Long time scale blinking kinetics of cyanine fluorophores conjugated to DNA and its effect on Förster resonance energy transfer

The blinking kinetics of individual Cy5 fluorophores conjugated to DNA are directly measured using single-molecule spectroscopy. Under deoxygenated aqueous conditions, Cy5 fluorescence exhibits spontaneous and reversible on/off fluctuations with a period lasting seconds. This blinking is observed when directly exciting Cy5 with 640 nm light and by Forster resonance energy transfer (FRET). We find that Cy5 blinking is influenced by the proximity of the donor, the structure of the donor, the presence of 514 nm excitation, and FRET. In the context of single-molecule FRET, blinking of the acceptor produces anticorrelated donor-acceptor intensity fluctuations, which can be difficult to discern from variations in the interdye distance. Slow blinking is, in particular, problematic because it overlaps with biologically relevant time scales. By employing an alternating 514640 nm laser excitation scheme, we show that the dark states can be readily resolved and discriminated from FRET distance fluctuations.     

Joint statistical analysis of multichannel time series from single quantum dot-(Cy5)n constructs

One of the major challenges in single-molecule studies is how to extract reliable information from the inevitably noisy data. Here, we demonstrate the unique capabilities of multichannel joint statistical analysis of multispectral time series using F?ster resonance energy transfer (FRET) in single quantum dot (QD)-organic dye hybrids as a model system. The multispectral photon-by-photon registration allows model-free determination of intensity change points of the donor and acceptor channels independently. The subsequent joint analysis of these change points gives high-confidence assignments of acceptor photobleaching events despite the interference from background noise and from intermittent blinking of the QD donors and acceptors themselves. Finally, the excited-state lifetimes of donors and acceptors are calculated using the joint maximum likelihood estimation (MLE) method on the donor and acceptor decay profiles, guided by a four-state kinetics model.     

Carbocyanine dyes as efficient reversible single-molecule optical switch

We demonstrate that commercially available unmodified carbocyanine dyes such as Cy5 (usually excited at 633 nm) can be used as efficient reversible single-molecule optical switch, whose fluorescent state after apparent photobleaching can be restored at room temperature upon irradiation at shorter wavelengths. Ensemble photobleaching and recovery experiments of Cy5 in aqueous solution irradiating first at 633 nm, then at 337, 488, or 532 nm, demonstrate that restoration of absorption and fluorescence strongly depends on efficient oxygen removal and the addition of the triplet quencher beta-mercaptoethylamine. Single-molecule fluorescence experiments show that individual immobilized Cy5 molecules can be switched optically in milliseconds by applying alternating excitation at 633 and 488 nm between a fluorescent and nonfluorescent state up to 100 times with a reliability of >90% at room temperature. Because of their intriguing performance, carbocyanine dyes volunteer as a simple alternative for ultrahigh-density optical data storage. Measurements on single donor/acceptor (tetramethylrhodamine/Cy5) labeled oligonucleotides point out that the described light-driven switching behavior imposes fundamental limitations on the use of carbocyanine dyes as energy transfer acceptors for the study of biological processes.     

Intramolecular directional förster resonance energy transfer at the single-molecule level in a dendritic system

We report on the directional F?rster resonance energy transfer (FRET) process taking place in single molecules of a first (T1P4) and a second (T2P8) generation of a perylenemonoimide (P)-terrylenediimide (T)-based dendrimer in which the chromophores are separated by rigid polyphenylene arms. At low excitation powers, single-molecule detection and spectroscopy of T1P4 and T2P8 dendrimers point to a highly efficient directional FRET from P donors to the central T acceptor, optical excitation at 488 nm resulting in exclusively acceptor emission in the beginning of the detected fluorescence intensity. Donor emission is seen only upon the bleaching of the acceptor. High-resolution time-resolved single-molecule fluorescence data measured with a microchannel plate photomultiplier reveal, for T2P8, a broad range of FRET rates as a result of a broad range of distances and orientations experienced by the donor-acceptor dendrimers when immobilized in a polymer matrix. Single-molecule data from T2P8 on 488 nm excitation are indicative for the presence, after terrylenediimide bleaching, of a P-P excited dimer characterized by a broad emission spectrum peaking around 600 nm and by fluctuating fluorescence decay times. At high excitation powers, single T1P4 and T2P8 molecules display simultaneous emission from both donor and acceptor chromophores. The effect, called "exciton blockade", occurs due to the presence of multiple excitations in a single molecule.     

Photobleaching of reduced nicotinamide adenine dinucleotide and the development of highly fluorescent lesions in rat basophilic leukemia cells during multiphoton microscopy

Endogenous reduced nicotinamide adenine dinucleotide (NADH) fluorescence provides an intrinsic indicator of the cellular metabolic state, but prolonged monitoring is limited by photobleaching and/or phototoxicity. Multiphoton excitation of NADH by ultrashort, 740-nm laser pulses provides a significant improvement over UV excitation by eliminating peripheral photobleaching; however, molecules within the subfemtoliter excitation volume remain susceptible. We have investigated the photophysical mechanisms responsible for multiphoton photobleaching of NADH in living cells to permit the imaging technique to be optimized. The loss of fluorescence because of multiphoton photobleaching was measured by repetitively imaging individual planes within rat basophilic leukemia cells. The photobleaching rate was proportional to the fourth power of the laser intensity. Based on these measurements, we propose a double-biphotonic, four-photon photobleaching mechanism and estimate the quantum yield of photobleaching of intracellular NADH to be 0.0073 +/- 0.0002 by this mechanism. In addition to photobleaching, the development of bright, punctate fluorescent lesions can also be observed. The frequency of lesion formation also increased approximately as the fourth power of the laser intensity after an intensity-dependent threshold number of images had been exceeded. The consequences for two-photon metabolic imaging are discussed.     

Origin of simultaneous donor-acceptor emission in single molecules of peryleneimide-terrylenediimide labeled polyphenylene dendrimers

F?rster type resonance energy transfer (FRET) in donor-acceptor peryleneimide-terrylenediimide dendrimers has been examined at the single molecule level. Very efficient energy transfer between the donor and the acceptor prevent the detection of donor emission before photobleaching of the acceptor. Indeed, in solution, on exciting the donor, only acceptor emission is detected. However, at the single molecule level, an important fraction of the investigated individual molecules (about 10-15%) show simultaneous emission from both donor and acceptor chromophores. The effect becomes apparent mostly after photobleaching of the majority of donors. Single molecule photon flux correlation measurements in combination with computer simulations and a variety of excitation conditions were used to determine the contribution of an exciton blockade to this two-color emission. Two-color defocused wide-field imaging showed that the two-color emission goes hand in hand with an unfavorable orientation between one of the donors and the acceptor chromophore.     

Unfolded protein and peptide dynamics investigated with single-molecule FRET and correlation spectroscopy from picoseconds to seconds

Single-molecule fluorescence spectroscopy and correlation methods are finding increasing applications in the investigation of biomolecular dynamics, especially together with F?rster resonance energy transfer (FRET). Here, we use the combination of start-stop experiments and classical fluorescence correlation spectroscopy (FCS) to obtain complete intensity auto- and cross-correlation functions from picoseconds to seconds for investigating the dynamics of unfolded proteins and peptides. In combination with distance information from single-molecule transfer efficiency histograms, we can analyze the data in terms of a diffusive process on a potential of mean force to obtain intramolecular diffusion coefficients. This allows us to extend our previous analysis of the time scales of chain dynamics into the low nanosecond range for peptides and into the microsecond range for a small cold shock protein (Csp). Dynamics in short unstructured peptides can be detected down to a time scale of about 10 ns, placing a lower limit on the time scales accessible with correlation methods and currently used dye pairs. We find no evidence for microsecond fluctuations in unfolded Csp, suggesting that its global chain dynamics occur predominantly in the tens of nanosecond range. We further investigate the position dependence of these dynamics by placing donor and acceptor dyes at different positions within the chain and find a decrease in the intramolecular diffusion coefficient by a factor of 3 upon moving one of the dyes toward the center of the polypeptide. Obtaining dynamic information on a wide range of time scales from single-molecule photon statistics will be of increasing importance for the study of unfolded proteins and for biomolecules in general.     

Correlations of structure and rates of energy transfer for through-bond energy-transfer cassettes

Fluorescent DNA-labeling cassettes are designed to have a common absorbing chromophore matched to a single exciting laser wavelength, but up to four different emitters. Experiments reported here have examined the energy-transfer rates and fluorescence polarization characteristics for two different types of cassette, involving three distinct relative orientations of the donor and acceptor transition moments and the axis of the rigid linker. Energy-transfer times range from <200 fs to approximately 20 ps, the fastest transfer times occurring when the transition moments of the donor and acceptor species are aligned parallel to the linker axis. Experimental evidence is presented that supports a through-bond energy-transfer mechanism, in contrast with a commercial DNA-labeling agent, which exhibits much slower transfer times controlled by FRET. These rigid cassettes also exhibit polarized fluorescence from the acceptor species, so that this particular type of DNA-labeling probe has some of the advantages of single-molecule probes such as rhodamine and coumarin dyes.     

Fluorescent, through-bond energy transfer cassettes for labeling multiple biological molecules in one experiment

Through-bond energy transfer cassettes based on a fluorescein donor component electronically conjugated to rhodamine-like acceptors have been designed and synthesized. They absorb strongly at 488 nm (Ar-laser emission) and efficiently transfer the energy to the acceptor component that emits strongly. Further, the cassettes are more stable to photobleaching than fluorescein, making them potentially more suitable for single-molecule detection methods than fluorescein itself. These studies form the basis for improved detection of chain-terminated DNA in high-throughput sequencing and other applications in biotechnology.     

Intramolecular Förster energy transfer in a dendritic system at the single molecule level

The photophysics of a dendrimer containing four donor chromophores and one acceptor chromophore are studied at the single-molecule level. Upon excitation of the donors exclusive acceptor emission is observed due to efficient F?rster energy transfer. For 70% of the molecules donor emission is observed after bleaching of the acceptor, leading to a reduction of the F?rster energy transfer efficiency. Furthermore, we demonstrate that in this molecular system the donor chromophores do not bleach by a triplet-sensitized photooxidation.     

绿色荧光蛋白为传能对的供体光漂白法测定FRET效率的探讨

探讨以两种新荧光蛋白MiCy,mKo为传能对并应用供体光漂白法测量荧光共振能量转移(FRET)效率.首先通过基因工程方法表达纯化了这两种蛋白,并测量了荧光光谱及光漂白性质,表明MiCy极易光漂白而mKo抗光漂白.进一步以Ni-NTA-agarose为FRET模型,在Confocal上对MiCy进行光漂白时间常数的测量,并计算了FRET效率.结果表明MiCy-mKo传能对适合用供体光漂白法测量FRET效率,此传能对将在蛋白质相互作用研究中有广泛应用.     

Investigation of photobleaching and saturation of single molecules by fluorophore recrossing events

A method for investigation of photobleaching and saturation of single molecules by fluorophore recrossing events in a laser beam is described. The diffraction-limited probe volumes encountered in single-molecule detection (SMD) produce high excitation irradiance, which can decrease available signal. The single molecules of several dyes were detected and the data was used to extract interpeak times above a defined threshold value. The interpeak times revealed the number of fluorophore recrossing events. The number of molecules detected that were within 2 ms of each other represented a molecular recrossing for this work. Calcein, fluorescein and R-phycoerythrin were analyzed and the saturation irradiance and photobleaching effects were determined as a function of irradiance. This approach is simple and it serves as a method of optimizing experimental conditions for single-molecule detection.     

Single-Molecule Photoactivation FRET: A General and Easy-To-Implement Approach To Break the Concentration Barrier

Single-molecule fluorescence resonance energy transfer (sm-FRET) has become a widely used tool to reveal dynamic processes and molecule mechanisms hidden under ensemble measurements. However, the upper limit of fluorescent species used in sm-FRET is still orders of magnitude lower than the association affinity of many biological processes under physiological conditions. Herein, we introduce single-molecule photoactivation FRET (sm-PAFRET), a general approach to break the concentration barrier by using photoactivatable fluorophores as donors. We demonstrate sm-PAFRET by capturing transient FRET states and revealing new reaction pathways during translation using μm fluorophore labeled species, which is 2–3 orders of magnitude higher than commonly used in sm-FRET measurements. sm-PAFRET serves as an easy-to-implement tool to lift the concentration barrier and discover new molecular dynamic processes and mechanisms under physiological concentrations.     

Fluorescent resonant energy transfer: correlated fluctuations of donor and acceptor

Mounting evidence suggests that in single-molecule fluorescent resonant energy transfer (FRET) measurements, correlation between fluctuations in donor and acceptor may be important. We present a general theory to describe this correlation and its effect on the FRET rate. The correlation arises from low-energy excitations (e.g., acoustic phonons) of the molecule to which a donor-acceptor pair is attached, and results in an effective interaction between local environments or baths associated with the donor and the acceptor. The correlation is found to reduce the transfer rate, in particular, at short donor-acceptor distances. The theory can quantitatively explain recent measurements of polyproline peptides.     

Concentration-dependent energy transfer studies in ternary dye mixture of Stilbene-420, Coumarin-540 and Nile Blue

The energy transfer studies in the case of ternary dye mixture [Stilbene-420 (donor)+Coumarin-540 (intermediator)+Nile Blue (acceptor)] have been done and discussed through optical gain characteristics at various acceptor concentrations under nitrogen laser excitation. The concentration of the other two dyes were kept constant. It is observed that the concentration of the acceptor dye plays a very critical role in energy transfer dye laser (ETDL) as small change in its concentration varies the intensity of the laser output in the red region by large amount. Also, the highest laser output in the red region is obtained when the concentration of the acceptor dye is slightly higher than that of the intermediator dye. The present studies are helpful in deciding the optimum concentration of the acceptor dye to be used in ternary dye mixture for maximum gain and tuning range. The ternary dye mixture under study provides an ETDL tuning range up to 700 nm.     

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

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

Breakdown of Born‐Oppenheimer Approximation as a Physical Mechanism for Ultrafast Hydrogen Migrations in Strong Laser Driven Molecules

We propose a physical mechanism based on breakdown of the Born‐Oppenheimer approximation to rationalize the ultrafast hydrogen migration in strong laser driven isomerization reactions. A three nuclei (proton, donor, and acceptor) model is employed to develop a three step solution scheme. The proton‐donor Coulomb repulsion is shown to be responsible for the high proton mobility. We identify a proton tunneling process and use the Keldysh‐Faisal‐Reiss theory to calculate the tunneling probability. The effect of laser parameters (intensity, frequency, polarization, and pulse duration) has been studied and found to be consistent with recent experiments.     

Two-color two-photon excitation using femtosecond laser pulses

The use of two-color two-photon (2c2p) excitation easily extends the wavelength range of Ti:sapphire lasers to the UV, widening the scope of its applications especially in biological sciences. We report observation of 2c2p excitation fluorescence of p-terphenyl (PTP), 2-methyl-5-t-butyl-p-quaterphenyl (DMQ) and tryptophan upon excitation with 400 and 800 nm wavelengths using the second harmonic and fundamental wavelength of a mode-locked Ti:sapphire femtosecond laser. This excitation is energetically equivalent to a one-photon excitation wavelength at 266 nm. The fluorescence signal is observed only when both wavelengths are spatially and temporally overlapping. Adjustment of the relative delay of the two laser pulses renders a cross correlation curve which is in good agreement with the pulse width of our laser. The fluorescence signal is linearly dependent on the intensity of each of the two colors but quadratically on the total incident illumination power of both colors. In fluorescence microscopy, the use of a combination of intense IR and low-intensity blue light as a substitute for UV light for excitation can have numerous advantages. Additionally, the effect of differently polarized excitation photons relative to each other is demonstrated. This offers information about different transition symmetries and yields deeper insight into the two-photon excitation process.     

Photoblinking and photobleaching of rylene diimide dyes

We investigate photoblinking and photobleaching of perylene diimide (PDI) and its higher homologue terrylene diimide (TDI). Single molecule fluorescence trajectories of the dye molecules embedded in PMMA under ambient conditions exhibit "on"-"off" blinking in the time range from ms to s. Due to the limited statistics of individual trajectories we construct ensemble distributions of "on" and "off" times which follow power laws with similar power law coefficients (m(on) ≈ 1.18, m(off) ≈ 1.31). The blinking is attributed to reversible formation of radical cations which are presumably created by electron transfer from higher excited triplet states T(n) of the molecules to acceptor levels in the PMMA host. This view is corroborated by the properties of TDI, which blinks at an excitation wavelength of 520 nm but does not at lower energy excitation (647 nm). In line with this observation, T(1)-T(n) absorption data of TDI (and PDI) indicate that above a certain illumination wavelength population of higher excited triplet states T(n) does not occur, preventing blinking. It is furthermore argued that the long-lived dark ("off") states, i.e. the radical cations, are precursors for the photobleaching process of the dye molecules. Consequently, the photobleaching quantum yield Y(bl) for TDI is very small at an excitation wavelength of 647 nm (Y(bl) = 2 × 10(-10)) but increases by two orders of magnitude at 520 nm (Y(bl) = 2 × 10(-8)), which lies in the range observed for PDI investigated with an excitation wavelength of 488 nm. Additional studies of a PDI-TDI donor-acceptor dyad give further insights into the blinking and bleaching processes. Important findings include the observation of power law blinking of TDI and PDI (after bleaching of TDI) with similar coefficients as found for the isolated chromophores. Furthermore, in the dyad the photostability of TDI decreases due to efficient population of the states T(n) by singlet-triplet annihilation, while that of PDI (after bleaching of TDI) is the same as for the isolated dye. These findings support the conclusions drawn for the isolated chromophores, in particular the involvement of the triplet manifold in the blinking (and bleaching) behavior.