RT Journal Article
SR Electronic
T1 Multi-parameter photon-by-photon hidden Markov modeling
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2021.04.08.439035
DO 10.1101/2021.04.08.439035
A1 Harris, Paul David
A1 Weiss, Shimon
A1 Lerner, Eitan
YR 2021
UL http://biorxiv.org/content/early/2021/04/10/2021.04.08.439035.abstract
AB Single molecule FRET (smFRET) is a useful tool for studying biomolecular sub-populations and their dynamics. Advanced smFRET-based techniques often track multiple parameters simultaneously, increasing the information content of the measurement. Photon-by-photon hidden Markov modelling (H2MM) is a smFRET analysis tool that quantifies FRET dynamics of single biomolecules, even if they occur in sub-milliseconds. However, sub-populations can be characterized by additional experimentally-derived parameters other than the FRET efficiency. We introduce multi-parameter H2MM (mpH2MM) that identifies sub-populations and their transition dynamics based on multiple experimentally-derived parameters, simultaneously. We show the use of this tool in deciphering the number of underlying sub-populations, their mean characteristics and the rate constants of their transitions for a DNA hairpin exhibiting milliseconds FRET dynamics, and for the RNA polymerase promoter open complex exhibiting sub-millisecond FRET dynamics of the transcription bubble. Overall, we show that using mpH2MM facilitates the identification and quantification of biomolecular sub-populations in smFRET measurements that are otherwise difficult to identify. Finally we provide the means to use mpH2MM in analyzing FRET dynamics in advanced multi-color smFRET-based measurements.Competing Interest StatementThe authors have declared no competing interest.