Locally Denatured DNA Compaction by Divalent Cations

The denaturation of DNA is a critical process in biologyand hasmany biotechnological applications. We investigated the compactionof locally denatured DNA by a chemical denaturation agent, dimethylsulfoxide (DMSO), using magnetic tweezers (MTs), atomic force microscopy(AFM), and dynamic light scattering (DLS). Our results show that DMSOnot only is capable of denaturing DNA but also able to compact DNAdirectly. When the DMSO concentration is above 10%, DNA condensationoccurs due to the reduction in the persistence length of DNA and excludedvolume interactions. Meanwhile, locally denatured DNA is easily condensedby divalent cations, such as magnesium ions (Mg2+), contrastingwith no native DNA condensation by the classical divalent cations.Specifically, the addition of more than 3 mM Mg2+ to a5% DMSO solution leads to DNA condensation. The critical condensingforce (F (C)) increases from 6.4 to 9.5 pNwhen the Mg2+ concentration grows from 3 to 10 mM. However, F (C) decreases gradually with a further increasein Mg2+ concentration. For 3% DMSO solution, above 30 mMMg(2+) is needed to compact DNA and a weaker condensing forcewas measured. With increasing Mg2+ concentration, the morphologyof the DMSO partially denatured DNA complex changes from loosely randomcoils to a dense network structure, even forming a spherical condensationnucleus, and finally to a partially disintegrated network. These findingsshow that the elasticity of DNA plays an important role in its denaturationand condensation behavior.