Hettiarachchi Eshani, Grassian Vicki H
Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States.
Langmuir. 2024 Dec 31;40(52):27194-27205. doi: 10.1021/acs.langmuir.4c02501. Epub 2024 Dec 19.
Environmental DNA (eDNA), i.e., DNA found in the environment, can interact with various geochemical surfaces, yet little is known about these interactions. Mineral surfaces may alter the structure, stability, and reactivity of eDNA, impacting the cycling of genetic information and the reliability of eDNA-based detection tools. Understanding how eDNA interacts with surfaces is crucial for predicting its fate in the environment. In this study, we examined the surface interaction and stability of herring testes DNA, a model system for eDNA, on two common iron oxide phases present in the environment: α-FeOOH (goethite) and α-FeO (hematite). Utilizing spectroscopic probes, including attenuated total reflection Fourier-transform infrared (ATR-FTIR) and UV-vis spectroscopy, we quantified the DNA adsorption capacity at pH 5 and determined its secondary structure. DNA adsorbed irreversibly at pH 5 and 25 °C, primarily through its phosphate groups, and retained the solution-phase B-form structure. However, the infrared data also indicated some distortion of the B-form likely due to additional interactions between nitrogenous bases when adsorbed on the α-FeO particle surfaces. The distortion in the double helical structure of adsorbed DNA on α-FeO led to a lower melting temperature () of 60 °C compared to 70 °C for DNA in solution. In contrast, DNA adsorbed on α-FeOOH melted at higher temperatures relative to solution-phase DNA and in two distinct phases. Upon testing adsorbed DNA stability at higher pH values, there were distinct differences between the two iron oxide phases. For α-FeOOH, nearly 50% of the DNA desorbed from the surface when the solution pH changed from 5 to 8, while less than 5% desorbed from α-FeO under the same conditions. Overall, these findings underscore the importance of mineral-specific eDNA-surface interactions and their role in adsorbed eDNA stability, in terms of DNA melting and the impact of solution-phase pH changes.
环境DNA（eDNA），即在环境中发现的DNA，可与各种地球化学表面相互作用，但人们对这些相互作用知之甚少。矿物表面可能会改变eDNA的结构、稳定性和反应活性，影响遗传信息的循环以及基于eDNA的检测工具的可靠性。了解eDNA如何与表面相互作用对于预测其在环境中的命运至关重要。在本研究中，我们研究了鲱鱼睾丸DNA（一种eDNA模型系统）在环境中存在的两种常见氧化铁相：α-FeOOH（针铁矿）和α-Fe₂O₃（赤铁矿）上的表面相互作用和稳定性。利用光谱探针，包括衰减全反射傅里叶变换红外光谱（ATR-FTIR）和紫外可见光谱，我们量化了pH为5时的DNA吸附容量，并确定了其二级结构。在pH为5和25℃时，DNA主要通过其磷酸基团不可逆地吸附，并保留了溶液相的B型结构。然而，红外数据也表明，B型结构可能存在一些扭曲，这可能是由于吸附在α-Fe₂O₃颗粒表面时含氮碱基之间的额外相互作用所致。与溶液中的DNA相比，吸附在α-Fe₂O₃上的DNA双螺旋结构的扭曲导致其较低的解链温度（Tm）为60℃，而溶液中的DNA解链温度为70℃。相比之下，吸附在α-FeOOH上的DNA相对于溶液相DNA在更高的温度下解链，且分两个不同阶段。在测试更高pH值下吸附的DNA稳定性时，两种氧化铁相之间存在明显差异。对于α-FeOOH，当溶液pH从5变为8时，近50%的DNA从表面解吸，而在相同条件下，从α-Fe₂O₃解吸的DNA不到5%。总体而言，这些发现强调了矿物特异性eDNA-表面相互作用的重要性及其在吸附的eDNA稳定性方面的作用，包括DNA解链以及溶液相pH变化的影响。
