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

Chao Li,Yaqin Tao,Xiaoxia Mao,Yang Xiang,Liu Shi,Genxi Li

doi:10.1038/s41598-017-10459-y

Chao Li, Yaqin Tao + Show 4 more

Open Access

https://doi.org/10.1038/s41598-017-10459-y

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Journal: Scientific Reports	Publication Date: Aug 30, 2017
Citations: 4	License type: open-access

Affiliation: Nanjing University, Shanghai University

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.

Highlights

In DNA nanotechnology, toehold-mediated DNA strand displacement reaction (SDR) is a powerful tool to construct many dynamic devices such as nanomachines[1,2,3], sensors[4, 5], logic gates[6, 7], transformable structures[8,9,10] and catalytic amplifiers[11]
Since the toehold has been exposed directly, we expect that the exonuclease III (Exo III) could rapidly cleave from the 3′-end of strand I2 once the SDR starts, leading to the failure of DNA displacement
We report a series of Nucleic acid-related enzymes (NAEs)-based strategies for SDR regulation and offers additional information on how NAEs affect SDR

Summary

Introduction

In DNA nanotechnology, toehold-mediated DNA strand displacement reaction (SDR) is a powerful tool to construct many dynamic devices such as nanomachines[1,2,3], sensors[4, 5], logic gates[6, 7], transformable structures[8,9,10] and catalytic amplifiers[11]. Aptamers have been integrated into toehold sequence, making the SDR responds to adenosine triphosphate (ATP)[17, 18]. Protein enzymes such as glutathione transferase and urease that can induce the pH change of solution have been used to trigger the activation of SDR19. It is vital to study NAEs-controlled SDRs, which provides novel regulation approaches to the current strand displacement toolbox, and helps in understanding the influence of NAEs on SDR and SDR-based DNA nanodevices. Motivated by the above arguments, we have conducted a series of NAEs-based studies for flexible SDR control and have further made use of these strategies to realize keypad lock systems and biosensing

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