and solvent viscosity, particle diffusion in various solvents was evaluated using a fluorescence correlation spectroscopy. Upon analyzing the correlation functions of AF-647, Q-dot, and beads with different viscosity values, the diffusion time of all particles was observed to increase with increasing solvent viscosity, and the ratio of diffusion time to solvent viscosity, τ D /η, showed a linear dependence on particle size. The particle diffusion coefficients calculated from the diffusion time decreased with increasing solvent viscosity. Further, the hydrodynamic radii of AF-647, Q-dot, and beads were 0.98 ± 0.1 nm, 64.8 ± 3.23 nm, and 89.8 ± 4.91 nm, respectively, revealing a linear dependence on τ D /η, which suggests that the hydrodynamic radius of a particle strongly depends on both the physical size of the particle and solvent viscosity.

Analysis of quantum rod diffusion by polarized fluorescence correlation spectroscopy.

To measure the polarization dependence of fluorescent probes, a confocal-microscope-based polarized fluorescence correlation spectroscopy system was developed, and the polarization dependence on the rotational diffusion of well-defined quantum rods (Qrods) was investigated and characterized. The rotational diffusion region of the Qrods was observed over a time range of less than 10(-5) s in a water solution, and the rotational diffusion parameters were extracted using a rotational diffusion model in which the viscosity of the solution media was varied. Our work demonstrated that polarized fluorescence correlation spectroscopy (FCS) is useful for investigating both the rotational and translational diffusion of fluorescent probes.

Characterization of the triplet state of hybridization-sensitive DNA probe by using fluorescence correlation spectroscopy.

The nonradiative relaxation mechanism of the newly synthesized hybridized-sensitive DNA probe has not been fully understood until now. In this study, the transient dark state of the probe, which is a double fluorescent dye attached to a specific DNA sequence, was investigated using a fluorescence correlation spectroscopy (FCS). The transient dark state was measured in various solvents that are known to affect the intersystem crossing or photoisomerization of the DNA probe. On the basis of the experimental results, a simplified two energy state model of the probe was constructed, and this model provides an insight into the nonradiative relaxation mechanism of the fluorophore and the applications for DNA and RNA detection. The transient dark state that was measured in a time scale of a few microseconds is a triplet state and is related to photoisomerization, viscosity, oxygen concentration, and hybridization, all of which are important parameters for cellular microscopy. The transient dark state in a time scale of a sub-microseconds is sensitively changed after the addition of target DNA. The characterization can improve the probe's capability to identify target DNA/RNA by using FCS since the triplet state that occurred after hybridization is distinctive in the time scale with that occurred before hybridization.

The Ripple Effect of Graphite Nanofilm on Stretchable Polydimethylsiloxane for Optical Sensing.

Graphene-based optical sensing devices have been widely studied for their broad band absorption, high carrier mobility, and mechanical flexibility. Due to graphene's weak light absorption, studies on graphene-based optical sensing thus far have focused on hybrid heterostructure devices to enhance photo-absorption. Such hybrid devices need a complicated integration process and lead to deteriorating carrier mobility as a result of heterogeneous interfaces. Rippled or wrinkled graphene has been studied in electronic and optoelectronic devices. However, concrete demonstrations of the impact of the morphology of nanofilms (e.g., graphite and graphene) associated with light absorption in optical sensing devices have not been fully examined. This study explored the optical sensing potential of a graphite nanofilm surface with ripples induced by a stretchable polydimethylsiloxane (PDMS) supporting layer under different stretch:release ratios and then transferred onto silicon, both under experimental conditions and via simulation. The optical sensing potential of the rippled graphite nanofilm was significantly enhanced (260 mA/W at the stretch-release state of 30%), as compared to the pristine graphite/PDMS (20 mA/W at the stretch-release state of 0%) under laser illumination at a wavelength of 532 nm. In addition, the results of our simulated computation also confirmed the improved light absorption of rippled graphite nanofilm surface-based optical sensing devices, which was comparable with the results found in the experiment.

Reaction kinetics study of short DNA strands using a maximum entropy method and nonlinear curve fitting.

It is important to understand the formation of double-strand DNA (dsDNA) in a salt solution because it is one of the key reactions in life. A short cDNA strand pair was designed, and each single-strand DNA (ssDNA) was attached to a fluorescent dye that was either a donor or an acceptor of fluorescence resonance energy transfer. The fluorescence intensity was expected to change as time passed as the complementary pairs of ssDNAs formed dsDNAs. The concentration of dsDNA was theoretically calculated, and the measured data were consistent with theoretical results. The analysis of the nonlinear fitting method and the maximum entropy method detected that the reaction curve contains two major types of kinetics that likely represent the formation of dsDNA and mismatching.

Characterization of micellar film morphologies of semifluorinated block copolymers by AFM.

The micellar morphologies of well-defined amphiphilic block copolymers composed of 1H,1H-dihydroperfluorooctyl methacrylate (FOMA) and ethylene oxide (EO) blocks with different chain lengths were effectively investigated by using tapping mode-atomic force microscopy (TM-AFM). By spin-casting chloroform solutions, well-ordered spherical micellar films could be obtained for poly(FOMA(10k)-b-EO(10k)) and poly(FOMA(20k)-b-EO(20k)) copolymers. The atomic force microscopy (AFM) height and phase image analysis indicated that dark regions of the micelles corresponded to PEO blocks and the light regions were for PFOMA blocks. The spherical micelles with PEO corona and PFOMA core were also identified by transmission electron microscopy (TEM) and X-ray photoelectron spectrometer (XPS) analysis. The core diameters of the block-copolymer aggregates were 20 nm for poly(FOMA(10k)-b-EO(10k)) and 30 nm for poly(FOMA(20k)-b-EO(20k)) by TM-AFM, whereas slightly lower values of 17 and 26 nm were obtained from TEM. A detailed study on the inverted morphological change observed in the micelles films after annealing above glass transition temperature (T(g)) was also presented.

Ordering transitions of semifluorinated diblock copolymers.

A series of diblock copolymers consisting of a hydrophilic polyethylene oxide (PEO) and a hydrophobic poly(1H,1H-dihydroperfluorooctyl methacrylate) (PDHFOMA) block were synthesized with different chain lengths for application to self-assembled nanopatterning structures. The morphology of poly(DHFOMA5k-b-EO5k), poly(DHFOMA10k-b-EO10k), and poly(DHFOMA20k-b-EO20k) spin cast from micellar solution in chloroform at room temperature were spherical with average diameter of 12 nm, 17 nm and 26 nm, respectively by TEM analysis. The spherical structures were reorganized to different shapes with thermodynamically stable morphologies upon annealing above glass transition temperature (Tg). PDHFOMA block domains changed to well ordered cylindrical domains, inversed continuous phase, and large composite spherical domains for 5 k, 10 k, and 20 k block copolymer, respectively.

Highly intense room-temperature photoluminescence in V2O5 nanospheres.

Room-temperature photoluminescence (PL) in V2O5 nanospheres with zero-like dimensional structure was investigated. A large number of V4+ oxidation states in the nanospheres were observed by X-ray photoelectron spectroscopy (XPS) measurements. The nanospheres revealed high PL intensity compared with previous studies. In particular, they showed intense ultraviolet (UV) PL near a wavelength of 396 nm (3.13 eV). The intense UV PL was attributed to the enhanced transition probability due to the large number of V4+ (3d1) oxidation states. The PL properties showed strong dependencies on the oxidation states and their distribution.