A fluorescence-quencher pair for DNA hybridization studies based on hydrophobic base surrogates

Abstract The synthesis of the novel, fluorescent 3-aminobiphenyl-C-nucleoside M as well as the corresponding building block for oligodeoxynucleotide synthesis is described. M was incorporated into oligodeoxynucleotides via standard phosphoramidite chemistry and the thermal stabilities of duplexes with one and three consecutive M – M , M – P , and M – O pairs, where P denotes an unmodified biphenyl C-nucleoside and O a 3,5-dinitrobiphenyl-C-nucleoside, were determined. It was found that duplexes containing three consecutive M – O pairs were the most stable in the series, notably more stable than a duplex with one additional natural G–C pair instead of the modified residues. Furthermore it was found that the fluorescence of M is efficiently quenched in a duplex when placed opposite to the dinitrophenyl unit O . Thus M and O constitute a novel fluorophore/quencher pair that is orthogonal to natural base pairs in its recognition properties enabling its use as highly specific tags with reporting properties.