Duplex probes

The duplex probe configuration provides for a close proximity of the donor/acceptor pair and may lead to two mechanisms of quenching FRET and direct transfer (contact-mediated) quenching [78]. Placement of the fluorophore and quencher toward the centre of the duplex probe sequence may further add to the quenching efficiency as the ends of duplexes are known to breathe and are not as tightly bound as internal base pairs. Duplex probes are relatively easy to synthesize as the fluorophore and quencher moieties do not have to be incorporated into the same strand. 

Sudha, R. and Zenobi, R. (2002) The detection and stability of DNA duplexes probed by MALDI mass spectrometry. Hdv. Chim. Acta, 85 (10), 3136-3143. 

FIGURE 11.26 Scheme for capture, ligation,and exonuclease ladder generation on a duplex probe attached to a streptavidin-coated surfece. 

Rajagopalan, S. Zenobi, R. The detection and stabihty of DNA duplexes probed by Maldi mass spectrometry. Heh. Chim. Acta 2002, 85, 3136-3143. 

Sequence-dependent variations along DNA duplexes probed by nucleotide-independent nitroxide probes. Qin and co-workers reported that the R5/R5a probes (Fig. 2, I), which can be attached at the phosphate... 

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