Dynamics of supercoiled and linear pBluescript II SK(+) Phagemids probed with a long-lifetime metal-ligand complex.

We extended the measurable time scale of DNA dynamics to microsecond using [Ru(phen)(2)(dppz)](2+)(phen = 1,10-phenanthroline, dppz=dipyrido[3,2-a:2',3'-c]phenazine)(RuPD) , which displays a mean lifetime near 500 ns. To evaluate the usefulness of this luminophore (RuPD) for probing nucleic acid dynamics, its intensity and anisotropy decays when intercalated into supercoiled and linear pBluescript (pBS) II SK(+) phagemids were examined using frequency-domain fluorometry with a blue light-emitting diode (LED) as the modulated light source. The mean lifetime for the supercoiled phagemids (<tau> = 489.7 ns) was somewhat shorter than that for the linear phagemids (<tau> = 506.4 ns), suggesting a more efficient shielding from water by the linear phagemids. The anisotropy decay data also showed somewhat shorter slow rotational correlation times for supercoiled phagemids (997.2 ns) than for the linear phagemids (1175.6 ns). The slow and fast rotational correlation times appear to be consistent with the bending and torsional motions of the phagemids, respectively. These results indicate that RuPD can have applications in studies of both bending and torsional dynamics of nucleic acids.