Capillary Electrophoresis Can Detect the Simultaneous Presence of Hairpins and Self-Dimers in Non-Symmetric, Single-Stranded DNA Oligomers.

Free solution capillary electrophoresis (CE) has been used to show that non-symmetric, single-stranded DNA oligomers containing 26 nucleotides can exhibit peaks in the electropherograms that correspond to the simultaneous presence of self-dimers and hairpins in the solution. The overlapping hairpin and self-dimer peaks were observed at temperatures close to 15°C in background electrolytes containing at least 80 mM Na ions. With increasing temperature, the self-dimers were converted first into hairpins and then into random coils at still higher temperatures. The results suggest that hairpins can be an intermediary step in the pathway between DNA duplexes and single-strands.