Weihong Tan from the University of Florida and Zunyi Yang and Steven Benner from the Foundation for Applied Molecular Evolution, USA, have designed a molecular beacon that incorporates components of an artificially expanded genetic information system (AEGIS) into its stems to prevent the detection of false-positives. 

                 

Molecular beacons (MBs) are short oligonucleotide hybridization probes that can report the presence of specific nucleic acids. They are hairpin shaped molecules with an internally quenched fluorophore whose fluorescence is restored when they bind to a target nucleic acid sequence. 

Background fluorescence from various sources often arises in MBs. There is therefore a great need for probes that have a high signal-to-noise ratio with low background and false positive detection in complex biological environments. 

Tan and colleagues introduced a non-standard base pair, dZ-dP, into the stem region of the MB. dZ and dP do not bind to standard nucleotides and therefore the dZ-dP pair efficiently eliminated the mishybridization with non-targeted DNAs. 

Tan says that the 'future work would be to improve the sensitivity and specificity of the diagnostic assays, nucleic acids detection, and genotyping systems, through the combination of the orthogonal pairing and enzymology of AEGIS with the micro-array technology for the advanced practical application. ' 

'The next set of challenges is to develop these as commercial reagents, so that molecular biologists who want to use them, but do not have skills in synthetic organic chemistry, can benefit from their attributes, said Tan. 

Kathryn Sear