Visualisation of plasmid DNA molecules containing T₁₅A₁₅ repeat sequences by atomic force microscopy

We have used atomic force microscopy to examine the conformations of a DNA plasmid which contains a repeated sequence that is able to form an unusual DNA structure. About 16.8% of plasmid molecules containing the sequence (T₁₅A₁₅)₂ adopted a compacted rod-shaped form compared to 89.5% of control molecules without the repeated sequence. The secondary structure- forming sequence therefore changed the conformation of the supercoiled plasmid in the predicted manner. In about 40.2% of plasmids with the (T₁₅A₁₅)₂ sequence a short, branched structure was visible. We speculate that this object may represent a non-standard local DNA conformation, and suggest an interpretation of the structure.