Super-resolved FRET imaging by confocal fluorescence-lifetime single-molecule localization microscopy

FRET-based approaches are a unique tool for sensing the immediate surroundings and interactions of (bio)molecules. FRET imaging and FLIM (Fluorescence Lifetime Imaging Microscopy) enable the visualization of the spatial distribution of molecular interactions and functional states. However, conventional FLIM and FRET imaging provide average information over an ensemble of molecules within a diffraction-limited volume, which limits the spatial information, accuracy, and dynamic range of the observed signals. Here, we demonstrate an approach to obtain super-resolved FRET imaging based on single-molecule localization microscopy using an early prototype of a commercial time-resolved confocal microscope. DNA Points Accumulation for Imaging in Nanoscale Topography (DNA-PAINT) with fluorogenic probes provides a suitable combination of background reduction and blinking kinetics compatible with the scanning speed of usual confocal microscopes. A single laser is used to excite the donor, a broad detection band is employed to retrieve both donor and acceptor emission, and FRET events are detected from lifetime information

An alternative to MINFLUX that enables nanometer resolution in a confocal microscope

Localization of single fluorescent emitters is key for physicochemical and biophysical measurements at the nanoscale and beyond ensemble averaging. Examples include single-molecule tracking and super-resolution imaging by single-molecule localization microscopy. Among the numerous localization methods available, MINFLUX outstands for achieving a ~10-fold improvement in resolution over wide-field camera-based approaches, reaching the molecular scale at moderate photon counts. Widespread application of MINFLUX and related methods has been hindered by the technical complexity of the setups. Here, we present RASTMIN, a single-molecule localization method based on raster scanning a light pattern comprising a minimum of intensity. RASTMIN delivers ~1–2 nm localization precision with usual fluorophores and is easily implementable on a standard confocal microscope with few modifications. We demonstrate the performance of RASTMIN in localization of single molecules and super-resolution imaging of DNA origami structures.Fil: Masullo, Luciano Andrés. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Szalai, Alan Marcelo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Lopez, Lucía Fernanda. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; ArgentinaFil: Pilo Pais, Mauricio. Universite de Fribourg;Fil: Acuna, Guillermo P.. Universite de Fribourg;Fil: Stefani, Fernando Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentin

Distance dependence of single-molecule energy transfer to graphene measured with DNA origami nanopositioners

Despite the thorough investigation of graphene since 2004, altering its surface chemistry and reproducible functionalization remain challenging. This hinders fabrication of more complex hybrid materials with controlled architectures, and as a consequence the development of sensitive and reliable sensors and biological assays. In this contribution, we introduce DNA origami structures as nanopositioners for placing single dye molecules at controlled distances from graphene. The measurements of fluorescence intensity and lifetime of single emitters carried out for distances ranging from 3 to 58 nm confirmed the d–4 dependence of the excitation energy transfer to graphene. Moreover, we determined the characteristic distance for 50% efficiency of the energy transfer from single dyes to graphene to be 17.7 nm. Using pyrene molecules as a glue to immobilize DNA origami nanostructures of various shape on graphene opens new possibilities to develop graphene-based biophysics and biosensing

DNA origami assembled nanoantennas for manipulating single-molecule spectral emission

Optical nanoantennas can affect the decay rates of nearby emitters by modifying the local density of photonic states around them. In the weak-coupling limit, and according to the Fermi's Golden Rule, the emission spectrum of a dye is given by the energy of all the possible radiative transitions weighted by the probability of each of them to occur. By engineering the resonance of a nanoantenna, one can selectively enhance specific vibronic transitions of a dye molecule, thus shaping its emission spectrum. Since interactions between emitters and nanoantennas are known to be position dependent, we make here use of DNA origami to precisely place an individual dye at different positions around a gold nanorod. We show how this relative position between the nanorod and the emitter affects the emission spectrum of the latter. In particular, we observe the appearance of a second fluorescence peak whose wavelength and intensity are correlated with the fundamental plasmonic resonance of the nanorod, which we extract from its photoluminescence spectrum. This second peak results from the selective enhancement of transitions to different vibrational levels of the excitonic ground state, whose energies are in resonance with the plasmonic one. Furthermore, we argue that the drastic alteration of the fluorescence spectrum in some of our samples cannot be accounted for with Kasha's rule, which indicates that radiative and vibrational relaxation dye lifetimes can become comparable through the coupling to the gold nanorods

Plasmon-assisted Förster resonance energy transfer at the single-molecule level in the moderate quenching regime

Metallic nanoparticles were shown to affect Förster energy transfer between fluorophore pairs. However, to date, the net plasmonic effect on FRET is still under dispute, with experiments showing efficiency enhancement and reduction. This controversy is due to the challenges involved in the precise positioning of FRET pairs in the near field of a metallic nanostructure, as well as in the accurate characterization of the plasmonic impact on the FRET mechanism. Here, we use the DNA origami technique to place a FRET pair 10 nm away from the surface of gold nanoparticles with sizes ranging from 5 to 20 nm. In this configuration, the fluorophores experience only moderate plasmonic quenching. We use the acceptor bleaching approach to extract the FRET rate constant and efficiency on immobilized single FRET pairs based solely on the donor lifetime. This technique does not require a posteriori correction factors neither a priori knowledge of the acceptor quantum yield, and importantly, it is performed in a single spectral channel. Our results allow us to conclude that, despite the plasmon-assisted Purcell enhancement experienced by donor and acceptor partners, the gold nanoparticles in our samples have a negligible effect on the FRET rate, which in turns yields a reduction of the transfer efficiency

Strong plasmonic enhancement of single molecule photostability in silver dimer optical antennas

Photobleaching is an effect terminating the photon output of fluorophores, limiting the duration of fluorescence-based experiments. Plasmonic nanoparticles (NPs) can increase the overall fluorophore photostability through an enhancement of the radiative rate. In this work, we use the DNA origami technique to arrange a single fluorophore in the 12-nm gap of a silver NP dimer and study the number of emitted photons at the single molecule level. Our findings yielded a 30× enhancement in the average number of photons emitted before photobleaching. Numerical simulations are employed to rationalize our results. They reveal the effect of silver oxidation on decreasing the radiative rate enhancement.We acknowledge funding by a starting grant (SiMBA, EU 261162) of the European Research Council (ERC) and the Deutsche Forschungsgesellschaft (AC 279/2-1 and TI 329/9-1). IK is grateful for the support by the Mobility Plus grant 1269/MOB/IV/2015/0 from the Polish Ministry of Science and Higher Education (MNiSW). CV thanks a scholarship of the Studienstiftung des deutschen Volkes. AIF-D and AC-G acknowledge funding from the Spanish MINECO under Contracts FIS2015- 64951-R and MDM-2014-0377-16-4, respectively. AIF-D also acknowledges funding from EU Seventh Framework Programme under Grant Agreement FP7-PEOPLE- 2013-CIG-630996. GA and PT acknowledge funding of the state ministry for research of lower saxony in the frame of the “Quantum- and Nanometrology” (QUANOMET) strategic research area. Quanomet is part of the LUH-TUBS research allianc

Directing single-molecule emission with dna origami-assembled optical antennas

We demonstrate the capability of DNA self-assembled optical antennas to direct the emission of an individual fluorophore, which is free to rotate. DNA origami is used to fabricate optical antennas composed of two colloidal gold nanoparticles separated by a predefined gap and to place a single Cy5 fluorophore near the gap center. Although the fluorophore is able to rotate, its excitation and far-field emission is mediated by the antenna, with the emission directionality following a dipolar pattern according to the antenna main resonant mode. This work is intended to set out the basis for manipulating the emission pattern of single molecules with self-assembled optical antennas based on colloidal nanoparticles

Controlled reduction of photobleaching in DNA origami gold nanoparticle hybrids

The amount of information obtainable from a fluorescence-based measurement is limited by photobleaching: Irreversible photochemical reactions either render the molecules nonfluorescent or shift their absorption and/or emission spectra outside the working range. Photobleaching is evidenced as a decrease of fluorescence intensity with time, or in the case of single molecule measurements, as an abrupt, single-step interruption of the fluorescence emission that determines the end of the experiment. Reducing photobleaching is central for improving fluorescence (functional) imaging, single molecule tracking, and fluorescence-based biosensors and assays. In this single molecule study, we use DNA self-assembly to produce hybrid nanostructures containing individual fluorophores and gold nanoparticles at a controlled separation distance of 8.5 nm. By changing the nanoparticles? size we are able to systematically increase the mean number of photons emitted by the fluorophores before photobleaching.Fil: Pellegrotti, Jesica Vanesa. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; ArgentinaFil: Acuña, Guillermo. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; AlemaniaFil: Puchkova, Anastasiya. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; AlemaniaFil: Holzmeister, Phil. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; AlemaniaFil: Gietl, Andreas. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; AlemaniaFil: Lalkens, Birka. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; AlemaniaFil: Stefani, Fernando Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Centro de Investigaciones en Bionanociencias "Elizabeth Jares Erijman"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Física; ArgentinaFil: Tinnefeld, Philip. Technische Universität Braunschweig. Institute for Physical and Theoretical Chemistry. NanoBioSciences Group; Alemani

DNA‐mediated self‐assembly of plasmonic antennas with a single quantum dot in the hot spot

DNA self‐assembly is a powerful tool to arrange optically active components with high accuracy in a large parallel manner. A facile approach to assemble plasmonic antennas consisting of two metallic nanoparticles (40 nm) with a single colloidal quantum dot positioned at the hot spot is presented here. The design approach is based on DNA complementarity, stoichiometry, and steric hindrance principles. Since no intermediate molecules other than short DNA strands are required, the structures possess a very small gap (≈ 5 nm) which is desired to achieve high Purcell factors and plasmonic enhancement. As a proof‐of‐concept, the fluorescence emission from antennas assembled with both conventional and ultrasmooth spherical gold particles is measured. An increase in fluorescence is obtained, up to ≈30‐fold, compared to quantum dots without antenna