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Liang Y, Wang Q, Zhang X, Zhang M, Du B, Cheng W, Wang H, Li L, Hou G, Zhang W. Dual isothermal amplification all-in-one approach for rapid and highly sensitive quantification of plasma circulating MYCN gene of neuroblastoma. Anal Biochem 2022; 658:114922. [PMID: 36162447 DOI: 10.1016/j.ab.2022.114922] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 09/16/2022] [Accepted: 09/18/2022] [Indexed: 11/27/2022]
Abstract
A dual isothermal amplification assay with dual fluorescence signal detection strategy, named dual isothermal amplification all-in-one approach, was developed for rapid, one-step, highly sensitive quantification of plasma circulating MYCN copy number of neuroblastoma (NB). The developed strategy consisted of rolling circle amplification (RCA) and loop-mediated isothermal amplification (LAMP) on a real-time PCR system using highly specific probe, molecular beacon (MB), as detection probe. The developed strategy possessing a broad linear dynamic range of 10 aM to 1 pM for both target gene (MYCN) and reference gene (NAGK). The ratio of the MYCN copy number to NAGK copy number (M/N ratio) was detected by the developed approach in cell lines, NB tumor tissues, hepatoblastoma tumor tissues and Wilms' tumor tissues, to which the M/N ratios were consistent with previous reports. In particular, the M/N ratio in NB clinical tissue specimens and NB plasma specimens detected with the developed approach were in keeping with the standard RT-PCR approach. More importantly, the M/N ratio in NB tissue samples and corresponding plasma samples of NB patients were consistent with each other with a correlation coefficient of 0.9690, indicating that plasma circulating MYCN is a promising indicator for the risk classification of NB.
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Affiliation(s)
- Ying Liang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Qionglin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Xianwei Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Mengxin Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Bang Du
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Weyland Cheng
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Huanmin Wang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China
| | - Lifeng Li
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Guangjun Hou
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
| | - Wancun Zhang
- Henan Key Laboratory of Children's Genetics and Metabolic Diseases, Henan International Joint Laboratory for Pediatric Disease Prevention and Control, Children's Hospital Affiliated to Zhengzhou University, Zhengzhou, 450018, China.
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Park KW, Lee CY, Batule BS, Park KS, Park HG. Ultrasensitive DNA detection based on target-triggered rolling circle amplification and fluorescent poly(thymine)-templated copper nanoparticles. RSC Adv 2018; 8:1958-1962. [PMID: 35542615 PMCID: PMC9077274 DOI: 10.1039/c7ra11071e] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 12/26/2017] [Indexed: 11/21/2022] Open
Abstract
An ultrasensitive DNA detection method is developed based on target-triggered rolling circle amplification coupled with fluorescent poly(thymine)-templated copper nanoparticles.
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Affiliation(s)
- Kwan Woo Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Chang Yeol Lee
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Bhagwan S. Batule
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
| | - Ki Soo Park
- Department of Biological Engineering
- College of Engineering
- Konkuk University
- Seoul 05029
- Republic of Korea
| | - Hyun Gyu Park
- Department of Chemical and Biomolecular Engineering (BK 21+ Program)
- KAIST
- Daejeon 34141
- Republic of Korea
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Gao J, Ma L, Lei Z, Wang Z. Multiple detection of single nucleotide polymorphism by microarray-based resonance light scattering assay with enlarged gold nanoparticle probes. Analyst 2016; 141:1772-8. [DOI: 10.1039/c5an02510a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A gold nanoparticle enlargement assisted DNA microarray-based RLS assay has been developed for multiplexed detection of single nucleotide polymorphism with high sensitivity.
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Affiliation(s)
- Jiaxue Gao
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Lan Ma
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Zhen Lei
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
| | - Zhenxin Wang
- State Key Laboratory of Electroanalytical Chemistry
- Changchun Institute of Applied Chemistry
- Chinese Academy of Sciences
- Changchun
- P. R. China
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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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5
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Yoshimura T, Suzuki T, Mineki S, Ohuchi S. Controlled Microwave Heating Accelerates Rolling Circle Amplification. PLoS One 2015; 10:e0136532. [PMID: 26348227 PMCID: PMC4562646 DOI: 10.1371/journal.pone.0136532] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 08/04/2015] [Indexed: 11/19/2022] Open
Abstract
Rolling circle amplification (RCA) generates single-stranded DNAs or RNA, and the diverse applications of this isothermal technique range from the sensitive detection of nucleic acids to analysis of single nucleotide polymorphisms. Microwave chemistry is widely applied to increase reaction rate as well as product yield and purity. The objectives of the present research were to apply microwave heating to RCA and indicate factors that contribute to the microwave selective heating effect. The microwave reaction temperature was strictly controlled using a microwave applicator optimized for enzymatic-scale reactions. Here, we showed that microwave-assisted RCA reactions catalyzed by either of the four thermostable DNA polymerases were accelerated over 4-folds compared with conventional RCA. Furthermore, the temperatures of the individual buffer components were specifically influenced by microwave heating. We concluded that microwave heating accelerated isothermal RCA of DNA because of the differential heating mechanisms of microwaves on the temperatures of reaction components, although the overall reaction temperatures were the same.
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Affiliation(s)
- Takeo Yoshimura
- Department of Applied Biological Science, Tokyo University of Science, 264 Yamazaki, Noda, Chiba 305–8506, Japan
- * E-mail:
| | - Takamasa Suzuki
- Department of Applied Biological Science, Tokyo University of Science, 264 Yamazaki, Noda, Chiba 305–8506, Japan
| | - Shigeru Mineki
- Department of Applied Biological Science, Tokyo University of Science, 264 Yamazaki, Noda, Chiba 305–8506, Japan
| | - Shokichi Ohuchi
- Graduate School of Life Science and System Engineering, Kyushu Institute of Technology, 680–4 Kawazu, Iizuka, Fukuoka 820–8502, Japan
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Xiang Y, Zhu X, Huang Q, Zheng J, Fu W. Real-time monitoring of mycobacterium genomic DNA with target-primed rolling circle amplification by a Au nanoparticle-embedded SPR biosensor. Biosens Bioelectron 2015; 66:512-9. [DOI: 10.1016/j.bios.2014.11.021] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/13/2014] [Accepted: 11/14/2014] [Indexed: 10/24/2022]
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Lapitan LDS, Guo Y, Zhou D. Nano-enabled bioanalytical approaches to ultrasensitive detection of low abundance single nucleotide polymorphisms. Analyst 2015; 140:3872-87. [PMID: 25785914 PMCID: PMC4456783 DOI: 10.1039/c4an02304h] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A survey of the recent, significant developments on nanomaterials enabled ultrasensitive DNA and gene mutation assays is presented.
Single nucleotide polymorphisms (SNPs) constitute the most common types of genetic variations in the human genome. A number of SNPs have been linked to the development of life threatening diseases including cancer, cardiovascular diseases and neurodegenerative diseases. The ability for ultrasensitive and accurate detection of low abundant disease-related SNPs in bodily fluids (e.g. blood, serum, etc.) holds a significant value in the development of non-invasive future biodiagnostic tools. Over the past two decades, nanomaterials have been utilized in a myriad of biosensing applications due to their ability of detecting extremely low quantities of biologically important biomarkers with high sensitivity and accuracy. Of particular interest is the application of such technologies in the detection of SNPs. The use of various nanomaterials, coupled with different powerful signal amplification strategies, has paved the way for a new generation of ultrasensitive SNP biodiagnostic assays. Over the past few years, several ultrasensitive SNP biosensors capable of detecting specific targets down to the ultra-low regimes (ca. aM and below) and therefore holding great promises for early clinical diagnosis of diseases have been developed. This mini review will highlight some of the most recent, significant advances in nanomaterial-based ultrasensitive SNP sensing technologies capable of detecting specific targets on the attomolar (10–18 M) regime or below. In particular, the design of novel, powerful signal amplification strategies that hold the key to the ultrasensitivity is highlighted.
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Affiliation(s)
- Lorico D S Lapitan
- School of Chemistry and Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK.
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9
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Freage L, Wang F, Orbach R, Willner I. Multiplexed Analysis of Genes and of Metal Ions Using Enzyme/DNAzyme Amplification Machineries. Anal Chem 2014; 86:11326-33. [DOI: 10.1021/ac5030667] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Lina Freage
- Institute of Chemistry, The Center for Nanoscience and
Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and
Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Ron Orbach
- Institute of Chemistry, The Center for Nanoscience and
Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Itamar Willner
- Institute of Chemistry, The Center for Nanoscience and
Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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Wang F, Lu CH, Willner I. From cascaded catalytic nucleic acids to enzyme-DNA nanostructures: controlling reactivity, sensing, logic operations, and assembly of complex structures. Chem Rev 2014; 114:2881-941. [PMID: 24576227 DOI: 10.1021/cr400354z] [Citation(s) in RCA: 494] [Impact Index Per Article: 49.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Fuan Wang
- Institute of Chemistry, The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
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11
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Ali MM, Li F, Zhang Z, Zhang K, Kang DK, Ankrum JA, Le XC, Zhao W. Rolling circle amplification: a versatile tool for chemical biology, materials science and medicine. Chem Soc Rev 2014; 43:3324-41. [DOI: 10.1039/c3cs60439j] [Citation(s) in RCA: 650] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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12
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Cheng Y, Zhao J, Jia H, Yuan Z, Li Z. Ligase chain reaction coupled with rolling circle amplification for high sensitivity detection of single nucleotide polymorphisms. Analyst 2013; 138:2958-63. [PMID: 23535938 DOI: 10.1039/c3an36920j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We present a highly sensitive and homogeneous assay for the detection of single nucleotide polymorphisms (SNPs) by ligase chain reaction (LCR) coupled with rolling circle amplification (RCA). The LCR probes include one pair of probes and a padlock probe (PLP). In the LCR, one pair of probes composed of X and Y, perfectly hybridize with the upper strand of the target DNA after thermal denaturation. They are then ligated by the thermostable ligase to form the ligation product of XY. At the same time, the PLP hybridizes with the lower strand of the target DNA and are ligated to form the circular PLP (cPLP). After repeated cycles of denaturation, annealing, and ligation, the target DNA is amplified exponentially to generate a large number of XY and cPLPs. Subsequently, RCA is triggered by the cPLP as a template and XY as a primer, producing large numbers of long strand DNA products, which are detected by binding with the fluorescent dye, SYBR Green I, in a homogeneous manner. This method is simple, and avoids the need for detection of the LCR products with labeled probes and complex separation steps. The assay is sensitive and specific enough to detect a 1 fM target DNA molecule. It is possible to accurately determine the allele frequency as low as 1.0%. The LCR coupled with RCA assay extends the application of the LCR and RCA, and provides a new strategy for detecting SNPs as well as nucleic acid analysis, immunoassay, and molecular diagnosis.
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Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis, Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding, 071002, P. R. China.
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Zhang H, Li F, Dever B, Li XF, Le XC. DNA-mediated homogeneous binding assays for nucleic acids and proteins. Chem Rev 2012; 113:2812-41. [PMID: 23231477 DOI: 10.1021/cr300340p] [Citation(s) in RCA: 339] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hongquan Zhang
- Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada T6G 2G3
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14
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Tsukada H, Watanabe T, Kanayama N, Takarada T, Maeda M. Quantitative SNP genotyping by affinity capillary electrophoresis using PEG-oligodeoxyribonucleotide block copolymers with electroosmotic flow. Electrophoresis 2012; 33:2122-9. [PMID: 22821487 DOI: 10.1002/elps.201200073] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Quantitative SNP detection was demonstrated with an ACE using a PEG-oligodeoxyribonucleotide block copolymer (PEG-b-ODN) as a probe in the presence of an EOF. The probe's PEG segment with large molecular weight and small polydispersity yielded a high resolution in the separation of a chemically synthesized 60-base ssDNA (WT) and its single-base-substituted mutant (MT). A mixture of WT and MT was clearly separated within 10 min by simultaneously using two types of PEG-b-ODN probes whose ODN segments were complementary to WT and MT and whose PEG segments were of different lengths. The peak area ratio between WT and MT was in good agreement with the feed ratio. The averaged difference between the feed and observed ratio of MT was determined to be 0.23%, which is lower than that of any other methods. The ACE using the PEG-b-ODN probes in the presence of EOF could be utilized as a facile method for estimating SNP allele frequency in various research fields.
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Affiliation(s)
- Harumi Tsukada
- Bioengineering Laboratory, RIKEN Advanced Science Institute, Wako, Saitama, Japan
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15
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Cheng Y, Du Q, Wang L, Jia H, Li Z. Fluorescently Cationic Conjugated Polymer as an Indicator of Ligase Chain Reaction for Sensitive and Homogeneous Detection of Single Nucleotide Polymorphism. Anal Chem 2012; 84:3739-44. [DOI: 10.1021/ac300314c] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Yongqiang Cheng
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Qing Du
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Liyong Wang
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Hailian Jia
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
| | - Zhengping Li
- Key Laboratory of Medicine Chemistry and Molecular Diagnosis,
Ministry of Education, College of Chemistry and Environment Science, Hebei University, Baoding 071002, China
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Akter F, Mie M, Kobatake E. Immuno-rolling circle amplification using a multibinding fusion protein. Anal Biochem 2011; 416:174-9. [DOI: 10.1016/j.ab.2011.05.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Revised: 05/02/2011] [Accepted: 05/03/2011] [Indexed: 10/18/2022]
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