Self-aggregation of DNA oligomers with XGG trinucleotide repeats: kinetic and atomic force microscopy measurements

Turbidity measurements via absorbance monitoring at 320 nm were employed to obtain autocatalytic-like kinetic profiles of K+-induced aggregate formation of d(XGG)4 and some related oligomers, where X = A, C, G, and T. At least 1 M KCl is needed to observe the turbidity-measurable aggregation at pH 8, and the relative propensity for aggregate formation is shown to follow the order d(GGG)4 > d(AGG)4 approximately d(TGG)4 >> d(CGG)4. The presence of Mg2+ greatly facilitates and dramatically reduces the amount of K+ required to initiate aggregation and significantly enhances the thermal stabilities of the aggregates. Replacement of K+ by Na+ fails to induce a similar phenomenon. The Psi-type CD characteristics of aggregates are strongly dependent on the sequence and ionic conditions. Despite their ease of aggregate formation, oligomers with AGG trinucleotide repeats fail to exhibit Psi-CD formation. The propensity for aggregation is greatly affected by the chain length, with oligomers of four repeats being most facile. Appending X base at the 3' end of d(GGXGGXGGXGG) appears to provide a greater hindrance to aggregation than at the 5' end. Atomic force microscopic images support some of these findings and reveal the morphologies of these aggregates. The presence of MgCl2 in solutions appears to considerably elongate the K+-induced aggregates.