Quantifying Microsecond Solution-Phase Conformational Dynamics of a DNA Hairpin at the Single-Molecule Level.

Quantifying the rapid conformational dynamics of biological systems is fundamental to understanding the mechanism. However, biomolecules are complex, often containing static and dynamic heterogeneity, thus motivating the use of single-molecule methods, particularly those that can operate in solution. In this study, we measure microsecond conformational dynamics of solution-phase DNA hairpins at the single-molecule level using an anti-Brownian electrokinetic (ABEL) trap. Different conformational states were distinguished by their fluorescence lifetimes, and kinetic parameters describing transitions between these states were determined using two-dimensional fluorescence lifetime correlation (2DFLCS) analysis. Rather than combining fluorescence signals from the entire data set ensemble, long observation times of individual molecules allowed ABEL-2DFLCS to be performed on each molecule independently, yielding the underlying distribution of the system's kinetic parameters. ABEL-2DFLCS on the DNA hairpins resolved an underlying heterogeneity of fluorescence lifetimes and provided signatures of two-state exponential dynamics with rapid (

Pulsed-Interleaved-Excitation Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

We report on pulsed-interleaved-excitation two-dimensional fluorescence lifetime correlation spectroscopy (PIE 2D FLCS) to study biomolecular structural dynamics with high sensitivity and high time resolution using Förster resonance energy transfer (FRET). PIE 2D FLCS is an extension of 2D FLCS, which is a unique single-molecule fluorescence method that uses fluorescence lifetime information to distinguish different fluorescence species in equilibrium and resolves their interconversion dynamics with a submicrosecond time resolution. Because 2D FLCS has used only a single-color excitation so far, it was difficult to distinguish a very low-FRET (or zero-FRET) species from only donor-labeled species. We overcome this difficulty by implementing the PIE scheme (i.e., alternate excitation of the donor and acceptor dyes using two temporally interleaved excitations with different colors) to 2D FLCS, realizing two-color excitation and two-color fluorescence detection in 2D FLCS. After proof-of-principle PIE 2D FLCS analysis on the photon data synthesized with Monte Carlo simulation, we apply PIE 2D FLCS to a DNA-hairpin sample and show that this method readily distinguishes four fluorescent species, i.e., high-FRET, low-FRET, and two single-dye-labeled species. In addition, we show that PIE 2D FLCS can also quantitatively evaluate the contributions of the donor-acceptor spectral crosstalk, which often appears as artifacts in FRET studies and degrades the information obtained.

A Toxicogenic Interaction between Intracellular Amyloid-ß and Apolipoprotein-E.

Alzheimer's disease (AD) is associated with the aggregation of amyloid ß (Aß) and tau proteins. Why ApoE variants are significant genetic risk factors remains a major unsolved puzzle in understanding AD, although intracellular interactions with ApoE are suspected to play a role. Here, we show that specific changes in the fluorescence lifetime of fluorescently tagged small Aß oligomers in rat brain cells correlate with the cellular ApoE content. An inhibitor of the Aß-ApoE interaction suppresses these changes and concomitantly reduces Aß toxicity in a dose-dependent manner. Single-molecule techniques show changes both in the conformation and in the stoichiometry of the oligomers. Neural stem cells derived from hiPSCs of Alzheimer's patients also exhibit these fluorescence lifetime changes. We infer that intracellular interaction with ApoE modifies the N-terminus of the Aß oligomers, inducing changes in their stoichiometry, membrane affinity, and toxicity. These changes can be directly imaged in live cells and can potentially be used as a rapid and quantitative cellular assay for AD drug discovery.

Effects of dietary feed supplementation with heat-treated Lactobacillus sakei HS-1 on the health status, blood parameters, and fecal microbes of Japanese Black calves before weaning.

Background and Aim: Our previous research suggested that heat-killed Lactobacillus sakei HS-1 (HK-LS HS-1) is potentially beneficial for improving intestinal microbes and reducing the number of medical treatments. This study aimed to investigate the effect of HK-LS HS-1 as a supplement in milk replacers (MRs) on clinical health during the 1-month preweaning period. Materials and Methods: Eighteen female calves were randomly assigned to either a group receiving the HK-LS HS-1 supplement (n = 9) or a control group without it (n = 9). We then investigated the effect of including supplementary HK-LS HS-1; 0.2% in MRs twice daily at 09:00 and 16:00 on the health, serum biochemical parameters (measured using an automated biochemical analyzer), and fecal bacteriological changes of preweaning Japanese Black calves at the day of the start of supplementation (before HK-LS HS-1 supplementation; day 0), at weaning (day 30), and at 2 weeks (day 45) and 4 weeks (day 60) after weaning. Results: During the supplementation period (0-30 days), (1) an increase (p = 0.023) was observed in albumin, and there was a tendency of increase in total cholesterol level in the HK-LS HS-1 group but not in the control group; (2) substantial differences were obtained after the weaning period (30-60 days), although no differences were observed from 0-30 days in both groups. The anti-Müllerian hormone (AMH) level was substantially increased after weaning in the control group. No differences were observed in the amounts of Coliform spp. and Staphylococcaceae spp. between the two groups; thus, HK-LS HS-1 supplementation had similar antibacterial effects. A significant reduction was observed in the time to weaning of the HK-LS HS-1 group in the field trial. Conclusion: Supplementation with HK-LS HS-1 from an early stage after birth to weaning is a cost-effective treatment to improve the growth rate of preweaning calves. However, supplementation during only preweaning periods appears to have no beneficial effects on preventing weaning stress, especially in terms of AMH levels.

Single-photon smFRET. III. Application to pulsed illumination.

Förster resonance energy transfer (FRET) using pulsed illumination has been pivotal in leveraging lifetime information in FRET analysis. However, there remain major challenges in quantitative single-photon, single-molecule FRET (smFRET) data analysis under pulsed illumination including 1) simultaneously deducing kinetics and number of system states; 2) providing uncertainties over estimates, particularly uncertainty over the number of system states; and 3) taking into account detector noise sources such as cross talk and the instrument response function contributing to uncertainty; in addition to 4) other experimental noise sources such as background. Here, we implement the Bayesian nonparametric framework described in the first companion article that addresses all aforementioned issues in smFRET data analysis specialized for the case of pulsed illumination. Furthermore, we apply our method to both synthetic as well as experimental data acquired using Holliday junctions.

Scanning Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy: Conformational Dynamics of DNA Holliday Junction from Microsecond to Subsecond.

Single-molecule Förster resonance energy transfer (smFRET) is widely utilized to investigate the structural heterogeneity and dynamics of biomolecules. However, it has been difficult to simultaneously achieve a wide observation time window, a high structure resolution, and a high time resolution with the current smFRET methods. Herein, we introduce a new method utilizing two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) and surface immobilization techniques. This method, scanning 2D FLCS, enables us to examine the structural heterogeneity and dynamics of immobilized biomolecules on a time scale from microsecond to subsecond by slowly scanning the sample stage at the rate of ∼1 µm/s. Application to the DNA Holliday junction (HJ) complex under various [Mg2+] conditions demonstrates that scanning 2D FLCS enables tracking reaction kinetics from 25 µs to 30 ms with a time resolution as high as 1 µs. Furthermore, the high structure resolution of scanning 2D FLCS allows us to unveil the ensemble nature of each isomer state and the heterogeneity of the dynamics of the HJ.

Extraction of rapid kinetics from smFRET measurements using integrative detectors.

Hidden Markov models (HMMs) are used to learn single-molecule kinetics across a range of experimental techniques. By their construction, HMMs assume that single-molecule events occur on slower timescales than those of data acquisition. To move beyond that HMM limitation and allow for single-molecule events to occur on any timescale, we must treat single-molecule events in continuous time as they occur in nature. We propose a method to learn kinetic rates from single-molecule Förster resonance energy transfer (smFRET) data collected by integrative detectors, even if those rates exceed data acquisition rates. To achieve that, we exploit our recently proposed "hidden Markov jump process" (HMJP), with which we learn transition kinetics from parallel measurements in donor and acceptor channels. HMJPs generalize the HMM paradigm in two critical ways: (1) they deal with physical smFRET systems as they switch between conformational states in continuous time, and (2) they estimate transition rates between conformational states directly without having recourse to transition probabilities or assuming slow dynamics. Our continuous-time treatment learns the transition kinetics and photon emission rates for dynamic regimes that are inaccessible to HMMs, which treat system kinetics in discrete time. We validate our framework's robustness on simulated data and demonstrate its performance on experimental data from FRET-labeled Holliday junctions.

Microsecond Folding of preQ1 Riboswitch and Its Biological Significance Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

Riboswitches are regulatory elements of bacterial mRNA which function with conformational switching upon binding of specific cellular metabolites. In particular, transcriptional riboswitches regulate gene expression kinetically through the conformational change of the aptamer domain. In this study, we investigate the conformational dynamics and ligand binding mechanisms of the aptamer domain of a transcriptional prequeuosine (preQ1) riboswitch from Bacillus subtilis using two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS) with microsecond time resolution. The obtained time-resolved single-molecule data indicate that the aptamer domain undergoes folding/unfolding including three forms, which are attributed to hairpin (O), pseudoknot-like (pF), and H-type pseudoknot (fF) structures. It is found that a cofactor, Mg2+, binds only to the fF form with the conformational selection mechanism. In contrast, it is indicated that the ligand, preQ1, binds to the O form with the induced-fit mechanism and significantly accelerates the microsecond O → pF folding process. It is also shown that the binding with preQ1 substantially stabilizes the fF form that is generated from the pF form with a long time constant (>10 ms). Combining these results with the results of a former smFRET study on the slower time scale, we obtain an overall picture of the folding/unfolding dynamics of the aptamer domain as well as its energy landscape. On the basis of the picture obtained, we discuss the significance of the microsecond folding/unfolding of the aptamer domain for biological function of the riboswitch and propose the molecular mechanism of the gene expression controlled by the structural dynamics of the aptamer domain.

Microsecond Equilibrium Dynamics of Hairpin-Forming Oligonucleotides Quantified by Two-Color Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

RNA and DNA play distinct roles in biological systems. However, the underlying physicochemical difference has been poorly understood, in particular, that in dynamical aspects. In this paper, we report on a comparative study of the formation-dissociation dynamics of a hairpin structure of RNA and DNA with development of two-color two-dimensional fluorescence lifetime correlation spectroscopy (two-color 2D FLCS). In this extension of 2D FLCS, we newly introduce the two-color detection scheme to analyze not only donor fluorescence photons but also acceptor fluorescence photons from a doubly labeled Förster resonance energy transfer (FRET) pair. This new 2D FLCS is utilized to resolve multiple species present in an equilibrated condition with a microsecond time resolution and enhanced sensitivity, and the combined use with the filtered fluorescence correlation spectroscopy (FCS) method enables a quantitative discussion on microsecond structural dynamics occurring in the equilibrium. This integrated approach is applied to FRET-labeled RNA/DNA oligonucleotides having analogous hairpin-forming sequences, and it was revealed that the hairpin dissociation rate of RNA is an order of magnitude slower than that of DNA while their hairpin-forming rates are comparable. This marked difference is attributable to the distinct duplex structure of RNA and DNA. The present study demonstrates that the integrated approach combining two-color 2D FLCS and filtered FCS has a high potential for quantifying microsecond kinetics at the single-molecule level, which allows us to experimentally construct a free energy landscape.

Direct Photon-by-Photon Analysis of Time-Resolved Pulsed Excitation Data using Bayesian Nonparametrics.

Lifetimes of chemical species are typically estimated by either fitting time-correlated single-photon counting (TCSPC) histograms or phasor analysis from time-resolved photon arrivals. While both methods yield lifetimes in a computationally efficient manner, their performance is limited by choices made on the number of distinct chemical species contributing photons. However, the number of species is encoded in the photon arrival times collected for each illuminated spot and need not be set by hand a priori. Here, we propose a direct photon-by-photon analysis of data drawn from pulsed excitation experiments to infer, simultaneously and self-consistently, the number of species and their associated lifetimes from a few thousand photons. We do so by leveraging new mathematical tools within the Bayesian nonparametric. We benchmark our method for both simulated and experimental data for 1-4 species.

Microsecond Conformational Dynamics of Biopolymers Revealed by Dynamic-Quenching Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy with Single Dye Labeling.

The single-molecule Förster resonance energy transfer (smFRET) technique is widely used for studying conformational dynamics of biopolymers. However, smFRET requires double dye labeling and is usually utilized for detecting dynamics on slow time scales (≳ milliseconds). In this Letter, we report dynamic-quenching two-dimensional fluorescence lifetime correlation spectroscopy (DQ 2D FLCS) that can elucidate the microsecond conformational dynamics of biopolymers with only single dye labeling. In DQ 2D FLCS, the difference in solvent accessibility of the labeled dye makes the fluorescence lifetime different, which is used for distinguishing different conformers. By applying DQ 2D FLCS to a singly labeled DNA hairpin, we successfully detect microsecond interconversion dynamics between the open and closed forms and evaluate the state-specific solvent accessibility of each form with Stern-Volmer analysis. Because DQ 2D FLCS is sensitive to the local structural change, it is complementary to FRET-based 2D FLCS and thus is a new, powerful tool for studying structural dynamics of biopolymers.

Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation.

Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structure formation and stability. We use large parallel temperature replica exchange molecular dynamics ensembles to sample the full conformational landscape of these hairpin molecules so that we can identify the stable structures formed by the hairpin sequence. Our simulations show RNA adopts a narrower distribution of folded structures compared to DNA at room temperature, which forms both hairpins and many unfolded conformations. RNA is capable of forming twice as many hydrogen bonds than DNA which results in a higher melting temperature. We see that local chemical differences lead to emergent molecular properties such as increased persistence length in RNA that is weakly temperature dependant. These discoveries provide fundamental insight into how RNA forms complex folded tertiary structures which confer enzymatic-like function in ribozymes, whereas DNA retains structural motifs in order to facilitate function such as translation of sequence.

Highly Heterogeneous Nature of the Native and Unfolded States of the B Domain of Protein A Revealed by Two-Dimensional Fluorescence Lifetime Correlation Spectroscopy.

Elucidating the protein folding mechanism is crucial to understand how proteins acquire their unique structures to realize various biological functions. With this aim, the folding/unfolding of small globular proteins has been extensively studied. Interestingly, recent studies have revealed that even such small proteins represent considerably complex processes. In this study, we examined the folding/unfolding process of a small α-helical protein, the B domain of protein A (BdpA), at equilibrium using two-dimensional fluorescence lifetime correlation spectroscopy with 10 µs time resolution. The results showed that although the BdpA is a two-state folder, both the native and unfolded states are highly heterogeneous and the conformational conversion within each ensemble occurs within 10 µs. Furthermore, it was shown that the average structures of both ensembles gradually change and become more elongated as the denaturant concentration increases. The analysis on two mutants suggested that fraying of the N-terminal helix is the origin of the inhomogeneity of the native state. Because the direct observation of the ensemble nature of the native state at the single-molecule level has not been reported, the data obtained in this study give new insights into complex conformational properties of small proteins.

Correction of the afterpulsing effect in fluorescence correlation spectroscopy using time symmetry analysis.

Afterpulsing of a photon-counting detector is a common problem in fluorescence correlation spectroscopy. We have developed a numerical procedure which eliminates the afterpulsing effect by analyzing the time reversal asymmetry of photon data that are recorded with a time-correlated single photon counting device. This method was applied to experimental data and was compared with a previous method [Rev. Sci. Instrum. 76, 033102 (2005).]. It is demonstrated that the present method can completely eliminate the afterpulsing effect even in the case of a sample solution that contains multiple fluorophores having different fluorescence lifetimes, for which the previous method underestimates the correlation amplitude. We also show a modification of the previous method incorporating the time symmetry analysis.

Microsecond protein dynamics observed at the single-molecule level.

How polypeptide chains acquire specific conformations to realize unique biological functions is a central problem of protein science. Single-molecule spectroscopy, combined with fluorescence resonance energy transfer, is utilized to study the conformational heterogeneity and the state-to-state transition dynamics of proteins on the submillisecond to second timescales. However, observation of the dynamics on the microsecond timescale is still very challenging. This timescale is important because the elementary processes of protein dynamics take place and direct comparison between experiment and simulation is possible. Here we report a new single-molecule technique to reveal the microsecond structural dynamics of proteins through correlation of the fluorescence lifetime. This method, two-dimensional fluorescence lifetime correlation spectroscopy, is applied to clarify the conformational dynamics of cytochrome c. Three conformational ensembles and the microsecond transitions in each ensemble are indicated from the correlation signal, demonstrating the importance of quantifying microsecond dynamics of proteins on the folding free energy landscape.

Two-dimensional fluorescence lifetime correlation spectroscopy. 1. Principle.

Fluorescence correlation spectroscopy (FCS) is a unique tool for investigating microsecond molecular dynamics of complex molecules in equilibrium. However, application of FCS in the study of molecular dynamics has been limited, owing to the complexity in the extraction of physically meaningful information. In this work, we develop a new method that combines FCS and time-correlated single photon counting (TCPSC) to extract unambiguous information about equilibrium dynamics of complex molecular systems. In this method, which we name two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS), we analyze the correlation of the fluorescence photon pairs, referring to the fluorescence lifetime. We first obtain the correlations of the photon pairs with respect to the excitation-emission delay times in the form of a two-dimensional (2D) map. Then, the 2D map is converted to the correlations between different species that have distinct fluorescence lifetimes using inverse Laplace transformation. This 2D FLCS is capable of visualizing the equilibration dynamics of complex molecules with microsecond time resolution at the single-molecule level. We performed a kinetic Monte Carlo simulation of a TCPSC-FCS experiment as a proof-of-principle example. The result clearly shows the validity of the proposed method and its high potential in analyzing the photon data of dynamic systems.

Two-dimensional fluorescence lifetime correlation spectroscopy. 2. Application.

In the preceding article, we introduced the theoretical framework of two-dimensional fluorescence lifetime correlation spectroscopy (2D FLCS). In this article, we report the experimental implementation of 2D FLCS. In this method, two-dimensional emission-delay correlation maps are constructed from the photon data obtained with the time-correlated single photon counting (TCSPC), and then they are converted to 2D lifetime correlation maps by the inverse Laplace transform. We develop a numerical method to realize reliable transformation, employing the maximum entropy method (MEM). We apply the developed actual 2D FLCS to two real systems, a dye mixture and a DNA hairpin. For the dye mixture, we show that 2D FLCS is experimentally feasible and that it can identify different species in an inhomogeneous sample without any prior knowledge. The application to the DNA hairpin demonstrates that 2D FLCS can disclose microsecond spontaneous dynamics of biological molecules in a visually comprehensible manner, through identifying species as unique lifetime distributions. A FRET pair is attached to the both ends of the DNA hairpin, and the different structures of the DNA hairpin are distinguished as different fluorescence lifetimes in 2D FLCS. By constructing the 2D correlation maps of the fluorescence lifetime of the FRET donor, the equilibrium dynamics between the open and the closed forms of the DNA hairpin is clearly observed as the appearance of the cross peaks between the corresponding fluorescence lifetimes. This equilibrium dynamics of the DNA hairpin is clearly separated from the acceptor-missing DNA that appears as an isolated diagonal peak in the 2D maps. The present study clearly shows that newly developed 2D FLCS can disclose spontaneous structural dynamics of biological molecules with microsecond time resolution.

Note: Simple calibration of the counting-rate dependence of the timing shift of single photon avalanche diodes by photon interval analysis.

The counting-rate dependence of the temporal response of single photon avalanche diodes (SPADs) is a critical issue for the accurate determination of the fluorescence lifetime. In this study, the response of SPADs was examined with analyzing the time interval of the detected photons. The results clearly show that the shift of the detection timing causes the counting-rate dependence of the temporal response, and this timing shift is solely determined by the time interval from the preceding photon. We demonstrate that this timing instability is readily calibrated by utilizing the macrotime data taken with the time-tag mode that is implemented in the time-correlated single photon counting modules.

Coherent nuclear dynamics in ultrafast photoinduced structural change of bis(diimine)copper(I) complex.

The photoinduced structural change of a prototype metal complex, [Cu(dmphen)(2)](+) (dmphen = 2,9-dimethyl-1,10-phenanthroline), was studied by ultrafast spectroscopy with time resolution as high as 30 fs. Time-resolved absorption measured with direct S(1) excitation clearly showed spectral changes attributable to the D(2d) (perpendicular) → D(2) (flattened) structural change occurring in the metal-to-ligand charge transfer singlet excited state ((1)MLCT) and the subsequent S(1) → T(1) intersystem crossing. It was confirmed that the two processes occur with time constants of ~0.8 ps (structural change) and ~10 ps (intersystem crossing), and their time scales are clearly well-separated. A distinct oscillation of the transient absorption signal was observed in the femtosecond region, which arises from the coherent nuclear motion of the perpendicular S(1) state that was directly generated by photoexcitation. This demonstrated that the perpendicular S(1) state has a well-defined vibrational structure and can vibrate within its subpicosecond lifetime. In other words, the S(1) state stays undistorted in a short period, and the coherent nuclear motion is maintained in this state. Time-dependent density functional theory (TDDFT) calculations gave consistent results, indicating a very flat feature and even a local minimum at the perpendicular structure on the S(1) potential energy surface. The vibrational assignments of the S(1) nuclear wavepacket motion were made on the basis of the TDDFT calculation. It was concluded that photoexcitation induces a(1) vibrations containing the Cu-ligand bond length change and a b(1) vibration attributed to the ligand-twisting motion that has the same symmetry as the flattening distortion. Ultrafast spectroscopy and complementary quantum chemical calculation provided an overall picture and new understanding of the photoinduced structural change of the prototypical metal complex.

Exploration of the correlation between solvation dynamics and internal dynamics of a protein.

Protein function is intimately related to the dynamics of the protein as well as to the dynamics of the solvent shell around the protein. Although it has been argued extensively that protein dynamics is slaved to solvent dynamics, experimental support for this hypothesis is scanty. In this study, measurements of fluorescence anisotropy decay kinetics have been used to determine the motional dynamics of the fluorophore acrylodan linked to several locations in a small protein barstar in its various structural forms, including the native and unfolded states as well as the acid and protofibril forms. Fluorescence upconversion and streak camera measurements have been used to determine the solvation dynamics around the fluorophore. Both the motional dynamics and solvent dynamics were found to be dependent upon the location of the probe as well as on the structural form of the protein. While the (internal) motional dynamics of the fluorophore occur in the 0.1-3 ns time domain, the observed mean solvent relaxation times are in the range of 20-300 ps. A strong positive correlation between these two dynamical modes was found in spite of the significant difference in their time scales. This observed correlation is a strong indicator of the coupling between solvent dynamics and the dynamics in the protein.