Table 3.

Melting temperatures of DNA duplexes in the presence and the absence of coralyne (Supplementary Figure S18)

Name	Sequence	Tm (°C) w/o coralyne	Tm (°C) with coralyne
(A·B)	5′-_______AAAAAAAA_______-3′	34.5	63.0
	3′-_______AAAAAAAA_______-5′
	One substitution
(1A·B)	5′-_______AAAA7AAA_______-3′	34.5	59.5
	3′-_______AAAAAAAA_______-5′
(A·1B)	5′-_______AAAAAAAA_______-3′	33.5	59.0
	3′-_______AAAA7AAA_______-5′
	Two substitutions
(2A·B)	5′-_______AA7A7AAA_______-3′	33.5	59.0
	3′-_______AAAAAAAA_______-5′
(A·2B)	5′-_______AAAAAAAA_______-3′	32.5	59.5
	3′-_______AA7A7AAA_______-5′
(A·3B)	5′-_______AAAAAAAA_______-3′	33.5	58.0
	3′-_______AAA7A7AA_______-5′
(A·4B)	5′-_______AAAAAAAA_______-3′	34.5	58.5
	3′-_______AAA77AAA_______-5′
(1A·1B)	5′-_______AAAA7AAA_______-3′	33.5	59.0
	3′-_______AAAA7AAA_______-5′
	Three substitutions
(1A·2B)	5′-_______AAAA7AAA_______-3′	33.0	55.0
	3′-_______AA7A7AAA_______-5′
(1A·3B)	5′-_______AAAA7AAA_______-3′	33.0	53.0
	3′-_______AAA7A7AA_______-5′
(1A·4B)	5′-_______AAAA7AAA_______-3′	34.5	51.5
	3′-_______AAA77AAA_______-5′
(2A·1B)	5′-_______AA7A7AAA_______-3′	33.0	53.5
	3′-_______AAAA7AAA_______-5′
	Four substitutions
(2A·2B)	5′-_______AA7A7AAA_______-3′	34.0	50.0
	3′-_______AA7A7AAA_______-5′
(2A·3B)	5′-_______AA7A7AAA_______-3′	34.0	50.0
	3′-_______AAA7A7AA_______-5′
(2A·4B)	5′-_______AA7A7AAA_______-3′	34.0	50.5
	3′-_______AAA77AAA_______-5′
(3A·B)	5′-_______AA7777AA_______-3′	34.5	53.5
	3′-_______AAAAAAAA_______-5′
	Five substitutions
(3A·1B)	5′-_______AA7777AA_______-3′	34.0	52.0
	3′-_______AAAA7AAA_______-5′
(3A·2B)	5′-_______AA7777AA_______-3′	34.0	45.5
	3′-_______AA7A7AAA_______-5′
(3A·3B)	5′-_______AA7777AA_______-3′	35.5	48.0
	3′-_______AAA7A7AA_______-5′
(3A·4B)	5′-_______AA7777AA_______-3′	34.5	48.0
	3′-_______AAA77AAA_______-5′

7 = 7-deaza-deoxyadenosine. All sequences have the same flanking Watson–Crick base-paired regions. For example, (A·B) is the duplex formed by oligos A and B:

A = 5′-GACCCGCAAAAAAAACCTCGCC-3′; B = 3′-CTGGGCGAAAAAAAAGGAGCGG-5′