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Revealing Three Stages of DNA-Cisplatin Reaction by a Solid-State Nanopore.

Zhou Z, Hu Y, Shan X, Li W, Bai X, Wang P, Lu X - Sci Rep (2015)

Bottom Line: The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time.In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts.In the third stage, the capture rate decreases again as a result of DNA aggregation.

View Article: PubMed Central - PubMed

Affiliation: Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.

ABSTRACT
The dynamic structural behavior in DNA due to interaction with cisplatin is essential for the functionality of platinum-based anti-cancer drugs. Here we report a novel method to monitor the interaction progress in DNA-cisplatin reaction in real time with a solid-state nanopore. The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time. In the first stage, the capture rate decreases rapidly due to DNA discharging as the positive-charged hydrated cisplatin molecules initially bond to the negative-charged DNA and form mono-adducts. In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts. In the third stage, the capture rate decreases again as a result of DNA aggregation. Our study demonstrates a new single-molecule tool in exploring dynamic behaviors during drug-DNA reactions and may have future application in fast drug screening.

No MeSH data available.


Stage I.(a) Temporal evolution of capture rate in stage I. The data is fitted with a second-order reaction model (red line, see SI-3 for the details). Inset: schematic of DNA-cisplatin mono-adducts. (b) The evolution of the derived linear charge density ρ(t) in the first stage. (c) Current traces taken at 35 and 90 minutes since injection of cisplatin molecules.
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f3: Stage I.(a) Temporal evolution of capture rate in stage I. The data is fitted with a second-order reaction model (red line, see SI-3 for the details). Inset: schematic of DNA-cisplatin mono-adducts. (b) The evolution of the derived linear charge density ρ(t) in the first stage. (c) Current traces taken at 35 and 90 minutes since injection of cisplatin molecules.

Mentions: DNA molecules are negatively charged with about 2 electrons per nm in the sodium acetate buffer, similar to that in 1 M KCl electrolyte environment30. When cisplatin is mixed with DNA solution, they diffusively approach the DNA molecules, firstly bond to the guanine base to form mono-adducts by which only one covalent bond is established with each attached cisplatin molecule (see the schematic inset of Fig. 3a). Since each cisplatin molecule (hydrated form) carries two positive charges, the effective charge density of DNA-cisplatin adducts reduces as more and more cisplatin molecules are attached. Consider charge as the distinct variable in stage I, the capture rate J(t) in equation (2) can be simplified to:where A1 is a constant, ρ(t) is the effect charge density of DNA-cisplatin mono-adducts, and if ΔV equals 500 mV, as derived from data in reference28. Since the formation of mono-adduct is a second order reaction, the explicit form of ρ(t), and then J(t), can be derived (see SI-3 for the detailed derivation). Figure 3a shows the zoom-in plot of stage I in Fig. 2c. Fitting the data derives a reaction rate of 0.22 ± 0.08 μM−1 h−1 for the initial bonding of cisplatin to DNA (see SI-3 for details). The typical time of this period is about 70 minutes. Figure 3(b) presents the change in charge density during the stage. Figure 3(c) shows two current traces taken at 35 and 90 minutes since injection of cisplatin, where the reduction in capture rate can be clearly seen.


Revealing Three Stages of DNA-Cisplatin Reaction by a Solid-State Nanopore.

Zhou Z, Hu Y, Shan X, Li W, Bai X, Wang P, Lu X - Sci Rep (2015)

Stage I.(a) Temporal evolution of capture rate in stage I. The data is fitted with a second-order reaction model (red line, see SI-3 for the details). Inset: schematic of DNA-cisplatin mono-adducts. (b) The evolution of the derived linear charge density ρ(t) in the first stage. (c) Current traces taken at 35 and 90 minutes since injection of cisplatin molecules.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4493569&req=5

f3: Stage I.(a) Temporal evolution of capture rate in stage I. The data is fitted with a second-order reaction model (red line, see SI-3 for the details). Inset: schematic of DNA-cisplatin mono-adducts. (b) The evolution of the derived linear charge density ρ(t) in the first stage. (c) Current traces taken at 35 and 90 minutes since injection of cisplatin molecules.
Mentions: DNA molecules are negatively charged with about 2 electrons per nm in the sodium acetate buffer, similar to that in 1 M KCl electrolyte environment30. When cisplatin is mixed with DNA solution, they diffusively approach the DNA molecules, firstly bond to the guanine base to form mono-adducts by which only one covalent bond is established with each attached cisplatin molecule (see the schematic inset of Fig. 3a). Since each cisplatin molecule (hydrated form) carries two positive charges, the effective charge density of DNA-cisplatin adducts reduces as more and more cisplatin molecules are attached. Consider charge as the distinct variable in stage I, the capture rate J(t) in equation (2) can be simplified to:where A1 is a constant, ρ(t) is the effect charge density of DNA-cisplatin mono-adducts, and if ΔV equals 500 mV, as derived from data in reference28. Since the formation of mono-adduct is a second order reaction, the explicit form of ρ(t), and then J(t), can be derived (see SI-3 for the detailed derivation). Figure 3a shows the zoom-in plot of stage I in Fig. 2c. Fitting the data derives a reaction rate of 0.22 ± 0.08 μM−1 h−1 for the initial bonding of cisplatin to DNA (see SI-3 for details). The typical time of this period is about 70 minutes. Figure 3(b) presents the change in charge density during the stage. Figure 3(c) shows two current traces taken at 35 and 90 minutes since injection of cisplatin, where the reduction in capture rate can be clearly seen.

Bottom Line: The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time.In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts.In the third stage, the capture rate decreases again as a result of DNA aggregation.

View Article: PubMed Central - PubMed

Affiliation: Beijing National Laboratory for Condensed-Matter Physics and Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People's Republic of China.

ABSTRACT
The dynamic structural behavior in DNA due to interaction with cisplatin is essential for the functionality of platinum-based anti-cancer drugs. Here we report a novel method to monitor the interaction progress in DNA-cisplatin reaction in real time with a solid-state nanopore. The interaction processes are found to be well elucidated by the evolution of the capture rate of DNA-cisplatin complex, which is defined as the number of their translocation events through the nanopore in unit time. In the first stage, the capture rate decreases rapidly due to DNA discharging as the positive-charged hydrated cisplatin molecules initially bond to the negative-charged DNA and form mono-adducts. In the second stage, by forming di-adducts, the capture rate increases as DNA molecules are softened, appears as the reduced persistence length of the DNA-cisplatin adducts. In the third stage, the capture rate decreases again as a result of DNA aggregation. Our study demonstrates a new single-molecule tool in exploring dynamic behaviors during drug-DNA reactions and may have future application in fast drug screening.

No MeSH data available.