A DNA nanoswitch-controlled reversible nanosensor

Peng, Pai; Shi, Lili; Li, Tao

doi:10.1093/nar/gkw1146

Cited by 39 publications

(27 citation statements)

References 37 publications

(38 reference statements)

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“…( C ) Electrophoretograms of DNA nanostructures in panel (B) upon addition of 200 μM ATP. An observable shift in the electrophoretic mobility of the (3+4)WJ nanoarchitecture originates from two ATP molecules captured by the split aptamer (lane 1 versus lane 2, compared to panel B), consistent with previous observations (5). ( D ) Electrophoretograms of DNA nanostructures in panel C upon adjusting pH to 8.…”

Section: Resultssupporting

confidence: 91%

Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device

Shi

Peng

et al. 2017

Nucleic Acids Research

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Four-stranded DNAs including G-quadruplexes and i-motifs are formed from four stretches of identical bases (G or C). A challenge remains in controlling the intermolecular folding of different G-rich or C-rich strands due to the self-association of each component. Here, we introduce a well-designed bimolecular i-motif that does not allow the dimerization of the same strand, and illustrate its usefulness in a pH-switched ATP-sensing DNA molecular device. We analyze two groups of i-motif DNAs containing two stretches of different C-residues (Cn-1TmCn and CnTmCn-1; n = 3−6, m = 1, 3) and show that their bimolecular folding patterns (L- and H-form) noticeably differs in the thermal stability. The L-form structures generally display a relatively low stability, with a bigger difference from that of conventional i-motifs formed by CnTmCn. It inspires us to at utmost improving the structural stability by extending the core of L-form bimolecular i-motifs with a few flanking noncanonical base pairs, and therefore to avoid the dimeric association of each component. This meaningful bimolecular i-motif is then incorporated into a three-way junction (3WJ) and a four-way junction (4WJ) functionalized with two components of a ATP-binding split DNA aptamer, allowing the pH-triggered directional assembly of 3WJ and 4WJ into the desired (3+4)WJ structure that is verified by gel electrophoresis. It therefore enables the ATP-induced association of the split aptamer within the (3+4)WJ structure, as monitored by fluorescence quenching. In this way, the designed DNA system behaves as a pH-switched reversible molecular device, showing a high sensitivity and selectivity for fluorescent ATP analysis. The i-motif folding topology-programmed DNA nanoassembly may find more applications in the context of larger 2D/3D DNA nanostructures like lattices and polyhedra.

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Section: Resultssupporting

confidence: 91%

Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device

Shi

Peng

et al. 2017

Nucleic Acids Research

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“…For example, Li and coworkers applied TSDR modules to build reversible DNA nanoswitch for the dynamic detection of ATP. [ 36 ] Furthermore, the directional regulation of DNA strand displacement can be applied to the detection of multiple biomolecules. For instance, Yuan and coworkers constructed a direction‐controlled biosensor using TSDR modules, which acts as a bidirectional DNA walking machine driven by a dual microRNA (microRNA‐21 and microRNA‐155) (Figure 3c).…”

Section: Biosensing Applications Based On Low‐order Dna‐crnsmentioning

confidence: 99%

DNA‐Based Chemical Reaction Networks for Biosensing Applications

Jiang

Yuan

et al. 2020

Advanced Intelligent Systems

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The nature of biosensing is a biochemical reaction. DNA‐based chemical reaction networks (DNA‐CRNs) as a powerful programming language for describing behaviors of chemical reactions have shown great potential in designs and applications of biosensors. Due to their programmability, modularity, and versatility of the DNA strand, the performance of different detection strategies can be improved mainly by the rational design of DNA‐CRNs. Herein, an overview of the fundamental theory and biosensing processes of DNA‐CRNs is provided. Various detection strategies of DNA‐CRNs are introduced, either in a simple low‐order reaction model or in a complicated high‐order reaction type, in combination with some typical cases for the different detection purposes. In addition, an overview of the recent development of DNA‐CRNs for monitoring the cell microenvironment is presented, which is of significance to uncover some specific cell behaviors and functions. Finally, the roles of DNA‐CRNs in the rational design of high‐performance biosensors are summarized by pointing out the remaining challenges that impede the precise biosensing using DNA‐CRNs in complicated biological environments.

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“…These devices have even been implemented in living cells to probe pH (4,76) or detect ion concentrations (100), and they have been in full organisms, such as Caenorhabditis elegans, to measure local pH (101). In addition, these devices can be functionalized with, for example, targeting moieties (76,101,102) or other aptamers that enable detection of specific molecular targets (103).…”

Section: Dynamic Dna Nanostructuresmentioning

confidence: 99%

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research

Castro

Choi

2018

Annu. Rev. Biomed. Eng.

111

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Structural DNA nanotechnology utilizes synthetic or biologic DNA as designer molecules for the self-assembly of artificial nanostructures. The field is founded upon the specific interactions between DNA molecules, known as Watson-Crick base pairing. After decades of active pursuit, DNA has demonstrated unprecedented versatility in constructing artificial nanostructures with significant complexity and programmability. The nanostructures could be either static, with well-controlled physicochemical properties, or dynamic, with the ability to reconfigure upon external stimuli. Researchers have devoted considerable effort to exploring the usability of DNA nanostructures in biomedical research. We review the basic design methods for fabricating both static and dynamic DNA nanostructures, along with their biomedical applications in fields such as biosensing, bioimaging, and drug delivery.

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A DNA nanoswitch-controlled reversible nanosensor

Cited by 39 publications

References 37 publications

Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device

Programmable i-motif DNA folding topology for a pH-switched reversible molecular sensing device

DNA‐Based Chemical Reaction Networks for Biosensing Applications

Structural DNA Nanotechnology: Artificial Nanostructures for Biomedical Research

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