Fig. 3: AV simulations predicting distances between the fluorophores at different stages of recombination.
From: Direct observation of subunit rotation during DNA strand exchange by serine recombinases
The accessible volumes (AV) of the donor fluorophore (green) and the acceptor fluorophore (red) are illustrated as surfaces48. The dye pairs used in our experiments are indicated on the Figure. The FRET-averaged donor-acceptor distances, <RDA>, were determined using Atto 532/ Cy5 (SUL25 + Sin Q115R) and Cy3B/ Cy5 (UL25 + Tn3 NM) FRET pairs and are shown with standard deviation (SD) in brackets. The expected E values for the Alexa 488/Cy5 FRET pair are also shown. Donor and acceptor positions are illustrated for each conformation expected during recombination (lnr, ligated non-recombinant; cnr, cleaved non-recombinant; cr, cleaved recombinant; lr, ligated recombinant). Note that the lnr structures shown for both Tn3 and Sin are models based on existing crystal structures, as high-resolution structures for these intermediates have not yet been solved. A (Sin Q115R): The models are based on the same structures as for Tn3 NM resolvase, but the fluorophores are at their positions in the SUL25 substrate. B (Tn3 NM resolvase): The lnr model was created previously by juxtaposition of two γδ resolvase-site I structures (1GDT)7,11. The cnr and cr models are based on the crystal structure of a γδ resolvase-site I cleaved synaptic intermediate (1ZR4)7,11, and the LR model is based on a single 1GDT structural unit. See text for details.
