Table 1.

Comparison of DSN Action on Perfect and Mismatched 10 bp DNA Duplexes

Duplex Name	Target Structurea	ΔFm/ΔFp for signal probe:
F1-5′-gccctatagt-3′TAMRA	F1-5′-gccctatagt-3′DABCYL
TP	5′-actcactatagggcgaat-3′	1.00	1.00
T1C	5′-actcCctatagggcgaat-3′	0.04	0.48
T1G	5′-actcGctatagggcgaat-3′	0.04	0.25
T1T	5′-actcTctatagggcgaat-3′	0.04	0.42
T2A	5′-actcaAtatagggcgaat-3′	0.05	0.36
T2G	5′-actcaGtatagggcgaat-3′	0.02	0.46
T2T	5′-actcaTtatagggcgaat-3′	0.02	0.24
T3A	5′-actcacAatagggcgaat-3′	0.02	0.27
T3C	5′-actcacCatagggcgaat-3′	0.01	0.09
T3G	5′-actcacGatagggcgaat-3′	0.02	0.22
T4C	5′-actcactCtagggcgaat-3′	0.02	0.10
T4G	5′-actcactGtagggcgaat-3′	0.03	0.18
T4T	5′-actcactTtagggcgaat-3′	0.03	0.18
T5A	5′-actcactaAagggcgaat-3′	0.01	0.11
T5C	5′-actcactaCagggcgaat-3′	0.03	0.14
T5G	5′-actcactaGagggcgaat-3′	0.02	0.13
T6C	5′-actcactatCgggcgaat-3′	0.06	0.14
T6G	5′-actcactatGgggcgaat-3′	0.04	0.16
T6T	5′-actcactatTgggcgaat-3′	0.01	0.22
T7A	5′-actcactataAggcgaat-3′	0.03	0.07
T7C	5′-actcactataCggcgaat-3′	0.01	0.10
T7T	5′-actcactataTggcgaat-3′	0.06	0.09
T8A	5′-actcactatagAgcgaat-3′	0.04	0.06
T8C	5′-actcactatagCgcgaat-3′	0.05	0.01
T8T	5′-actcactatagTgcgaat-3′	0.06	0.05
T9A	5′-actcactataggAcgaat-3′	0.05	0.03
T9C	5′-actcactataggCcgaat-3′	0.08	0.03
T9T	5′-actcactataggTcgaat-3′	0.07	0.03
T10A	5′-actcactatagggAgaat-3′	0.03	0.03
T10G	5′-actcactatagggGgaat-3′	0.07	0.08
T10T	5′-actcactatagggTgaat-3′	0.05	0.15

Duplexes were generated from 10-mer signal probes and 18-mer synthetic targets. Fluorescence values, ΔF, were normalized according to the formula: ΔF = Fi-Fo, where Fi is the fluorescence of substrate after DSN treatment and Fo represents fluorescence at the start of the reaction. The ratio of DSN activity on mismatched (ΔFm) and perfect (ΔFp) duplexes was determined. 

^aSequence complementary to signal probes is underlined; mismatch position is marked by capital letter.