Closing the lid on DNA end-to-end stacking interactions.

Recent experiments suggest that short DNA strands associate by end-to-end stacking. Here, we report interactions between DNAs with modified ends. DNA duplexes, 20 bp long, were capped with short T(4) loops at 2, 1 or 0 ends, and were placed in solutions containing 20 mM Mg(2+). Association was observed only in constructs with one or more uncapped ends. DNA-DNA interactions were characterized by measuring variations in small angle x-ray scattering (SAXS) curves at the lowest scattering angles. Second virial coefficients were computed from the SAXS data. Our results confirm that end-to-end stacking plays an important role in short strand DNA-DNA interactions.