Effect of pH on the stability of DNA origami

The response of DNA origami nanostructures to pH is systematically investigated from two aspects in this work. At first, self-assembly of DNA origami triangle in different pH buffer was tested by putting M13 scaffold and staple strands into a series of sodium citrate buffer (10 mmol/L with 12.5 mmol/L Mg²⁺), the as-prepared sample was characterized by AFM. The formation of the origami structure was affected by pH and the structure was observed only in the pH range of 6-9. Tolerance of DNA origami to pH in the external environment was investigated by immersing them (pH = 8) into acidic and basic solutions for 2 h at room temperature, followed by characterization of the samples by AFM and 0.5% agarose gel respectively. The AFM results showed that the DNA origami triangle maintained the original structure at pH range of 5-10, and the structure was broken at higher or lower pH. The agarose gel suggested that the most stable state of DNA origami triangle was in pH range of 7-8, where the intensity and mobility of the sample band remained the same. Compared with the origami self-assembled in different pH buffers, the pre-prepared origami showed better resistance to acidic and alkali environments. In order to test the long time-stability of DNA origami, pH value of the prepared triangle origami was adjusted in the range of 5-10 and the reaction time was extended to 12 h. AFM test results indicated that the DNA origami could maintain its original structure for at least 12 h. Another common origami nanostructure was also tested; like origami triangle, rectangle structure showed a similar pH tolerance which could keep the stability at pH range of 5-10 for at least 12 h. The long time pH stability experiment of the triangle and the rectangle structures indicated that the origami structure based on M13 owned a relatively high pH tolerance. Based on the above results, possible mechanism of pH effect on DNA origami stability was also proposed. In the process of the origami preparation, excess H⁺ or OH-will affect the formation of the hydrogen bond thus affecting the hybridization of DNA double helixes. In the pH tolerance experiment, excessive H⁺ or OH-will attack the formed hydrogen bonds and make the origami structure floppy. In both aspects, more H+ or OH-will undermine the primary structure of DNA, and eventually affect the formation and stability of DNA origami structures.