This is a very difficult task, and if you lack any information about the potential interaction site, you are most probably lost.

Of course, you could raise the question, whether certain different binding poses or interaction mechanisms are preferred over each other, and then investigate the different systems using calculations. Without any experimental link, however, this remains a purely theoretical investigation of the suggested conformations.

And remember, that it is still a large leap from a set of energy-minimized structures (in solvent) to an actual, dynamic biological system with counter ions and small molecules interacting with your biomolecule.

In summary, you can study different interaction complexes with different structures and rank them e.g. via their total or interaction energy; but you have to be very careful to extrapolate your model findings to real systems.

DNA is too big for quantum chemistry. I'm afraid that there only molecular mechanics can be used .

While DNA is too big for quantum chemistry, if you simplify the structure of DNA by only looking at a couple of base pairs, DFT starts to become manageable. QM/MM and ONIOM, which model the interesting part (the interaction) with a higher level of theory than the rest of the system, are also worth looking at.

As was said above it is possible to carry out calculations on a few base pairs which might be enough depending on what exactly you plan to do. As well as QM/MM it may be worth looking at some of the linear scaling DFT methods depending on the size of your system it maybe applicable. Also ab initio MD maybe. There are few references below of examples of calculation which can be done on a few base pairs in DNA and bases from RNA for your information.

Hunter, R. S.; van Mourik, T., DNA base stacking: The stacked uracil/uracil and thymine/thymine minima. Journal of Computational Chemistry 2012, 33 (27), 2161-2172.

Danilov, V.; Dailidonis, V.; Mourik, T.; Früchtl, H., A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach. cent.eur.j.chem. 2011, 9 (4), 720-727

Danilov, V. I.; van Mourik, T.; Poltev, V. I., Modeling of the ‘hydration shell’ of uracil and thymine in small water clusters by DFT and MP2 methods. Chemical Physics Letters 2006, 429 (1–3), 255-260.