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Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing.

ABSTRACT: Toehold-mediated DNA strand displacement reaction (SDR) plays pivotal roles for the construction of diverse dynamic DNA nanodevices. To date, many elements have been introduced into SDR system to achieve controllable activation and fine regulation. However, as the most relevant stimuli for nucleic acid involved reaction, nucleic acid-recognizing enzymes (NAEs) have received nearly no attention so far despite SDR often takes place in NAEs-enriched environment (i.e., biological fluids). Herein, we report a set of NAEs-controlled SDR strategies, which take full advantage of NAEs' properties. In this study, three different kinds of enzymes belonging to several classes (i.e., exonuclease, endonuclease and polymerase) have been used to activate or inhibit SDR, and more importantly, some mechanisms behind these strategies on how NAEs affect SDR have also been revealed. The exploration to use NAEs as possible cues to operate SDR will expand the available toolbox to build novel stimuli-fueled DNA nanodevices and could open the door to many applications including enzyme-triggered biocomputing and biosensing.

SUBMITTER: Li C

PROVIDER: S-EPMC5577262 | biostudies-literature | 2017 Aug

REPOSITORIES: biostudies-literature

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Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing.

Li Chao C Shi Liu L Tao Yaqin Y Mao Xiaoxia X Xiang Yang Y Li Genxi G

Scientific reports 20170830 1

Toehold-mediated DNA strand displacement reaction (SDR) plays pivotal roles for the construction of diverse dynamic DNA nanodevices. To date, many elements have been introduced into SDR system to achieve controllable activation and fine regulation. However, as the most relevant stimuli for nucleic acid involved reaction, nucleic acid-recognizing enzymes (NAEs) have received nearly no attention so far despite SDR often takes place in NAEs-enriched environment (i.e., biological fluids). Herein, we ...[more]

PMID: 28855676

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Project description:A novel thiazole phenol conjugate, 2-aminothiazolesalicylaldehyde (receptor1) was designed and synthesized for the first time through a single step process via Schiff base condensation reaction. The formation of receptor1 was confirmed by FTIR, 13C NMR, and 1H NMR. The IR spectra confirmed the presence of the aldimine formation. It is further supported by the proton NMR, showing the disappearance of aldehyde peaks and the formation of a new imine peak. This is further corroborated by the 13C NMR. The receptor1 complexing with various metal ions were studied through fluorescence spectroscopy showed its selectivity toward Fe2+ ion following a reverse photoinduced electron transfer (PET) process compared to all other potentially competing ions. The receptor1 was applied as a sensor to sense Fe2+ ion in water samples. The detection limit for Fe2+ ion in drinking water was substantially lower (0.003 µM) than the EPA (environmental protection agency) recommendation (5.37 M). The capability of receptor1 in recovering Fe2+ ion in bore water, tap water, and drinking water was up to 99.5%. The receptor1 was also used as a chelating ligand (receptor1) in molecular docking and it was assessed as a potential inhibitor of NUDT5, a silence hormone signaling for breast cancer. The test compound (PDB: 5NWH) showed good affinity toward the target receptor1 with the binding energy of - 5.23 kcal mol-1. Furthermore, the receptor1 showed excellent reversibility property on adding EDTA solution. Due to the marvelous reversible property, a molecular-scale sequential information processing circuit is designed for the multi-task behavior such as 'Writing-Reading-Erasing-Reading' in the form of binary logic gate. The consecutive addition of Fe2+ ion and EDTA solution to receptor1 paves a way for the construction of INHIBIT logic gate. Additionally, the receptor1 showed the mimicking behavior of molecular keypad lock.Supplementary informationThe online version contains supplementary material available at 10.1007/s11696-022-02373-z.

Dataset Information

Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing.

Publications

Flexible regulation of DNA displacement reaction through nucleic acid-recognition enzyme and its application in keypad lock system and biosensing.

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