Table 4.

Sequence discrimination ability of six- and eight-ring polyamides

Ring sequence	ΔGbind*	All†			TATA box†			Fraction‡
		A	B	C	A	B	C
IIIPPI	−7.74	935	63	24	10	0	0	0.014
IIPPPI	−8.71	959	47	16	10	0	0	0.018
IPIPPI	−8.71	959	47	16	10	0	0	0.018
IPPPPI	−9.68	991	31	0	10	0	0	0.023
IIIPPP	−8.75	955	51	16	8	2	0	0.018
IIPPPP	−9.72	975	39	8	8	2	0	0.023
IPIPPP	−9.72	975	39	8	6	4	0	0.023
IPPPPP	−10.69	991	31	0	6	4	0	0.029
IIIIPPPI	−9.10	3,863	175	56	10	0	0	0.005
IIIPPPPI	−10.07	3,920	127	48	10	0	0	0.007
IIPIPPPI	−10.07	3,919	127	48	10	0	0	0.007
IIPPPPPI	−11.04	3,967	95	32	10	0	0	0.007
IPIIPPPI	−10.07	3,919	127	48	10	0	0	0.009
IPIPPPPI	−11.04	3,967	95	32	10	0	0	0.009
IPPIPPPI	−11.04	3,967	95	32	10	0	0	0.009
IPPPPPPI	−12.01	4,031	63	0	10	0	0	0.011
IIIIPPPP	−10.11	3,911	139	44	10	0	0	0.007
IIIPPPPP	−11.08	3,959	103	32	10	0	0	0.008
IIPIPPPP	−11.08	3,959	103	32	10	0	0	0.008
IIPPPPPP	−12.05	3,999	79	16	10	0	0	0.011
IPIIPPPP	−11.08	3,959	103	32	9	1	0	0.008
IPIPPPPP	−12.05	3,999	79	16	8	2	0	0.011
IPPIPPPP	−12.05	3,999	79	16	9	1	0	0.011
IPPPPPPP	−13.02	4,031	63	0	8	2	0	0.014

I and P defined in Table 1. 

^*Estimated binding free energy to the target sequence (AGAAA for six-ring polyamides and AGAAAA for eight-ring polyamides) in kcal/mol. 

^†Number of sequences for which the estimated polyamide binding constant is: (A) less than one-tenth of the target sequence; (B) greater than one-tenth that of the target sequence, but less than that of the target sequence; and (C) greater than that of the target sequence. Results are tabulated for all possible 5-bp sequences or all possible 6-bp sequences, excluding the target sequence and its complement, and for the 10 unique 5-bp sequences or for the 10 unique 6-bp sequences from the TATA box consensus sequence TATA(A,T)A(A,T). 

^‡Fraction of bound drug that is bound to the target sequence when this target sequence is 50% saturated.