Pulsed-interleaved excitation FRET measurements on single duplex DNA molecules inside C-shaped nanoapertures

Lasing from Micro- and Nano-Scale Photonic Disordered Structures for Biomedical Applications

A disordered photonic medium is one in which scatterers are distributed randomly. Light entering such media experiences multiple scattering events, resulting in a "random walk"-like propagation. Micro- and nano-scale structured disordered photonic media offer platforms for enhanced light-matter interaction, and in the presence of an appropriate gain medium, coherence-tunable, quasi-monochromatic lasing emission known as random lasing can be obtained. This paper discusses the fundamental physics of light propagation in micro- and nano-scale disordered structures leading to the random lasing phenomenon and related aspects. It then provides a state-of-the-art review of this topic, with special attention to recent advancements of such random lasers and their potential biomedical imaging and biosensing applications.

Numerical Study on a Bound State in the Continuum Assisted Plasmonic Refractive Index Sensor

Plasmonic sensors have attracted intensive attention due to their high sensitivity. However, due to intrinsic metallic loss, plasmonic sensors usually have a large full width at half maximum (FWHM) that limits the wavelength resolution. In this paper, we numerically investigate and propose a dielectric grating-assisted plasmonic device, leveraging the bound states in the continuum (BIC) effect to suppress the FWHM of the resonance. We initiate quasi-SP-BIC modes at 1559 nm and 1905 nm wavelengths by slightly tilting the incident angle at 2° to break the symmetry, featuring a narrow linewidth of 1.8 nm and 0.18 nm at these two wavelengths, respectively. Refractive index sensing has also been investigated, showing high sensitivity of 938 nm/RIU and figure of merit (FOM) of 521/RIU at 1559 nm and even higher sensitivity of 1264 nm/RIU and FOM of 7022/RIU at 1905 nm.

Plasmonic Metasurfaces for Medical Diagnosis Applications: A Review

Plasmonic metasurfaces have been widely used in biosensing to improve the interaction between light and biomolecules through the effects of near-field confinement. When paired with biofunctionalization, plasmonic metasurface sensing is considered as a viable strategy for improving biomarker detection technologies. In this review, we enumerate the fundamental mechanism of plasmonic metasurfaces sensing and present their detection in human tumors and COVID-19. The advantages of rapid sampling, streamlined processes, high sensitivity, and easy accessibility are highlighted compared with traditional detection techniques. This review is looking forward to assisting scientists in advancing research and developing a new generation of multifunctional biosensors.

Enhancing Single-Molecule Fluorescence Spectroscopy with Simple and Robust Hybrid Nanoapertures

Plasmonic nanoapertures have found exciting applications in optical sensing, spectroscopy, imaging, and nanomanipulation. The subdiffraction optical field localization, reduced detection volume (~attoliters), and background-free operation make them particularly attractive for single-particle and single-molecule studies. However, in contrast to the high field enhancements by traditional "nanoantenna"-based structures, small field enhancement in conventional nanoapertures results in weak light-matter interactions and thus small enhancement of spectroscopic signals (such as fluorescence and Raman signals) of the analytes interacting with the nanoapertures. In this work, we propose a hybrid nanoaperture design termed "gold-nanoislands-embedded nanoaperture" (AuNIs-e-NA), which provides multiple electromagnetic "hotspots" within the nanoaperture to achieve field enhancements of up to 4000. The AuNIs-e-NA was able to improve the fluorescence signals by more than 2 orders of magnitude with respect to a conventional nanoaperture. With simple design and easy fabrication, along with strong signal enhancements and operability over variable light wavelengths and polarizations, the AuNIs-e-NA will serve as a robust platform for surface-enhanced optical sensing, imaging, and spectroscopy.

Zero-mode waveguides can be made better: fluorescence enhancement with rectangular aluminum nanoapertures from the visible to the deep ultraviolet

Nanoapertures milled in metallic films called zero-mode waveguides (ZMWs) overcome the limitations of classical confocal microscopes by enabling single molecule analysis at micromolar concentrations with improved fluorescence brightness. While the ZMWs have found many applications in single molecule fluorescence studies, their shape has been mainly limited to be circular. Owing to the large parameter space to explore and the lack of guidelines, earlier attempts using more elaborate shapes have led to unclear conclusions whether or not the performance was improved as compared to a circular ZMW. Here, we comparatively analyze the performance of rectangular-shaped nanoapertures milled in aluminum to enhance the fluorescence emission rate of single molecules from the near infrared to the deep ultraviolet. Our new design is based on rational principles taking maximum advantage of the laser linear polarization. While the long edge of the nanorectangle is set to meet the cut-off size for the propagation of light into the nanoaperture, the short edge is reduced to 30 nm to accelerate the photodynamics while maintaining bright fluorescence rates. Our results show that both in the red and in the ultraviolet, the nanorectangles provide 50% brighter photon count rates as compared to the best performing circular ZMWs and achieve fluorescence lifetimes shorter than 300 ps. These findings can be readily used to improve the performance of ZMWs, especially for fast biomolecular dynamics, bright single-photon sources, and ultraviolet plasmonics.

Long-Range Single-Molecule Förster Resonance Energy Transfer between Alexa Dyes in Zero-Mode Waveguides

Zero-mode waveguide (ZMW) nano-apertures milled in metal films were proposed to improve the Förster resonance energy transfer (FRET) efficiency and enable single-molecule FRET detection beyond the 10 nm barrier, overcoming the restrictions of diffraction-limited detection in a homogeneous medium. However, the earlier ZMW demonstrations were limited to the Atto 550-Atto 647N fluorophore pair, asking the question whether the FRET enhancement observation was an artifact related to this specific set of fluorescent dyes. Here, we use Alexa Fluor 546 and Alexa Fluor 647 to investigate single-molecule FRET at large donor-acceptor separations exceeding 10 nm inside ZMWs. These Alexa fluorescent dyes feature a markedly different chemical structure, surface charge, and hydrophobicity as compared to their Atto counterparts. Our single molecule data on Alexa 546-Alexa 647 demonstrate enhanced FRET efficiencies at large separations exceeding 10 nm, extending the spatial range available for FRET and confirming the earlier conclusions. By showing that the FRET enhancement inside a ZMW does not depend on the set of fluorescent dyes, this report is an important step to establish the relevance of ZMWs to extend the sensitivity and detection range of FRET, while preserving its ability to work on regular fluorescent dye pairs.

Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis

In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100–300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.

Extending Single-Molecule Förster Resonance Energy Transfer (FRET) Range beyond 10 Nanometers in Zero-Mode Waveguides

Single-molecule Förster resonance energy transfer (smFRET) is widely used to monitor conformations and interaction dynamics at the molecular level. However, conventional smFRET measurements are ineffective at donor-acceptor distances exceeding 10 nm, impeding the studies on biomolecules of larger size. Here, we show that zero-mode waveguide (ZMW) apertures can be used to overcome the 10 nm barrier in smFRET. Using an optimized ZMW structure, we demonstrate smFRET between standard commercial fluorophores up to 13.6 nm distance with a significantly improved FRET efficiency. To further break into the classical FRET range limit, ZMWs are combined with molecular constructs featuring multiple acceptor dyes to achieve high FRET efficiencies together with high fluorescence count rates. As we discuss general guidelines for quantitative smFRET measurements inside ZMWs, the technique can be readily applied for monitoring conformations and interactions on large molecular complexes with enhanced brightness.

Plasmonic zero mode waveguide for highly confined and enhanced fluorescence emission

We fabricate a plasmonic nanoslot that is capable of performing enhanced single molecule detection at 10 μM concentrations. The nanoslot combines the tiny detection volume of a zero-mode waveguide and the field enhancement of a plasmonic nanohole. The nanoslot is fabricated on a bi-metallic film formed by the sequential deposition of gold and aluminum on a transparent substrate. Simulations of the structure yield an average near-field intensity enhancement of two orders of magnitude at its resonant frequency. Experimentally, we measure the fluorescence stemming from the nanoslot and compare it with that of a standard aluminum zero-mode waveguide. We also compare the detection volume for both structures. We observe that while both structures have a similar detection volume, the nanoslot yields a 25-fold fluorescence enhancement.

Combining gold nanoparticle antennas with single-molecule fluorescence resonance energy transfer (smFRET) to study DNA hairpin dynamics

The association of a plasmonic nano-antenna with single-molecule FRET technique presents new prospects to investigate the dynamics of biological molecules. However, the presence of a plasmonic nano-antenna significantly modifies the FRET rate and efficiency; this makes its applicability to the prevalent single-molecule FRET experiments unclear. Herein, using gold nanoparticle antennas of different sizes and DNA hairpins labelled with FRET pairs (Cy3 and Cy5) as the model system, we performed experiments to study the folding dynamics of single DNA hairpins at various salt concentrations. Our results indicate that gold nanoparticle antennas can enhance single-molecule fluorescence of Cy3 and Cy5 up to 3-5 folds, substantially reduce the FRET efficiency, and alter the obtained FRET efficiency histograms. However, the folding dynamics of DNA hairpins remains unaffected, and the correct kinetic and dynamic information can still be extracted from the seriously modified FRET efficiencies. Therefore, our experiments demonstrate the feasibility and compatibility for applying plasmonic nano-antennas to the mostly used single-molecule FRET assays, which provide a broad range of possibilities for the future applications of these nano-antennas in studying various essential biological processes.

Single-molecule detection at high concentrations with optical aperture nanoantennas

Single-molecule detection has become an indispensable technology in life science, and medical research. In order to get meaningful information on many biological processes, single-molecule analysis is required in micro-molar concentrations. At such high concentrations, it is very challenging to isolate a single molecule with conventional diffraction-limited optics. Recently, optical aperture nanoantennas (OANs) have emerged as a powerful tool to enhance the single-molecule detection under a physiological environment. The OANs, which consist of nano-scale apertures on a metallic film, have the following unique properties: (1) nanoscale light confinement; (2) enhanced fluorescence emission; (3) tunable radiation pattern; (4) reduced background noise; and (5) massive parallel detection. This review presents the fundamentals, recent developments and future perspectives in this emerging field.

FRET enhancement in aluminum zero-mode waveguides

Zero-mode waveguides (ZMWs) can confine light into attoliter volumes, which enables single molecule fluorescence experiments at physiological micromolar concentrations. Of the fluorescence spectroscopy techniques that can be enhanced by ZMWs, Förster resonance energy transfer (FRET) is one of the most widely used in life sciences. Combining zero-mode waveguides with FRET provides new opportunities to investigate biochemical structures or follow interaction dynamics at micromolar concentrations with single-molecule resolution. However, prior to any quantitative FRET analysis on biological samples, it is crucial to establish first the influence of the ZMW on the FRET process. Here, we quantify the FRET rates and efficiencies between individual donor-acceptor fluorophore pairs that diffuse into aluminum zero-mode waveguides. Aluminum ZMWs are important structures thanks to their commercial availability and the large amount of literature that describe their use for single-molecule fluorescence spectroscopy. We also compared the results between ZMWs milled in gold and aluminum, and found that although gold has a stronger influence on the decay rates, the lower losses of aluminum in the green spectral region provide larger fluorescence brightness enhancement factors. For both aluminum and gold ZMWs, we observed that the FRET rate scales linearly with the isolated donor decay rate and the local density of optical states. Detailed information about FRET in ZMWs unlocks their application as new devices for enhanced single-molecule FRET at physiological concentrations.

Nanophotonic enhancement of the Förster resonance energy-transfer rate with single nanoapertures

Tailoring the light-matter interaction and the local density of optical states (LDOS) with nanophotonics provides accurate control over the luminescence properties of a single quantum emitter. This paradigm is also highly attractive to enhance the near-field Förster resonance energy transfer (FRET) between two fluorescent emitters. Despite the wide applications of FRET in nanosciences, using nanophotonics to enhance FRET has remained a debated and complex challenge. Here we demonstrate enhanced energy transfer within single donor-acceptor fluorophore pairs confined in single gold nanoapertures. Experiments monitoring both the donor and the acceptor emission photodynamics clearly establish a linear dependence of the FRET rate on the LDOS in nanoapertures, demonstrating that nanophotonics can be used to intensify the near-field energy transfer. Strikingly, we observe a significant six-fold increase in the FRET rate for large donor-acceptor separations exceeding 13 nm. Exciting opportunities are opened to investigate biochemical structures with donor-acceptor distances much beyond the classical Förster radius. Importantly, our approach is fully compatible with the detection of single biomolecules freely diffusing in water solution under physiological conditions.

Single-molecule detection and radiation control in solutions at high concentrations via a heterogeneous optical slot antenna

We designed a heterogeneous optical slot antenna (OSA) that is capable of detecting single molecules in solutions at high concentrations, where most biological processes occur. A heterogeneous OSA consists of a rectangular nanoslot fabricated on heterogeneous metallic films formed by sequential deposition of gold and aluminum on a glass substrate. The rectangular nanoslot gives rise to large field and fluorescence enhancement for single molecules. The near-field intensity inside a heterogeneous OSA is 170 times larger than that inside an aluminum zero-mode waveguide (ZMW), and the fluorescence emission rate of a molecule inside the heterogeneous OSA is about 70 times higher than that of the molecule in free space. Our proposed heterogeneous optical antenna enables excellent balance between performance and cost. The design takes into account the practical experimental conditions so that the parameters chosen in the simulation are well within the reach of current nano-fabrication technologies. Our results can be used as a direct guidance for designing high-performance, low-cost plasmonic nanodevices for the study of bio-molecule and enzyme dynamics at the single-molecule level.

Placing individual molecules in the center of nanoapertures

While nanophotonic devices are unfolding their potential for single-molecule fluorescence studies, metallic quenching and steric hindrance, occurring within these structures, raise the desire for site-specific immobilization of the molecule of interest. Here, we refine the single-molecule cut-and-paste technique by optical superresolution routines to immobilize single fluorescent molecules in the center of nanoapertures. By comparing their fluorescence lifetime and intensity to stochastically immobilized fluorophores, we characterize the electrodynamic environment in these nanoapertures and proof the nanometer precision of our loading method.

Ensemble and single-molecule detected time-resolved FRET methods in studies of protein conformations and dynamics

Most proteins are nanomachines that are selected to execute specific functions and therefore should have some degree of flexibility. The driving force that excites specific motions of domains and smaller chain elements is the thermal fluctuations of the solvent bath which are channeled to selected modes of motions by the structural constraints. Consequently characterization of the ensembles of conformers of proteins and their dynamics should be expressed in statistical terms, i.e., determination of probability distributions of the various conformers. This can be achieved by measurements of time-resolved dynamic non-radiative excitation energy transfer (trFRET) within ensembles of site specifically labeled protein molecules. Distributions of intramolecular segmental end-to-end distances and their fast fluctuations can be determined, and fast and slow conformational transitions within selected sections of the molecule can be monitored and analyzed. Both ensemble and single-molecule detection methods can be applied for data collection. In combination with synchronization methods, time-resolved FRET was also used for studies of fast conformational transitions, in particular the folding/unfolding transitions.

Multiple-pulse pumping for enhanced fluorescence detection and molecular imaging in tissue

Applications of fluorescence based imaging techniques for detection in cellular and tissue environments are severely limited by autofluorescence of endogenous components of cells, tissue, and the fixatives used in sample processing. To achieve sufficient signal-to-background ratio, a high concentration of the probe needs to be used which is not always feasible. Since typically autofluorescence is in the nanosecond range, long-lived fluorescence probes in combination with time-gated detection can be used for suppression of unwanted autofluorescence. Unfortunately, this requires the sacrifice of the large portion the probe signal in order to sufficiently filter the background. We report a simple and practical approach to achieve a many-fold increase in the intensity of a long-lived probe without increasing the background fluorescence. Using controllable, well separated bursts of closely spaced laser excitation pulses, we are able to highly increase the fluorescence signal of a long-lived marker over the endogenous fluorescent background and scattering, thereby greatly increasing detection sensitivity. Using a commercially available confocal microscopy system equipped with a laser diode and time correlated single photon counting (TCSPC) detection, we are able to enhance the signal of a long-lived Ruthenium (Ru)-based probe by nearly an order of magnitude. We used 80 MHz bursts of pulses (12.5 ns pulse separation) repeated with a 320 kHz repetition rate as needed to adequately image a dye with a 380 ns lifetime. Just using 10 pulses in the burst increases the Ru signal almost 10-fold without any increase in the background signal.

Elimination of autofluorescence in fluorescence correlation spectroscopy using the AzaDiOxaTriAngulenium (ADOTA) fluorophore in combination with time-correlated single-photon counting (TCSPC)

Fluorescence correlation spectroscopy (FCS) is a frequently applied technique that allows for the precise and sensitive analysis of molecular diffusion and interactions. However, the potential of FCS for in vitro or ex vivo studies has not been fully realized due in part to artifacts originating from autofluorescence (fluorescence of inherent components and fixative-induced fluorescence). Here, we propose the azadioxatriangulenium (ADOTA) dye as a solution to this problem. The lifetime of the ADOTA probe, about 19.4 ns, is much longer than most components of autofluorescence. Thus, it can be easily separated by time-correlated single-photon counting methods. Here, we demonstrate the suppression of autofluorescence in FCS using ADOTA-labeled hyaluronan macromolecules (HAs) with Rhodamine 123 added to simulate diffusing fluorescent background components. The emission spectrum and decay rate of Rhodamine 123 overlap with the usual sources of autofluorescence, and its diffusion behavior is well known. We show that the contributions from Rhodamine 123 can be eliminated by time gating or by fluorescence lifetime correlation spectroscopy (FLCS). While the pairing of ADOTA and time gating is an effective strategy for the removal of autofluorescence from fluorescence imaging, the loss of photons leads to erroneous concentration values with FCS. On the other hand, FLCS eliminates autofluorescence without such errors. We then show that both time gating and FLCS may be used successfully with ADOTA-labeled HA to detect the presence of hyaluronidase, the overexpression of which has been observed in many types of cancer.

Pulsed interleaved excitation: principles and applications

Pulsed interleaved excitation (PIE) is the methodology of interleaved or alternating excitation of different fluorophores on the nanosecond timescale, which allows quasi-simultaneous, yet independent measurements to be performed. PIE simplifies quantification of several fluorescence techniques such as FCCS and FRET experiments. Foremost, it allows to specifically filter out spectral emission bleedthrough (crosstalk) and direct excitation without a decrease in the signal-to-noise ratio (SNR) of the experiment. Next, PIE allows determination of the absolute FRET efficiency from FCCS experiments in the case of nonperfect labeling. In recent years, PIE has been utilized in many different advanced FFS techniques. Combining MFD with PIE allows highly accurate and species-specific spFRET analyses to be performed. The combination of scanning FFS techniques with PIE combines the best of both techniques and allows for false-positive free measurements of molecular interactions in vitro and in living cells. In succession, a comprehensive overview of the principle and versatility of the PIE technique is discussed, the theory for analysis with PIE is outlined by comparing CW- and PIE-FCCS and finally, some of the most important applications of the PIE technique in literature are reviewed.

Modulation of physiological and pathological activities of lysozyme by biological membranes

The molecular details of interactions between lipid membranes and lysozyme (Lz), a small polycationic protein with a wide range of biological activities, have long been the focus of numerous studies. The biological consequences of this process are considered to embrace at least two aspects: i) correlation between antimicrobial and membranotropic properties of this protein, and ii) lipid-mediated Lz amyloidogenesis. The mechanisms underlying the lipid-assisted protein fibrillogenesis and membrane disruption exerted by Lz in bacterial cells are believed to be similar. The present investigation was undertaken to gain further insight into Lz-lipid interactions and explore the routes by which Lz exerts its antimicrobial and amyloidogenic actions. Binding and Förster resonance energy transfer studies revealed that upon increasing the content of anionic lipids in lipid vesicles, Lz forms aggregates in a membrane environment. Total internal reflection fluorescence microscopy and pyrene excimerization reaction were employed to study the effect of Lz on the structural and dynamic properties of lipid bilayers. It was found that Lz induces lipid demixing and reduction of bilayer free volume, the magnitude of this effect being much more pronounced for oligomeric protein.

Single-molecule tools elucidate H2A.Z nucleosome composition

Although distinct epigenetic marks correlate with different chromatin states, how they are integrated within single nucleosomes to generate combinatorial signals remains largely unknown. We report the successful implementation of single molecule tools constituting fluorescence correlation spectroscopy (FCS), pulse interleave excitation-based Förster resonance energy transfer (PIE-FRET) and fluorescence lifetime imaging-based FRET (FLIM-FRET) to elucidate the composition of single nucleosomes containing histone variant H2A.Z (Htz1p in yeast) in vitro and in vivo. We demonstrate that yeast nucleosomes containing Htz1p are primarily composed of H4 K12ac and H3 K4me3 but not H3 K36me3 and that these patterns are conserved in mammalian cells. Quantification of epigenetic modifications in nucleosomes will provide a new dimension to epigenetics research and lead to a better understanding of how these patterns contribute to the targeting of chromatin-binding proteins and chromatin structure during gene regulation.

OS-FRET: a new one-sample method for improved FRET measurements

Fluorescence resonance energy transfer (FRET) is a powerful tool for studying macromolecular assemblies in vitro under near-physiological conditions. Here we present a new type of one-sample FRET (OS-FRET) method employing a novel, nonfluorescent methanethiosulfonate-linked acceptor that can be reversibly coupled to a target sulfhydryl residue via a disulfide bond. After the quenched donor emission is quantitated, the acceptor is removed by reduction, allowing measurement of unquenched donor emission in the same sample. Previous one-sample methods provide distinct advantages in specific FRET applications. The new OS-FRET method is a generalizable spectrochemical approach that can be applied to macromolecular systems lacking essential disulfide bonds and eliminates the potential systematic errors of some earlier one-sample methods. In addition, OS-FRET enables quantitative FRET measurements in virtually any fluorescence spectrometer or detection device. Compared to conventional multisample FRET methods, OS-FRET conserves sample, increases the precision of data, and shortens the time per measurement. The utility of the method is illustrated by its application to a protein complex of known structure formed by CheW and the P4-P5 fragment of CheA, both from Thermotoga maritima. The findings confirm the practicality and advantages of OS-FRET. Anticipated applications of OS-FRET include analysis of macromolecular structure, binding and conformational dynamics, and high-throughput screening for interactions and inhibitors.

Nano-biophotonics: new tools for chemical nano-analytics

The nondestructive chemical analysis of biological processes in the crowded intracellular environment, at cellular membranes, and between cells with a spatial resolution well beyond the diffraction limit is made possible through Nano-Biophotonics. A number of sophisticated schemes employing nanoparticles, nano-apertures, or shaping of the probe volume in the far field have significantly extended our knowledge about lipid rafts, macromolecular complexes, such as chromatin, vesicles, and cellular organelles, and their interactions and trafficking within the cell. Here, I review some of the most recent developments in Nano-Biophotonics that already are or soon will become relevant to the analysis of intracellular processes. The pros and cons of the various techniques will be discussed and an outlook of their prospects for the near future will be provided.

Selective aluminum passivation for targeted immobilization of single DNA polymerase molecules in zero-mode waveguide nanostructures

Optical nanostructures have enabled the creation of subdiffraction detection volumes for single-molecule fluorescence microscopy. Their applicability is extended by the ability to place molecules in the confined observation volume without interfering with their biological function. Here, we demonstrate that processive DNA synthesis thousands of bases in length was carried out by individual DNA polymerase molecules immobilized in the observation volumes of zero-mode waveguides (ZMWs) in high-density arrays. Selective immobilization of polymerase to the fused silica floor of the ZMW was achieved by passivation of the metal cladding surface using polyphosphonate chemistry, producing enzyme density contrasts of glass over aluminum in excess of 400:1. Yields of single-molecule occupancies of approximately 30% were obtained for a range of ZMW diameters (70-100 nm). Results presented here support the application of immobilized single DNA polymerases in ZMW arrays for long-read-length DNA sequencing.

Single-molecule fluorescence resonance energy transfer in nanopipets: improving distance resolution and concentration range

In recent years fluorescence resonance energy transfer (FRET) has widely been used to measure distances, binding, and distance dynamics at the single-molecule (sm) level. Some basic constraints of smFRET are the limited distance resolution owing to low photon statistics and the restriction to high affinity interactions. We demonstrate that by confining molecules in nanopipets with an inner diameter of approximately 100 nm at the tip, FRET can be measured with improved photon statistics and at up to 50-fold higher concentrations. The flow of the donor/acceptor (Cy3B/ATTO647N) labeled double-stranded DNA conjugates was established by electrokinetic forces. Because of the small inner diameter of the nanopipet, every molecule passing the tip is detected applying alternating laser excitation (ALEX). Thus, the technique offers the advantage to study interactions with smaller association constants (<10(9) M-1) using minute sample amounts (<5 microL). The improved photon statistics reduces shot-noise contributions and results in sharper FRET distributions. Experimental results are supported by Monte Carlo simulations which also explain the occurrence of two populations in burst size distributions measured in nanopipet experiments. Because of the confinement of the molecules in nanopipets, the widths of FRET histograms are reduced to a degree where shot-noise is not the only limiting factor but also conformational dynamics of the linkers used to attach the chromophores have to be considered. In addition, our experiments emphasize the influence of photoinduced dark states on both the mean energy transfer efficiency and the width of FRET histograms.