The use of the BTX molecule raises the issue as to its behavior relative to the well-characterized
TX molecule whose helix axes are roughly co-planar.17 We have characterized the frictional
and thermal properties of the BTX molecule and have compared them to a TX molecule; the
TX molecule is the same one described in reference 17. Figure 3a shows the Ferguson plots of
the non-overhanging BTX molecule, the TX molecule and a linear duplex DNA molecule, all
42 nucleotide pairs long. The Ferguson plot of gel mobility vs. acrylamide concentration is a
means of estimating the friction constant of the molecule, because the slope of the plot is
proportional to this quantity.18 The slope of the BTX molecule (.175) is similar to that of the
TX molecule (.165) but is still somewhat higher, suggesting that two unequally sized surfaces
interact differently with the gel matrix than two roughly equal surfaces. Figure 3b shows the
differential melting curve of the same TX and BTX molecules. The BTX molecule melts
(Tmax = 64.9 °C) below the TX molecule (Tmax = 68.1 °C). This difference may be a
consequence of the electrostatic repulsion likely to result from the closer approach of the outer
helices to each other in the BTX molecule. Both molecules exhibit post-melting transitions,
and the BTX molecule might also exhibit a pre-melting transition. Figure 3c shows the
Ferguson plots of the BTX, the 6HB, the 4HB and the 8HB molecules. The BTX and the 6HB
molecules are 63 nucleotides long here, and the 4HB and the 8HB molecules are 84 nucleotides
long. One can model the slopes as being proportional surface area, assuming that the interiors
of 6HB and 8HB do not interact with the gel matrix, and therefore do not contribute to the
friction constant. The plot of the relative surface areas of the six species represented in Figure
3c has a 94.8% correlation with this model (data not shown).