Some of the subject methods may be used to sequence single molecules of polynucleotides of interest. The methods of the invention employ fluorescent intercalators as a donor in FRET (fluorescence resonance energy transfer). Fluorescent intercalators intercalate within the double-stranded region of the primed template. The intercalators may be used as donors in FRET. Additional molecules of the fluorescent intercalator may be incorporated into the newly formed double-stranded regions that are formed as the primer is extended.