Exploring the binding of carbon dots to calf thymus DNA: From green synthesis to fluorescent molecular probe
Graphical abstract
Introduction
In the early 2000s, carbon dots (CDs) have been discovered by Xu and co-workers through the purification of single-walled carbon nanotubes derived from an arc-discharge soot [1]. However, due to the traditional semiconductor Quantum dots (QDs) are mainly composed of heavy metals and due to the often high cytotoxicity of fluorescence dyes, and there are obvious limitations in cell and in vivo studied. CDs have become more and more important in the development of carbon nanomaterials because of their generally high biocompatibility, chemical inertness, low toxicity, ease of functionalization, simple synthetic routes, low environmental impact, fluorescence stability, resistance to photobleaching, excitation-wavelength dependent emission, and high electrical conductivity, This list of properties is generally considered advantageous, especially compared to QDs and fluorescence dyes. CDs are useful in numerous industrial applications, including optoelectronic devices, electrocatalyst, photocatalysts, gene delivery, drug delivery, anticancer treatment, bioimaging, biosensing, nanocarbon electrochemistry and electroanalysis. Some of these applications were mimic, compete, or go beyond those already derived from QDs [[2], [3], [4], [5], [6], [7], [8]]. However, the disadvantageous of CDs as described below are apparent. Therefore, for system compare, quantum yield and fluorescence decay of CDs, it is particularly critical to study different types of CDs. Generally, full-color light-emitting is not easy to tune and it is often difficult to produce CDs with controlled size and properties, while the photoluminescence mechanism of CDs is still not fully understood [[9], [10], [11]]. Therefore, obtaining answers to this list of questions remain a critical, albeit unmet, scientific goal.
In recent years, CDs have attracted increasing attention in the scientific community and the synthetic routes typically include two different approaches: top-down methods also include physical methods that generally break down larger carbon structures to reach nanoscale particles, a process that is particularly important in arc discharge, laser ablation, electrochemical oxidation, plasma treatment and confined combustion [12,13]. However, these approaches frequently require expensive precursors and synthetic processes as well as post-treatments are often complex. Through chemical methods used in the synthesis of such materials, bottom-up methods are often used in an effort to solve these issues. Bottom-up methods imply that small particles can be produced in a nanoscale form. Examples for such processes include thermal decomposition, microwave or ultrasonic processes, hydrothermal, water phase reflow, and template approaches [[14], [15], [16]]. Due to the economic efficiency and green production as well as simple post-treatment, this article selected the water phase reflow method for the synthesis of CDs.
The interaction of DNA with small molecules represents an important topic in various research fields, including applications in medicinal chemistry, life science, clinical medicine, etc. [17]. The interaction of CDs with biomacromolecules has been studied by various research groups around the globe. Molecular docking has been a helpful tool for the study of small molecule drugs with targeting macromolecules. Presumably, molecular docking may also exhibit suitable properties for future studies involving the interactions between CDs and biomacromolecules. Molecular dynamics simulations have been applied in the study of proteins, and hopefully, this technique may also be applicable for the future study of DNA [[18], [19], [20], [21], [22]]. The binding mode of small molecules to the DNA double helical structure features three major modes of non-covalent interactions, including electrostatic interactions, groove binding and intercalation [23].
CDs exhibit various advantages that are potentially useful in anticancer treatment applications. ctDNA is the carrier of genetic information and represents the target of various drugs in vivo. In this research, the binding modes between CDs and ctDNA have been studied and a bottom-up synthetic route was selected. Compare with the huang's group that the synthesis method for fluorescent carbon dots to label-free and highly selective recognition of DNA, the synthesis approach of this paper that one-pot green synthesis, require low temperature, synthesis processes and carrying out post-treatments are often simple [24]. Via one-pot green synthesis using ascorbic acid as carbon precursor and polyethylene glycol (PEG-600) as surface passivation reagent with water phase reflow at 90 °C, the corresponding CDs could be prepared. The quantum yield of CDs was 13.3%. Nowadays, the fluorescence probes of ctDNA used to study the interaction of ctDNA with a drug are often toxic organic dyes. Therefore, the development of new and nontoxic fluorescent probes remains a crucial, albeit unmet, scientific topic. In doing so, the binding modes of the interaction between CDs and ctDNA could be determined to be due to intercalation. Therefore it is believed that nontoxic CDs may replace organic fluorescent dyes in the future to become a promising fluorescent probe of ctDNA.
Section snippets
Materials
Ascorbic acid and polyethylene glycol (PEG-600) were purchased from Sinopharm Chemical Reagent. Calf thymus DNA was obtained from Sigma-Aldrich (St. Louis, MO). Na2HPO4-NaH2PO4 (PBS) with a purity of no less than 99.5%. All reagents used throughout this study were of analytical purity. The ctDNA solution was dissolved in buffer solution and was stored at 4 °C for one day before further purification. The purity of ctDNA was verified by monitoring the ratio of absorbance at 260/280 nm
Characterization of CDs
Generally appreciated is the notion that parameters like the ratio between carbon source and surface passivation reagent, reactant amount of carbon source, time of reaction, pH of reaction, reaction temperature etc. significantly affect the fluorescence intensity of CDs. Furthermore, these parameters significantly affect the experimental fluorescence properties of CDs. Fig. 1A shows the reaction condition effect of the as-synthesized CDs. The fluorescence intensity was stronger upon increasing
Conclusions
In this study, CDs were prepared that emit green-yellow light, different than CDs that have been synthesized in the past using ascorbic acid as carbon precursor. Compared to organic dyes, the as-prepared CDs featured properties such as small size, high QY, good dispersibility, excitation wavelength dependent emission, and suitable optical properties. The fluorescence intensity stability was found to be highest at pH values ranging between 4.2 and 10.2 and was also found to be temperature
Acknowledgements
This work was supported by the national natural science foundation of China (No. 21273065), the foundation of key laboratory of analytical chemistry for biology and medicine (ministry of education), Wuhan University (No. ACBM2016002), and Hubei key laboratory of pollutant analysis & reuse technology, Hubei normal university, China (No. PA150210).
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