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

Evidence of a Three-State Mechanism in DNA Hairpin Folding

DNA hairpins are a model system for biomolecule folding as well as key structures in biology and nanotechnology. However, limitations in traditional solution-phase spectroscopy shorten the window of observable kinetics and cannot account for static heterogeneity. Here, we show that the application of two-dimensional fluorescence lifetime correlation spectroscopy (2DFLCS) to a solution-phase molecule trapped in an anti-Brownian electrokinetic (ABEL) trap bypasses those limitations, enabling kinetic analysis of the dynamics of single solution-phase molecules on a broad range of time scales down to microseconds. The analysis unambiguously shows that DNA hairpin folding proceeds via a three-state system, where hairpins fold initially on the scale of tens to hundreds of microseconds from a random coil to a partially closed intermediate and then form a stable fully closed state.

Non-convergence of the blinking timescale of twelve-faceted perovskite nanocrystals observed through an advanced fluorescence correlation spectroscopy study

Single-particle photoluminescence measurements have been extensively utilized to investigate the charge carrier dynamics in quantum dots (QDs). Among these techniques, single dot blinking studies are effective for probing relatively slower processes with timescales >10 ms, whereas fluorescence correlation spectroscopy (FCS) studies are suited for recording faster processes with timescales typically <1 ms. In this study, we utilized scanning FCS (sFCS) to bridge the ms gap, thereby enabling the tracking of carrier dynamics across an extended temporal window ranging from μs to subsecond. We compared the sFCS data recorded on surface-immobilized twelve-faceted CsPbBr3 dodecahedron perovskite nanocrystals (d-PNCs) with the FCS data of the same nanocrystals in the solution phase. Although the two datasets exhibited similarities in a qualitative sense, they revealed notable quantitative differences. This is primarily attributed to the significantly varying immediate environments of PNCs in these two techniques, as well as the different temporal sizes of the observation windows available for the recording of carrier dynamics. The most intriguing finding of our study lies in the non-converging blinking timescale (τR) of d-PNCs in sFCS, despite this technique providing an extended temporal window size (≤328 ms) for studying carrier dynamics. We attribute this observation to PL blinking following power-law statistics, which causes the mean ON/OFF duration of blinking persuasive to the experimental integration time, making blinking occur across all timescales.

Macromolecular crowding effects on protein dynamics

Macromolecular crowding experiments bridge the gap between in-vivo and in-vitro studies by mimicking some of the cellular complexities like high viscosity and limited space, while still manageable for experiments and analysis. Macromolecular crowding impacts all biological processes and is a focus of contemporary research. Recent reviews have highlighted the effect of crowding on various protein properties. One of the essential characteristics of protein is its dynamic nature; however, how protein dynamics get modulated in the crowded milieu has been largely ignored. This article discusses how protein translational, rotational, conformational, and solvation dynamics change under crowded conditions, summarizing key observations in the literature. We emphasize our research on microsecond conformational and water dynamics in crowded milieus and their impact on enzymatic activity and stability. Lastly, we provided our outlook on how this field might move forward in the future.

Competition among recombination pathways in single FAPbBr3 nanocrystals

Single particle level microscopy of immobilized FAPbBr3 nanocrystals (NCs) has elucidated the involvement of different processes in their photoluminescence (PL) intermittency. Four different blinking patterns are observed in the data from more than 100 NCs. The dependence of PL decays on PL intensities brought out in fluorescence lifetime intensity distribution (FLID) plots is rationalized by the interplay of exciton- and trion-mediated recombinations along with hot carrier (HC) trapping. The high intensity-long lifetime component is attributed to neutral exciton recombination, the low intensity-short lifetime component is attributed to trion assisted recombination, and the low intensity-long lifetime component is attributed to hot carrier recombination. Change-point analysis (CPA) of the PL blinking data reveals the involvement of multiple intermediate states. Truncated power law distribution is found to be more appropriate than power law and lognormal distribution for on and off events. Probability distributions of PL trajectories of single NCs are obtained for two different excitation fluences and wavelengths (λex = 400, 440 nm). Trapping rate (kT) prevails at higher power densities for both excitation wavelengths. From a careful analysis of the FLID and probability distributions, it is concluded that there is competition between the HC and trion assisted blinking pathways and that the contribution of these mechanisms varies with excitation wavelength as well as fluence.

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.

Single-Particle Dynamics of ZnS Shelling Induced Replenishment of Carrier Diffusion for Individual Emission Centers in CuInS2 Quantum Dots

Insights into blinking and photoactivation of aqueous copper indium sulfide (CIS) quantum dots have been obtained using fluorescence correlation spectroscopy (FCS) and fluorescence lifetime correlation spectroscopy (FLCS). An unusual excitation wavelength-dependence of photoactivation/photocorrosion is manifested in an increase in the initial correlation amplitude G(0) for λ_ex = 532 nm, but a decrease for λ_ex = 405 nm. This has been rationalized in terms of different contributions from surface-assisted recombination in the two cases. Blinking times obtained from the autocorrelation functions (ACFs) of the 100-200 ns lifetime component (core Cu-mediated recombination) are almost unaffected by shelling, but those from the ACF for the 10-30 ns lifetime (surface states) increase significantly. Absence of cross-correlation between the two recombinative states of bare CIS QDs and the emergence of an anticorrelation with the introduction of the ZnS shell are observed, indicating the diffusive nature of the two states for CIS-ZnS. The diffusion is inhibited in bare CIS QDs due to the preponderance of surface states.

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.