Single-molecule analysis of restriction DNA fragments using fluorescence correlation spectroscopy

A fluorescence correlation spectroscopy-based enzyme assay for human Dicer

We used fluorescence correlation spectroscopy (FCS) to establish an in vitro assay to investigate RNase activity of human Dicer (Werner et al., Biol Chem 393(3):187-193). FCS allows investigating the interactions of different particles due to their differing diffusion mobility, provided that one of the interacting partners exhibit a fluorescence label. In our case we used a fluorophore-labeled double-stranded RNA (dsRNA) as substrate to monitor Dicer activity. The dsRNA was cleaved by the enzyme resulting in a five-nucleotide-short single-stranded RNA (ssRNA) fragment carrying the fluorophore, which could be distinguished from the substrate and unlabeled second product by FCS. Furthermore, we refer to additional (control) experiments to confirm obtained data.

A rapid and high-throughput quantitation assay of the nuclear factor κB activity using fluorescence correlation spectroscopy in the setting of clinical laboratories

Background

Transcription factor nuclear factor-κB (NF-κB) plays a key role in the regulation of immune responses to inflammation. However, convenient assay systems to quantitate the NF-κB activity level in a timely manner are not available in the setting of clinical laboratories. Therefore, we developed a novel and high-throughput quantitative assay based on fluorescence correlation spectroscopy (FCS) to detect the NF-κB activity level in cellular nuclear extracts and evaluated the performance of this method. The basic principle of this assay is to calculate the binding fraction of NF-κB to fluorescent-labeled DNA probes, which contain NF-κB binding sites.

Methods

Non-fluorescent competitive probes are employed to normalize the influence of the viscosity of the nuclear extracts between samples and to eliminate the influence of nonspecific binding of the fluorescent probes. To confirm accurate quantitation, human recombinant NF-κB p50 was mixed into U937 cell nuclear extracts, and the binding fraction of the fluorescent probes to NF-κB in the mixture was calculated for quantitation. To evaluate whether this method can be applied to measure the NF-κB activity in human lymphocytes, the NF-κB activity levels of systemic inflammatory response syndrome patients during perioperative periods were measured.

Results

The percentage recovery was 88.9%. The coefficients of variation of the intra-assay were approximately 10%. NF-κB activity levels during the perioperative period can were successfully measured. The assay time for the FCS measurement was within 20 minutes.

Conclusions

This assay system can be used to quantitate NF-κB activity levels in a timely manner in the setting of hospital laboratories.

Nanoaperture-enhanced signal-to-noise ratio in fluorescence correlation spectroscopy

The fluorescence enhancement found in gold nanoapertures is demonstrated to increase the signal-to-noise ratio (SNR) in fluorescence correlation spectroscopy (FCS). Starting from a general discussion on noise in FCS experiments, we show that fluorescence enhancement leads to a dramatic increase in the SNR. This prediction is confirmed by experiments where we report an experimental gain in SNR of about 1 order of magnitude, corresponding to a 100-fold reduction of the experiment duration. This technique is then applied to monitor the kinetics of a fast enzymatic cleavage reaction. This set of experiments evidence the feasibility of FCS analysis with fast integration times of about 1 s, opening the way to the monitoring of a variety of biochemical reactions at reduced time scales.

Fluorescence correlation spectroscopy analysis of the hydrophobic interactions of protein 4.1 with phosphatidyl serine liposomes

Fluorescence correlation spectroscopy (FCS) was applied to examine the interactions between a protein and a membrane lipid. The protein 4.1-phosphatidyl serine (PS) interactions served as the model system to demonstrate the membrane lipid-protein interactions. This protein was labeled with rhodamine and its interactions with PS-liposomes were measured by FCS. The present results clearly demonstrated that a small protein molecule, protein 4.1, interacts specifically with a large particle, a PS-liposome. This interaction appears to be hydrophobic and not electrostatic, since the bound protein 4.1 did not dissociate in solution and was specifically released from PS-liposomes by treatment with phospholipase A(2) (PLA(2)). In the present study, using FCS we could demonstrate that the serine residue of PS is required for protein 4.1 to bind to PS-liposomes and that the bound protein 4.1 is closely associated with the fatty acid of the PS molecule in the liposomes.

Detection of weak ligand interactions of leukocyte Ig-like receptor B1 by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) can directly and quickly detect the translational diffusion of individual fluorescence-labeled molecules in solutions. Although FCS analyses for protein-protein interactions have been performed, the very weak interactions generally observed in cell-cell recognition of the immune system have not been examined in detail. Here, we report the FCS analysis for low-affinity and fast-kinetic binding (K(d) greater than muM range) of the human inhibitory immune cell surface receptor, leukocyte immunoglobulin-like receptor B1 (LILRB1), to its ligands, MHC (major histocompatibility complex) class I molecules (MHCIs) by using the single-molecule FCS detection system which requires only a small amount of sample. Since the random labeling technique for LILRB1 disturbed the MHCI binding, we performed site-specific labeling of LILRB1 by introducing a cysteine residue at the C-terminus, which could be covalently attached with the fluorescence reagent, Alexa647. This technique can be applied to other type I membrane receptors. The low-affinity binding of LILRB1-Alexa647 to MHCIs (HLA-Cw4, and -G1) was detected by FCS, even though non-labeled MHCIs were only twice as big as the labeled LILRB1. Their dissociation constants (7.5 muM (HLA-Cw4) and 5.7 muM (HLA-G1)) could be determined and were consistent with surface plasmon resonance (SPR) data. These results indicate that the single-molecule FCS detection system is capable of analyzing the binding characteristics of immune cell surface receptors even in difficult cases such as (1) small amount of protein samples, (2) small difference in molecular weight and (3) weak affinity. Therefore, it is a powerful tool for characterization and high throughput inhibitor screening of a wide variety of cell-cell recognition receptors involved in immunologically relevant events.

Application of surface plasmon coupled emission to study of muscle

Muscle contraction results from interactions between actin and myosin cross-bridges. Dynamics of this interaction may be quite different in contracting muscle than in vitro because of the molecular crowding. In addition, each cross-bridge of contracting muscle is in a different stage of its mechanochemical cycle, and so temporal measurements are time averages. To avoid complications related to crowding and averaging, it is necessary to follow time behavior of a single cross-bridge in muscle. To be able to do so, it is necessary to collect data from an extremely small volume (an attoliter, 10(-18) liter). We report here on a novel microscopic application of surface plasmon-coupled emission (SPCE), which provides such a volume in a live sample. Muscle is fluorescently labeled and placed on a coverslip coated with a thin layer of noble metal. The laser beam is incident at a surface plasmon resonance (SPR) angle, at which it penetrates the metal layer and illuminates muscle by evanescent wave. The volume from which fluorescence emanates is a product of two near-field factors: the depth of evanescent wave excitation and a distance-dependent coupling of excited fluorophores to the surface plasmons. The fluorescence is quenched at the metal interface (up to approximately 10 nm), which further limits the thickness of the fluorescent volume to approximately 50 nm. The fluorescence is detected through a confocal aperture, which limits the lateral dimensions of the detection volume to approximately 200 nm. The resulting volume is approximately 2 x 10(-18) liter. The method is particularly sensitive to rotational motions because of the strong dependence of the plasmon coupling on the orientation of excited transition dipole. We show that by using a high-numerical-aperture objective (1.65) and high-refractive-index coverslips coated with gold, it is possible to follow rotational motion of 12 actin molecules in muscle with millisecond time resolution.

Protein-protein interaction analysis by C-terminally specific fluorescence labeling and fluorescence cross-correlation spectroscopy

Here, we describe novel puromycin derivatives conjugated with iminobiotin and a fluorescent dye that can be linked covalently to the C-terminus of full-length proteins during cell-free translation. The iminobiotin-labeled proteins can be highly purified by affinity purification with streptavidin beads. We confirmed that the purified fluorescence-labeled proteins are useful for quantitative protein–protein interaction analysis based on fluorescence cross-correlation spectroscopy (FCCS). The apparent dissociation constants of model protein pairs such as proto-oncogenes c-Fos/c-Jun and archetypes of the family of Ca²⁺-modulated calmodulin/related binding proteins were in accordance with the reported values. Further, detailed analysis of the interactions of the components of polycomb group complex, Bmi1, M33, Ring1A and RYBP, was successfully conducted by means of interaction assay for all combinatorial pairs. The results indicate that FCCS analysis with puromycin-based labeling and purification of proteins is effective and convenient for in vitro protein–protein interaction assay, and the method should contribute to a better understanding of protein functions by using the resource of available nucleotide sequences.

Lateral mobility of membrane-binding proteins in living cells measured by total internal reflection fluorescence correlation spectroscopy

Total internal reflection fluorescence correlation spectroscopy (TIR-FCS) allows us to measure diffusion constants and the number of fluorescent molecules in a small area of an evanescent field generated on the objective of a microscope. The application of TIR-FCS makes possible the characterization of reversible association and dissociation rates between fluorescent ligands and their receptors in supported phospholipid bilayers. Here, for the first time, we extend TIR-FCS to a cellular application for measuring the lateral diffusion of a membrane-binding fluorescent protein, farnesylated EGFP, on the plasma membranes of cultured HeLa and COS7 cells. We detected two kinds of diffusional motion-fast three-dimensional diffusion (D(1)) and much slower two-dimensional diffusion (D(2)), simultaneously. Conventional FCS and single-molecule tracking confirmed that D(1) was free diffusion of farnesylated EGFP close to the plasma membrane in cytosol and D(2) was lateral diffusion in the plasma membrane. These results suggest that TIR-FCS is a powerful technique to monitor movement of membrane-localized molecules and membrane dynamics in living cells.

Quantification of size distribution of restriction fragments in mitochondrial genome using fluorescence correlation spectroscopy

A crucial investigation is to quantify restriction fragment length polymorphisms without gel electrophoresis, as the distribution of fragment size is mainly evaluated on the gel, which cannot be easily quantified. We developed a method to determine the fragmentation of the mitochondrial genome caused by restriction enzymes using fluorescence correlation spectroscopy (FCS). Distribution of fragment size was evaluated by the decrease in amplitude of the fluorescence correlation function while the mitochondrial genome PCR product was digested with Hga I or Hae III. Using a multicomponent model, which was considered as a fragment length-weighted correlation function, we calculated the correlation amplitude theoretically expected and compared it to that measured by FCS. These amplitudes for Hga I were coincident, whereas the measured amplitude for Hae III was more than the theoretical one. Because of tetra-nucleotide recognition by Hae III, there were many more fragments than with Hga I. Therefore, the amplitude measured by FCS would be a very useful index for primary screening for alterations in the entire mitochondrial genome with restriction enzymes that have several polymorphic restriction sites in the genome.

Molecular dynamics of STAT3 on IL-6 signaling pathway in living cells

Signal transducer and activator of transcription 3 (STAT3) is a critical signal transducer of interleukin-6 (IL-6) signaling. To investigate the mobility and the dynamics of STAT3 complex on IL-6 signaling in living cells, we generated a chimeric gene consisting of STAT3 fused to enhanced green fluorescence protein, STAT3-GFP. STAT3-GFP was expressed in Hep3B cells and the dynamics of this protein were analyzed by fluorescence correlation spectroscopy. After IL-6 stimulation, STAT3 translocated from the cytoplasm to the nucleus, as shown previously. According to the analysis of STAT3 diffusion in stable transformants, the number of STAT3 molecules at the cytoplasmic membrane and in the cytoplasm decreased after IL-6 stimulation. In the nucleus, the diffusion speed of STAT3 complex strongly decreased after IL-6 stimulation. Furthermore, we found that STAT3 existed as a complex whose molecular weight was less than 400kDa before IL-6 addition. However, IL-6 stimulation induced the formation of STAT3 dimer as a megacomplex form whose molecular weight was more than 1MDa at the cytoplasm and a very slow diffusion complex in the nucleus.

Systematic error in fluorescence correlation measurements identified by a simple saturation model of fluorescence

The distortion of the fluorescence correlation function of a dye solution becomes larger with the increase in the excitation power, and eventually the parameters, such as the number of molecules and the diffusion time, obtained by the fluorescence correlation function systematically change. The most fundamental reason for this change is thought to be the distortion of the Gaussian excitation-detection field due to the saturation of the photocycle of the chromophore. The deviation from linearity of the fluorescence intensity causes the distortion of the fluorescence correlation function. Consequently, a smaller excitation power reduces the distortion and ensures an accurate measurement of the absolute value of these parameters. At the same time, the measurements at a fixed excitation power can be used to quantitatively determine the relative value of concentration and of the diffusion time. The deviation in the linearity of the fluorescence intensity and the deviation of the parameters show a high degree of correlation, and a 10% deviation of the intensity results in a prediction of a approximately 10% deviation in the number of molecules and a approximately 5% in the diffusion time.

Amphiphilic p-sulfonatocalix[4]arene-coated CdSe/ZnS quantum dots for the optical detection of the neurotransmitter acetylcholine

Water-soluble CdSe/ZnS (core-shell) semiconductor quantum dots surface-modified with tetrahexyl ether derivatives of p-sulfonatocalix[4]arene were synthesized for the optical detection of the neurotransmitter acetylcholine.

Calixarene-coated water-soluble CdSe–ZnS semiconductor quantum dots that are highly fluorescent and stable in aqueous solution

A simple method for the preparation of highly fluorescent and stable, water-soluble CdSe-ZnS quantum dots is reported using calix[4]arene carboxylic acids as surface coating agents; the coating of the surface with the calixarene and the conjugation of antibodies to the quantum dots are confirmed by fluorescence correlation spectroscopy.

Detection of protein–DNA interactions in crude cellular extracts by fluorescence correlation spectroscopy

Fluorescence correlation spectroscopy (FCS) is a methodology to examine directly the translational diffusion of individual fluorescence-labeled molecules in solutions. Recent studies using FCS have quantified various bimolecular reactions without any need for amplification. To evaluate further the applicability of FCS, we studied the specific binding between proteins and DNA in crude biological samples. Using an automated FCS system that was recently developed in our laboratories and is capable of distinguishing two or more molecular species in a multicomponent analysis, we detected the binding of two representative transcription factors, activator protein-1 (AP-1) and nuclear factor kappa B (NF-kappaB), in nuclear extracts of HeLa cells quantitatively with each sequence-specific DNA. The binding rates of these specific interactions were markedly augmented when cells were treated with tumor necrosis factor alpha which is known to activate both AP-1 and NF-kappaB. We also observed the pyrrolidine-dithiocarbamate-induced reciprocal regulation of these transcription factors. These results indicated that FCS is a useful tool for the analysis of complex interactions of transcription factors with DNA even in crude cellular extracts, suggesting that it is a powerful methodology for the study of a wide variety of molecular events under various experimental conditions.

In situ observation of mobility and anchoring of PKCbetaI in plasma membrane

We employed fluorescence correlation spectroscopy (FCS) to analyze the characteristics of biomolecules in living cells. Protein kinase C (PKC) changes its subcellular localization from cytosol to the plasma membrane by its ligand. Using FCS, we found PKCbetaI labeled with enhanced green fluorescent protein freely diffusing in cytosol. Upon 12-O-tetradecanoylphorbol-13-acetate activation, a large part of PKCbetaI is anchored in the plasma membrane but some PKCbetaI still moves freely near the plasma membrane. These results indicate that a diffusion-driven transport mechanism is appropriate for the molecular mechanism of the PKCbetaI localization change.

Dual-color fluorescence cross-correlation spectroscopy for monitoring the kinetics of enzyme-catalyzed reactions

Dual-color fluorescence correlation spectroscopy is a biophysical technique that enables precise and sensitive analyzes of molecular interactions. It is unique in its ability to analyze reactions in real time at nanomolar substrate concentrations and below, especially when applied to the monitoring of enzyme-catalyzed reactions. Furthermore, it offers a wide range of accessible reactions, restricted only by the prerequisite that a chemical bond or a physical interaction between two spectrally distinguishable fluorophores is established or broken. Recently, the optical setup of dual-color fluorescence correlation spectroscopy has been extended toward two-photon excitation, resulting in several advantages compared with standard excitation, such as lower fluorescence background, an even larger spectrum of potential fluorescence dyes to be used, as well as a more stable and simplified optical setup. So far, the method has been successfully employed to analyze the kinetics of nucleic acid and peptide modifications catalyzed by nucleases, polymerases, and proteases.

Fluorescently labeled model DNA sequences for exonucleolytic sequencing

We describe here the enzyme-catalyzed, low-density labeling of DNAs with fluorescent dyes. Firstly, for "natural" template DNAs, dNTPs were partially substituted in the labeling reactions by the respective fluorophore-bearing analogs. The DNAs were labeled by PCR using Taq DNA polymerase. The covalent incorporation of dye-dNTPs decreased in the following order: rhodamine-green-5-dUTP (Molecular Probes, the Netherlands), tetramethylrhodamine-4-dUTP (FluoroRed, Amersham Pharmacia Biotech), Cy5-dCTP (Amersham Pharmacia Biotech). Exonucleolytic degradation by the 3'-->5' exonuclease activity of T7 DNA polymerase (wild type) in the presence of excess reduced thioredoxin proceeded to complete breakdown of the labeled DNAs. The catalytic cleavage constants determined by fluorescence correlation spectroscopy were between 0.5 and 1.5 s(-1) at 16 degrees C, normalized for the covalently incorporated dye-nucleotides. Secondly, rhodamine-green-X-dUTP (Roche Diagnostics), tetramethylrhodamine-6-dUTP (Roche Diagnostics), and Cy5-dCTP were covalently incorporated into the antisense strand of "synthetic" 218-b DNA template constructs (master sequences) at well defined positions, starting from the primer binding site, by total substitution for the naturally occurring dNTPs. The 218-b DNA constructs were labeled by PCR with a thermostable 3'-->5' exonuclease deficient mutant of the Tgo DNA polymerase which we have selected. The advantage of the special, synthetic DNA constructs as compared to natural DNAs lies in the possibility of obtaining tailor-made nucleic acids, optimized for testing the performance of exonucleolytic sequencing. The number of incorporated fluorescent nucleotides determined by complete exonucleolytic degradation and fluorescence correlation spectroscopy were six out of six possible incorporations for rhodamine-green-X-dUTP and tetramethylrhodamine-6-dUTP, respectively. Their covalent and base-specific incorporations were confirmed by the novel analysis methodology of re-sequencing (i.e. mobility-shift gel electrophoresis, reversion-PCR and re-sequencing) first developed in the paper Földes-Papp et al. (2001) and in this paper. This methodology was then used by other groups within the whole sequencing project.

Probes for detection of specific DNA sequences at the single-molecule level

A method has been developed for highly sensitive detection of specific DNA sequences in a homogeneous assay using labeled oligonucleotide molecules in combination with single-molecule photon burst counting and identification. The fluorescently labeled oligonucleotides are called smart probes because they report the presence of complementary target sequences by a strong increase in fluorescence intensity. The smart probes consist of a fluorescent dye attached at the terminus of a hairpin oligonucleotide. The presented technique takes advantage of the fact that the used oxazine dye JA242 is efficiently quenched by complementary guanosine residues. Upon specific hybridization to the target DNA, the smart probe undergoes a conformational change that forces the fluorescent dye and the guanosine residues apart, thereby increasing the fluorescence intensity about six fold in ensemble measurements. To increase the detection sensitivity below the nanomolar range, a confocal fluorescence microscope was used to observe the fluorescence bursts from individual smart probes in the presence and absence of target DNA as they passed through the focused laser beam. Smart probes were excited by a pulsed diode laser emitting at 635 nm with a repetition rate of 64 MHz. Each fluorescence burst was identified by three independent parameters: (a) the burst size, (b) the burst duration, and (c) the fluorescence lifetime. Through the use of this multiparameter analysis, higher discrimination accuracies between smart probes and hybridized probe-target duplexes were achieved. The presented multiparameter detection technique permits the identification of picomolar target DNA concentrations in a homogeneous assay, i.e., the detection of specific DNA sequences in a 200-fold excess of labeled probe molecules.

Fluorescence correlation spectroscopy: molecular recognition at the single molecule level

Fluorescence correlation spectroscopy (FCS) is a fluorescence microscopy technique that allows the study of molecular interactions in extremely low volumes, at nanomolar concentrations, even when binding is not accompanied by a fluorescence change. It can be applied directly in living cells. FCS clearly considerably extends the possibilities of the classical techniques used in molecular recognition studies and can be considered to belong to a growing group of techniques that allow detection at the single molecule level. In this review, several applications of FCS, both in vitro and in vivo, will be discussed.

Analysis of the RNase T1 mediated cleavage of an immobilized gapped heteroduplex via fluorescence correlation spectroscopy

We report a new method for studying the activity of hydrolytic enzymes. Fluorescence correlation spectroscopy was used to observe online the hydrolyzation of a rhodamine B-labeled substrate by ribonuclease T1. A gapped heteroduplex substrate - a hybrid of a ribooligonucleotide and two smaller complementary deoxyribooligonucleotides - was immobilized via biotin to a streptavidin-coated surface of a coverslip. The reported method opens the possibility to study the cleavage of small substrates differing only slightly in molecular weight from the enzyme reaction product. The use of fluorescence correlation spectroscopy allows the detection of very low enzyme concentrations (down to 10(-21) mol 0.05 fM of RNase T1, corresponding to about 600 RNase T1 molecules in 0.02 ml).

Effect of electrostatic interactions on the binding of charged substrate to GroEL studied by highly sensitive fluorescence correlation spectroscopy

The binding processes of GroEL with apo cytochrome c (apo-cyt c) and disulfide-reduced apo alpha-lactalbumin (rLA) in homogeneous solution at low concentration were analyzed by fluorescence correlation spectroscopy (FCS) with extremely high sensitivity. Although apo-cyt c, a positively charged substrate, was tightly bound to GroEL in both the absence and the presence of 200 mM KCl, the strength of the binding was changed with varying salt concentration. Results from experiments when two different salts (KCl or MgCl(2)) were titrated into a sample solution containing GroEL and apo-cyt c clearly showed that the binding strength decreased with increasing salt concentration. On the other hand, the binding affinity of GroEL for rLA, a negatively charged substrate, increased by adding of 200 mM KCl. These results indicate that electrostatic interactions substantially contribute to the binding interactions by manipulating the binding affinity of charged substrates.

Single-molecule detection of DNA separations in microfabricated capillary electrophoresis chips employing focused molecular streams

DNA separations have been performed using microfabricated capillary electrophoresis chips and detected using a single-molecule fluorescence burst counting technique. We enhanced the percentage of electromigrating DNA molecules that were detected by focusing the sample through the 1-microm-diameter focused laser beam. The sample was focused by introducing a taper in the separation channel and by a sheath flow delivered from cross channels. The sample stream width, single-molecule velocities, and single-molecule count rates varied linearly with the current density ratio as expected. The optimal laser power for each focusing condition was investigated using dilute solutions of pBluescript DNA. Although fluorescence burst heights and background varied with laser power, the signal-to-noise ratio was only weakly dependent on this parameter using our single-molecule counting technique. Focused single-molecule counting was used to detect separations of a 100-1000-bp DNA sizing ladder. The increase in molecular detection efficiency was quantified by applying a focusing current midway through the ladder separation and comparing observed count rates to the known molecular concentration in the bands. The molecular detection efficiency varied linearly with the applied current density ratio, and greater than 3-fold enhancements in detection efficiency were achieved.