Abstract: A method for using an organic compound to label polynucleotides is described. The method utilizes an organic compound including an oligonucleotide, and electrophilic active site, an active complex, and a phosphate binding site. The oligonucleotide has a sequence that is complimentary to a specific region of a polynucleotide. This facilitates labeling of DNA or RNA at a specific site in its sequence. The active site consists of a stable precursor, and only becomes reactive upon activation. Leaving and protecting functional groups may be attached to the active site in order to facilitate the formation of a stable precursor and subsequent activation. The active complex may be a drug, polypeptide or a reporter molecule such as an isotope or fluorescing compound. The phosphate binding sites may be any functional group capable of forming ionic bonds with phosphate oxygens. Nucleotide labeling using this compound does not interfere with a polynucleotide sequence.