From signal-off to signal-on: polyT linker alters signal response mode and enhances signal change of aptamer beacon probe

A molecular beacon is an oligonucleotide hybridization probe that can report the presence of specific nucleic acids in homogeneous solutions. Using an aptamer has allowed an aptamer-based molecular beacon-aptamer beacon to be developed, which has shown advantages of simplicity, rapidity, and sensitivity in imaging and sensing non-nucleic acid substances. However, due to requirement for a deliberate DNA hairpin structure for the preparation of a molecular beacon, not any given aptamer is suitable for designing an aptamer beacon probe. This paper provides a general design strategy for the preparation of an aptamer beacon probe, which theoretically can be used for any given aptamer. Through coupling an aptamer and a short complementary DNA into one DNA molecule via a rational poly thymidine (T) linker, novel molecular beacon probes are successfully prepared and used for the detection of targets (aflatoxin B1 and ochratoxin A). The working mechanism of this aptamer beacon probe is based on intramolecular hybridization/dehybridization, which is more efficient than commonly aptasensor strategies based on intermolecular reactions. This aptamer beacon probe shows advantages of low background, a signal-on response, a large signal change, as well as simplicity and rapidity of analysis, which have promising application potential.