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. Author manuscript; available in PMC: 2011 Mar 22.
Published in final edited form as: Bioorg Med Chem Lett. 2009 Mar 24;19(14):3919–3923. doi: 10.1016/j.bmcl.2009.03.072

Table 5.

Relative binding affinities for polyamides

R1,R2 T·A A·T C·G G·C
graphic file with name nihms-279883-t0017.jpg OH, H 1.0 1.0 <0.01 <0.01
F,H 1.0 0.8 <0.01 <0.01
H, OH 1.0 1.3 1.4 0.8
H, F 1.0 0.6 0.6 <0.01

Relative binding affinities are reported as ratios of binding affinities (Ka) as determined by DNase I footprinting titration experiments for polyamides targeting 5′-WGGWW-3′ Sites containing G·C at the hairpin position have relative affinities <0.01 (not shown).