Design and synthesis of hairpin probe for specific mis-match discrimination

A single stranded hairpin probe labeled with fluorescein at its 5'-end and terminates with deoxyguanosine nucleotide at 3'- end, as quencher, has been designed and synthesized in an automated DNA synthesizer. The system has been used as an alternative to molecular beacon. The deoxyguanosine residues have been kept at the 3'-end of the complementary arm strand to quench the fluorescence intensity of the fluorophore, making the hairpin probe behave like a conventional molecular beacon. The proposed probe has been used to find a correlation between fluorescence and thermal behaviour on hybridizing it with several mismatched target oligonucleotides. The designed probe has shown greater degree of specificity with perfectly matched target oligonucleotide, while it shows a variable degree of destabilization with mismatched (A/C) target complementary oligonucleotides.