Ethanol induces condensation of single DNA molecules

Abstract

As a widely used precipitation agent for DNA extraction, ethanol is used to induce single molecule DNA condensation. This process is studied with force-measuring magnetic tweezers and atomic force microscopy (AFM). Our experiments provide direct evidence of the metastable intermediate racquet states in DNA collapse induced by ethanol. The measured condensing force is less than 0.2 pN even at 50% ethanol concentration, which is much less than those induced by multivalent cations and cationic surfactants. We confirmed the A-B transition of DNA in ethanol and found that the tensile modulus of A-form DNA is larger than that of B-form. The single molecule pulling experiment shows very different features of neutral ethanol from those of multivalent cations. The pulling curve contains a wide range of step sizes, ranging from tens of nanometres to a few micrometres, contrasting with the relatively uniform interval (about 200 nm) in multivalent cations. Meanwhile, the persistence length of DNA decreases monotonically with the increasing ethanol concentration. The condensing morphologies by the weak attraction of DNA segments in the less polar solvent are loose and flowerlike structures composed of many annealed irregular racquets. The analysis of pulling experiments is supported by AFM direct imaging. We concluded that the dominant factor in DNA condensation induced by ethanol is solvent exclusion rather than the charge neutralization correlation effect.