Dinucleotides - High-Temperature Results

    A plot of experimental cross section vs. temperature is shown at right for dAT and dTA. The 80 K ATDs for dAT and dTA show two peaks that correspond to the stacked and open conformers. The collision cross sections obtained from the two peaks are identical for each dinucleotide (the increase in cross section below 300 K is due to the ion-He interaction potential [Wyttenbach, T.; von Helden, G.; Batka, Jr., J.J.; Carlat, D.; Bowers, M.T. J. Am. Soc. Mass Spectrom. 1997, 8, 275-282]). However, the stacked conformer is the dominant (90%) form of dTA but the open conformer is the dominant (95%) form of dAT. By 200 K, the two conformers isomerize, yielding one peak in the ATD and one averaged collision cross section.
    Between 200 and 400 K, the experimental cross section for dAT is larger than that of dTA. This is due to the fact that even though the stacked and open conformers are isomerizing in the drift cell, the average drift time is weighted by the relative amounts of each conformer. The dinucleotide dAT, with a high percentage of open conformers will therefore have a larger average cross section than dTA, which has a high percentage of the smaller stacked conformers. However, between 400 and 600 K, the experimental cross sections of dAT and dTA merge to the same value.
    The plots at left compare the experimental cross sections to values calculated for the theoretically determined open and stacked dinucleotide structures. For dAT, the experimental cross section agrees well with the theoretical value of the open form from 200 to 600 K. For dTA, the experimental cross section agrees well with the theoretical value of the stacked form between 200 and 300 K but begins to agree with the open form between 400 and 600 K. This indicates that the dTA are "opening up" at higher temperatures, favoring the open forms. In fact, all of the dinucleotides that favored the stacked or H-bonded forms at lower temperatures "opened up" between 400 and 600 K.