Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States.
ACS Nano. 2011 Dec 27;5(12):9345-53. doi: 10.1021/nn203764j. Epub 2011 Nov 16.
Nanopores in thin solid-state membranes are used to rapidly analyze individual RNA/drug complexes. The interactions of a truncated A-site RNA model of the prokaryotic ribosome with aminoglycoside antibiotics are characterized by passing individual molecules through a 3-3.5 nm diameter pore fabricated in a 8-10 nm thick silicon nitride membrane. Complexes of the A-site RNA with aminoglycosides can be distinguished from unbound A-site based on the ion current signatures produced as they pass through the nanopores. Counting the fraction of free and drug-bound molecules affords label-free drug-RNA binding isotherms consistent with literature reports and with data generated using independent fluorescence-based assays. Our measurements are supported by molecular dynamics simulations, which illustrate the relationship between the ionic current and complexation of the A-site RNA with paramomycin, a prototypical aminoglycoside antibiotic.
在薄固态膜中的纳米孔被用于快速分析单个 RNA/药物复合物。通过将单个分子穿过在 8-10nm 厚的氮化硅膜中制造的 3-3.5nm 直径的孔，来对原核核糖体的 A 位 RNA 模型与氨基糖苷类抗生素的相互作用进行表征。可以根据它们穿过纳米孔时产生的离子电流特征来区分与未结合的 A 位 RNA 结合的氨基糖苷类复合物。通过计算游离和药物结合的分子分数，可以获得无标记的药物-RNA 结合等温线，这与文献报道以及使用独立的荧光测定法生成的数据一致。我们的测量结果得到了分子动力学模拟的支持，该模拟说明了 A 位 RNA 与代表氨基糖苷类抗生素的帕拉霉素的离子电流和络合之间的关系。
