Fig. 19. DNA-sensitized reaction centers and polyamide driven assembly of dyes to DNA duplexes. (A) Modified structure of the reaction center (RC) from Rhodobacter sphaeroides 2.4.1 (PDB 2J8C10) with sequences of the three-arm-DNA construct shown. Cofactors of the RC are colored, those active in electron transfer reactions are designated by letters: P, bacteriochlorophyll pair; BA, bacteriochlorophyll monomer; HA, bacteriopheophytin; QA, ubiquinone. The arrows in the DNA structure point in the direction of the 3′-end of DNA strands. The 3′-amine-modified strand-1 (purple) of the three-arm DNA is conjugated to one of the Cys (shown in red) on the surface of the RC. Other two strands (strand-2 and -3, in green and red, respectively) hybridize to strand-1 to form the three-arm-DNA junction. Inter-Cys distances on the RC marked as dotted lines. Reproduced with permission from ref. 259 Copyright 2014 American Chemical Society. (B) Top: Structure of the fluorophore-tethered pyrrole-imidazole polyamides where 1 binds the sequence 5′-ATGGACA-3′ while 2,3 bind to 5′-TACTGCT-3′. Bottom: Schematic of the ds 30 bp Pacific Blue (PB), Alexa 488 (A488), Alexa 532 (A532), Cy3.5 multiFRET construct. Reproduced from ref. 260 with permission from Springer Nature, copyright 2013.