Two-dimensional X-ray correlation spectroscopy (2DXCS) signals of the isolated DNA bases and Watson-Crick base pairs which contain multiple absorbing nitrogen atoms are calculated. Core-hole excited states are calculated using density functional theory with the B3LYP functional and 6-311G** basis set. Sum over states calculations of the signals reveal changes in cross-peak intensities between hydrogen-bonded and stacked base pairs. Nucleobase analogues are proposed for investigating base-stacking and hydrogen-bonding interactions.