After fifty years of DNA targeting through intercalators and groove binders and related studies now the current focus is in RNA targeting. Polyadenylic acid [poly(A)] tail of mRNA has been recently established as a potential drug target due to its significant role in the initiation of translation, maturation and stability of mRNA as well as in the production of alternate proteins in eukaryotic cells. Isoquinoline group of alkaloids have their importance in contemporary biomedical research and drug discovery programme due to extensive pharmacological and biological activity. Very recently some small molecule alkaloids of the isoquinoline group have been found to bind poly(A) with remarkably high affinity leading to self structure formation. The alkaloids have a high binding affinity towards single stranded poly(A) whereas their binding with double stranded poly(A) is weak. Among the alkaloids discussed here, berberine and coralyne are found to be capable to induce self-structure in poly(A). All the binding phenomena are characterized by electrostatic interaction between RNA and the alkaloids and the mode of binding revealed as full or partial intercalation. This review focuses on the structural and biological significance of poly(A) and the recent developments in the use of plant alkaloids and their synthetic analogs to control the structure and function of this RNA for the development of new alkaloid based molecules specifically targeted to poly(A) structures.