Self-Assemblies, Folding, and Properties of Perylene Monomers, Oligomers, and Polymers - Molecular Self-Assembly: Advances and Applications - page 152

with the absorption band of the DDP, fluorescence resonance energy
transfer (FRET) quenches the blue emitter and yellow emission
dominates the fluorescence spectrum. Subsequently, the hybrid
foldamer was exposed to various oligonucleotides, having either
the complementary sequence or one or two mismatched base pairs.
Quantitative analyses reveal that the DNA chromophore hybrid

foldamers can distinguish the complementary oligonucleotide from
the others that have one or two base-pair mismatches.

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−

Figure 5.12 The DNA chromophore hybrid foldamers can function as

gene sensors. In the folded structure, fluorescence energy
transfer results in the emission of the fluorescent acceptor
like DDP. Upon DNA recognition, the unfolded structures
have little or no energy transfer, thus emitting the fluorescent
donor color like HSB.

Molecular beacons can be conceptually regarded as the simplest
version of the hybrid DNA chromophore foldamers (Fig. 5.13).

The structure of molecular beacons has one DNA sequence flanked
by two dyes or one dye and one quencher. First, the dye

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DNA
quencher construct was used to discriminate alleles in real-time
PCR assays of genomic DNA. For example, a quencher (4-(4

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′

-
dimethylaminophenylazo)benzoic acid) was paired up with either
fluorescin or rhodamine to form the desired molecular beacons
[43]. A set of overlapping such molecular beacons was employed
to detect mutations in the Mycobacterium tuberculosis rpoB gene.
Molecular beacons correctly analyzed mutations in all of the 52
rifampin-resistant strains and none of the 23 rifampin-susceptible