The design of molecules that recognize specific sequence on the deoxyribonucleic acid (DNA) double helix would provide interesting tools to interfere with DNA information processing at an early stage of gene expression. This chapter describes in detail the protocol of conjugation between terminally phosphorylated oligonucleotides and chemically or biologically active ligands possessing electrophilic or nucleophilic functional groups. The synthetic procedure includes chemical activation of oligonucleotide terminal phosphate and introduction in this way of a nucleophilic or electrophilic group (such as amino or carboxyl groups) into oligonucleotide terminus using aliphatic amino group of a ligand or a linker. The attachment of a topoisomerase inhibitor camptothecin to a triple helix-forming oligonucleotide is taken as an example of such synthesis. The described method has general interest because any functional ligand containing a primary or secondary amino group or aliphatic carboxyl group could be attached to the terminal phosphate of an oligonucleotide in a similar way.