3 '-minor groove binder-DNA probes increase sequence specificity at PCR extension temperatures

DNA probes with conjugated minor groove binder (MGB) groups form extremely stable duplexes with single-stranded DNA targets, allowing shorter probes t o be used for hybridization based assays. In this paper, sequence specifici ty of 3'-MGB probes was explored. In comparison with unmodified DNA, MGB pr obes had higher melting temperature (T-m) and increased specificity, especi ally when a mismatch was in the MGB region of the duplex. To exploit these properties, fluorogenic MGB probes were prepared and investigated in the 5' -nuclease PCR assay (realtime PCR assay, TaqMan assay). A 12mer MGB probe h ad the same T-m (65 degrees C) as a no-MGB 27mer probe. The fluorogenic MGB probes were more specific for single base mismatches and fluorescence quen ching was more efficient, giving increased sensitivity. ATT rich duplexes w ere stabilized more than G/C rich duplexes, thereby leveling probe T-m and simplifying design. In summary, MGB probes were more sequence specific than standard DNA probes, especially for single base mismatches at elevated hyb ridization temperatures.