Detection of Terminal Mismatches on DNA Duplexes in Homogeneous Assays or with Immobilized Probes

Abstract

We recently reported the design of new fluorescent oligo-2′-deoxyribonucleotides (FODNs) for the detection of terminal mismatches on DNA duplexes in homogeneous assays. We now report the validation of this method in homogeneous assays with other sequences and the feasibility of the detection of terminal mismatches with immobilized FODNs. In all cases studied, the mismatched duplexes were more fluorescent than the perfect ones and results confirmed that the discrimination factor is sequence-dependent.

Keywords:

• DNA
• terminal mismatch detection
• fluorescent oligonucleotides
• thiazole orange
• non-stringent conditions

We thank the CNRS “Programme Puces à ADN” for financial support, H. Meudal and C. Buré for recording the NMR spectra and for running the electrospray mass spectrometer.