Liu Lu, Li Siqiao, Mao Anwen, Wang Guyu, Liu Yiran, Ju Huangxian, Ding Lin
State Key Laboratory of Analytical Chemistry for Life Science , School of Chemistry and Chemical Engineering , Chemistry and Biomedicine Innovation Center (ChemBIC) , Nanjing University , Nanjing 210023 , China . Email:
Chem Sci. 2020 Jan 2;11(6):1665-1671. doi: 10.1039/c9sc04161c. eCollection 2020 Feb 14.
Given the powerful regulation roles of chemical modification networks in protein structures and functions, it is of vital importance to acquire the spatiotemporal chemical modification pattern information in a protein-specific fashion, which is by far a highly challenging task. Herein, we design a localized DNA automaton, equipped with an - sequential propagation algorithm, for visualization of a given protein subtype with two chemical modifications of interest on the cell surface. The automaton is composed of three probes respectively for the protein and two types of modifications. Once anchored on the cell surface and triggered, the automaton performs sequential protein-localized, DNA hybridization-based computations on the proximity status of each modification type with the protein and contracts the set of close proximity information into a single fluorescence signal turn-on using the designed algorithm. The modular and scalable features of the automaton enable its operation in scaled-down versions for protein-specific identification of one given modification. Thus, this work opens up the possibility of using automata for revealing complex regulation mechanisms of protein posttranslational modifications.
鉴于化学修饰网络在蛋白质结构和功能中具有强大的调控作用，以蛋白质特异性方式获取时空化学修饰模式信息至关重要，而这目前是一项极具挑战性的任务。在此，我们设计了一种配备顺序传播算法的局部DNA自动机，用于可视化细胞表面具有两种感兴趣化学修饰的给定蛋白质亚型。该自动机由分别针对蛋白质和两种修饰类型的三个探针组成。一旦锚定在细胞表面并被触发，自动机就会对每种修饰类型与蛋白质的接近状态进行基于蛋白质定位和DNA杂交的顺序计算，并使用设计的算法将紧密接近信息集收缩为单个荧光信号开启。自动机的模块化和可扩展特性使其能够以缩小版本运行，用于对一种给定修饰进行蛋白质特异性识别。因此，这项工作开启了利用自动机揭示蛋白质翻译后修饰复杂调控机制的可能性。
