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, C4T4G4T5-8; HP1-TG series, C4T4G4T1-4G4. In NaCl at concentrations up to 200 mM, the melting profiles of these oligomers are characterized by single inflection points whose Tm 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 T5-8 or T1-4G4. 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 G4 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.(ABSTRACT TRUNCATED AT 250 WORDS)