Quantitative analysis of the flexibility effect of cisplatin on circular DNA

We study the effects of cisplatin on the circular configuration of DNA using atomic force microscopy (AFM) and observe that the DNA gradually transforms to a complex configuration with an intersection and interwound structures from a circlelike structure. An algorithm is developed to extract the configuration profiles of circular DNA from AFM images and the radius of gyration is used to describe the flexibility of circular DNA. The quantitative analysis of the circular DNA demonstrates that the radius of gyration gradually decreases and two processes on the change of flexibility of circular DNA are found as the cisplatin concentration increases. Furthermore, a model is proposed and discussed to explain the mechanism for understanding the complicated interaction between DNA and cisplatin.

Figure 1

(a) A 20-μl mixture was deposited on a mica surface. (b) After 15 min, the mixture solution was washed with 200 μl of ddH${}_2$O. (c) The sample was blown dry using a gentle stream of nitrogen gas.

Figure 2

(a) The AFM images of pUC19 DNA on a mica surface. (b)–(d) The AFM images of pUC19 DNA in the presence of the following cisplatin concentrations: (b) 0.5 μM, (c) 1 μM, and (d) 2 μM. The white scale bar is 500 nm for all images.

Figure 3

Weight of DNA configurations, including circlelike, intersection, and interwound structures, at the following concentrations of cisplatin: 0, 0.12, 0.25, 0.5, 1.0, and 2.0 μM, respectively.

Figure 4

(a) Original AFM images of a single circular DNA molecule. (b) The thinning process was performed to extract the configuration profile of the DNA molecule. (c) The skeleton backbone of the DNA molecule was obtained using a pruning process. (d) The configuration of the DNA molecule was expressed by successive points tracing the skeleton backbone. (e) The new point $X_n$${}_{+1}$ was found using the initial point $X_n$${}_{-1}$ and the center $X_n$ of a circle. (f) The next new point $X_n$${}_{+2}$ was also found using the new initial point $X_n$ and the new center $X_n$${}_{+1}$.

Figure 5

Radius of gyration of pUC19 DNA plotted against the cisplatin concentration curve. The error bar is the standard deviation of means for independent samples ($n$ $=$ 3).

Figure 6

(a) Aquatic chemistry of cisplatin in solution. (b) Two possible factors of aqueous cisplatin influence the configuration of circular DNA in solution: (1) the cisplatin as a diadduct binds on circular DNA to result in the formation of kinks and (2) cisplatin as a divalent cation may leads to weakness of electrostatic repulsion on circular DNA.

Figure 7

Schematic diagram of the algorithm recognizing aspects of the DNA configurations.