Molecular assemblies held together by weak intermolecular bonds exhibit a rich variety of geometries. Even a simple complex formed by only two molecules can adopt several conformations corresponding to different geometrical isomers. Isomers of small polar dimers can be isolated nondestructively by taking advantage of a selective and reversible ionization process, with the use of a mass spectrometry method that allows the determination and control of the geometrical configuration of neutral or negatively charged molecular complexes in supersonic beams. Here, the method is applied to isolated nucleic acid base pairs that can be selected in stacked or H-bonded configurations.