GOLD can be used to dock ligands to DNA and RNA structures, however it has not been specifically parametrised to handle these and extensive validation work has not, as yet, been carried out in this area. Some initial research has been carried out, see for example:
Y. Li, J. Shen, X. Sun, W. Li, G. Liu and Y. Tang, J. Chem. Inf. Model., 50, 1134–1146, 2010, [DOI: 10.1021/ci9004157].
GOLD was originally designed to handle proteins rather than DNA/RNA. Consequently, GOLD solutions from nucleic acid targets can be somewhat unreliable (consistent with other docking programs).