Single Label Interactions

For achieving a specific detection most assays rely on use of labeled probe molecules. Only one label is necessary when the hybridization strongly affects the

Label Hydrogen Bond Dna

Intercalation

Fig. 4.2.2. Binding modes of typical stains used for homogenous detection of double stranded DNA. Binding to the minor groove or intercalation between base pairs can lead to fluorescence enhancement.

Intercalation

Fig. 4.2.2. Binding modes of typical stains used for homogenous detection of double stranded DNA. Binding to the minor groove or intercalation between base pairs can lead to fluorescence enhancement.

fluorescence properties. Fluorescence polarization anisotropy measurements can detect the hybridization-induced alteration of molecular weight. The underlying principle is that a fluorophore that is excited by polarized light also emits polarized light if molecular rotations are slow compared with the fluorescence lifetime. It was, for example, shown that the fluorescence anisotropy of the labeled probe 1 is enhanced by binding to the complementary DNA strand (Figure 4.2.3) [11]. The observed anisotropy differences are, however, not pronounced, even when high molecular weight PCR DNA is targeted (see 2) [12].

The fluorescence of many fluorophores is environmentally sensitive and is, therefore, in principle, suitable for reporting a hybridization event. Meehan and coworkers attached a pyrene chromophore to the 5 '-end of an oligonucleotide (Figure

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