DNA/RNA bifunctional transduction molecules. The molecules shown were designed to help in the examination of DNA-DNA binding (left panel, with introduction of 5'-TACCT-3' annealing complement, see  for details) and DNA-protein binding (right panel, DNA Y-aptamer with TATA binding site, examined upon introduction of TATA Binding Protein, see  for details). Each molecule is designed to have a length of blunt-ended duplex DNA that is to be captured by the channel, that length is "terminated" such that the captured end is perched directly above the limiting aperture of the channel, free to move, bind to channel, and un-bind, in the high electrophoretic field strength concentration at the limiting aperture. For the termination with 3 T mismatch "bulges", a length of 9 base-pairs suffices for good channel blockade modulation; for termination at the Y-branching chosen, a length of 10 base-pairs works best.
Winters-Hilt BMC Bioinformatics 2007 8(Suppl 7):S9 doi:10.1186/1471-2105-8-S7-S9