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We report a study of dynamics with a dsDNA-specific dye called Pico-Green bound to plasmid DNA (3.4 kb), and show that at low dye⁄DNA phosphate ratios (1 : 100 and below), PicoGreen dynamics reflect the motional dynamics of dsDNA. | Enhanced DNA dynamics due to cationic reagents topological states of dsDNA and high mobility group box 1 as probed by PicoGreen Sunil K. Noothi1 Mamata Kombrabail2 Tapas K. Kundu3 G. Krishnamoorthy2 and Basuthkar J. Rao1 1 Department of BiologicalSciences Tata Institute of FundamentalResearch Mumbai India 2 Department of ChemicalSciences Tata Institute of FundamentalResearch Mumbai India 3 Molecular Biology and Genetics Unit JawaharlalNehru Centre for Advanced Scientific Research Bangalore India Keywords anisotropy decay kinetics chromatin remodelling DNA dynamics HMGB1 PicoGreen Correspondence B. J. Rao Department of Biological Sciences Tata Institute of Fundamental Research Homi Bhabha Road Mumbai 400005 India Fax 91 22 2280 4610 2280 4611 Tel 91 22 2278 2606 E-mail bjrao@tifr.res.in G. Krishnamoorthy Department of Chemical Sciences Tata Institute of Fundamental Research Homi Bhabha Road Mumbai 400005 India Fax 91 22 2280 4610 2280 4611 Tel 91 22 2278 2301 E-mail gk@tifr.res.in Received 18 September 2008 revised 6 November 2008 accepted 14 November 2008 We report a study of dynamics with a dsDNA-specific dye called PicoGreen bound to plasmid DNA 3.4 kb and show that at low dye DNA phosphate ratios 1 100 and below PicoGreen dynamics reflect the motional dynamics of dsDNA. We further evaluated the usefulness of this probe by measuring the time-resolved fluorescence dynamics of PicoGreen bound to dsDNA in the presence of cationic reagents that affect DNA dynamics MgCl2 and polyethyleneimine PEI and also with plasmid DNA in different topological states. Among these conditions MgCl2 PEI and the supercoiled form of plasmid resulted in increases in the very short component 0.2-0.4 ns of the rotational correlation time. Separately HMGB1 protein enhanced DNA dynamics as observed from the rotational correlation times of very short 0.2-0.4 ns and short 2-4 ns rotational correlation timescale components. By studying the effect of specific deletion mutants HMGB1-DA deletion .
