1
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Sun LZ, Ying YJ. Moving dynamics of a nanorobot with three DNA legs on nanopore-based tracks. NANOSCALE 2023; 15:15794-15809. [PMID: 37740362 DOI: 10.1039/d3nr03747a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/24/2023]
Abstract
DNA nanorobots have garnered increasing attention in recent years due to their unique advantages of modularity and algorithm simplicity. To accomplish specific tasks in complex environments, various walking strategies are required for the DNA legs of the nanorobot. In this paper, we employ computational simulations to investigate a well-designed DNA-legged nanorobot moving along a nanopore-based track on a planar membrane. The nanorobot consists of a large nanoparticle as the robot core and three single-stranded DNAs (ssDNAs) as the robot legs. The nanopores linearly embedded in the membrane serve as the toeholds for the robot legs. A charge gradient along the pore distribution mainly powers the activation of the nanorobot. The nanorobot can move in two modes: a walking mode, where the robot legs sequentially enter the nanopores, and a jumping mode, where the robot legs may skip a nanopore to reach the next one. Moreover, we observe that the moving dynamics of the nanorobot on the nanopore-based tracks depends on pore-pore distance, pore charge gradient, external voltage, and leg length.
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Affiliation(s)
- Li-Zhen Sun
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
| | - Yao-Jun Ying
- Department of Applied Physics, Zhejiang University of Technology, Hangzhou 310023, China.
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2
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Wu K, Kong F, Zhang J, Tang Y, Chen Y, Chao L, Nie L, Huang Z. Recent Progress in Single-Nucleotide Polymorphism Biosensors. BIOSENSORS 2023; 13:864. [PMID: 37754098 PMCID: PMC10527258 DOI: 10.3390/bios13090864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/23/2023] [Accepted: 08/26/2023] [Indexed: 09/28/2023]
Abstract
Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.
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Affiliation(s)
| | | | | | | | | | | | - Libo Nie
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (K.W.); (F.K.); (J.Z.); (Y.T.); (Y.C.); (L.C.)
| | - Zhao Huang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, Hunan University of Technology, Zhuzhou 412007, China; (K.W.); (F.K.); (J.Z.); (Y.T.); (Y.C.); (L.C.)
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3
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Yarra SS, Ashok G, Mohan U. "Toehold Switches; a foothold for Synthetic Biology". Biotechnol Bioeng 2023; 120:932-952. [PMID: 36527224 DOI: 10.1002/bit.28309] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 08/24/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Toehold switches are de novo designed riboregulators that contain two RNA components interacting through linear-linear RNA interactions, regulating the gene expression. These are highly versatile, exhibit excellent orthogonality, wide dynamic range, and are highly programmable, so can be used for various applications in synthetic biology. In this review, we summarized and discussed the design characteristics and benefits of toehold switch riboregulators over conventional riboregulators. We also discussed applications and recent advancements of toehold switch riboregulators in various fields like gene editing, DNA nanotechnology, translational repression, and diagnostics (detection of microRNAs and some pathogens). Toehold switches, therefore, furnished advancement in synthetic biology applications in various fields with their prominent features.
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Affiliation(s)
- Sai Sumanjali Yarra
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Ganapathy Ashok
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
| | - Utpal Mohan
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education & Research (NIPER) Kolkata, Kolkata, West Bengal, India
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4
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A renewable platform based on the entropy-driven catalytic amplification and element labeling inductively coupled plasma mass spectrometry for microRNA analysis. Anal Chim Acta 2023; 1254:341112. [PMID: 37005022 DOI: 10.1016/j.aca.2023.341112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/15/2023] [Accepted: 03/16/2023] [Indexed: 03/19/2023]
Abstract
The element labeling inductively coupled plasma mass spectrometry (ICP-MS) strategy has been increasingly applied to the bioanalysis for various bio-targets. Herein, a renewable analysis platform with element labeling ICP-MS was firstly proposed for microRNA (miRNA) analysis. The analysis platform was established on the magnetic bead (MB) with entropy-driven catalytic (EDC) amplification. When the EDC reaction was initiated by target miRNA, numerous strands labeled with Ho element were released from MBs, and 165Ho in the supernatant detected by ICP-MS could reflect the amount of target miRNA. After detection, the platform was easily regenerated by adding strands to reassemble EDC complex on MBs. This MB platform could be used four times, and the limit of detection for miRNA-155 was 8.4 pmol L-1. Moreover, the developed regeneration strategy based on EDC reaction can be easily expanded to other renewable analysis platforms, such as, the renewable platform involving EDC and rolling circle amplification technology. Overall, this work proposed a novel regenerated bioanalysis strategy to reduce the consumption of reagent and time for probe preparation, profiting the development of bioassay based on element labeling ICP-MS strategy.
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5
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Ding S, Yu X, Zhao Y, Zhao C. Identification of single nucleotide polymorphisms by a peptide nucleic acid-based sandwich hybridization assay coupled with toehold-mediated strand displacement reactions. Anal Chim Acta 2023; 1242:340810. [PMID: 36657895 DOI: 10.1016/j.aca.2023.340810] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 01/03/2023] [Accepted: 01/05/2023] [Indexed: 01/07/2023]
Abstract
In this work, we developed a simple and accurate peptide nucleic acid (PNA)-based sandwich hybridization assay for single nucleotide polymorphisms (SNPs) in the p53 gene. Our approach combines the enzyme-free toehold-mediated strand displacement reaction (SDR) with real-time enzyme-linked immunosorbent assay (ELISA) to detect SNPs with high sensitivity and specificity. A PNA-DNA heteroduplex with an external toehold is designed and fixed on well surface of a 96-well plate. The strand displacement from PNA-DNA heteroduplexes is initiated by the hybridization of target sequence with the toehold domain and ends with the fully displacing of the incumbent DNA. Finally, the as formed PNA-target DNA duplex with overhang at its 5'-end hybridizes with a biotin-labeled reporter PNA to form a sandwich structure on surface for signal amplification. The proposed PNA-based sandwich biosensor displays high sensitivity and greatly enhanced discriminability to target p53 gene segments against single-base mutant sequences compared to its all-DNA counterpart. Furthermore, the probe design is elegantly simple and the sensing procedure is easy to operate. We believe that this strategy may provide a simple and universal strategy for SNPs detection through easily altering the sequences of probes according to the sequences around target SNPs.
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Affiliation(s)
- Shuyu Ding
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Xiaomeng Yu
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China
| | - Yang Zhao
- College of Science and Technology, Ningbo University, Ningbo 315300, PR China
| | - Chao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo 315211, PR China.
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6
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Toehold-mediated biosensors: Types, mechanisms and biosensing strategies. Biosens Bioelectron 2022; 220:114922. [DOI: 10.1016/j.bios.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/13/2022] [Accepted: 11/15/2022] [Indexed: 11/18/2022]
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7
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Zarubiieva I, Spaccasassi C, Kulkarni V, Phillips A. Automated Leak Analysis of Nucleic Acid Circuits. ACS Synth Biol 2022; 11:1931-1948. [PMID: 35544754 DOI: 10.1021/acssynbio.2c00084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nucleic acids are a powerful engineering material that can be used to implement a broad range of computational circuits at the nanoscale, with potential applications in high-precision biosensing, diagnostics, and therapeutics. However, nucleic acid circuits are prone to leaks, which result from unintended displacement interactions between nucleic acid strands. Such leaks can grow combinatorially with circuit size, are challenging to mitigate, and can significantly compromise circuit behavior. While several techniques have been proposed to partially mitigate leaks, computational methods for designing new leak mitigation strategies and comparing their effectiveness on circuit behavior are limited. Here we present a general method for the automated leak analysis of nucleic acid circuits, referred to as DSD Leaks. Our method extends the logic programming functionality of the Visual DSD language, developed for the design and analysis of nucleic acid circuits, with predicates for leak generation, a leak reaction enumeration algorithm, and predicates to exclude low probability leak reactions. We use our method to identify the critical leak reactions affecting the performance of control circuits, and to analyze leak mitigation strategies by automatically generating leak reactions. Finally, we design new control circuits with substantially reduced leakage including a sophisticated proportional-integral controller circuit, which can in turn serve as building blocks for future circuits. By integrating our method within an open-source nucleic acid circuit design tool, we enable the leak analysis of a broad range of circuits, as an important step toward facilitating robust and scalable nucleic acid circuit design.
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8
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Mana T, Bhattacharya B, Lahiri H, Mukhopadhyay R. XNAs: A Troubleshooter for Nucleic Acid Sensing. ACS OMEGA 2022; 7:15296-15307. [PMID: 35571783 PMCID: PMC9096816 DOI: 10.1021/acsomega.2c00581] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/12/2022] [Indexed: 06/15/2023]
Abstract
The strategies for nucleic acid sensing based on nucleic acid hybridization between the target sequence and the capture probe sequence are considered to be largely successful as far as detection of a specific target of known sequence is concerned. However, when compared with other complementary methods, like direct sequencing, a number of results are still found to be either "false positives" or "false negatives". This suggests that modifications in these strategies are necessary to make them more accurate. In this minireview, we propose that one way toward improvement could be replacement of the DNA capture probes with the xeno nucleic acid or XNA capture probes. This is because the XNAs, especially the locked nucleic acid, the peptide nucleic acid, and the morpholino, have shown better single nucleobase mismatch discrimination capacity than the DNA capture probes, indicating their capacity for more precise detection of nucleic acid sequences, which is beneficial for detection of gene stretches having point mutations. Keeping the current trend in mind, this minireview will include the recent developments in nanoscale, fluorescent label-free applications, and present the cases where the XNA probes show clear advantages over the DNA probes.
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Affiliation(s)
- Tanushree Mana
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Budhaditya Bhattacharya
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Hiya Lahiri
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
| | - Rupa Mukhopadhyay
- School
of Biological Sciences, Indian Association
for the Cultivation of Science, Jadavpur, Kolkata 700032, India
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9
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Kabza AM, Kundu N, Zhong W, Sczepanski JT. Integration of chemically modified nucleotides with DNA strand displacement reactions for applications in living systems. WILEY INTERDISCIPLINARY REVIEWS-NANOMEDICINE AND NANOBIOTECHNOLOGY 2021; 14:e1743. [PMID: 34328690 DOI: 10.1002/wnan.1743] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 06/26/2021] [Accepted: 07/06/2021] [Indexed: 01/21/2023]
Abstract
Watson-Crick base pairing rules provide a powerful approach for engineering DNA-based nanodevices with programmable and predictable behaviors. In particular, DNA strand displacement reactions have enabled the development of an impressive repertoire of molecular devices with complex functionalities. By relying on DNA to function, dynamic strand displacement devices represent powerful tools for the interrogation and manipulation of biological systems. Yet, implementation in living systems has been a slow process due to several persistent challenges, including nuclease degradation. To circumvent these issues, researchers are increasingly turning to chemically modified nucleotides as a means to increase device performance and reliability within harsh biological environments. In this review, we summarize recent progress toward the integration of chemically modified nucleotides with DNA strand displacement reactions, highlighting key successes in the development of robust systems and devices that operate in living cells and in vivo. We discuss the advantages and disadvantages of commonly employed modifications as they pertain to DNA strand displacement, as well as considerations that must be taken into account when applying modified oligonucleotide to living cells. Finally, we explore how chemically modified nucleotides fit into the broader goal of bringing dynamic DNA nanotechnology into the cell, and the challenges that remain. This article is categorized under: Diagnostic Tools > In Vivo Nanodiagnostics and Imaging Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Diagnostic Tools > Biosensing.
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Affiliation(s)
- Adam M Kabza
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Nandini Kundu
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
| | - Wenrui Zhong
- Department of Chemistry, Texas A&M University, College Station, Texas, USA
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10
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Xu M, Xing S, Zhao Y, Zhao C. Peptide nucleic acid-assisted colorimetric detection of single-nucleotide polymorphisms based on the intrinsic peroxidase-like activity of hemin-carbon nanotube nanocomposites. Talanta 2021; 232:122420. [PMID: 34074407 DOI: 10.1016/j.talanta.2021.122420] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 10/21/2022]
Abstract
Here, taking the advantage of single-stranded (ss) DNA specific nuclease (S1) and peptide nucleic acid (PNA), we demonstrated a novel, rapid, and label-free colorimetric nanosensor for the sensitive and accurate detection of SNPs based on the intrinsic peroxidase-like activity of hemin-functionalized single-walled carbon nanotubes (hemin-SWCNTs). PNA, a man-made mimic of DNA with extraordinary stability toward enzymatic degradation, can effectively protect DNA in the fully matched DNA/PNA duplexes from nuclease digestion. While the DNA in DNA/PNA duplexes containing a mismatch can be cleaved into small fragments. This difference can be visually monitored from the specific color change of TMB/H2O2 system by employing the peroxidase activity of hemin-SWCNTs because of its different aggregation states responding to ssPNA or DNA/PNA duplex. Under optimized conditions, the SNPs in the human tumor suppressor gene TP53 have been successfully genotyped in a linear range of 50-1000 nM with a detection limit of 0.11 nM. Moreover, this platform can effectively discriminate a series of single-base mismatches. This assay avoids the assistance of sophisticated instruments and complicated modifications of probes or nanomaterials, and function well for both cell lysate samples and PCR amplicons from standard cell lines, implying its potential practical applications for bioanalysis and biosensors.
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Affiliation(s)
- Mengjia Xu
- Affiliated Cixi Hospital, Wenzhou Medical University, Cixi, 315300, Zhejiang, PR China
| | - Shu Xing
- Cixi Institute of Biomedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315201, PR China
| | - Yang Zhao
- College of Science and Technology, Ningbo University, Ningbo, 315300, PR China
| | - Chao Zhao
- School of Materials Science and Chemical Engineering, Ningbo University, Ningbo, 315211, PR China.
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11
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Wu Y, Ali S, White RJ. Use of Electrocatalysis for Differentiating DNA Polymorphisms and Enhancing the Sensitivity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part II. ACS Sens 2020; 5:3842-3849. [PMID: 33305566 DOI: 10.1021/acssensors.0c02363] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Single-nucleotide polymorphisms (SNPs), insertion/deletion (indel) polymorphisms, and DNA methylation are the most frequent types of genetic variations. As such, DNA polymorphisms play significant roles in genetic mapping and diagnostics. Thus, analytical methods enabling DNA polymorphism detection will provide an invaluable means for early disease diagnosis. However, no single electrochemical nucleic acid-based sensor has achieved the detection of the three major polymorphisms (SNPs, indel polymorphisms, and DNA methylation) with sufficient specificity and sensitivity. In response, we explore the utilization of a catalytic reaction between methylene blue (MB) covalently linked to surface-bound nucleic acid and freely diffusing ferricyanide (Fe(CN)63-) to improve specificity and sensitivity of DNA polymorphism detection. We find that the dynamics of the nucleic acid tether is an additional rate-limiting factor for the electrocatalytic reaction, in addition to the more traditional kinetic and excess factors. Our proof-of-concept experiments demonstrate that the use of electrocatalysis enables differentiation of the three polymorphisms when target sequences are present at 10 nM. We hypothesize that this ability is a result of the distinct dynamics of the DNA probe with each respective polymorphism. In addition to the specificity the sensor displays, the sensor achieves a 20 pM limit of detection. We believe that the electrocatalysis between nucleic acid-tethered MB and Fe(CN)63- is highly promising for electrochemical nucleic acid-based sensors to achieve better specificity and sensitivity.
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Affiliation(s)
| | - Sufyaan Ali
- Walnut Hills High School, Cincinnati, Ohio 45207, United States
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12
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Tan Y, Zhong W, Tang W, Fan J, Zhang X, Guo D, Wu X, Liu Y. Improvement of Molecular Diagnosis Using Domain-Level Single-Nucleotide Variants by Eliminating Unexpected Secondary Structures. Chemistry 2020; 26:16256-16260. [PMID: 32964533 DOI: 10.1002/chem.202003592] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Indexed: 01/06/2023]
Abstract
Identification of single-nucleotide variants (SNVs) is of great significance in molecular diagnosis. The problem that should not be ignored in the identification process is that the unexpected secondary structure of the target nucleic acid may greatly affect the detection accuracy. Herein, we proposed a conditional domain-level SNV diagnosis strategy, in which the subsequent SNV detection can only be carried out after eliminating the unexpected secondary structure of target DNA. Specifically, the target DNA is assembled into a rigid double strand, which makes folding the target DNA difficult and the unexpected secondary structure is eliminated. Based on this double-stranded structure, specially designed probes are used to detect double-stranded properties and report abundant domain-level oligonucleotide information to improve the effective information in the detection results and complete domain-level SNV diagnosis. If the unexpected secondary structure is not eliminated, the detector will first detect it and feed back to us, ensuring the accuracy of the subsequent detection results. With the occurrence (or not) of SNV and the change of the SNV site, in the proof-of-concept experiment, we successfully identified the four homologous sequences to be tested related to BRAF gene.
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Affiliation(s)
- Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Jin Fan
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaohui Zhang
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Donghua Guo
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Xiaolong Wu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Nanhai Avenue 3688, Nanshan District, Shenzhen, Guangdong, CN, 518060, P. R. China
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13
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Lu H, Ding B, Tong L, Wu F, Yi X, Wang J. Toehold-Mediated Strand Displacement Reaction for Dual-Signal Electrochemical Assay of Apolipoprotein E Genotyping. ACS Sens 2020; 5:2959-2965. [PMID: 32869976 DOI: 10.1021/acssensors.0c01511] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Apolipoprotein E (apoE) polymorphic genes are one of the main genetic determinants of Alzheimer's disease (AD) risk. Relying on the toehold-mediated strand displacement reaction (SDR), the dual-signal electrochemical assay of apoE genotyping with potential applications in the early diagnosis of AD has been achieved. The displacement of the surface-confined methylene blue- and ferrocene-capped detection probe-modified gold nanoparticles (AuNPs) by the complementary sequences (Tc 1 and Tc 2, fragment of allele ε4 at codon 112 and that of allele ε3 or ε4 at codon 158, respectively), triggered by the highly specific SDR, results in decreased voltammetric signals. In contrast, partial strand displacement caused by the single mismatched sequences (Tsm 1 and Tsm 2, fragment of allele ε2 or ε3 at codon 112 and that of allele ε2 at codon 158, respectively) produces larger voltammetric signals. The proposed method serves as a versatile platform for the discrimination of six apoE genotypes, including three homozygotes (ε2/2, ε3/3, and ε4/4) and three heterozygotes (ε2/3, ε2/4, and ε3/4), and for the quantification of apoE ε3/3 from genomic DNA extracts of AD patients.
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Affiliation(s)
- Hanwen Lu
- Hunan Provincial Key Laboratory of Micro Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Binrong Ding
- Department of Geriatrics, The Third Xiangya Hospital of Central South University, Changsha, Hunan 510060, P. R. China
| | - Liujuan Tong
- Hunan Provincial Key Laboratory of Micro Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Fan Wu
- Hunan Provincial Key Laboratory of Micro Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Xinyao Yi
- Hunan Provincial Key Laboratory of Micro Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
| | - Jianxiu Wang
- Hunan Provincial Key Laboratory of Micro Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan 410083, P. R. China
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14
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Lu H, Hailin T, Yi X, Wang J. Three-Dimensional DNA Nanomachine Combined with Toehold-Mediated Strand Displacement Reaction for Sensitive Electrochemical Detection of MiRNA. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:10708-10714. [PMID: 32804511 DOI: 10.1021/acs.langmuir.0c01415] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
MicroRNA (miRNA) serves as an ideal biomarker for diagnosis, prognosis, and therapy of various human cancers. The rationally designed three-dimensional (3D) DNA nanomachine was constructed on the matrixes of magnetic beads, and the high density of gold nanoparticles (AuNPs) on each magnetic bead and further enlargement of the AuNPs lead to the anchoring of numerous DNA walkers and signal probes on the AuNPs. With the combination of toehold-mediated strand displacement reaction (SDR), amplified electrochemical detection of miRNA is performed. The existence of miRNA triggers the toehold-mediated SDR and the released DNA walker probe is hybridized with the ferrocene (Fc)-tagged signal probe. The cleavage of the duplex by the nicking endonuclease detaches the signal probe from the magnetic nanocomposites. The oxidation current of Fc moieties was found to be inversely proportional to the concentrations of miRNA-182 between 1.0 fM and 2 pM. The assay is highly selective for discrimination of miRNAs with similar sequences. The feasibility of the method for sensitive detection of the expression levels of miRNA-182 from serum samples of glioma patients at different stages was demonstrated. The sensing protocol holds great promise for early diagnosis and prognosis of the cancer cases with abnormal miRNA expression.
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Affiliation(s)
- Hanwen Lu
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan P. R. China 410083
| | - Tang Hailin
- SunYat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangzhou, Guangdong P. R. China 510060
| | - Xinyao Yi
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan P. R. China 410083
| | - Jianxiu Wang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha, Hunan P. R. China 410083
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15
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Dual-output toehold-mediated strand displacement amplification for sensitive homogeneous electrochemical detection of specie-specific DNA sequences for species identification. Biosens Bioelectron 2020; 161:112256. [PMID: 32365011 DOI: 10.1016/j.bios.2020.112256] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 12/11/2022]
Abstract
The determination of specie-specific DNA sequences is a key factor for identification of animal species and detection of meat adulteration. Herein, a simple homogeneous electrochemical biosensor was developed for sensitive detection of specie-specific DNA sequences from meat products based on high efficient and specific dual-output toehold-mediated strand displacement (TMSD). After incubation with target DNA, large amount of methylene blue (electrochemical signal molecule) labeled probes (MB-P) were released from preformed DNA duplex structures by the process of dual-output TMSD amplification. The free MB-P could be further digested by Exonuclease I, and the enzymatic products contain little negative charge could diffuse to the surface of indium tin oxide electrode, generating significantly electrochemical signal. As a result, the designed biosensor showed a broad dynamic range from 0.01 pM to 100 pM, with a low detection limit of 8.2 fM, and ideal selectivity and reproducibility. Meanwhile, the approach exhibited acceptable accuracy for the detection of specie-specific DNA sequences, and possessed the potential application for the identification of animal species from meat products.
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16
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Xu H, Wu B, Wang J, Cao H, Yang J, Hao K, Chen S, Ye S, Shen Z. Label-free detection of cancer related gene based on target recycling and palindrome-mediated strand displacement amplification. Talanta 2020; 215:120897. [PMID: 32312442 DOI: 10.1016/j.talanta.2020.120897] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/29/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022]
Abstract
STAT3 plays an important role in regulating gene expression and is closely related with cancer. Thus, the sensitive and specific detection of the STAT3 biomarker is of great importance for disease diagnosis and therapeutics. In this study, by combining the target recycling amplification (TRA) with strand displacement amplification (SDA), we have developed a label-free and highly sensitive method for the dual-amplified detection of STAT3. The assay system consists of polymerization primer and label-free hairpin probe (HP) containing palindromic fragment and nicking site. In the presence of STAT3, the stem of the HP is opened, followed by the primer binding to initiate TRA and SDA with the help of Klenow Fragment (KF) and nickase. After multiple replication, nicking, and strand displacement, STAT3 was released and initiated the next round of reactions, generating a large number of terminal palindrome-contained fragments. Subsequently, the intermolecular hybridization between palindromic fragments occurred and the bidirectional extension by polymerase takes place, forming the dsDNAs. The double-stranded DNA products can be quantified by measuring the fluorescence intensity of SYBR Green I. The proposed strategy shows the excellent specificity and high sensitivity with a detection limit as low as 50 pM. In addition, this designed protocol can be successfully applied to detect the STAT3 in human serum, indicating great potential for the practical application in early diagnosis and prognosis.
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Affiliation(s)
- Huo Xu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Cancer Metastasis Alert and Prevention Center, Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, And Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, 350002, China; Institute of Oceanography, Minjiang University, Fuzhou, Fujian, 350108, China
| | - Biting Wu
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jue Wang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China; Cancer Metastasis Alert and Prevention Center, Biopharmaceutical Photocatalysis of State Key Laboratory of Photocatalysis on Energy and Environment, And Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, Fuzhou University, Fuzhou, 350002, China
| | - Hongwen Cao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Jie Yang
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Kaixuan Hao
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Si Chen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China
| | - Sheng Ye
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine, Ministry of Education of China, And Zhejiang Provincial Key Laboratory of Medical Genetics, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, 325035, China.
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17
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Tang W, Zhong W, Tan Y, Wang GA, Li F, Liu Y. DNA Strand Displacement Reaction: A Powerful Tool for Discriminating Single Nucleotide Variants. Top Curr Chem (Cham) 2020; 378:10. [PMID: 31894426 DOI: 10.1007/s41061-019-0274-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/06/2019] [Indexed: 01/01/2023]
Abstract
Single-nucleotide variants (SNVs) that are strongly associated with many genetic diseases and tumors are important both biologically and clinically. Detection of SNVs holds great potential for disease diagnosis and prognosis. Recent advances in DNA nanotechnology have offered numerous principles and strategies amenable to the detection and quantification of SNVs with high sensitivity, specificity, and programmability. In this review, we will focus our discussion on emerging techniques making use of DNA strand displacement, a basic building block in dynamic DNA nanotechnology. Based on their operation principles, we classify current SNV detection methods into three main categories, including strategies using toehold-mediated strand displacement reactions, toehold-exchange reactions, and enzyme-mediated strand displacement reactions. These detection methods discriminate SNVs from their wild-type counterparts through subtle differences in thermodynamics, kinetics, or response to enzymatic manipulation. The remarkable programmability of dynamic DNA nanotechnology also allows the predictable design and flexible operation of diverse strand displacement probes and/or primers. Here, we offer a systematic survey of current strategies, with an emphasis on the molecular mechanisms and their applicability to in vitro diagnostics.
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Affiliation(s)
- Weiyang Tang
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Weiye Zhong
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Yun Tan
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China
| | - Guan A Wang
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada
| | - Feng Li
- Department of Chemistry, Centre for Biotechnology, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON, L2S 3A1, Canada. .,College of Chemistry, Sichuan University, Chengdu, 610064, China.
| | - Yizhen Liu
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, People's Republic of China. .,Key Laboratory of Analytical Chemistry for Biology and Medicine (Ministry of Education), Wuhan University, Wuhan, China.
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18
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Zhang W, Li J, Salena B, Li Y. A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions. Chemistry 2019; 26:592-596. [PMID: 31475757 DOI: 10.1002/chem.201903536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 08/28/2019] [Indexed: 01/24/2023]
Abstract
DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson-Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15-25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35-90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.
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Affiliation(s)
- Wenqing Zhang
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Jiuxing Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Bruno Salena
- Department of Medicine, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
| | - Yingfu Li
- M.G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, DeGroote School of Medicine, McMaster University, 1280 Main Street West, Hamilton, ON, L8S 4K1, Canada
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19
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Gu C, Kong X, Liu X, Gai P, Li F. Enzymatic Biofuel-Cell-Based Self-Powered Biosensor Integrated with DNA Amplification Strategy for Ultrasensitive Detection of Single-Nucleotide Polymorphism. Anal Chem 2019; 91:8697-8704. [DOI: 10.1021/acs.analchem.9b02510] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Chengcheng Gu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xinke Kong
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Xiaojuan Liu
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Panpan Gai
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
| | - Feng Li
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, P. R. China
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20
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Li Y, Chen H, Dai Y, Chen T, Cao Y, Zhang J. Cellular interface supported toehold strand displacement cascade for amplified dual-electrochemical signal and its application for tumor cell analysis. Anal Chim Acta 2019; 1064:25-32. [PMID: 30982514 DOI: 10.1016/j.aca.2019.03.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 01/17/2023]
Abstract
In this work, toehold strand displacement cascade (TSDC) has been delicately designed and carried out on the cellular interface for the amplification and output of dual-electrochemical signal. Specifically, antibody cross-linked T strand can recognize cell which is linked with immune-magnetic bead. Subsequently, T strand on the cellular interface can mediate the occurrence of TSDC, resulting the change of SN3/S1-MB to SN3/S2-Fc ratio in the supernatant after magnetic separation. The resultant SN3/S1-MB and SN3/S2-Fc can be immobilized on the electrode interface through click chemistry and give the amplified double electrochemical signal. So the tumor cell amount can closely correlate with the change of the double signal. Except for output of the double signal for improvement of analytical accuracy, the double magnetic separation not only eliminate the interference of the complicated substances in serum, but also remove the influence of cell on click reaction on the electrode interface. So based on cellular interface supported TSDC for amplified dual-electrochemical signal, the established method has been successfully applied to analyze the tumor cells in serum accurately and sensitively.
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Affiliation(s)
- Yifei Li
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China; CAS Key Lab of Bio-Medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, 215163, PR China
| | - Hong Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Yuhao Dai
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Tingjun Chen
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China
| | - Ya Cao
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
| | - Juan Zhang
- Center for Molecular Recognition and Biosensing, School of Life Sciences, Shanghai University, 200444, PR China.
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21
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Simmel FC, Yurke B, Singh HR. Principles and Applications of Nucleic Acid Strand Displacement Reactions. Chem Rev 2019; 119:6326-6369. [PMID: 30714375 DOI: 10.1021/acs.chemrev.8b00580] [Citation(s) in RCA: 367] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Dynamic DNA nanotechnology, a subfield of DNA nanotechnology, is concerned with the study and application of nucleic acid strand-displacement reactions. Strand-displacement reactions generally proceed by three-way or four-way branch migration and initially were investigated for their relevance to genetic recombination. Through the use of toeholds, which are single-stranded segments of DNA to which an invader strand can bind to initiate branch migration, the rate with which strand displacement reactions proceed can be varied by more than 6 orders of magnitude. In addition, the use of toeholds enables the construction of enzyme-free DNA reaction networks exhibiting complex dynamical behavior. A demonstration of this was provided in the year 2000, in which strand displacement reactions were employed to drive a DNA-based nanomachine (Yurke, B.; et al. Nature 2000, 406, 605-608). Since then, toehold-mediated strand displacement reactions have been used with ever increasing sophistication and the field of dynamic DNA nanotechnology has grown exponentially. Besides molecular machines, the field has produced enzyme-free catalytic systems, all DNA chemical oscillators and the most complex molecular computers yet devised. Enzyme-free catalytic systems can function as chemical amplifiers and as such have received considerable attention for sensing and detection applications in chemistry and medical diagnostics. Strand-displacement reactions have been combined with other enzymatically driven processes and have also been employed within living cells (Groves, B.; et al. Nat. Nanotechnol. 2015, 11, 287-294). Strand-displacement principles have also been applied in synthetic biology to enable artificial gene regulation and computation in bacteria. Given the enormous progress of dynamic DNA nanotechnology over the past years, the field now seems poised for practical application.
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Affiliation(s)
| | - Bernard Yurke
- Micron School of Materials Science and Engineering , Boise State University , Boise , ID 83725 , United States
| | - Hari R Singh
- Physics Department , TU München , 85748 Garching , Germany
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22
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Xing Y, Li X, Yuan T, Cheng W, Li D, Yu T, Ding X, Ding S. Engineering high-performance hairpin stacking circuits for logic gate operation and highly sensitive biosensing assay of microRNA. Analyst 2018; 142:4834-4842. [PMID: 29160870 DOI: 10.1039/c7an01624g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Recently, hairpin stacking circuits (HSC) based on toehold-mediated strand displacement have been engineered to detect nucleic acids and proteins. However, the three metastable hairpins in a HSC system can potentially react non-specifically in the absence of a catalyst, limiting its practical application. Here, we developed a unique hairpin design guideline to eliminate circuit leakage of HSC, and the high-performance HSC was successfully implemented on logic gate building and biosensing. We began by analyzing the sources of circuit leakage and optimizing the toehold lengths of hairpins in the HSC system based on the surface plasmon resonance (SPR) technique. Next, a novel strategy of substituting two nucleotides in a specific domain, termed 'loop-domain substitution', was introduced to eliminate leakages. We also systematically altered the positions and numbers of the introduced substitutions to probe their potential contribution to circuit leakage suppression. Through these efforts, the circuit leakage of HSC was significantly reduced. Finally, by designing different DNA input strands, the logic gates could be activated to achieve the output signal. Using miRNA as a model analyte, this strategy could detect miRNA down to pM levels with minimized circuit leakage. We believe these work indicate significant progress in the DNA circuitry.
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Affiliation(s)
- Yueli Xing
- The Affiliated Hospital of Binzhou Medical University, Shandong 256603, China
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23
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Xu J, Wu ZS, Shen W, Le J, Zheng T, Li H, Jia L. Programmable nanoassembly consisting of two hairpin-DNAs for p53 gene determination. Biosens Bioelectron 2017; 94:626-631. [DOI: 10.1016/j.bios.2017.03.052] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 03/16/2017] [Accepted: 03/24/2017] [Indexed: 12/12/2022]
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24
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Chang Y, Zhuo Y, Chai Y, Yuan R. Host–Guest Recognition-Assisted Electrochemical Release: Its Reusable Sensing Application Based on DNA Cross Configuration-Fueled Target Cycling and Strand Displacement Reaction Amplification. Anal Chem 2017; 89:8266-8272. [DOI: 10.1021/acs.analchem.7b01272] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Yuanyuan Chang
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ying Zhuo
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Yaqin Chai
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
| | - Ruo Yuan
- Key Laboratory of Luminescent
and Real-Time Analytical Chemistry (Southwest University), Ministry
of Education, College of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, P.R. China
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25
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Ultrasensitive chemiluminescence assay for the lung cancer biomarker cytokeratin 21-1 via a dual amplification scheme based on the use of encoded gold nanoparticles and a toehold-mediated strand displacement reaction. Mikrochim Acta 2017. [DOI: 10.1007/s00604-017-2430-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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26
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Wang S, Yang F, Jin D, Dai Q, Tu J, Liu Y, Ning Y, Zhang GJ. Toehold Mediated One-Step Conformation-Switchable “Signal-On” Electrochemical DNA Sensing Enhanced with Homogeneous Enzymatic Amplification. Anal Chem 2017; 89:5349-5356. [PMID: 28452219 DOI: 10.1021/acs.analchem.6b05171] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Siqi Wang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Fan Yang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Dan Jin
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Qi Dai
- Huangjia
Lake Hospital, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Jiyuan Tu
- School
of Pharmacy, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Yanju Liu
- School
of Pharmacy, Hubei University of Chinese Medicine, 1 Huangjia
Lake West Road, Wuhan, Hubei 430065, China
| | - Yong Ning
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
| | - Guo-Jun Zhang
- School
of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan, Hubei 430065, China
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27
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Wu Y, Wang L, Jiang W. Toehold-mediated strand displacement reaction-dependent fluorescent strategy for sensitive detection of uracil-DNA glycosylase activity. Biosens Bioelectron 2017; 89:984-988. [DOI: 10.1016/j.bios.2016.10.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Revised: 10/09/2016] [Accepted: 10/19/2016] [Indexed: 01/27/2023]
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28
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Dual-cyclical nucleic acid strand-displacement polymerization based signal amplification system for highly sensitive determination of p53 gene. Biosens Bioelectron 2016; 86:1024-1030. [DOI: 10.1016/j.bios.2016.07.029] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Revised: 07/07/2016] [Accepted: 07/08/2016] [Indexed: 01/15/2023]
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29
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Wang L, Tian J, Huang Y, Lin X, Yang W, Zhao Y, Zhao S. Homogenous fluorescence polarization assay for the DNA of HIV A T7 by exploiting exonuclease-assisted quadratic recycling amplification and the strong interaction between graphene oxide and ssDNA. Mikrochim Acta 2016. [DOI: 10.1007/s00604-016-1844-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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30
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Gao ZF, Huang YL, Ren W, Luo HQ, Li NB. Guanine nanowire based amplification strategy: Enzyme-free biosensing of nucleic acids and proteins. Biosens Bioelectron 2016; 78:351-357. [DOI: 10.1016/j.bios.2015.11.070] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 11/20/2015] [Accepted: 11/23/2015] [Indexed: 01/25/2023]
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31
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Yang F, Wang S, Zhang Y, Tang L, Jin D, Ning Y, Zhang GJ. Toehold enabling stem-loop inspired hemiduplex probe with enhanced sensitivity and sequence-specific detection of tumor DNA in serum. Biosens Bioelectron 2016; 82:32-9. [PMID: 27040528 DOI: 10.1016/j.bios.2016.03.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 03/08/2016] [Accepted: 03/21/2016] [Indexed: 11/26/2022]
Abstract
The sensitivity of structure-switchable electrochemical DNA (E-DNA) sensors is generally limited by the irremovable redox labels that are close to or distant from the sensing interface. To address this issue, we design a semiduplex probe inspired by the stem-loop structure, in which the "nicked loop" domain can serve as toehold to mediate a target-responsive strand-displacement reaction. Such a reaction can fundamentally eliminate the post-responsive background current that arises from the irremovable probe, and thus improve the sensitivity. This novel toehold E-DNA (tE-DNA) sensor is able to achieve a detection limit as low as 0.2pM, which is lower than that of the classic stem-loop structured sensor by two orders of magnitude. Moreover, the toehold domain endows the sensor an excellent selectivity against a single-base mismatched sequence and high binding kinetics. By combining this heterogeneous surface-based dynamic self-assembly design with a homogeneous enzyme amplification strategy, the sensitivity can be further improved by three orders of magnitude to sub-femtomolar level. Additionally, this unique biosensor presents reliable reusability, and is capable of probing low abundance of target DNA directly in complex matrices, such as human serum, with minimal interference. These advantages make our tE-DNA sensor a promising contender in the E-DNA sensor family for clinical diagnostics.
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Affiliation(s)
- Fan Yang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Siqi Wang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Yulin Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Lina Tang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Dan Jin
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China
| | - Yong Ning
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
| | - Guo-Jun Zhang
- School of Laboratory Medicine, Hubei University of Chinese Medicine, 1 Huangjia Lake West Road, Wuhan 430065, China.
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32
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Yuan R, Ding S, Yan Y, Zhang Y, Zhang Y, Cheng W. A facile and pragmatic electrochemical biosensing strategy for ultrasensitive detection of DNA in real sample based on defective T junction induced transcription amplification. Biosens Bioelectron 2016; 77:19-25. [DOI: 10.1016/j.bios.2015.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 08/25/2015] [Accepted: 09/04/2015] [Indexed: 11/30/2022]
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33
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Huang J, Wang Z, Kim JK, Su X, Li Z. Detecting Arbitrary DNA Mutations Using Graphene Oxide and Ethidium Bromide. Anal Chem 2015; 87:12254-61. [DOI: 10.1021/acs.analchem.5b03369] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Jiahao Huang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Zhenyu Wang
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Jang-Kyo Kim
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Xuefen Su
- School of Public
Health and Primary Care, Faculty of Medicine, Prince of Wales Hospital, The Chinese University of Hong Kong,
Shatin, New Territories, Hong Kong
| | - Zhigang Li
- Department
of Mechanical and Aerospace Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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34
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Abstract
Isothermal amplification of nucleic acids is a simple process that rapidly and efficiently accumulates nucleic acid sequences at constant temperature. Since the early 1990s, various isothermal amplification techniques have been developed as alternatives to polymerase chain reaction (PCR). These isothermal amplification methods have been used for biosensing targets such as DNA, RNA, cells, proteins, small molecules, and ions. The applications of these techniques for in situ or intracellular bioimaging and sequencing have been amply demonstrated. Amplicons produced by isothermal amplification methods have also been utilized to construct versatile nucleic acid nanomaterials for promising applications in biomedicine, bioimaging, and biosensing. The integration of isothermal amplification into microsystems or portable devices improves nucleic acid-based on-site assays and confers high sensitivity. Single-cell and single-molecule analyses have also been implemented based on integrated microfluidic systems. In this review, we provide a comprehensive overview of the isothermal amplification of nucleic acids encompassing work published in the past two decades. First, different isothermal amplification techniques are classified into three types based on reaction kinetics. Then, we summarize the applications of isothermal amplification in bioanalysis, diagnostics, nanotechnology, materials science, and device integration. Finally, several challenges and perspectives in the field are discussed.
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Affiliation(s)
- Yongxi Zhao
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Feng Chen
- Key Laboratory of Biomedical Information Engineering of Education Ministry, School of Life Science and Technology, Xi'an Jiaotong University , Xianning West Road, Xi'an, Shaanxi 710049, China
| | - Qian Li
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboraotory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China.,School of Life Science & Technology, ShanghaiTech University , Shanghai 200031, China
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35
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Dong H, Wu ZS, Xu J, Ma J, Zhang H, Wang J, Shen W, Xie J, Jia L. Novel multifunction-integrated molecular beacon for the amplification detection of DNA hybridization based on primer/template-free isothermal polymerization. Biosens Bioelectron 2015; 72:182-90. [DOI: 10.1016/j.bios.2015.04.090] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/20/2015] [Accepted: 04/27/2015] [Indexed: 01/10/2023]
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36
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Gao ZF, Chen DM, Lei JL, Luo HQ, Li NB. A regenerated electrochemical biosensor for label-free detection of glucose and urea based on conformational switch of i-motif oligonucleotide probe. Anal Chim Acta 2015; 897:10-6. [PMID: 26515000 DOI: 10.1016/j.aca.2015.09.045] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2014] [Revised: 03/24/2015] [Accepted: 09/18/2015] [Indexed: 01/21/2023]
Abstract
Improving the reproducibility of electrochemical signal remains a great challenge over the past decades. In this work, i-motif oligonucleotide probe-based electrochemical DNA (E-DNA) sensor is introduced for the first time as a regenerated sensing platform, which enhances the reproducibility of electrochemical signal, for label-free detection of glucose and urea. The addition of glucose or urea is able to activate glucose oxidase-catalyzed or urease-catalyzed reaction, inducing or destroying the formation of i-motif oligonucleotide probe. The conformational switch of oligonucleotide probe can be recorded by electrochemical impedance spectroscopy. Thus, the difference of electron transfer resistance is utilized for the quantitative determination of glucose and urea. We further demonstrate that the E-DNA sensor exhibits high selectivity, excellent stability, and remarkable regenerated ability. The human serum analysis indicates that this simple and regenerated strategy holds promising potential in future biosensing applications.
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Affiliation(s)
- Zhong Feng Gao
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Dong Mei Chen
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
| | - Jing Lei Lei
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 400044, China
| | - Hong Qun Luo
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
| | - Nian Bing Li
- Key Laboratory of Eco-environments in Three Gorges Reservoir Region (Ministry of Education), School of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China.
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37
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Meng TT, Liu YX, Liu MT, Long JB, Cao QF, Yan SY, Meng XX. Lineal DNA logic gate for microRNA diagnostics with strand displacement and fluorescence resonance energy transfer. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2015.05.039] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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38
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Shen W, Tian Y, Ran T, Gao Z. Genotyping and quantification techniques for single-nucleotide polymorphisms. Trends Analyt Chem 2015. [DOI: 10.1016/j.trac.2015.03.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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39
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Chang K, Deng S, Chen M. Novel biosensing methodologies for improving the detection of single nucleotide polymorphism. Biosens Bioelectron 2015; 66:297-307. [DOI: 10.1016/j.bios.2014.11.041] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 10/28/2014] [Accepted: 11/20/2014] [Indexed: 12/11/2022]
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40
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Protected DNA strand displacement for enhanced single nucleotide discrimination in double-stranded DNA. Sci Rep 2015; 5:8721. [PMID: 25735213 PMCID: PMC4348642 DOI: 10.1038/srep08721] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2014] [Accepted: 01/23/2015] [Indexed: 12/18/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are a prime source of genetic diversity. Discriminating between different SNPs provides an enormous leap towards the better understanding of the uniqueness of biological systems. Here we report on a new approach for SNP discrimination using toehold-mediated DNA strand displacement. The distinctiveness of the approach is based on the combination of both 3- and 4-way branch migration mechanisms, which allows for reliable discrimination of SNPs within double-stranded DNA generated from real-life human mitochondrial DNA samples. Aside from the potential diagnostic value, the current study represents an additional way to control the strand displacement reaction rate without altering other reaction parameters and provides new insights into the influence of single nucleotide substitutions on 3- and 4-way branch migration efficiency and kinetics.
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41
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Sensitive detection of point mutation using exponential strand displacement amplification-based surface enhanced Raman spectroscopy. Biosens Bioelectron 2015; 65:191-7. [DOI: 10.1016/j.bios.2014.10.035] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 09/29/2014] [Accepted: 10/13/2014] [Indexed: 12/29/2022]
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42
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Xu H, Deng W, Huang F, Xiao S, Liu G, Liang H. Enhanced DNA toehold exchange reaction on a chip surface to discriminate single-base changes. Chem Commun (Camb) 2014; 50:14171-4. [DOI: 10.1039/c4cc07272c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
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