Rhodamine-based fluorophores useful as labeling reagents

The invention generally relates to methods of labeling organic compounds for fluorescent detection. More particularly, the invention relates to rhodamine-based fluorophores which are made useful by derivatization with organic molecules, and have application so as to label biomolecules such as synthetic oligonucleotides and proteins. The fluorophores are single isomers, are stable and reactive in standard phosphite chemistry, and the conjugates remain fluorescent. Fluorescent dyes based on rhodamine are derivatized to form labeled conjugates that fluoresce upon excitation with light of an appropriate wavelength. Particularly preferred embodiments are certain single isomer form rhodamine phosphoramidites. These rhodamine phosphoramidites enhance the efficiency of synthesizing rhodamine-labeled oligonucleotides by solid phase methods. Conjugate embodiments of the invention are prevented from being converted to a non-fluorescent lactam form due to having a fully substituted amide linkage derived from the 3-position carboxylate.