Trapping intermediates in the melting transition of DNA oligomers

We present a new method to study the melting transition of DNA oligonucleotides, which can quantify the presence of intermediate states. The approach is to combine UV spectroscopy with a method based on trapping intermediate states by quenching. The measurements yield both the average fraction of open base pairs ( f ) and the fraction of completely open molecules ( p ). If intermediate (partially open) states are not present, then p = f throughout the transition. In the presence of intermediate states, p < f . We demonstrate the method on the example of a 48mer sequence which is designed to open at one end and thus have intermediate states during melting. Then we show a different sequence design where the melting appears essentially as a two-states process. These experiments demonstrate the role played by end effects and sequence design in controlling the nature of the melting transition for DNA oligomers.