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. 2004 Sep 30;32(17):5192–5197. doi: 10.1093/nar/gkh854

Figure 1.

Figure 1

Design of the double-labeled DNA construct for FRET analysis of binding and DNA bending by GCN4-bZIP protein. (a) Original DNA construction with DNA ‘base’ sequence between two A5-bulges and the arms, described in (9). The distance (Rda) between FAM (donor) and TAMRA (acceptor) attached to the 5′ ends was 54 Å. (b) Insertion of 10 bp DNA fragment (one full turn) containing target sequences, AP-1 or ATF/CREB, for binding of GCN4-bZIP protein increases the dye-to-dye distance (Rda) by 34 Å. Insertion of the A4-tracts into the arms decreases Rda to 80 Å. (c) Modeling of the DNA construct used for the quantitative calculation of the bend angle of the binding site from the measured Rda by Equation 1. (d) The sequences used for the construction of the U-shaped DNA.