A novel denaturing heteroduplex tracking assay for genotypic prediction of HIV-1 tropism

► A novel denaturing heteroduplex tracking assay. ► The use of a single-stranded fluorescent probe based on the consensus V3 sequence of HIV-1 CCR5 tropic viruses. ► The use of Locked Nucleic Acid (LNA) “clamps” at both ends of heteroduplex DNA. ► The partially denaturing gel electrophoresis with formamide induced significant mobility shifts of heteroduplex DNA based on patterns of mutations. ► A useful research method for analysis of viral quasispecies and for genotypic prediction of HIV-1 tropism.