1
|
Fazel M, Vallmitjana A, Scipioni L, Gratton E, Digman MA, Pressé S. Fluorescence lifetime: Beating the IRF and interpulse window. Biophys J 2023; 122:672-683. [PMID: 36659850 PMCID: PMC9989884 DOI: 10.1016/j.bpj.2023.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 11/29/2022] [Accepted: 01/11/2023] [Indexed: 01/20/2023] Open
Abstract
Fluorescence lifetime imaging captures the spatial distribution of chemical species across cellular environments employing pulsed illumination confocal setups. However, quantitative interpretation of lifetime data continues to face critical challenges. For instance, fluorescent species with known in vitro excited-state lifetimes may split into multiple species with unique lifetimes when introduced into complex living environments. What is more, mixtures of species, which may be both endogenous and introduced into the sample, may exhibit 1) very similar lifetimes as well as 2) wide ranges of lifetimes including lifetimes shorter than the instrumental response function or whose duration may be long enough to be comparable to the interpulse window. By contrast, existing methods of analysis are optimized for well-separated and intermediate lifetimes. Here, we broaden the applicability of fluorescence lifetime analysis by simultaneously treating unknown mixtures of arbitrary lifetimes-outside the intermediate, Goldilocks, zone-for data drawn from a single confocal spot leveraging the tools of Bayesian nonparametrics (BNP). We benchmark our algorithm, termed BNP lifetime analysis, using a range of synthetic and experimental data. Moreover, we show that the BNP lifetime analysis method can distinguish and deduce lifetimes using photon counts as small as 500.
Collapse
Affiliation(s)
- Mohamadreza Fazel
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona
| | - Alexander Vallmitjana
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Lorenzo Scipioni
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Enrico Gratton
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Michelle A Digman
- Department of Biomedical Engineering, University of California Irvine, Irvine, California; Laboratory of Fluorescence Dynamics, The Henry Samueli School of Engineering, University of California Irvine, Irvine, California
| | - Steve Pressé
- Center for Biological Physics, Arizona State University, Tempe, Arizona; Department of Physics, Arizona State University, Tempe, Arizona; School of Molecular Science, Arizona State University, Tempe, Arizona.
| |
Collapse
|
2
|
Blanchard AT, Li Z, Duran EC, Scull CE, Hoff JD, Wright KR, Pan V, Walter NG. Ultra-photostable DNA FluoroCubes: Mechanism of Photostability and Compatibility with FRET and Dark Quenching. NANO LETTERS 2022; 22:6235-6244. [PMID: 35881934 PMCID: PMC10080265 DOI: 10.1021/acs.nanolett.2c01757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
DNA-based FluoroCubes were recently developed as a solution to photobleaching, a ubiquitous limitation of fluorescence microscopy (Niekamp; ; Stuurman; ; Vale Nature Methods, 2020). FluoroCubes, that is, compact ∼4 × 4 × 5.4 nm3 four-helix bundles coupled to ≤6 fluorescent dyes, remain fluorescent up to ∼50× longer than single dyes and emit up to ∼40× as many photons. The current work answers two important questions about the FluoroCubes. First, what is the mechanism by which photostability is enhanced? Second, are FluoroCubes compatible with Förster resonance energy transfer (FRET) and similar techniques? We use single particle photobleaching studies to show that photostability arises through interactions between the fluorophores and the four-helix DNA bundle. Supporting this, we discover that smaller ∼4 × 4 × 2.7 nm3 FluoroCubes also confer ultraphotostability. However, we find that certain dye-dye interactions negatively impact FluoroCube performance. Accordingly, 4-dye FluoroCubes lacking these interactions perform better than 6-dye FluoroCubes. We also demonstrate that FluoroCubes are compatible with FRET and dark quenching applications.
Collapse
Affiliation(s)
- Aaron T. Blanchard
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Michigan Society of Fellows, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Zi Li
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Elizabeth C. Duran
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Catherine E. Scull
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - J. Damon Hoff
- Single Molecule Analysis in Real-Time (SMART) Center, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Keenan R. Wright
- Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Victor Pan
- Department of Biomedical Engineering, Emory University and the Georgia Institute of Technology, Atlanta, Georgia, 30322
| | - Nils G. Walter
- Single Molecule Analysis Group, Department of Chemistry, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, Michigan, 48109, United States
| |
Collapse
|