Single-molecule dynamic DNA junctions for engineering robust molecular switches

Cai, Shuang; Deng, Yingnan; Fu, Shengnan; Li, Junjie; Chen, Yu; Su, Xin

doi:10.1039/c9sc03389k

Cited by 8 publications

(4 citation statements)

References 43 publications

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“…The stimulus-responsive assembly of Y-shaped DNA is mainly motivated by the static or dynamic self-assembly approach . The traditional static self-assembly represents a simple way to obtain a Y-shaped DNA construct yet is constrained with limited sensitivity for each analyte contributes to only one Y-shaped DNA unit . To resolve this obstruction, the static self-assembly of Y-shaped DNA is often integrated with protein enzymes to achieve a more sensitive analyte assay. − However, these combined strategies are often confronted with the relatively complicated design and tedious enzyme modification procedures.…”

mentioning

confidence: 99%

A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA

Wan

Zou

et al. 2021

Anal. Chem.

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Functional DNA nanostructures have been widely used in various bioassay fields. Yet, the programmable assembly of functional DNA nanostructures in living cells still represents a challenging goal for guaranteeing the sensitive and specific biosensing utility. In this work, we report a self-catalytic DNA assembly (SDA) machine by using a feedback deoxyribozyme (DNAzyme)-amplified branched DNA assembly. This SDA system consists of catalytic self-assembly (CSA) and DNAzyme amplification modules for recognizing and amplifying the target analyte. The analyte initiates the CSA reaction, leading to the formation of Y-shaped DNA that carries two RNA-cleaving DNAzymes. One DNAzyme can then successively cleave the corresponding substrate and generate numerous additional inputs to activate new CSA reactions, thus realizing a self-catalytic amplification reaction. Simultaneously, the other DNAzyme is assembled as a versatile signal transducer for cleaving the fluorophore/quencher-modified substrate, leading to the generation of an amplified fluorescence readout. By incorporating a flexible auxiliary sensing module, the SDA system can be converted into a universal sensing platform for detecting cancerous biomarkers, e.g., a well-known oncogene microRNA-21 (miR-21). Moreover, the SDA system realized the precise intracellular miR-21 imaging in living cells, which is attributed to the reciprocal amplification property between CSA reactions and DNAzyme biocatalysis. This compact SDA amplifier machine provides a universal and facile toolbox for the highly efficient identification of cancerous biomarkers and thus holds great potential for early cancer diagnosis.

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confidence: 99%

A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA

Wan

Zou

et al. 2021

Anal. Chem.

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“…A DNA navigator operating at a single-molecule level can be used in solving mazes by real-time tracking of the reaction path . A recent study demonstrated a robust molecular switch engineered by single-molecule dynamic DNA junctions . Due to the real-time tracking techniques at the single-molecule level, the kinetics-based outputs or the leakage can be distinguished.…”

Section: Introductionmentioning

confidence: 99%

“…22 A recent study demonstrated a robust molecular switch engineered by single-molecule dynamic DNA junctions. 23 Due to the real-time tracking techniques at the single-molecule level, the kinetics-based outputs or the leakage can be distinguished. Hence, an investigation of the single-molecule methods could bring special advantages to detecting and measuring DNA computing.…”

Section: ■ Introductionmentioning

confidence: 99%

Single-Molecule Resettable DNA Computing via Magnetic Tweezers

et al. 2022

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DNA-based Boolean logic computing has emerged as a leading technique in biosensing, diagnosis, and therapeutics. Due to the development of the biological and chemical methods, especially the toehold-mediated DNA strand displacement (TMSD) reaction, different logic gates as well as circuits can be performed. However, most of these methods have been conducted at the bulk level, which may lead to missing information and be less controllable. Herein, we engineered single-molecule DNA computing controlled by stretching forces using magnetic tweezers. By tracking the real-time signals of the DNA extension, the output can be determined at a single base-pair resolution. A kinetics-controllable TMSD reaction was realized in the range of a ∼19-fold change of the reaction rate by different stretching forces. OR, AND, and NOT gates were also achieved. In addition, resettable DNA computing using force stretching cycles has been further exemplified. Overall, such a real-time, label-free, and force-controlled single-molecule DNA computing system provided new insight into molecular computing.

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“…There are several technologies available for nucleic acid detection and analysis such as hybridization, strand displacement, and enzymatic and nonenzymatic amplification assays. − These techniques employ either single-molecule or ensemble approaches including optical, electrochemical, and colorimetric assays. ,− Although hybridization-based assays offer a simple and fast analysis of nucleic acid targets, they typically exhibit poor specificity between the target with perfect complementarity and the one with a point mutation. , Therefore, any sensing approach that is sensitive down to single-nucleotide mismatch can be a very useful attribute to ensure specificity of diagnosis. Although enzymatic amplification approaches such as polymerase chain reaction (PCR), reverse transcriptase PCR (RT-PCR), and digital PCR are simple and highly sensitive, they rely on target amplification and are susceptible to false negatives/positives. − This is problematic because false negatives run the risk of instilling a false sense of security and false positives may result in unnecessary panic. − Therefore, novel single-molecule and ensemble techniques including DNA nanotechnology platforms with improved sensitivity and specificity are continuously emerging in recent years. − Nonetheless, most of these methods are rather complicated and have limited applications.…”

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confidence: 99%

Single-Molecule FRET-Based Dynamic DNA Sensor

2021

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Selective and sensitive detection of nucleic acid biomarkers is of great significance in early-stage diagnosis and targeted therapy. Therefore, the development of diagnostic methods capable of detecting diseases at the molecular level in biological fluids is vital to the emerging revolution in the early diagnosis of diseases. However, the vast majority of the currently available ultrasensitive detection strategies involve either target/signal amplification or involve complex designs. Here, using a p53 tumor suppressor gene whose mutation has been implicated in more than 50% of human cancers, we show a background-free ultrasensitive detection of this gene on a simple platform. The sensor exhibits a relatively static mid-FRET state in the absence of a target that can be attributed to the time-averaged fluorescence intensity of fast transitions among multiple states, but it undergoes continuous dynamic switching between a low-and a high-FRET state in the presence of a target, allowing a high-confidence detection. In addition to its simple design, the sensor has a detection limit down to low femtomolar (fM) concentration without the need for target amplification. We also show that this sensor is highly effective in discriminating against single-nucleotide polymorphisms (SNPs). Given the generic hybridization-based detection platform, the sensing strategy developed here can be used to detect a wide range of nucleic acid sequences enabling early diagnosis of diseases and screening genetic disorders.

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Single-molecule dynamic DNA junctions for engineering robust molecular switches

Abstract: Highly robust DNA molecule switches were engineered by utilizing single-molecule dynamic three-way junctions.

Cited by 8 publications

References 43 publications

A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA

A Deoxyribozyme-Initiated Self-Catalytic DNA Machine for Amplified Live-Cell Imaging of MicroRNA

Single-Molecule Resettable DNA Computing via Magnetic Tweezers

Single-Molecule FRET-Based Dynamic DNA Sensor

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