Synthesis of fluorophore and quencher monomers for use in Scorpion primers and nucleic acid structural probes

Article abstract of DOI:10.1039/b301859h

The synthesis of monomers to incorporate fluorescein and methyl red within sequence and at the termini of modified oligonucleotides was reported. These monomers were used in the solid-phase synthesis of fluorogenic oligonucleotides for genetic analysis and the study of multi-stranded nucleic acid structures. Fluorescence quenching and energy transfer were also used to study the structural, thermodynamic and kinetic properties of higher order nucleic acid structures.