DNA Mechanics Affected by Small DNA Interacting Ligands

We have investigated the mechanics of individual DNA strands exposed to DNA binding ligands. The interaction of these agents with individual dsDNA strands measured by optical tweezers clearly indicates the ligand-DNA binding mode. As expected, if the compound is intercalating then an increase of contour length is detected. Groove binders affect the overstretching capabilities of the formerly “naked” dsDNA strand. We interacted SYBR® Green I with naked dsDNA. The binding mode of this compound, which is used for nucleic acid gel staining, is not known. The mechanics of the interaction of SYBR® is revealed by optical tweezers experiments. The force extension curves on single dsDNA fragments show a groove-binding mode, which does not affect the contour length of the molecule but significantly alters the overstretching behaviour of the dsDNA.