Analysis of photon count data from single-molecule fluorescence experiments

Burzykowski, Tomasz; Szubiakowski, Jacek P.; Rydén, Tobias

doi:10.1016/s0301-0104(03)00034-x

Cited by 18 publications

(15 citation statements)

References 18 publications

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“…Figures 9(d) and 9(e) show histograms of N B and τ B . Critically, N B and τ B follow an exponential distribution as predicted by the theory involving quantum jumps between weak and strong transitions [27,28].…”

Section: Fluorescence Switching Of Polynucleotidesmentioning

confidence: 71%

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Stochastic fluorescence switching of nucleic acids under visible light illumination

Dong¹,

Almassalha²,

Soetikno³

et al. 2017

Opt. Express

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We report detailed characterizations of stochastic fluorescence switching of unmodified nucleic acids under visible light illumination. Although the fluorescent emission from nucleic acids under the visible light illumination has long been overlooked due to their apparent low absorption cross section, our quantitative characterizations reveal the high quantum yield and high photon count in individual fluorescence emission events of nucleic acids at physiological concentrations. Owing to these characteristics, the stochastic fluorescence switching of nucleic acids could be comparable to that of some of the most potent exogenous fluorescence probes for localization-based super-resolution imaging. Therefore, utilizing the principle of single-molecule photon-localization microscopy, native nucleic acids could be ideal candidates for optical labelfree super-resolution imaging.

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Section: Fluorescence Switching Of Polynucleotidesmentioning

confidence: 71%

“…Likewise, by assuming that during the "on" period the triplet transition takes place at a constant rate, this produces the average "on" time τ B as a function of I e x that is given by [28] …”

Section: Fluorescence Switching Of Polynucleotidesmentioning

confidence: 99%

Stochastic fluorescence switching of nucleic acids under visible light illumination

Dong¹,

Almassalha²,

Soetikno³

et al. 2017

Opt. Express

View full text Add to dashboard Cite

show abstract

“…The latter is also used in ref. [19], albeit for the analysis of photon counts, not individual photons. Recently a HMM approach for fluorescence resonance energy transfer (FRET) trajectories was proposed [20] and validated on experimental data.…”

Section: Related Workmentioning

confidence: 99%

Analysis of Single‐Molecule Fluorescence Spectroscopic Data with a Markov‐Modulated Poisson Process

Jäger¹,

Kiel²,

Herten³

et al. 2009

ChemPhysChem

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We present a photon-by-photon analysis framework for the evaluation of data from single-molecule fluorescence spectroscopy (SMFS) experiments using a Markov-modulated Poisson process (MMPP). A MMPP combines a discrete (and hidden) Markov process with an additional Poisson process reflecting the observation of individual photons. The algorithmic framework is used to automatically analyze the dynamics of the complex formation and dissociation of Cu2+ ions with the bidentate ligand 2,2'-bipyridine-4,4'dicarboxylic acid in aqueous media. The process of association and dissociation of Cu2+ ions is monitored with SMFS. The dcbpy-DNA conjugate can exist in two or more distinct states which influence the photon emission rates. The advantage of a photon-by-photon analysis is that no information is lost in preprocessing steps. Different model complexities are investigated in order to best describe the recorded data and to determine transition rates on a photon-by-photon basis. The main strength of the method is that it allows to detect intermittent phenomena which are masked by binning and that are difficult to find using correlation techniques when they are short-lived.

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“…Numerous methods that are based on specific kinetic systems were introduced to characterize the dynamics in these experimental trajectories under the assumption of hidden Markov chains, for example through Bayesian analysis [16][17][18], photon counting histograms [19], or maximum likelihood analysis [20,21]. These methods are appropriate for experiments with a well-known number of accessible states, for example in the case of single molecule blinking, or enzymatic turnovers, which can be approximated as ''on'' and ''off'' states.…”

Section: Introductionmentioning

confidence: 99%

Statistical identification of structural rearrangement events in molecular dynamics trajectories

Bingemann

2013

Computer Physics Communications

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Analysis of photon count data from single-molecule fluorescence experiments

Cited by 18 publications

References 18 publications

Stochastic fluorescence switching of nucleic acids under visible light illumination

Stochastic fluorescence switching of nucleic acids under visible light illumination

Analysis of Single‐Molecule Fluorescence Spectroscopic Data with a Markov‐Modulated Poisson Process

Statistical identification of structural rearrangement events in molecular dynamics trajectories

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