SELF-ASSEMBLY OF DNA OLIGOMERS INTO HIGH-MOLECULAR-WEIGHT SPECIES

Thermal denaturation, gel electrophoresis, and circular dichroism methods were used to characterize DNA oligomers possessing one or two segments of four contiguous G bases in order to investigate their environmentally dependent conformational properties. The sequences of the oligomers studied were the following: HP1-T series, C(4)T(4)G(4)T(5-8); HP1-TG series, C(4)T(4)G(4)T(1-4)G(4). In NaCl at concentrations up to 200 mM, the melting profiles of these oligomers are characterized by single inflection points whose T-m values are independent of DNA concentration. In addition, these oligomers run as single bands in polyacrylamide gels under those same conditions as well as in 100 mM K+ or 20 mM Mg2+. These data suggest that these oligomers exist as intramolecular hairpins comprised of four G:C base pairs in the stems, loops of four T bases, and 3'-overhangs of T-5-8 or T(1-4)G(4). In the presence of 100 mM K+ plus 20 mM Mg2+, however, gel electrophoresis indicates that oligomers of the HP1-T series exist as equilibria between parent hairpins and four-stranded structures (i.e., quadraplexes). Quadraplex formation for any member of the HP1-T series requires unfolding of the hairpin, exposing the G(4) Segment prior to quadraplexation. Members of the HP1-TG series self-assemble into multistranded species of high molecular weight in the presence of 100 mM K+ plus 20 mM Mg2+. For this series of oligomers, the data suggest that these higher order species arise from successive additions of parent oligomer to an initially formed quadraplex. Since the self-assembly is not observed with K+ or Mg2+ alone, these cations behave in a synergistic manner in the formation and/or stability of the supermolecular self-assemblies.