Book of Abstracts: Albany 2003
June 17-21 2003
Protonation Induced Structures of Homo-and Hetero-polymer of Guanine-cytosine and Their Binding to Berberine: Spectroscopic Studies
Polypurine-polypyrimidine sequences located in regions of regulatory importance can exist in a variety of non-canonical structures that may play important organizing and regulatory roles in vivo. To understand their possible conformational alterations, protonation induced structural rearrangements in poly(dG)·poly(dC) and its alternating polymer poly(dG-dC)·poly(dG-dC) has been studied in detail. At pH 3.4 and low ionic strength, both polynucleotides adopted a unique and stable structure different from the canonical B-form structure. The protonated alternating polymer structure is further established as left handed with guanine-cytosine adopting Hoogsteen pairing (1,2), while the homo polymer is Watson-Crick base paired B-form structure with different base stacking arrangements. Further investigations on the nature of these new structures were carried out through their binding to the isoquinoline plant alkaloid berberine that exhibits simultaneous intercalative and groove binding properties with B-form DNA (3-6). Binding of berberine to alternating polymer resulted in intrinsic circular dichroic changes and generation of extrinsic circular dichroic bands with opposite signs and magnitude for the protonated form compared to B-form while with the homo polymer no such reversal of extrinsic circular dichroic band was seen. This further lends strength to a model with changed stacking arrangements for protonated structure of homo polymer. Scatchard analysis of the binding data, however, indicated non-cooperative binding of berberine to B-form and protonated form of both polymers. These results suggest that berberine can be used as a probe to detect the change in structural handedness of alternating GC polymer on protonation that could potentiate its use in regulatory roles in biological functions.
G. Suresh Kumar
Biophysical Chemistry Laboratory