Dinucleotides - Experimental Results - ATDs

    Typical ATDs for the deprotonated dinucleotides, measured at different drift temperatures using the MALDI-Sector instrument, are shown below. At 300 K and higher temperatures, only one peak appears in the ATDs. However, multiple peaks are present in the lower-temperature ATDs. Since the ions are mass-selected before they enter the drift cell and the injection energies are kept low enough to prevent significant fragmentation, the multiple peaks in the ATDs must represent different conformations (with significantly different collision cross sections) of the dinucleotide ion.

    The number of peaks in the 80 K ATDs and their relative intensities are base- and sequence-dependent. However, each dinucleotide can be grouped into one of four distinct categories based on similarities observed in the ATDs. These groups and their 80 K ATDs are shown at right.
    In Group 1, two peaks are present in the 80 K ATDs and are separated by 25 μs (corresponding to a difference in cross section of 20-22 Ų). The shortest-time peak is always more intense than the longest-time peak. The dinucleotides dAA, dCA, dTA, and dAG, dCG are members of this group.
    In Group 2, two peaks are also present in the 80 K ATDs and again separated by 25 μs. However, in this case, the longest-time peak is always more intense than the shortest-time peak. The dinucleotides dAT, dCT, dGT, dTT, and dTG are members of this group.
    In Group 3, two peaks are present in the 80 K ATDs and are separated by 12 μs (corresponding to a difference in cross section of 10-12 Ų). The dinucleotides dGA and dGG are members of this group.
    In Group 4, three peaks are present in the 80 K ATDs. Each one is separated by 12 μs. The intermediate-time peak is always the most intense peak in the spectra. The dinucleotides dAC, dCC, dGC, and dTC are members of this group.