A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

The folding of a dye-quencher labeled DNA hairpin molecule was investigated using fluorescence autocorrelation and cross-correlation spectroscopy (FCS) and photon counting histogram analysis (PCH). The autocorrelation and cross-correlation measurements revealed the flow and diffusion times of the DNA molecules through two spatially offset detection volumes, the relaxation time of the folding reaction, and the total concentration of DNA molecules participating in the reaction. The PCH measurements revealed the equilibrium distribution of DNA molecules in folded and unfolded conformations and the specific brightnesses of the fluorophore in each conformational state. These measurements were carried out over a range of NaCl concentrations, from those that favored the open form of the DNA hairpin to those that favored the closed form. DNA melting curves obtained from each sample were also analyzed for comparison. It was found that the reactant concentrations were depleted as the reaction progressed and that the equilibrium distributions measured by FCS and PCH deviated from those obtained from the melting curve analyses. These observations suggest a three-state mechanism for the DNA hairpin folding reaction that involves a stable intermediate form of the DNA hairpin. The reaction being probed by FCS and PCH is suggested to be a rapid equilibrium between open and intermediate conformations. Formation of the fully closed DNA hairpin is suggested to occur on a much longer time scale than the FCS and PCH measurement time. The closed form of the hairpin thus serves as a sink into which the reactants are depleted as the reaction progresses.     

Panorama of DNA hairpin folding observed via diffusion-decelerated fluorescence correlation spectroscopy

Based on a confocal microscopy platform, we extended the FCS time window by three orders of magnitude to the s timescale by attaching a polystyrene microsphere. We simultaneously monitored the relaxations of multiple intermediates involved in DNA hairpin folding, thus offering a much more detailed view of the kinetics of hairpin folding experimentally.     

Probing the binding kinetics of proinflammatory cytokine-antibody interactions using dual color fluorescence cross correlation spectroscopy

Dual color fluorescence cross correlation spectroscopy (FCCS) was used to investigate quantitatively the binding kinetics of tumor necrosis factor (TNFα) with TNFα antibody (anti-TNFα) following fluorescent labeling. Through the analysis of the auto correlation curves of fluorescence correlation spectroscopy (FCS), diffusion coefficients of 100.06 ± 4.9 μm(2) s(-1) and 48.96 ± 2.52 μm(2) s(-1) for Alexa488-TNFα and Atto647N-anti-TNFα were obtained. In addition, the calculated hydrodynamic diameters of the Alexa488-TNFα and Atto647N-anti-TNFα were approximately 4.89 ± 0.24 nm and 9.99 ± 0.52 nm, respectively, which agrees with the values of 5.20 ± 1.23 nm and 9.28 ± 0.86 nm for the native TNFα and the anti-TNFα as determined from dynamic light scattering measurements. For the binding kinetics, association (k(on)) and dissociation (k(off)) rate constants were (1.13 ± 0.08) × 10(4) M(-1) s(-1) and (1.53 ± 0.19) × 10(-3) s(-1) while the corresponding dissociation constant (K(d)) at 25 °C was (1.36 ± 0.10) × 10(-7) M. We believe this is the first report on the binding kinetics for TNFα-antibody recognition in the homogeneous phase. Using this technology, we have shown that controlled experiments can be performed to gain insight into molecular mechanisms involved in the immune response.     

Probing the mechanisms of an air amplifier using a LTQ-FT-ICR-MS and fluorescence spectroscopy

We report the first quantitative assessment of electrosprayed droplet/ion focusing enabled by the use of a voltage-assisted air amplifier between an electrospray ionization emitter and a hybrid linear ion trap Fourier transform ion cyclotron resonance mass spectrometer (ESI-LTQ-FT-ICR-MS). A solution of fluorescent dye was electrosprayed with a stainless steel mesh screen placed in front of the MS inlet capillary acting as a gas-permeable imaging plate for fluorescence spectroscopy. Without use of the air amplifier, no detectable FT-ICR signal was observed, as well as no detectable fluorescence on the screen upon imaging using a fluorescence scanner. When the air amplifier was turned ON while electrospraying the fluorescent dye, FT-ICR mass spectra with high signal to noise ratio were obtained with an average ion injection time of 21 ms for an AGC target value of 5 x 10(5). Imaging of the screen using a fluorescence scanner produced a distinct spot of cross-sectional area approximately 33.5 mm(2) in front of the MS inlet capillary. These experimental results provide direct evidence of aerodynamic focusing of electrosprayed droplets/ions enabled by an air amplifier, resulting in improved electrospray droplet/ion capture efficiency and reduced ion injection time. A second set of experiments was carried out to explore whether the air amplifier assists in desolvation. By electrospraying a mix of quaternary amines, ratios of increasingly hydrophobic molecules were obtained. Observation of the solvophobic effect associated with electrospray ionization resulted in a higher abundance of the hydrophobic molecule. This bias was eliminated when the air amplifier was turned ON and a response indicative of the respective component concentrations of the molecules in the bulk solution was observed.     

Binding of hairpin polyamides to DNA studied by fluorescence correlation spectroscopy for DNA nanoarchitectures

We have recently constructed a “DNA strut” consisting of two DNA-binding hairpin polyamides of Dervan-type connected via a long flexible linker and were able to show that this strut can be used to sequence-selectively connect DNA helices. This approach provides a second structural element (besides the Watson–Crick base pairing) for the assembly of higher-order DNA nanoarchitectures from smaller DNA building blocks. Since none of the existing analytical techniques for studying this kind of system were found suitable for detection and quantification of the formation of the resulting complexes, we chose fluorescence correlation spectroscopy (FCS). In the present study we show that FCS allowed us in a versatile and fast way to investigate the binding of Dervan polyamides to DNA. In particular it also shows its power in the quantitative detection of the formation of multimeric complexes and the in investigation of binding under nonphysiological conditions. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits

Catalyzed hairpin assembly (CHA) is a robust enzyme-free signal-amplification reaction that has a wide range of potential applications, especially in biosensing. Although most studies of the analytical applications of CHA have focused on the measurement of concentrations of biomolecules, we show here that CHA can also be used to probe the spatial organization of biomolecules such as single-stranded DNA. The basis of such detection is the fact that a DNA structure that brings a toehold and a branch-migration domain into close proximity can catalyze the CHA reaction. We quantitatively studied this phenomenon and applied it to the detection of domain reorganization that occurs during DNA self-assembly processes such as the hybridization chain reaction (HCR). We also show that CHA circuits can be designed to detect certain types of hybridization defects. This principle allowed us to develop a "signal on" assay that can simultaneously respond to multiple types of mutations in a DNA strand in one simple reaction, which is of great interest in genotyping and molecular diagnostics. These findings highlight the potential impacts of DNA circuitry on DNA nanotechnology and provide new tools for further development of these fields.     

Probing the interaction between fluorophores and DNA nucleotides by fluorescence correlation spectroscopy and fluorescence quenching

We have investigated the association interactions between the fluorescent dyes TAMRA, Cy3B and Alexa-546 and the DNA deoxynucleoside monophosphates by means of fluorescence quenching and fluorescence correlation spectroscopy (FCS). The interactions of Cy3B and TAMRA with the nucleotides produce a decrease in the apparent diffusion coefficient of the dyes, which result in a shift toward longer times in the FCS autocorrelation decays. Our results with Cy3B demonstrate the existence of Cy3B-nucleotide interactions that do not affect the fluorescence intensity or lifetime of the dye significantly. The same is true for TAMRA in the presence of dAMP, dCMP and dTMP. In contrast, the diffusion coefficient of Alexa 546 remains practically unchanged even at high concentrations of nucleotide. These results demonstrate that interactions between this dye and the four dNMPs are not significant. The presence of the negatively charged sulfonates and the bulky chlorine atoms in the phenyl group of Alexa 546 possibly prevent strong interactions that are otherwise possible for TAMRA. The characterization of dye-DNA interactions is important in biophysical research because they play an important role in the interpretation of energy transfer experiments, and because they can potentially affect the structure and dynamics of the DNA.     

Probing actinide electronic structure using fluorescence and multi-photon ionization spectroscopy

The role of the 5f orbitals in actinide bond formation is one of the central issues of actinide chemistry. This question can be explored using relativistic quantum chemistry calculations, but the theoretical methods must be validated using definitive experimental data. For simple ionic compounds such as actinide oxides and halides, the electronic structure can be examined using electronic and photoelectron spectroscopy of gas phase molecules. The present article surveys recent spectroscopic and theoretical studies of the oxides of thorium and uranium. The results show that the 5f-like states are spectators and that the complex patterns of low-lying electronic states for these molecules can be understood in terms of a semi-empirical ligand field model. Comparisons with recent high-level theoretical calculations are presented and discussed.     

Single-molecule fluorescence spectroscopy of protein folding.

Single-molecule spectroscopy is an important new approach for studying the intrinsically heterogeneous process of protein folding. This Review illustrates how different single-molecule fluorescence techniques have improved our understanding of mechanistic aspects in protein folding, exemplified by a series of recent experiments on a small protein.     

DNA microelectrophoresis using double focus fluorescence correlation spectroscopy

Double focus fluorescence correlation spectroscopy (dfFCS) was used to determine electrophoretic mobilities of short double-stranded DNA (dsDNA)-fragments (75 base pairs (bp) -1019 bp) in microfluidic channels. The electrokinetic flow profile across a microchannel was measured with 1 microm spatial resolution and separated in electroosmotic and electrophoretic contributions. Experiments show that the free solution mobility is independent of DNA length. The diffusion constant is additionally determined by FCS and follows a length dependent rod-diffusion model. We interpret the electrophoretic mobilities using a modified Nernst Einstein relation, which additionally takes Manning condensation and counterion induced hydrodynamic retardation forces into account. In 3% w/v polyethylene oxide (PEO)-network (M(r) 3 .10(5) Dalton) the electrophoretic velocities become size-dependent with a power-law exponent be-tween 0.28 and 0.31. Mixtures of dsDNA-fragments exhibit distinguishable peaks in the dfFCS cross-correlation function. The potential of dfFCS for realtime micro-analysis in terms of speed and spatial resolution is discussed.     

Circumvention of fluorophore photobleaching in fluorescence fluctuation experiments: a beam scanning approach.

Photobleaching is a fluorophore-damaging process that commonly afflicts single-molecule fluorescence studies. It becomes an especially severe problem in fluorescence fluctuation experiments when studying slowly diffusing particles. One way to circumvent this problem is to use beam scanning to decrease the residence time of the fluorophores in the excitation volume. We report a systematic study of the effects of circular beam scanning on the photobleaching of fluorescent particles as observed in single-photon excitation fluorescence fluctuation experiments. We start by deriving a simple expression relating the average detected fluorescence to the photobleaching cross section of the fluorophores. We then perform numerical calculations of the spatial distribution of fluorescent particles in order to understand under which conditions beam scanning can prevent the formation of a photobleaching hole. To support these predictions, we show experimental results obtained for large unilamellar vesicles containing a small amount of the fluorescent lipophilic tracer DiD. We establish the required scanning radius and frequency range in order to obtain sufficient reduction of the photobleaching effect for that system. From the detected increase in fluorescence upon increase in scanning speed, we estimate the photobleaching cross section of DiD.     

Probing the bottom of a folding funnel using conformationally gated electron transfer reactions

The effect of global stability on the kinetics of interconversion between the native (N) and a compact, partially unfolded form (I) of iso-1-cytochrome c stabilized by His73-heme ligation is investigated using a novel conformationally gated ET method. For the K73H variant and the 2-fold less stable AcH73 variant, the N and I conformers are of nearly equal stability at pH 7.5. The pH jump kinetic data yield kobs = kNI + kIN of 35-40 s-1 at final pH values from 6 to 8 for the AcH73 variant, about 3-fold faster than for the more stable K73H variant. Gated ET measurements give kNI = 28 s-1 and kIN = 13 s-1 for the AcH73 variant, 10- and 2-fold greater than that for the more stable K73H variant. Thus, funneled landscapes have evolved such that loss of global stability lowers barriers at the bottom of a folding funnel, still allowing for efficient folding.     

基于双发射免标记核酸探针的比率型荧光传感器用于银的检测

构建了一种新型免标记的双发射荧光比率核酸探针(GelRed/[G40]/Tb^3+)并用于Ag+的检测。对于GelRed/[G40]/Tb^3+探针,GelRed作为一种核酸染料嵌入到单链DNA-[G40]中,形成的GelRed/[G40]作为稳定的内置参照标准,在激发波长290 nm处,发射荧光强度固定不变的红色荧光(发射波长为635 nm),而[G40]/Tb^3+作为敏感的响应信号,随着Ag^+浓度的增加,产生的绿色荧光逐渐增强(发射波长为545 nm),[G40]/Tb3+与GelRed/[G40]发射的荧光强度比值也发生相应的改变,从而实现对Ag^+的定量检测。在优化的实验条件下,[G40]/Tb^3+与GelRed/[G40]荧光强度比值和Ag^+浓度在0~7.5μmol/L的范围内具有较好的线性关系,Ag^+检出限为0.156μmol/L。本传感器在10 min内就可完成对Ag^+的分析。方法已用于自来水样中Ag^+的检测,与ICP-MS法检测结果一致。     

Probing redox proteins on a gold surface by single molecule fluorescence spectroscopy

The interaction between the fluorescently labeled redox protein, azurin, and a thin gold film is characterized using single-molecule fluorescence intensity and lifetime measurements. Fluorescence quenching starts at distances below 2.3 nm from the gold surface. At shorter distances the quantum yield may decrease down to fourfold for direct attachment of the protein to bare gold. Outside of the quenching range, up to fivefold enhancement of the fluorescence is observed on average with increasing roughness of the gold layer. Fluorescence-detected redox activity of individual azurin molecules, with a lifetime switching ratio of 0.4, is demonstrated for the first time close to a gold surface.     

Study of binding and denaturation dynamics of IgG and anti-IgG using dual color fluorescence correlation spectroscopy

In this article, we present a systematic study on IgG and Fab fragment of anti-IgG molecules using fluorescence auto- and cross-correlation spectroscopy to investigate their diffusion characteristics, binding kinetics, and the effect of small organic molecule, urea on their binding. Through our analysis, we found that the diffusion coefficient for IgG and Fab fragment of anti-IgG molecules were 37 ± 2 μm² s⁻¹ and 56 ± 2 μm² s⁻¹, respectively. From the binding kinetics study, the respective forward (k_a) and backward (k_d) reaction rates were (5.25 ± 0.25) × 10⁶ M⁻¹ s⁻¹ and 0.08 ± 0.005 s⁻¹, respectively and the corresponding dissociation binding constant (K_D) was 15 ± 2 nM. We also found that urea inhibits the binding of these molecules at 4 M concentration due to denaturation.     

pH-controlled reversible drug binding and release using a cytosine-rich hairpin DNA

Here we report that a cytosine-rich DNA carrier, that oscillates between a hairpin and an i-motif structure in its response to pH variation, can be used as a drug binding and release device.     

Ultrafast site-specific fluorescence quenching of 2-aminopurine in a DNA hairpin studied by femtosecond down-conversion

The ΔP(-)PBS analog of the DNA primary binding sequence (PBS) of the HIV-1 genome labeled at different positions by 2-aminopurine (2-AP) is investigated by a novel femtosecond fluorescence down-conversion experiment with 0.3-ps time resolution. The high signal-to-noise ratio of the fluorescence kinetics makes it possible to reveal four distinct decay times ranging from 0.8 ps to 2-3 ns for all the three labeling positions. This suggests the existence of at least four different quenching conformations of 2-AP with its nearest neighbors, and underscores the structural heterogeneity of the loop region of ΔP(-)PBS. Sub-5-ps components are found and attributed to stacking interactions of 2-AP with the flanking guanine (G) side chains, consistent with the NMR structure of ΔP(-)PBS. The observation of a significant increase of their total amplitude when 2-AP is positioned close to the rigid 3'-half of the G-rich stem gives further support to this assignment. Only a minor portion of conformations involves slow nanosecond collisional quenching.     

Probing the mechanisms of ambient ionization by laser‐induced fluorescence spectroscopy

The ionization mechanisms of several atmospheric pressure ion sources based on desorption and ionization of samples deposited on a surface were studied. Home‐built desorption electrospray ionization (DESI), laserspray ionization (LSI), and atmospheric pressure matrix‐assisted laser desorption/ionization (AP‐MALDI) sources were characterized using low‐molecular‐weight compounds, in particular fluorescent dyes. Detection of the desorbed and ionized species was performed by laser‐induced fluorescence and ion cyclotron resonance mass spectrometry. The dependences of the signal intensities on various experimental parameters were studied. The data obtained reveals common features, such as formation of solvated species and clusters in the ionization processes, in all of the techniques considered. Copyright © 2012 John Wiley & Sons, Ltd.     

Monitoring DNA structures by dual fluorescence of pyrene derivatives

We have developed a nucleotide modified by a pyrene derivative with dual fluorescence. The dual fluorescence of the fluorophore, which was incorporated into DNA, was effectively controlled at ambient temperature according to DNA structural status. Our nucleoside with dual fluorescence is effective as a conceptually new probe for monitoring DNA hybridization by the color change without multilabeling with fluorescent dyes.