Bern: Molecular beacons with higher specificity

Licensing opportunity

Researchers at the University of Bern, Switzerland, have designed a new way to create molecular beacons using non-nucleosidic building blocks. This enables a more specific hybridisation with a given nucleotide sequence. The technique does away with the need for expensive fluorophores and quenchers, and so provides synthesis cheaper and more simply. The technique, the subject of a patent application, is now available for licensing.

The researchers, Robert Häner and Simon Langenegger, believe the technique has uses as probes for diagnostic markers in the early diagnosis of genetic diseases. It is also applicable to tests to prove parenthood, in forensic cases, and for identifiying SNPs, single-nucleotide polymorphisms. It can also be used as a research tool, for example in PCR, the polymerase chain reaction.

Molecular beacons (single stranded oligonucleotide hybridization probes that form a stem-and-loop structure) are widely used as detector probes in diagnostic assays. Usually, a fluorophore is linked to the end of one arm and a quencher molecule to the end of the second arm; when the molecular beacon hybridises to a target sequence the quencher is separated from the fluorophore and a fluorescence signal is observed.

A serious problem of common molecular beacons is their unspecificity due to  cross-hybridisation of the stem region, which is composed of natural nucleosides with sequences similar to the target.

The researchers say that their entirely novel design of the stem region prevents
unspecific cross-hybridisation of the usual nucleoside substitutes (poly-aromatic hydrocarbons) to their counterparts in the stem region. In addition, the excimer formation of the pyrene building blocks in the stem region take over the function of a fluorophore. The hybridization is monitored by the emission of a light signal, which is stimulated by irradiation.

As a further variation, the excimer formation can be inhibited by the presence of a polyaromatic hydrocarbon, such as phenanthrene or 1,10- phenanthroline. 

The use of pyrene building blocks simplifies the synthesis of the beacons by replacing the current need for a fluorophore and a quencher.