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. Author manuscript; available in PMC: 2009 Dec 11.
Published in final edited form as: ACS Chem Biol. 2009 Oct 16;4(10):844–854. doi: 10.1021/cb900167m

TABLE 1.

Apparent Kd values (μM) as measured in competition experiments

Compound Kd without
competitorsa 		Kd with
HIV-1Δbulgeb 		Kd with
HIV-1wtbulgec 		Degree of
nonspecificity		 Degree of direct
competition		 Relative specificity
for bulge		 Hill
coefficientd
Cinchonidine 193.2 ± 21.3 n.d. n.d. n.d. n.d. n.d. 1.5 ± 0.15
Butamben 39.4 ± 7.0 n.d. n.d. n.d. n.d. n.d. 1.7 ± 0.2
Idarubicin 9.1 ± 1.3 17.6 ± 2.4 81.7 ± 3.4 17.6 ± 3.5% 81.6 ± 12.1% 4.7 ± 1.2 1.0 ± 0.15
Doxorubicin 2.8 ± 0.4 8.4 ± 0.9 37.8 ± 6.1 27.3 ± 4.9% 77.2 ± 16.7% 2.8 ± 0.8 1.5 ± 0.15
a

Compounds were titrated into 2 μM HIV-1screen in 3 replicate experiments. Mean apparent Kd and SEM are indicated.

b

n.d. = not determined. 20 μM HIV-1Δbulge was included in the titrations. This is a 10-fold molar excess of RNA relative to the HIV-1screen RNA containing the 2-aminopurine reporter.

c

20 μM HIV-1wtbulge was included in the titrations. This is a 10-fold molar excess of RNA relative to the HIV-1screen RNA containing the 2-aminopurine reporter.

d

Hill coefficient errors are shown as standard errors resulting from the least-squares fit.