Berberine, the plant alkaloid, was recently shown to induce self-structure in poly(A) by a unique dilution technique. The interaction of berberine and five 9-(u-amino) alkyl ether analogues with polyadenylic acid [poly (A)] has been studied to understand the role of an additional anchoring module in the formation and/or amplification of self-structure in poly(A). The binding was characterized by absorption and fluorescence titration, Job's plot and isothermal titration calorimetry. All the molecules bound cooperatively to poly(A). Self-structure formation was confirmed by circular dichroic melting, optical melting, and dilution experiments. Energetics of the interaction revealed that as the alkyl chain length increased, the binding was more entropy dominated. The results showed that berberine and all the analogues induced self-structure formation in poly(A). The length of the alkyl chain had a significant influence on the ease of formation of self-structure. New insights in terms of structural and thermodynamic aspects into self-structure formation in poly(A) by berberine analogues are revealed from these studies.