Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor

Single-molecule fluorescence spectroscopy and microscopy of biomolecular motors

The methods of single-molecule fluorescence spectroscopy and microscopy have been recently utilized to explore the mechanism of action of several members of the kinesin and myosin biomolecular motor protein families. Whereas ensemble averaging is removed in single-molecule studies, heterogeneity in the behavior of individual motors can be directly observed, without synchronization. Observation of translocation by individual copies of motor proteins allows analysis of step size, rate, pausing, and other statistical properties of the process. Polarization microscopy as a function of nucleotide state has been particularly useful in revealing new and highly rotationally mobile forms of particular motors. These experiments complement X-ray and biochemical studies and provide a detailed view into the local dynamical behavior of motor proteins.

Dynamics of single biomolecules in free solution

Instrumental advances have allowed the continuous observation of single-molecule trajectories in free solution. Diffraction-limited spectral resolution at video frame rates is routinely achieved by using commercial, intensified, charge-coupled device cameras, low-power continuous-wave lasers, and standard optical microscopes. Either the native fluorescence from large biomolecules or emission from conjugated fluorescence labels can be employed to follow multiple molecules over many seconds. Both molecular motion at the liquid/solid interface and in bulk solution can be recorded. The former reveals adsorption and desorption probabilities that are related to chromatographic retention processes and to the applicability of biocompatible materials. The latter allows the manipulation of particles and large biomolecules to facilitate separation and identification.

Three-dimensional orientational colocalization of individual donor–acceptor pairs

We report on the determination of the three-dimensional orientation of the donor and acceptor transition dipoles in individual fluorescence resonance energy transfer (FRET) pairs by means of scanning optical microscopy with annular illumination. Knowledge of the mutual orientation of the donor and acceptor dipole is mandatory for reliable distance determination based on FRET efficiency measurements. In our model system perylenediimide as the donor and terryelenediimide as the acceptor are coupled via a stiff p-terphenyl linker. The absorption dipoles of the donor and acceptor are selectively addressed by the 488 nm and 647 line of an Ar/Kr mixed gas laser, respectively. A clear deviation from collinearity is observed with a distribution of misalignment angles peaked around 22 degrees.

Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules

We use alternating-laser excitation to achieve fluorescence-aided molecule sorting (FAMS) and enable simultaneous analysis of biomolecular structure and interactions at the level of single molecules. This was performed by labeling biomolecules with fluorophores that serve as donor-acceptor pairs for Förster resonance energy transfer, and by using alternating-laser excitation to excite directly both donors and acceptors present in single diffusing molecules. Emissions were reduced to the distance-dependent ratio E, and a distance-independent, stoichiometry-based ratio S. Histograms of E and S sorted species based on the conformation and association status of each species. S was sensitive to the stoichiometry and relative brightness of fluorophores in single molecules, observables that can monitor oligomerization and local-environment changes, respectively. FAMS permits equilibrium and kinetic analysis of macromolecule-ligand interactions; this was validated by measuring equilibrium and kinetic dissociation constants for the interaction of Escherichia coli catabolite activator protein with DNA. FAMS is a general platform for ratiometric measurements that report on structure, dynamics, stoichiometries, environment, and interactions of diffusing or immobilized molecules, thus enabling detailed mechanistic studies and ultrasensitive diagnostics.

Simultaneous atomic-force and two-photon fluorescence imaging of biological specimens in vivo

We describe in this paper a home-built scanning-probe setup that combines the high spatial resolution of a commercial atomic-force microscope (AFM) with the high sensitivity and the discriminative power of a confocal two-photon fluorescence microscope. This scheme offers the ability of acquiring simultaneous, directly correlated topography and optical images with high sensitivity and resolution, and was successfully tested using model systems, such as dye-loaded latex beads. As a first biological application, we studied the (un)stacking of grana membranes in the envelope-free plant chloroplasts. The topographs showed two grana layers attached together in a "native unit" 15-16 nm thick and 4 nm protrusions on their surface, which we assign to Photosystem II reaction center. The optical imaging did not resolve single photosynthetic proteins, but helped in identifying the grana and indicated that the protein conformation and the chromophore binding are intact. Furthermore, our instrument allowed a direct comparison between the cell morphology and the distribution of the signaling protein H-Ras in living cells, i.e. mouse fibroblasts. With our approach the nanometer-scale resolving power of AFM is improved with the chemical identification capabilities of optical techniques, thus opening up interesting possibilities in various areas of research, including material and life sciences.

SINGLE-MOLECULE OPTICS

We review recent developments in single-molecule spectroscopy and microscopy. New optical methods provide access to the absorption, emission, or excitation spectra of single nano-objects and can determine either the positions of these objects with subwavelength accuracy or the full three-dimensional orientation of their transition dipole moments. Recent work aims at using single molecules as nanoparts or nanoelements in a variety of molecular-scale devices, from triggered sources of single photons to single-molecular switches. A prominent new direction explores the various interactions between molecules within individual multichromophoric systems obtained by chemical synthesis. These systems are the models for natural self-assembled systems such as the light-harvesting proteins of bacteria and green plants, which are currently studied on a single-molecule basis. Another important class of multichromophoric systems are conjugated polymers. The combination of microscopy with time- and frequency-resolved spectroscopy is opening a wide field of new and exciting applications to individual nano-objects.

Single-molecule imaging analysis of Ras activation in living cells

A single-molecule fluorescence resonance energy transfer (FRET) method has been developed to observe the activation of the small G protein Ras at the level of individual molecules. KB cells expressing H- or K-Ras fused with YFP (donor) were microinjected with the fluorescent GTP analogue BodipyTR-GTP (acceptor), and the epidermal growth factor-induced binding of BodipyTR-GTP to YFP-(H or K)-Ras was monitored by single-molecule FRET. On activation, Ras diffusion was greatly suppressed/immobilized, suggesting the formation of large, activated Ras-signaling complexes. These complexes may work as platforms for transducing the Ras signal to effector molecules, further suggesting that Ras signal transduction requires more than simple collisions with effector molecules. GAP334-GFP recruited to the membrane was also stationary, suggesting its binding to the signaling complex. The single-molecules FRET method developed here provides a powerful technique to study the signal-transduction mechanisms of various G proteins.

Optical studies of single molecules at room temperature

Recent developments in optical studies of single molecules at room temperature are reviewed, with an emphasis on the underlying principles and the potential of single-molecule experiments. Examples of single-molecule studies are given, including photophysics and photochemistry pertinent to single-molecule measurements, spectral fluctuations, Raman spectroscopy, diffusional motions, conformational dynamics, fluorescence resonant energy transfer, exciton dynamics, and enzymatic turnovers. These studies illustrate the information obtainable with the single-molecule approach that is hidden in ensemble-averaged measurements.

Conformational flexibility of four-way junctions in RNA

Helical junctions are common architectural features in RNA. They are particularly important in autonomously folding molecules, as exemplified by the hairpin ribozyme. We have used single-molecule fluorescence spectroscopy to study the dynamic properties of the perfect (4H) four-way helical junction derived from the hairpin ribozyme. In the presence of Mg(2+), the junction samples parallel and antiparallel conformations and both stacking conformers, with a bias towards one antiparallel stacking conformer. There is continual interconversion between the forms, such that there are several transitions per second under physiological conditions. Our data suggest that interconversion proceeds via an open intermediate with reduced cation binding in which coaxial stacking between helices is disrupted. The rate of interconversion becomes slower at higher Mg(2+) concentrations, yet the activation barrier decreases under these conditions, indicating that entropic effects are important. Transitions also occur in the presence of Na(+) only; however, the coaxial stacking appears incomplete under these conditions. The polymorphic and dynamic character of the four-way RNA junction provides a source of structural diversity, from which particular conformations required for biological function might be stabilised by additional RNA interactions or protein binding.

Single-molecule imaging of cooperative assembly of gamma-hemolysin on erythrocyte membranes

Single-molecule fluorescence imaging was used to investigate assembly of Staphylococcus aureus LukF and HS monomers into pore-forming oligomers (gamma-hemolysin) on erythrocyte membranes. We distinguished the hetero-oligomers from the monomers, as indicated by fluorescence resonance energy transfer between different dyes attached to monomeric subunits. The stoichiometry of LukF (donor) and HS (acceptor) subunits in oligomers was deduced from the acceptor emission intensities during energy transfer and by direct acceptor excitation, respectively. Based on populations of monomeric and oligomeric intermediates, we estimated 11 sequential equilibrium constants for the assembly pathway, beginning with membrane binding of monomers, proceeding through single pore oligomerization, and culminating in the formation of clusters of pores. Several stages are highly cooperative, critically enhancing the efficiency of assembly.

Photon antibunching and collective effects in the fluorescence of single bichromophoric molecules

The fluorescence of individual pairs of perylenemonoimide chromophores coupled via a short rigid linker is investigated. Photon antibunching is reported, indicating collective effects in the fluorescence, which are further substantiated by the observation of collective triplet off times and triplet lifetime shortening. The experimental findings are analyzed in terms of singlet-singlet and singlet-triplet annihilation based on Förster type energy transfer. The results reported here demonstrate that the statistical properties of the emission light of isolated single quantum systems can serve as a hallmark of intermolecular interactions.

Single-molecule measurement of protein folding kinetics

In order to investigate the behavior of single molecules under conditions far from equilibrium, we have coupled a microfabricated laminar-flow mixer to a confocal optical system. This combination enables time-resolved measurement of Förster resonance energy transfer after an abrupt change in solution conditions. Observations of a small protein show the evolution of the intramolecular distance distribution as folding progresses. This technique can expose subpopulations, such as unfolded protein under conditions favoring the native structure, that would be obscured in equilibrium experiments.

Fluorescence spectroscopy of single molecules under ambient conditions: methodology and technology

This review presents an overview of the fluorescence detection and spectroscopy of single molecules (SMS) in liquids and on surfaces under ambient conditions. The various techniques of SMS, such as confocal epifluorescence detection and wide-field imaging are presented and discussed, together with the different methods of data analysis such as fluorescence correlation spectroscopy and burst-by-burst analysis. Selected applications of the various techniques in physics, chemistry, and biology are described.

A four-way junction accelerates hairpin ribozyme folding via a discrete intermediate

The natural form of the hairpin ribozyme comprises two major structural elements: a four-way RNA junction and two internal loops carried by adjacent arms of the junction. The ribozyme folds into its active conformation by an intimate association between the loops, and the efficiency of this process is greatly enhanced by the presence of the junction. We have used single-molecule spectroscopy to show that the natural form fluctuates among three distinct states: the folded state and two additional, rapidly interconverting states (proximal and distal) that are inherited from the junction. The proximal state juxtaposes the two loop elements, thereby increasing the probability of their interaction and thus accelerating folding by nearly three orders of magnitude and allowing the ribozyme to fold rapidly in physiological conditions. Therefore, the hairpin ribozyme exploits the dynamics of the junction to facilitate the formation of the active site from its other elements. Dynamic interplay between structural elements, as we demonstrate for the hairpin ribozyme, may be a general theme for other functional RNA molecules.

Single-molecule transition-state analysis of RNA folding

How RNA molecules fold into functional structures is a problem of great significance given the expanding list of essential cellular RNA enzymes and the increasing number of applications of RNA in biotechnology and medicine. A critical step toward solving the RNA folding problem is the characterization of the associated transition states. This is a challenging task in part because the rugged energy landscape of RNA often leads to the coexistence of multiple distinct structural transitions. Here, we exploit single-molecule fluorescence spectroscopy to follow in real time the equilibrium transitions between conformational states of a model RNA enzyme, the hairpin ribozyme. We clearly distinguish structural transitions between effectively noninterchanging sets of unfolded and folded states and characterize key factors defining the transition state of an elementary folding reaction where the hairpin ribozyme's two helical domains dock to make several tertiary contacts. Our single-molecule experiments in conjunction with site-specific mutations and metal ion titrations show that the two RNA domains are in a contact or close-to-contact configuration in the transition state even though the native tertiary contacts are at most partially formed. Such a compact transition state without well formed tertiary contacts may be a general property of elementary RNA folding reactions.

Atomic force microscopy and scanning near-field optical microscopy studies on the characterization of human metaphase chromosomes

A better knowledge of biochemical and structural properties of human chromosomes is important for cytogenetic investigations and diagnostics. Fluorescence in situ hybridization (FISH) is a commonly used technique for the visualization of chromosomal details. Localizing specific gene probes by FISH combined with conventional fluorescence microscopy has reached its limit. Also, microdissecting DNA from G-banded human metaphase chromosomes by either a glass tip or by laser capture needs further improvement. By both atomic force microscopy (AFM) and scanning near-field optical microscopy (SNOM), local information from G-bands and chromosomal probes can be obtained. The final resolution allows a more precise localization compared to standard techniques, and the extraction of very small amounts of chromosomal DNA by the scanning probe is possible. Besides new strategies towards a better G-band and fluorescent probe detection, this study is focused on the combination of biochemical and nanomanipulation techniques which enable both nanodissection and nanoextraction of chromosomal DNA.

One-dimensional transport with dynamic disorder

We study the mean quenching time distribution and its moments in a one-dimensional N-site donor-bridge-acceptor system where all sites are coupled to a two-state jump bath for arbitrary disorder and an arbitrary ratio kappa identical with <k>/R of the bath jump rate R and the average hopping rate <k>. When kappaN approximately 1, the quenching time distribution has long power-law tails even when the waiting times are exponentially distributed. These disappear for kappaN<<1 where the hopping rate self-averages on the bath relaxation time scale. In the absence of disorder or for small kappa, the mean quenching time scales linearly with N. Otherwise, we observe a power law, approximately N1+gamma, with a crossover to linear scaling (gamma=0) for large N. Distributions of particle position, its second moment, velocity and diffusion coefficient are computed in the infinite N limit. For times longer than R-1, the dynamic disorder self-averages and the average position, velocity, and diffusion coefficient scale linearly in time.

Photodestruction intermediates probed by an adjacent reporter molecule

We used a fluorescence resonance energy transfer donor molecule to probe the multiple intermediates in the photoinduced destruction of an acceptor molecule. These intermediates are nonemitting but are still able to quench the fluorescence of the donor at a distance scale shorter than conventional fluorescence resonance energy transfer, suggesting novel biophysical applications.

High-throughput single molecule screening of DNA and proteins

We report a novel imaging technology for real time comprehensive analysis of molecular alterations in cells and tissues appropriate for automation and adaptation to high-throughput applications. With these techniques it should eventually be possible to perform simultaneous analysis of the entire contents of individual biological cells with a sensitivity and selectivity sufficient to determine the presence or absence of a single copy of a targeted analyte (e.g., DNA region, RNA region, protein), and to do so at a relatively low cost. The technology is suitable for DNA and RNA through sizing or through fluorescent hybridization probes, and for proteins and small molecules through fluorescence immunoassays. This combination of the lowest possible detection limit and the broadest applicability to biomolecules represents the final frontier in bioanalysis. The general scheme is based on novel concepts for single molecule detection (SMD) and characterization recently demonstrated in our laboratory. Since minimal manipulation is involved, it should be possible to screen large numbers of cells in a short time to facilitate practical applications. This opens up the possibility of finding single copies of DNA or proteins within single biological cells for disease markers without performing polymerase chain reaction or other biological amplification.

Biology and polymer physics at the single-molecule level

The ability to look at individual molecules has given us new insights into molecular processes. Examples of our recent work are given to illustrate how behaviour that may otherwise be hidden from view can be clearly seen in single-molecule experiments.

Single-molecule folding

Recent developments in fluorescence and force spectroscopy enable us to go beyond the ensemble average and measure the behavior of individual biomacromolecules. These single-molecule approaches can directly resolve transient intermediate states and multiple reaction pathways, and thus are uniquely powerful in characterizing the complex dynamics of biological processes. Recent applications of these two techniques to the protein and RNA folding problems have led to exciting new results.

Single-molecule reader for proteomics and genomics

Recent developments in ultrasensitive fluorescence microscopy enabled the detection and detailed characterization of individual biomolecules in their native environment. New types of information can be obtained from studying individual molecules, which is not accessible from ensemble measurements. Moreover, this methodological advance matches the need of bioscience to downscale the sample amount required for screening devices. It is envisioned that concentrations as low as approximately 1000 molecules contained in a sample of 1 nl can be detected in a chip-based assay. In this review, we overview state-of-the-art single molecule microscopy with respect to its applicability to ultrasensitive screening. Quantitative estimations will be given, based on a novel apparatus designed for large area screening at single molecule sensitivity.

Excitation energy transfer in dendritic host-guest donor-acceptor systems

We report on a study of a physically formed host-guest system, which was designed to be investigated by fluorescence energy transfer. All donor and acceptor molecules used were cyanine dyes. Investigation was performed at the ensemble level as well as at the single-molecule level. The ensemble measurements revealed a distribution of binding sites as well for the donor as for the acceptor. Accordingly, we found a distribution of the energy transfer efficiency. At the single-molecule level, these distributions are still present. We could discriminate entities that show very efficient energy transfer, some that do not show any energy transfer and systems whose energy transfer efficiency is only about 50%. The latter allowed the time-resolved detection of energy transfer of single entities through the acceptor decay. Finally, we discuss the observation that the energy transfer efficiency fluctuates as a function of time.

Single-molecule fluorescence of nucleic acids

Less than a decade old, single-molecule fluorescence of nucleic acids has rapidly become an important tool in the arsenal of biological probes. A variety of novel approaches to investigate conformational dynamics, catalytic mechanisms, folding pathways and protein-nucleic-acid interactions have recently been devised for nucleic acids using this technique. Combined with biomechanical tools and ensemble measurements, single-molecule fluorescence methods extend our ability to observe and understand biomolecules and complex biological processes.

Single molecule fluorescence and force microscopy

The investigation of biomolecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states occurring highly correlated in space and time within an arrangement of various elements. Recent advances in the development of new microscopy techniques with sensitivity at the single molecule have gained access to essentially new types of information obtainable from imaging biomolecular samples. These methodologies are described here in terms of their applicability to the in vivo detection and visualization of molecular processes on surfaces, membranes, and cells. First examples of single molecule microscopy on cell membranes revealed new basic insight into the lateral organization of the plasma membrane, providing the captivating perspective of an ultra-sensitive methodology as a general tool to study local processes and heterogeneities in living cells.

Initiation and re-initiation of DNA unwinding by the Escherichia coli Rep helicase

Helicases are motor proteins that couple conformational changes induced by ATP binding and hydrolysis with unwinding of duplex nucleic acid, and are involved in several human diseases. Some function as hexameric rings, but the functional form of non-hexameric helicases has been debated. Here we use a combination of a surface immobilization scheme and single-molecule fluorescence assays--which do not interfere with biological activity--to probe DNA unwinding by the Escherichia coli Rep helicase. Our studies indicate that a Rep monomer uses ATP hydrolysis to move toward the junction between single-stranded and double-stranded DNA but then displays conformational fluctuations that do not lead to DNA unwinding. DNA unwinding initiates only if a functional helicase is formed via additional protein binding. Partial dissociation of the functional complex during unwinding results in interruptions ('stalls') that lead either to duplex rewinding upon complete dissociation of the complex, or to re-initiation of unwinding upon re-formation of the functional helicase. These results suggest that the low unwinding processivity observed in vitro for Rep is due to the relative instability of the functional complex. We expect that these techniques will be useful for dynamic studies of other helicases and protein-DNA interactions.

Why are sweet proteins sweet? Interaction of brazzein, monellin and thaumatin with the T1R2-T1R3 receptor

Sweet tasting proteins interact with the same receptor that binds small molecular weight sweeteners, the T1R2-T1R3 G-protein coupled receptor, but the key groups on the protein surface responsible for the biological activity have not yet been identified. I propose that sweet proteins, contrary to small ligands, do not bind to the 'glutamate-like' pocket but stabilize the free form II of the T1R2-T1R3 receptor by attachment to a secondary binding site. Docking of brazzein, monellin and thaumatin with a model of the T1R2-T1R3 sweet taste receptor shows that the most likely complexes can indeed stabilize the active form of the receptor.

Microscope-based techniques to study cell adhesion and migration

Modern light microscopy has evolved to provide a variety of quantitative imaging techniques and also the capability to perturb structure-function relationships in living cells. The advances have been especially useful in the study of cell adhesion and migration. This review will focus on how such microscopy-based techniques can be useful in situ to study the molecular interactions and dynamics, to locally perturb actin-based structures and to measure the traction forces exerted by motile cells.

Imaging of the fluorescence spectrum of a single fluorescent molecule by prism-based spectroscopy

We have devised a novel method to visualize the fluorescence spectrum of a single fluorescent molecule using prism-based spectroscopy. Equipping a total internal reflection microscope with a newly designed wedge prism, we obtained a spectral image of a single rhodamine red molecule attached to an essential light chain of myosin. We also obtained a spectral image of single-pair fluorescence resonance energy transfer between rhodamine red and Cy5 in a double-labeled myosin motor domain. This method could become a useful tool to investigate the dynamic processes of biomolecules at the single-molecule level.

Fluorescence resonance energy transfer (FRET) and competing processes in donor-acceptor substituted DNA strands: a comparative study of ensemble and single-molecule data

We studied the fluorescence resonance energy transfer (FRET) efficiency of different donor-acceptor labeled model DNA systems in aqueous solution from ensemble measurements and at the single molecule level. The donor dyes: tetramethylrhodamine (TMR); rhodamine 6G (R6G); and a carbocyanine dye (Cy3) were covalently attached to the 5'-end of a 40-mer model oligonucleotide. The acceptor dyes, a carbocyanine dye (Cy5), and a rhodamine derivative (JA133) were attached at modified thymidine bases in the complementary DNA strand with donor-acceptor distances of 5, 15, 25 and 35 DNA-bases, respectively. Anisotropy measurements demonstrate that none of the dyes can be observed as a free rotor; especially in the 5-bp constructs the dyes exhibit relatively high anisotropy values. Nevertheless, the dyes change their conformation with respect to the oligonucleotide on a slower time scale in the millisecond range. This results in a dynamic inhomogeneous distribution of donor/acceptor (D/A) distances and orientations. FRET efficiencies have been calculated from donor and acceptor fluorescence intensity as well as from time-resolved fluorescence measurements of the donor fluorescence decay. Dependent on the D/A pair and distance, additional strong fluorescence quenching of the donor is observed, which simulates lower FRET efficiencies at short distances and higher efficiencies at longer distances. On the other hand, spFRET measurements revealed subpopulations that exhibit the expected FRET efficiency, even at short D/A distances. In addition, the measured acceptor fluorescence intensities and lifetimes also partly show fluorescence quenching effects independent of the excitation wavelength, i.e. either directly excited or via FRET. These effects strongly depend on the D/A distance and the dyes used, respectively. The obtained data demonstrate that besides dimerization at short D/A distances, an electron transfer process between the acceptor Cy5 and rhodamine donors has to be taken into account. To explain deviations from FRET theory even at larger D/A distances, we suggest that the pi-stack of the DNA double helix mediates electron transfer from the donor to the acceptor, even over distances as long as 35 base pairs. Our data show that FRET experiments at the single molecule level are rather suited to resolve fluorescent subpopulations in heterogeneous mixture, information about strongly quenched subpopulations gets lost.

Cell biology beyond the diffraction limit: near-field scanning optical microscopy

Throughout the years, fluorescence microscopy has proven to be an extremely versatile tool for cell biologists to study live cells. Its high sensitivity and non-invasiveness, together with the ever-growing spectrum of sophisticated fluorescent indicators, ensure that it will continue to have a prominent role in the future. A drawback of light microscopy is the fundamental limit of the attainable spatial resolution – ∼250 nm – dictated by the laws of diffraction. The challenge to break this diffraction limit has led to the development of several novel imaging techniques. One of them, near-field scanning optical microscopy (NSOM), allows fluorescence imaging at a resolution of only a few tens of nanometers and, because of the extremely small near-field excitation volume, reduces background fluorescence from the cytoplasm to the extent that single-molecule detection sensitivity becomes within reach. NSOM allows detection of individual fluorescent proteins as part of multimolecular complexes on the surface of fixed cells, and similar results should be achievable under physiological conditions in the near future.

Detection and characterization of single biomolecules at surfaces

The investigation of bio-molecules has entered a new age since the development of methodologies capable of studies at the level of single molecules. In biology, most molecules show a complex dynamical behavior, with individual motions and transitions between different states, occurring as highly correlated in space and time within an arrangement of various elements. In order to resolve such dynamical changes in ensemble average techniques, one would have to synchronize all molecules, which is hard to achieve and might interfere with important system properties. Single molecule studies, in contrast, do not require pretreatment of the system and resume, therefore, much less invasive methodologies. Here, we review recent employments for the investigation of bio-molecules on surfaces, in which the high local and temporal resolution of two complementary techniques, atomic force microscopy and single molecule fluorescence microscopy, is used to address single molecules. Novel methodologies for the characterization of biologically relevant parameters, functions and dynamical aspects of individual molecules are described.

Duplex Scorpion primers in SNP analysis and FRET applications

Scorpions are fluorogenic PCR primers with a probe element attached at the 5'-end via a PCR stopper. They are used in real-time amplicon-specific detection of PCR products in homogeneous solution. Two different formats are possible, the 'stem-loop' format and the 'duplex' format. In both cases the probing mechanism is intramolecular. We have shown that duplex Scorpions are efficient probes in real-time PCR. They give a greater fluorescent signal than stem-loop Scorpions due to the vastly increased separation between fluorophore and quencher in the active form. We have demonstrated their use in allelic discrimination at the W1282X locus of the ABCC7 gene and shown that they can be used in assays where fluorescence resonance energy transfer is required.

Single-molecule fluorescence resonance energy transfer

Fluorescent resonance energy transfer (FRET) is a powerful technique for studying conformational distribution and dynamics of biological molecules. Some conformational changes are difficult to synchronize or too rare to detect using ensemble FRET. FRET, detected at the single-molecule level, opens up new opportunities to probe the detailed kinetics of structural changes without the need for synchronization. Here, we discuss practical considerations for its implementation including experimental apparatus, fluorescent probe selection, surface immobilization, single-molecule FRET analysis schemes, and interpretation.

Ratiometric single-molecule studies of freely diffusing biomolecules

We outline recent developments in biological single-molecule fluorescence detection with particular emphasis on observations by ratiometric fluorescence resonance energy transfer (FRET) of biomolecules freely diffusing in solution. Single-molecule-diffusion methodologies were developed to minimize perturbations introduced by interactions between molecules and surfaces. Confocal microscopy is used in combination with sensitive detectors to observe bursts of photons from fluorescently labeled biomolecules as they diffuse through the focal volume. These bursts are analyzed to extract ratiometric observables such as FRET efficiency and polarization anisotropy. We describe the development of single-molecule FRET methodology and its application to the observation of the Förster distance dependence and the study of protein folding and polymer physics problems. Finally, we discuss future advances in data acquisition and analysis techniques that can provide a more complete picture of the accessible molecular information.