Journal: Nucleic Acids Research

Article Title: G-quadruplex recognition and remodeling by the FANCJ helicase

doi: 10.1093/nar/gkw574

Figure Lengend Snippet: Mechanism of FANCJ-mediated G4-unfolding and refolding. ( A ) Regions of the single-molecule G4-unfolding FRET time-courses for each FANCJ construct containing FRET transitions were globally analyzed by the ebFRET Matlab suite. The resulting transition density plots (TDPs) for each FANCJ construct show four major FRET states with mean FRET values of 0.13 (ssDNA; 1), 0.32 (G2), 0.49 (G3) and 0.64 (G4). Additional, albeit infrequent state (FRET ≈ 0.73) represents a parallel G-quadruplex (P). The scale bar for transition frequency is shown on the right of each respective TDP where the brighter peaks correspond to more frequent transitions. ( B ) Schematic representation of the TDP, observed FRET states and their corresponding DNA conformations, and transitions. ( C ) FANCJ-, bioFANCJ- and FANCJ HD -mediated G4-unfolding and refolding proceeded through the same intermediates and mechanism based on the TDPs. The TDP for the bioFANCJ K141/K142A -mediated process shows a reduction in the G2⇔G4 and G3⇔G4 interconversions.

Article Snippet: The ebFRET Matlab library was used to statistically determine the number of FRET states observed during the course of G4 melting, and the mean lower bound was used to evaluate the number of states that best described each time series.

Techniques: Construct

Journal: Cell

Article Title: Cohesin mediates DNA loop extrusion by a “swing and clamp” mechanism

doi: 10.1016/j.cell.2021.09.016

Figure Lengend Snippet:

Article Snippet: Plots were generated by the plotTDP MATLAB script ( http://ebfret.github.io/ ), using a variance of 0.003, and normalized for the total number of frames in each condition (‘normbyframes’).

Techniques: Virus, Recombinant, Lambda DNA Preparation, Avidin-Biotin Assay, Software