Chapter 9 Minor Groove Recognition of T , A Base Pairs by Benzothiophene / Pyrrole Pairs

Polyamides are designed oligomers that can bind to DNA in a sequence-specific manner with affinities comparable to those of natural DNA-binding proteins. Recently, an N-terminal 3-chloro-6-fluorobenzothiophene polyamide bound in the minor groove of DNA was co-crystallized at 1.1 Å resolution as an antiparallel dimer. In addition, antimicrobial screenings for this polyamide family and the development of N-terminal 3chlorothiophene as a T-specific recognition element have been disclosed. These results inspired us to measure the affinities and specificities of N-terminal 3-substituted benzothiophene hairpin polyamides by DNase I footprint titration experiments. While the four polyamides bound with high affinity, none showed specificity for A•T over T•A or vice versa. This observation suggests that N-terminal 3-substituted benzothiophene polyamides prefer to adopt the rotational conformation that directs the sulfur atom towards the floor of the minor groove, a conclusion that is consistent with the recently solved crystal structure.