A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer

Ioannis Sgouralis, Shreya Madaan, Franky Djutanta, Rachael Kha, Rizal Hariadi, Steve Presse

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

We develop a Bayesian nonparametric framework to analyze single molecule FRET (smFRET) data. This framework, a variation on infinite hidden Markov models, goes beyond traditional hidden Markov analysis, which already treats photon shot noise, in three critical ways: (1) it learns the number of molecular states present in a smFRET time trace (a hallmark of nonparametric approaches), (2) it accounts, simultaneously and self-consistently, for photophysical features of donor and acceptor fluorophores (blinking kinetics, spectral cross-talk, detector quantum efficiency), and (3) it treats background photons. Point 2 is essential in reducing the tendency of nonparametric approaches to overinterpret noisy single molecule time traces and so to estimate states and transition kinetics robust to photophysical artifacts. As a result, with the proposed framework, we obtain accurate estimates of single molecule properties even when the supplied traces are excessively noisy, subject to photoartifacts, and of short duration. We validate our method using synthetic data sets and demonstrate its applicability to real data sets from single molecule experiments on Holliday junctions labeled with conventional fluorescent dyes.

Original languageEnglish (US)
Pages (from-to)675-688
Number of pages14
JournalJournal of Physical Chemistry B
Volume123
Issue number3
DOIs
StatePublished - Jan 24 2019

Fingerprint

Bayes Theorem
Energy Transfer
Photons
Energy transfer
energy transfer
Cruciform DNA
Blinking
Molecules
Fluorescent Dyes
Artifacts
molecules
blinking
Shot noise
Kinetics
Fluorophores
kinetics
photons
shot noise
Hidden Markov models
estimates

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer. / Sgouralis, Ioannis; Madaan, Shreya; Djutanta, Franky; Kha, Rachael; Hariadi, Rizal; Presse, Steve.

In: Journal of Physical Chemistry B, Vol. 123, No. 3, 24.01.2019, p. 675-688.

Research output: Contribution to journalArticle

Sgouralis, Ioannis ; Madaan, Shreya ; Djutanta, Franky ; Kha, Rachael ; Hariadi, Rizal ; Presse, Steve. / A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer. In: Journal of Physical Chemistry B. 2019 ; Vol. 123, No. 3. pp. 675-688.
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