Figure 7.

Structure of TdT chimera as a ternary complex with a downstream dsDNA and the incoming dNTP. A, DNA substrates; the downstream DNA duplex is colored in blue and cyan. The incoming nucleotide and Loop1 are represented in dark gray and blue, respectively. The additional DNA strand, a triplex-forming oligonucleotide (TFO) is represented in gray. B, space-filling representation of the incoming ddNTP-binding site. The ddCTP is in ball-and-stick form, the downstream template strand is in cyan, and the surface of the Loop1 atoms is in dark blue. C, overall structure of the TdT-μ chimera downstream dsDNA. The incoming ddCTP makes Watson–Crick interactions with the in trans template strand. Loop1 is fully visible in the electron density map and is made of two 3₁₀ helices and one α helix. The exit channel for the 3′ protruding end is represented by a dashed cyan line. D, differences in the Loop1 conformation in the binary ddCTP complex (gold) and in the downstream dsDNA complex (dark blue). Loop1 conformation of TdT-WT apoenzyme is also represented as a reference (black).