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.

Charge inversion and condensation of DNA in solutions of trivalent and quadrivalent counterions are significantly influenced by the pH value of the solution. We systematically investigated the condensation and charge compensation of DNA by spermidine, hexammine cobalt(III) (cohex, [Co(NH₃)₆]³⁺) and spermine in solutions of a wide range of pH values from 3 to 9.3 by dynamic light scattering, magnetic tweezers, and atomic force microscopy. In trivalent counterion solution, we found that there is a critical concentration (0.75 mM for cohex and 0.5 mM for spermidine), under which the electrophoresis mobility of DNA initially increases, reaches a maximum, and finally decreases when the pH value is decreased. In contrast, above the critical concentration, the electrophoretic mobility of DNA increases monotonously with decreasing pH value of the solution. The corresponding condensing force has the same dependence on the pH value. However, for the case of quadrivalent counterions, the electrophoretic mobility of DNA is monotonously promoted by lowering the pH value of the solution at any concentration of counterions in which charge inversion of DNA may occur. In atomic force microscopy images and force spectroscopy of magnetic tweezers, we found that maximal charge neutralization and condensation force correspond to the most compact DNA condensation. We propose a mechanism of promoting DNA charge neutralization: small and highly mobile hydrogen ions tend to attach to the DNA–counterion complex to further neutralize its remaining charge, which is related to the surface area of the complex. Therefore, this further neutralization is prominent when the complex is toroidal which corresponds to the case of mild ion concentration while it is less prominent for more compact globules or rod complexes at high counterion concentration.

In the preset study, we report the suppression and promotion of DNA charge inversion by mixing a quadrivalent counterion (spermine) with mono-, di- and trivalent counterions by dynamic light scattering (DLS) and single molecule electrophoresis (SME) methods.

Gold nanoparticles' novel properties are widely realized in catalysis, plasmonics, electronics, and biomedical applications. For biomedical application, one challenge is to find a non-toxic chemical and/or physical method of functionalizing gold nanoparticles with biomolecular compounds that can promote efficient binding, clearance, and biocompatibility and to assess their safety to other biological systems and their long-term effects on human health and reproduction. In the present study, we describe a new method by using Tris(hydroxymethyl)aminomethane (Tris), a widely used buffer solvent of nucleic acid and proteins, as the reducing agent for synthesizing gold nanoparticles by one step. It is found that Tris carries out the reduction reactions in relatively mild conditions for biomacromolecules. Particularly, it can be used to modify the DNA during the process of preparation of gold nanoparticles. The morphology and size distribution of gold nanoparticles are consistent and were confirmed by many different approaches including dynamic light scattering (DLS), UV-visible (UV-vis) spectrophotometry, atomic force microscopy (AFM), and transmission electron microscopy (TEM).

We have quantitatively investigated the precipitation of DNA in different valence cations and in various ethanol concentration solution. In free ethanol condition, monovalent ion cannot induce DNA condensation and in turn to precipitation. Divalent ion can cause DNA precipitation as the concentrations of both Mg²⁺ (MgCl₂) and Ca²⁺ (CaCl₂) go up to a critical value of about 50 mM. After adding ethanol, monovalent ion and divalent ion can promote DNA precipitation significantly, but it has no effect on the process by trivalent ions. In monovalent ion solution of 100 mM, the critical volume ratio of ethanol is about 52% for DNA precipitation. However, the value decreases significantly to 4% in 25 mM divalent ion solution. Based on the precipitation curves, we quantitatively calculated the binding energies between the cations and phosphate group of DNA. For monovalent ions and in aqueous solution, the Na⁺‐DNA binding energy is about −5.52 KJ·Mol⁻¹ (−2.63 k_BT, the precipitation temperature is 253 Kelvin) and the K⁺‐DNA binding energy is about −4.77 KJ·Mol⁻¹ (−2.27 k_BT). For divalent ions and in the same condition, the Ca²⁺‐DNA binding energy is about −8.25 KJ·Mol⁻¹ (−3.93 k_BT) and the Mg²⁺‐DNA binding energy is about −8.67 KJ·Mol⁻¹ (−4.13 k_BT). The scenario of DNA precipitation modulation by ethanol and zwitterionic ions is demonstrated by atomic force microscopy (AFM) imaging intuitively.

DNA conformation is strongly dependent on the valence of counterions in solution, and a valence of at least three is needed for DNA compaction. Recently, we directly demonstrated DNA compaction and its regulation, mediated by divalent cations, by lowering the pH of a solution. In the present study, we found that the critical electrophoretic mobility of DNA is promoted to around −1.0 × 10⁻⁴ cm² V⁻¹ s⁻¹ to incur DNA compaction or condensation in a tri- and tetravalent counterions solution, corresponding to an about 89% neutralized charge fraction of DNA. This is also valid for DNA compaction by divalent counterions in a low pH solution. It is notable that the critical charge neutralization of DNA for compaction is only about 1% higher than the saturated charge fraction of DNA in a mild divalent ion solution. We also found that DNA compaction by divalent cations at low pH is weakened and even decondensed with an increasing concentration of counterions.