Many human diseases start with a defect in the genome. Cancer, for example, is a genetic disease that arises from a single cell that behaves abnormally, dividing uncontrollably and leading, eventually, to the development of a tumor. A critical step in diagnosing and treating cancer is to detect cancer cells that result from the mutated genes. In spite of the extensive biomedical research efforts during the last few decades, it is still difficult to detect cancer at its early stages — when a cancer is diagnosed it is often too late to cure. A novel way of achieving early detection of cancer is to detect mRNA transcripts that arise from mutated genes in living cells [1]. We have developed a FRET-enhanced molecular beacons methodology which, combined with the state-of-the-art fluorescence imaging techniques, has the potential to detect cancer cells. FRET (Fluorescence resonance energy transfer) refers to the non-radiative transfer of energy from a donor molecule to an acceptor molecule through dipole-dipole coupling. As shown schematically in Figure 1, molecular beacons are dual labeled antisense oligonucleotides (ODNs) with a fluorophore (A or D) at one end and a quencher (Q) at the other; they are designed to form a hairpin structure in the absence of a complimentary target such that fluorescence of the fluorophore is quenched. Upon hybridization with the target mRNA, the molecular beacon opens up, leading to fluorescence [2,3].

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