Abstract: Improved hybridization probe compositions and method for detecting nucleic acids of interest are provided. A hybridization probe constructed to contain thionucleotides and a detectable label is hybridized to a nucleotide sequence of interest in the absence of nonpolar solvents, reducing agents and volume exclusion agents. The thionucleotides serve to increase the mass of bound probe molecules, thereby amplifying the signal available to detect the presence of the nucleic acid sequence of interest. Certain cations interact specifically with the thiol moiety of phosphorothioate groups of nucelic acid molecules in a manner that can be exploited to amplify probe binding or convey a detectable label. Thus, the mass of bound probe molecules can be further increased by the presence of specified multivalent cations from the transition metal group, such as Cu.sup.2+ or Fe.sup.3+, during the annealing step.