The promotion and suppression of DNA charge neutralization by the cosolute ectoine

Visualization of DNA Damage and Protection by Atomic Force Microscopy in Liquid

DNA damage is closely related to cancer and many aging-related diseases. Peroxynitrite is a strong oxidant, thus a typical DNA damage agent, and is a major mediator of the inflammation-associated pathogenesis. For the first time, we directly visualized the process of DNA damage by peroxynitrite and DNA protection by ectoine via atomic force microscopy in liquid. We found that the persistence length of DNA decreases significantly by adding a small amount of peroxynitrite, but the observed DNA chains are still intact. Specifically, the persistence length of linear DNA in a low concentration of peroxynitrite (0 µM to 200 µM) solution decreases from about 47 nm to 4 nm. For circular plasmid DNA, we observed the enhanced superhelices of plasmid DNA due to the chain soften. When the concentration of peroxynitrite was above 300 µM, we observed the fragments of DNA. Interestingly, we also identified single-stranded DNAs during the damage process, which is also confirmed by ultraviolet spectroscopy. However, if we added 500 mM ectoine to the high concentration PN solution, almost no DNA fragments due to double strand breaks were observed because of the protection of ectoine. This protection is consistent with the similar effect for DNA damage caused by ionizing radiation and oxygenation. We ascribe DNA protection to the preferential hydration of ectoine.

DNA-Lysozyme Nanoarchitectonics: Quantitative Investigation on Charge Inversion and Compaction

The interaction between DNA and proteins is fundamentally important not only for basic research in biology, but also for potential applications in nanotechnology. In the present study, the complexes formed by λ DNA and lysozyme in a dilute aqueous solution have been investigated using magnetic tweezers (MT), dynamic light scattering (DLS), and atomic force microscopy (AFM). We found that lysozyme induced DNA charge inversion by measuring its electrophoretic mobility by DLS. Lysozyme is very effective at neutralizing the positive charge of DNA, and its critical charge ration to induce charge inversion in solution is only 2.26. We infer that the high efficiency of charge neutralization is due to the highly positively charged (+8 e) and compact structure of lysozyme. When increasing the concentration of lysozymes from 6 ng·µL-1 to 70 ng·µL-1, DNA mobility (at fixed concentration of 2 ng·µL-1) increases from -2.8 to 1.5 (in unit of 10-4 cm2·V-1·S), implying that the effective charge of DNA switches its sign from negative to positive in the process. The corresponding condensing force increased from 0 pN to its maximal value of about 10.7 pN at concentrations of lysozyme at 25 ng·µL-1, then decreases gradually to 3.8 pN at 200 ng·µL-1. The maximal condensing force occurs at the complete DNA charge neutralization point. The corresponding morphology of DNA-lysozyme complex changes from loosely extensible chains to compact globule, and finally to less compact flower-like structure due to the change of attached lysozyme particles as observed by AFM.

Demonstration of pH-controlled DNA-surfactant manipulation for biomolecules

The understanding of DNA-surfactant interactions is important for fundamental physical biology and developing biomedical applications. In the present study, we demonstrated a DNA-surfactant nano-machine model by modulating the compaction of DNA in dodecyldimethylamine oxide (DDAO) solutions. By controlling DDAO concentration and pH of solution, we are able to adjust the compacting force of DNA so as to pull biomolecular subunits connected to it. The pulling force of the machine depends on DDAO concentration and pH of solution, ranging from near zero to about 4.6 pN for 10 mM DDAO concentration at pH = 4. The response time of the machine is about 3 minutes for contracting and 2 minutes for releasing in 5 mM DDAO solution. We found that DDAO has no significant influence on DNA under basic conditions, but compacts DNA under acidic conditions, which is enhanced with decreasing pH of solution. Meanwhile, we found the accompanying charge inversion of DNA in the process of DNA compaction by DDAO.