1
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Duan X, Qin W, Hao J, Yu X. Recent advances in the applications of DNA frameworks in liquid biopsy: A review. Anal Chim Acta 2024; 1308:342578. [PMID: 38740462 DOI: 10.1016/j.aca.2024.342578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/02/2024] [Accepted: 04/03/2024] [Indexed: 05/16/2024]
Abstract
Cancer is one of the serious threats to public life and health. Early diagnosis, real-time monitoring, and individualized treatment are the keys to improve the survival rate and prolong the survival time of cancer patients. Liquid biopsy is a potential technique for cancer early diagnosis due to its non-invasive and continuous monitoring properties. However, most current liquid biopsy techniques lack the ability to detect cancers at the early stage. Therefore, effective detection of a variety of cancers is expected through the combination of various techniques. Recently, DNA frameworks with tailorable functionality and precise addressability have attracted wide spread attention in biomedical applications, especially in detecting cancer biomarkers such as circulating tumor cells (CTCs), exosomes and circulating tumor nucleic acid (ctNA). Encouragingly, DNA frameworks perform outstanding in detecting these cancer markers, but also face some challenges and opportunities. In this review, we first briefly introduced the development of DNA frameworks and its typical structural characteristics and advantages. Then, we mainly focus on the recent progress of DNA frameworks in detecting commonly used cancer markers in liquid-biopsy. We summarize the advantages and applications of DNA frameworks for detecting CTCs, exosomes and ctNA. Furthermore, we provide an outlook on the possible opportunities and challenges for exploiting the structural advantages of DNA frameworks in the field of cancer diagnosis. Finally, we envision the marriage of DNA frameworks with other emerging materials and technologies to develop the next generation of disease diagnostic biosensors.
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Affiliation(s)
- Xueyuan Duan
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Weiwei Qin
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China.
| | - Jicong Hao
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China
| | - Xiaoping Yu
- Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Science, China Jiliang University, Hangzhou, 310018, China.
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2
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Ma Z, Xu J, Hou W, Lei Z, Li T, Shen W, Yu H, Liu C, Zhang J, Tang S. Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography. Anal Chem 2024; 96:5195-5204. [PMID: 38520334 DOI: 10.1021/acs.analchem.3c05500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2024]
Abstract
The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.
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Affiliation(s)
- Ziyu Ma
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Junjie Xu
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Weilin Hou
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Zi Lei
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Tingting Li
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Wei Shen
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Hui Yu
- Department of Thoracic Surgery, Affiliated Hospital of Jiangsu University, No. 438, Jiefang Road, Zhenjiang 212000, Jiangsu, P. R. China
| | - Chang Liu
- School of Grain Science and Technology, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Jinghui Zhang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
| | - Sheng Tang
- School of Environmental and Chemical Engineering, Jiangsu University of Science and Technology, Zhenjiang 212003, Jiangsu, P. R. China
- College of Chemistry, Chemical Engineering and Materials Science, Soochow University, Suzhou 215123, P. R. China
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3
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Liang T, Qin X, Zhang Y, Yang Y, Chen Y, Yuan L, Liu F, Chen Z, Li X, Yang F. CRISPR/dCas9-Mediated Specific Molecular Assembly Facilitates Genotyping of Mutant Circulating Tumor DNA. Anal Chem 2023; 95:16305-16314. [PMID: 37874695 DOI: 10.1021/acs.analchem.3c03481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023]
Abstract
Breakthroughs in circulating tumor DNA (ctDNA) analysis are critical in tumor liquid biopsies but remain a technical challenge due to the double-stranded structure, extremely low abundance, and short half-life of ctDNA. Here, we report an electrochemical CRISPR/dCas9 sensor (E-dCas9) for sensitive and specific detection of ctDNA at a single-nucleotide resolution. The E-dCas9 design harnesses the specific capture and unzipping of target ctDNA by dCas9 to introduce a complementary reporter probe for specific molecular assembly and signal amplification. By efficient homogeneous assembly and interfacial click reaction, the assay demonstrates superior sensitivity (up to 2.86 fM) in detecting single-base mutant ctDNA and a broad dynamic range spanning 6 orders of magnitude. The sensor is also capable of measuring 10 fg/μL of a mutated target in excess of wild-type ones (1 ng/μL), equivalent to probing 0.001% of the mutation relative to the wild type. In addition, our sensor can monitor the dynamic expression of cellular genomic DNA and allows accurate analysis of blood samples from patients with nonsmall cell lung cancer, suggesting the potential of E-dCas9 as a promising tool in ctDNA-based cancer diagnosis.
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Affiliation(s)
- Tingting Liang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
- Department of Pharmacy, The Second Affiliated Hospital of Guangxi Medical University, Nanning 530007, China
| | - Xiaojie Qin
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yuyuan Zhang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yu Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Yu Chen
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Lin Yuan
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rhumatic Diseases, Hubei Minzu University, Enshi 445000, China
| | - Feng Liu
- Department of Blood Transfusion, the First Affiliated Hospital, Guangxi Medical University, Nanning 530021, China
| | - Zhizhong Chen
- Department of Clinical Laboratory, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning 530021, China
| | - Xinchun Li
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
| | - Fan Yang
- Key Laboratory of Micro-Nanoscale Bioanalysis and Drug Screening of Guangxi Education Department, Guangxi Key Laboratory of Pharmaceutical Precision Detection and Screening, State Key Laboratory of Targeting Oncology, Pharmaceutical College, Guangxi Medical University, Nanning 530021, China
- Hubei Provincial Key Laboratory of Occurrence and Intervention of Rhumatic Diseases, Hubei Minzu University, Enshi 445000, China
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4
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Meng X, O'Hare D, Ladame S. Surface immobilization strategies for the development of electrochemical nucleic acid sensors. Biosens Bioelectron 2023; 237:115440. [PMID: 37406480 DOI: 10.1016/j.bios.2023.115440] [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: 05/19/2022] [Revised: 05/20/2023] [Accepted: 05/27/2023] [Indexed: 07/07/2023]
Abstract
Following the recent pandemic and with the emergence of cell-free nucleic acids in liquid biopsies as promising biomarkers for a broad range of pathologies, there is an increasing demand for a new generation of nucleic acid tests, with a particular focus on cost-effective, highly sensitive and specific biosensors. Easily miniaturized electrochemical sensors show the greatest promise and most typically rely on the chemical functionalization of conductive materials or electrodes with sequence-specific hybridization probes made of standard oligonucleotides (DNA or RNA) or synthetic analogues (e.g. Peptide Nucleic Acids or PNAs). The robustness of such sensors is mostly influenced by the ability to control the density and orientation of the probe at the surface of the electrode, making the chemistry used for this immobilization a key parameter. This exhaustive review will cover the various strategies to immobilize nucleic acid probes onto different solid electrode materials. Both physical and chemical immobilization techniques will be presented. Their applicability to specific electrode materials and surfaces will also be discussed as well as strategies for passivation of the electrode surface as a way of preventing electrode fouling and reducing nonspecific binding.
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Affiliation(s)
- Xiaotong Meng
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK. https://in.linkedin.com/https://www.linkedin.com/profile/view?id=xiaotong-meng-888IC
| | - Danny O'Hare
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
| | - Sylvain Ladame
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
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5
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Jaradi B, Das T, Koo KM. Design and Analytical Evaluation of a Rapid Plasma Screening Assay for Circulating Human Papillomavirus DNA via Thermostable Enzyme Chemistries. Anal Chem 2023; 95:11172-11180. [PMID: 37441723 DOI: 10.1021/acs.analchem.3c02528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/15/2023]
Abstract
Infection with oncogenic strains of human papillomavirus (HPV), such as HPV-16 and HPV-18, can lead to malignant progression and tumorigenesis. As an adjunct to traditional invasive tissue sampling methods, the use of modern thermostable enzyme chemistries can aid in the development of innovative assay workflows to extract and detect circulating HPV DNA (cHPV-DNA) in liquid biopsies. In this work, we first successfully generated a model system to replicate fragmented cHPV-DNA in human plasma. Using this model system, we designed a novel thermostable enzyme chemistry-based cHPV-DNA assay for rapid clinical HPV screening and robustly evaluated its analytical assay performance. Our findings demonstrated that the use of thermostable enzymes provided faster cHPV-DNA extraction and amplification, leading to an overall three-fold improvement in overall assay time as compared to the current standard assay workflow and achieving clinically relevant levels of analytical specificity, sensitivity, and precision for accurate cHPV-DNA detection with excellent 100% sensitivity and specificity in contrived human plasma specimens. In summary, we have devised a rapid laboratory workflow to facilitate the emerging use of liquid biopsies for minimally invasive, rapid, and scalable HPV DNA testing. With facile assay modifications, our thermostable enzyme-based cHPV-DNA assay can be utilized for the detection of other clinically high-risk HPV genotypes.
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Affiliation(s)
- Binny Jaradi
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
| | - Tulika Das
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kevin M Koo
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, Brisbane, Queensland 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Herston, Queensland 4029, Australia
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6
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Qian Y, Gu Y, Deng J, Cai Z, Wang Y, Zhou R, Zhu D, Lu H, Wang Z. Combined SERS Microfluidic Chip with Gold Nanocone Array for Effective Early Lung Cancer Prognosis in Mice Model. Int J Nanomedicine 2023; 18:3429-3442. [PMID: 37383221 PMCID: PMC10295598 DOI: 10.2147/ijn.s411395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/19/2023] [Indexed: 06/30/2023] Open
Abstract
Introduction As the most common malignant tumor in the world, the prognosis of patients with advanced lung cancer remains poor even after treatment. There are many prognostic marker assays available, but there is still more room for the development of high-throughput and sensitive detection of circulating tumor DNA (ctDNA). Surface-enhanced Raman spectroscopy (SERS), a spectroscopic detection method that has received wide attention in recent years, can achieve exponential amplification of Raman signals by using different metallic nanomaterials. Integrating SERS with signal amplification strategy into the microfluidic chip and applying it to ctDNA detection is expected to be an effective tool for the prognosis of lung cancer treatment effect in the future. Methods To construct a high-throughput SERS microfluidic chip integrated with enzyme-assisted signal amplification (EASA) and catalytic hairpin self-assembly (CHA) signal amplification strategies, using hpDNA-functionalized Au nanocone arrays (AuNCAs) as capture substrates and cisplatin-treated lung cancer mice to simulate the detection environment for sensitive detection of ctDNA in serum of lung cancer patients after treatment. Results The SERS microfluidic chip constructed by this scheme, with two reaction zones, can simultaneously and sensitively detect the concentrations of four prognostic ctDNAs in the serum of three lung cancer patients with a limit of detection (LOD) as low as the aM level. The results of the ELISA assay are consistent with this scheme, and its accuracy is guaranteed. Conclusion This high-throughput SERS microfluidic chip has high sensitivity and specificity in the detection of ctDNA. This could be a potential tool for prognostic assessment of lung cancer treatment efficacy in future clinical applications.
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Affiliation(s)
- Yayun Qian
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yuexing Gu
- Institute of Translational Medicine, Medical College, Yangzhou University, Yangzhou, People’s Republic of China
| | - Jialin Deng
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People’s Republic of China
| | - Zhaoying Cai
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People’s Republic of China
| | - Yang Wang
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People’s Republic of China
| | - Ruoyu Zhou
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People’s Republic of China
| | - Dongxu Zhu
- Jiangsu Key Laboratory of Integrated Traditional Chinese and Western Medicine for Prevention and Treatment of Senile Diseases, Yangzhou University, Yangzhou, People’s Republic of China
| | - Hongmei Lu
- Department of Pathology, Yangzhou Maternal and Child Health Hospital, Yangzhou, People’s Republic of China
| | - Zheng Wang
- Department of Pathology, The Affiliated Hospital of Yangzhou University, Yangzhou University, Yangzhou, People’s Republic of China
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7
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Multifunctional Hybrid Nanozymes for Magnetic Enrichment and Bioelectrocatalytic Sensing of Circulating Tumor RNA during Minimal Residual Disease Monitoring. Catalysts 2023. [DOI: 10.3390/catal13010178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Iron oxide nanozymes are a form of nanomaterial with both superparamagnetic and enzyme-mimicking properties. Ongoing research efforts have been made to create multifunctional iron oxide hybrid nanozymes with auxiliary properties through biomolecular modifications. Such iron oxide hybrid nanozymes can be useful for rapid and cost-effective analysis of circulating tumor nucleic acids (ctNAs) in patient liquid biopsies during minimal residual disease (MRD) monitoring of cancer recurrence. Herein, the use of streptavidin-modified iron oxide hybrid nanozymes is reported for magnetic enrichment and bioelectrocatalytic sensing of three prostate cancer (PCa) ctRNA biomarkers with high detection specificity and sensitivity (10 copies) over an ultrabroad dynamic range (five orders of magnitude). Furthermore, the feasibility of ctRNA analysis for pre- and post-cancer treatment MRD monitoring is demonstrated using PCa urinary liquid biopsy samples.
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8
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Wu NJW, Aquilina M, Qian BZ, Loos R, Gonzalez-Garcia I, Santini CC, Dunn KE. The Application of Nanotechnology for Quantification of Circulating Tumour DNA in Liquid Biopsies: A Systematic Review. IEEE Rev Biomed Eng 2023; 16:499-513. [PMID: 35302938 DOI: 10.1109/rbme.2022.3159389] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Technologies for quantifying circulating tumour DNA (ctDNA) in liquid biopsies could enable real-time measurements of cancer progression, profoundly impacting patient care. Sequencing methods can be too complex and time-consuming for regular point-of-care monitoring, but nanotechnology offers an alternative, harnessing the unique properties of objects tens to hundreds of nanometres in size. This systematic review was performed to identify all examples of nanotechnology-based ctDNA detection and assess their potential for clinical use. Google Scholar, PubMed, Web of Science, Google Patents, Espacenet and Embase/MEDLINE were searched up to 23rd March 2021. The review identified nanotechnology-based methods for ctDNA detection for which quantitative measures (e.g., limit of detection, LOD) were reported and biologically relevant samples were used. The pre-defined inclusion criteria were met by 66 records. LODs ranged from 10 zM to 50nM. 25 records presented an LOD of 10fM or below. Nanotechnology-based approaches could provide the basis for the next wave of advances in ctDNA diagnostics, enabling analysis at the point-of-care, but none are currently used clinically. Further work is needed in development and validation; trade-offs are expected between different performance measures e.g., number of sequences detected and time to result.
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9
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Chang Y, Wang Y, Zhang J, Xing Y, Li G, Deng D, Liu L. Overview on the Design of Magnetically Assisted Electrochemical Biosensors. BIOSENSORS 2022; 12:bios12110954. [PMID: 36354462 PMCID: PMC9687741 DOI: 10.3390/bios12110954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/27/2022] [Accepted: 10/29/2022] [Indexed: 06/12/2023]
Abstract
Electrochemical biosensors generally require the immobilization of recognition elements or capture probes on the electrode surface. This may limit their practical applications due to the complex operation procedure and low repeatability and stability. Magnetically assisted biosensors show remarkable advantages in separation and pre-concentration of targets from complex biological samples. More importantly, magnetically assisted sensing systems show high throughput since the magnetic materials can be produced and preserved on a large scale. In this work, we summarized the design of electrochemical biosensors involving magnetic materials as the platforms for recognition reaction and target conversion. The recognition reactions usually include antigen-antibody, DNA hybridization, and aptamer-target interactions. By conjugating an electroactive probe to biomolecules attached to magnetic materials, the complexes can be accumulated near to an electrode surface with the aid of external magnet field, producing an easily measurable redox current. The redox current can be further enhanced by enzymes, nanomaterials, DNA assemblies, and thermal-cycle or isothermal amplification. In magnetically assisted assays, the magnetic substrates are removed by a magnet after the target conversion, and the signal can be monitored through stimuli-response release of signal reporters, enzymatic production of electroactive species, or target-induced generation of messenger DNA.
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Affiliation(s)
| | | | | | | | | | | | - Lin Liu
- Correspondence: (D.D.); (L.L.)
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10
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Ghafary Z, Salimi A, Hallaj R. Exploring the Role of 2D-Graphdiyne as a Charge Carrier Layer in Field-Effect Transistors for Non-Covalent Biological Immobilization against Human Diseases. ACS Biomater Sci Eng 2022; 8:3986-4001. [PMID: 35939853 DOI: 10.1021/acsbiomaterials.2c00607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Graphdiyne's (GDY's) outstanding features have made it a novel 2D nanomaterial and a great candidate for electronic gadgets and optoelectronic devices, and it has opened new opportunities for the development of highly sensitive electronic and optical detection methods as well. Here, we testified a non-covalent grafting strategy in which GDY serves as a charge carrier layer and a bioaffinity substrate to immobilize biological receptors on GDY-based field-effect transistor (FET) devices. Firm non-covalent anchoring of biological molecules via pyrene groups and electrostatic interactions in addition to preserved electrical properties of GDY endows it with features of an ultrasensitive and stable detection mechanism. With emerging new forms and extending the subtypes of the already existing fatal diseases, genetic and biological knowledge demands more details. In this regard, we constructed simple yet efficient platforms using GDY-based FET devices in order to detect different kinds of biological molecules that threaten human health. The resulted data showed that the proposed non-covalent bioaffinity assays in GDY-based FET devices could be considered reliable strategies for novel label-free biosensing platforms, which still reach a high on/off ratio of over 104. The limits of detection of the FET devices to detect DNA strands, the CA19-9 antigen, microRNA-155, the CA15-3 antigen, and the COVID-19 antigen were 0.2 aM, 0.04 pU mL-1, 0.11 aM, 0.043 pU mL-1, and 0.003 fg mL-1, respectively, in the linear ranges of 1 aM to 1 pM, 1 pU mL-1 to 0.1 μU mL-1, 1 aM to 1 pM, 1 pU mL-1 to 10 μU mL-1, and 1 fg mL-1 to 10 ng mL-1, respectively. Finally, the extraordinary performance of these label-free FET biosensors with low detection limits, high sensitivity and selectivity, capable of being miniaturized, and implantability for in vivo analysis makes them a great candidate in disease diagnostics and point-of-care testing.
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Affiliation(s)
- Zhaleh Ghafary
- Department of Chemistry, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Abdollah Salimi
- Department of Chemistry, University of Kurdistan, 66177-15175 Sanandaj, Iran.,Research Center for Nanotechnology, University of Kurdistan, 66177-15175 Sanandaj, Iran
| | - Rahman Hallaj
- Department of Chemistry, University of Kurdistan, 66177-15175 Sanandaj, Iran.,Research Center for Nanotechnology, University of Kurdistan, 66177-15175 Sanandaj, Iran
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11
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Wang D, Zhou H, Shi Y, Sun W. A FEN 1-assisted swing arm DNA walker for electrochemical detection of ctDNA by target recycling cascade amplification. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1922-1927. [PMID: 35527509 DOI: 10.1039/d2ay00364c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A flap endonuclease 1 (FEN 1)-assisted swing arm DNA walker was constructed to achieve the signal amplification detection of ctDNA. The MB-labeled hairpin DNA was designed as the track and a long swing-arm DNA strand as the capture probe. The introduction of ctDNA unlocked a helper hairpin DNA, which could be captured to form the DNA duplex walker with the capture probe, and also activated the catalyst hairpin assembly. The DNA duplex walker opened the hairpin track and formed a three-base overlapping DNA structure, which was recognized and cleaved by FEN 1. Driven by the FEN 1 and the high reaction temperature, the DNA walker was initiated to hybridize with the track DNA and release multiple MB-labeled flaps for signal amplification. Owing to the excellent amplification capacity of the target recycling-induced DNA walker and programmed catalysis hairpin assembly, the one-step biosensor showed a linear detection range from 1 fM to 100 pM with a detection limit of 0.33 fM. Moreover, the sensitive detection of ctDNA in serum samples was verified, suggesting its potential application in liquid biopsy for clinical diagnosis.
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Affiliation(s)
- Dongmei Wang
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Huan Zhou
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Yundong Shi
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
| | - Wanjun Sun
- School of Laboratory Medicine, Wannan Medical College, Wuhu, 241000, P. R. China.
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12
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Lázaro A, Maquieira Á, Tortajada-Genaro LA. Discrimination of Single-Nucleotide Variants Based on an Allele-Specific Hybridization Chain Reaction and Smartphone Detection. ACS Sens 2022; 7:758-765. [PMID: 35188365 PMCID: PMC8961872 DOI: 10.1021/acssensors.1c02220] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Massive DNA testing
requires novel technologies to support a sustainable
health system. In recent years, DNA superstructures have emerged as
alternative probes and transducers. We, herein, report a multiplexed
and highly sensitive approach based on an allele-specific hybridization
chain reaction (AS-HCR) in the array format to detect single-nucleotide
variants. Fast isothermal amplification was developed before activating
the HCR process on a chip to work with genomic DNA. The assay principle
was demonstrated, and the variables for integrating the AS-HCR process
and smartphone-based detection were also studied. The results were
compared to a conventional polymerase reaction chain (PCR)-based test.
The developed multiplex method enabled higher selectivity against
single-base mismatch sequences at concentrations as low as 103 copies with a limit of detection of 0.7% of the mutant DNA
percentage and good reproducibility (relative error: 5% for intra-assay
and 17% for interassay). As proof of concept, the AS-HCR method was
applied to clinical samples, including human cell cultures and biopsied
tissues of cancer patients. Accurate identification of single-nucleotide
mutations in KRAS and NRAS genes
was validated, considering those obtained from the reference sequencing
method. To conclude, AS-HCR is a rapid, simple, accurate, and cost-effective
isothermal method that detects clinically relevant genetic variants
and has a high potential for point-of-care demands.
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Affiliation(s)
- Ana Lázaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
| | - Ángel Maquieira
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
| | - Luis A. Tortajada-Genaro
- Instituto Interuniversitario de Investigación de Reconocimiento Molecular y Desarrollo Tecnológico (IDM), Universitat Politècnica de València, Universitat de València, Camino de Vera s/n, 46022 Valencia, Spain
- Unidad Mixta UPV-La Fe, Nanomedicine and Sensors, Av. Fernando Abril Martorell, 46026 Valencia, Spain
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Koo KM, Trau M. Molecular locker probe enrichment of gene fusion variants from matched patient liquid biopsy specimens for magneto-bioelectrocatalytic nanosensing. NANOSCALE 2022; 14:4225-4233. [PMID: 35234786 DOI: 10.1039/d1nr07845c] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The accurate and sensitive analysis of recurrent gene fusion mutant variants in circulating tumor nucleic acids (NAs) of patient liquid biopsy samples is crucial for realizing clinical potential for cancer screening, diagnostics, and therapeutics. Gene fusion analysis is especially challenging in patient liquid biopsy samples because of trace biotarget levels in high non-target background of highly similar native and variant NA sequences. Herein, we describe accurate analysis of three prostate cancer gene fusion mutant variants in matched plasma and urine specimens from real cancer patients and healthy controls (n = 80) by (i) direct locker probe enrichment of multiple gene fusion mutant variants without tedious upstream sample processing; (ii) magneto-bioelectrocatalytic cycling readout using both NA-intercalating and freely diffusive redox probes for superior signal enhancement. For each mutant variant, an ultrabroad dynamic range (10-105 copies) was achieved with enhanced 10 copies (zmol) detection limit. With the combination of locker probe enrichment and magneto-bioelectrocatalytic cycling readout for NA mutant variant analysis, the potential of non-invasive liquid biopsies may be exploited for the benefit of cancer patients.
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Affiliation(s)
- Kevin M Koo
- The University of Queensland Centre for Clinical Research (UQCCR), QLD 4029, Australia.
- XING Applied Research & Assay Development (XARAD) Division, XING Technologies Pty Ltd, QLD 4073, Australia
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, QLD 4072, Australia.
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD 4072, Australia
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14
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Abouali H, Hosseini SA, Purcell E, Nagrath S, Poudineh M. Recent Advances in Device Engineering and Computational Analysis for Characterization of Cell-Released Cancer Biomarkers. Cancers (Basel) 2022; 14:288. [PMID: 35053452 PMCID: PMC8774172 DOI: 10.3390/cancers14020288] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 12/21/2021] [Accepted: 01/04/2022] [Indexed: 02/04/2023] Open
Abstract
During cancer progression, tumors shed different biomarkers into the bloodstream, including circulating tumor cells (CTCs), extracellular vesicles (EVs), circulating cell-free DNA (cfDNA), and circulating tumor DNA (ctDNA). The analysis of these biomarkers in the blood, known as 'liquid biopsy' (LB), is a promising approach for early cancer detection and treatment monitoring, and more recently, as a means for cancer therapy. Previous reviews have discussed the role of CTCs and ctDNA in cancer progression; however, ctDNA and EVs are rapidly evolving with technological advancements and computational analysis and are the subject of enormous recent studies in cancer biomarkers. In this review, first, we introduce these cell-released cancer biomarkers and briefly discuss their clinical significance in cancer diagnosis and treatment monitoring. Second, we present conventional and novel approaches for the isolation, profiling, and characterization of these markers. We then investigate the mathematical and in silico models that are developed to investigate the function of ctDNA and EVs in cancer progression. We convey our views on what is needed to pave the way to translate the emerging technologies and models into the clinic and make the case that optimized next-generation techniques and models are needed to precisely evaluate the clinical relevance of these LB markers.
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Affiliation(s)
- Hesam Abouali
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Seied Ali Hosseini
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
| | - Emma Purcell
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Sunitha Nagrath
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109-2800, USA; (E.P.); (S.N.)
| | - Mahla Poudineh
- Department of Electrical and Computer Engineering, University of Waterloo, Waterloo, ON N2L 3G1, Canada; (H.A.); (S.A.H.)
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15
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Meng Y, Qin N, Hun X. ZnSe nanodisks:Ti 3C 2 MXenes-modified electrode for nucleic acid liquid biopsy with photoelectrochemical strategy. Mikrochim Acta 2021; 189:2. [PMID: 34855037 DOI: 10.1007/s00604-021-05117-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/20/2021] [Indexed: 01/13/2023]
Abstract
ZnSe nanodisks:Ti3C2 MXene complex was prepared for the first time. Based on its remarkable photoelectrochemical performance, combined with the enzyme-free toehold-mediated strand displacement reaction, a photoelectrochemical biosensor for the detection of the non-small-cell cancer biomarker ctDNA KRAS G12D was developed. ZnSe nanodisks were in situ grown on Ti3C2 MXene surface by two-step hydrothermal method. The high conductivity and adjustable band gap of MXene significantly enhanced the photoelectric response of ZnSe. Subsequently, the photoelectrochemical biosensor was prepared by combining with the signal amplification function of p-aminophenol and the enzyme-free toehold-mediated strand displacement reaction on the modified ITO electrode surface. Under the optimized conditions, the linear detection range is 0.5 ~ 100.0 fM, and the detection limit is 0.2 fM, which realizes the sensitive detection of KRAS G12D. The photoelectrochemical biosensor constructed opens up a new pathway for the preparation of new Mxene-based composite materials and the research of photoelectrochemical biosensor. Nucleic acid liquid biopsy with ZnSe nanodisks:Ti3C2 MXene photoelectroactive modified electrode.
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Affiliation(s)
- Yuchan Meng
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Qingdao University of Science and Technology, 266042, Qingdao, People's Republic of China
| | - Nana Qin
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Qingdao University of Science and Technology, 266042, Qingdao, People's Republic of China
| | - Xu Hun
- Key Laboratory of Optic-electric Sensing and Analytical Chemistry for Life Science, Qingdao University of Science and Technology, 266042, Qingdao, People's Republic of China.
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16
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An ultrasensitive biosensor for dual-specific DNA based on deposition of polyaniline on a self-assembled multi-functional DNA hexahedral-nanostructure. Biosens Bioelectron 2021; 179:113066. [PMID: 33571935 DOI: 10.1016/j.bios.2021.113066] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/29/2021] [Accepted: 01/31/2021] [Indexed: 11/21/2022]
Abstract
Kras and Braf are major oncogenes. The mutation of Kras codon 12 or Braf V600E can lead to ovarian carcinoma. The detection of oncogene-related DNAs and their mutations offers solution for early diagnosis of ovarian cancer. Herein, a size-tunable multi-functional DNA hexahedral-nanostructure (DHN) has been rationally designed and modified on the electrode to response to Kras and Braf DNA. The size of DHN is controlled via polyadenines (polyA). The complete self-assembly of DHN depends on the presence of both target DNAs and two assistant probes. Meanwhile, a HRP-mimicking DNAzyme forms in DHN, which catalyzes the polymerization of aniline. The produced polyaniline is utilized as the output signal through differential pulse voltammetry (DPV). The biosensor shows the linear range from 100 fM to 1 μM, with the detection limit of 48.7 fM for Kras gene; and the linear range from 100 fM to 100 nM, with the detection limit of 44.1 fM for Braf gene, respectively. Since the current response depends on both gene sequences, the high specificity of the biosensor endows it to operate in an "OR"-type logic gate to discriminate the mutation of both genes. When Kras codon 12 or Braf V600E mutation happens, the response decreases significantly due to the incomplete formation of DNAzyme in DHN. The practicability of the biosensor has been verified through challenging human serum samples. Thus, it has great potential for clinical diagnosis of ovarian cancer through simultaneous detection of Kras and Braf genes and their mutations.
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Liu ZG, Xiao M, Yang RZ, Zhou QQ, Ye HF, Yi CQ. Multiplexed Detection of Fe3+, Cobalamin and Folate Using Fluorescent Nanoprobe-Based Microarrays and a Smartphone. JOURNAL OF ANALYSIS AND TESTING 2021. [DOI: 10.1007/s41664-021-00163-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Zeng Y, Koo KM, Shen AG, Hu JM, Trau M. Nucleic Acid Hybridization-Based Noise Suppression for Ultraselective Multiplexed Amplification of Mutant Variants. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2006370. [PMID: 33325632 DOI: 10.1002/smll.202006370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Indexed: 06/12/2023]
Abstract
The analysis of mutant nucleic acid (NA) variants can provide crucial clinical and biological insights for many diseases. Yet, existing analysis techniques are generally constrained by nonspecific "noise" signals from excessive wildtype background sequences, especially under rapid isothermal multiplexed target amplification conditions. Herein, the molecular hybridization chemistry between NA bases is manipulated to suppress noise signals and achieve ultraselective multiplexed detection of cancer gene fusion NA variants. Firstly, modified locked NA (LNA) bases are rationally introduced into oligonucleotide sequences as designed "locker probes" for high affinity hybridization to wildtype sequences, leading to enrichment of mutant variants for multiplexed isothermal amplification. Secondly, locker probes are coupled with a customized "proximity-programmed" (SERS) readout which allows precise control of hybridization-based plasmonic signaling to specifically detect multiple target amplicons within a single reaction. Moreover, the use of triple bond Raman reporters endows NA noise signal-free quantification in the Raman silent region (≈1800-2600 cm-1 ). With this dual molecular hybridization-based strategy, ultraselective multiplexed detection of gene fusion NA variants in cancer cellular models is actualized with successful noise suppression of native wildtype sequences. The distinct benefits of isothermal NA amplification and SERS multiplexing ability are simultaneously harnessed.
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Affiliation(s)
- Yi Zeng
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Kevin M Koo
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- XING Technologies Pty Ltd, Sinnamon Park, Brisbane, QLD, 4073, Australia
- The University of Queensland Centre for Clinical Research (UQCCR), Brisbane, QLD, 4029, Australia
| | - Ai-Guo Shen
- School of Printing and Packaging, Wuhan University, Wuhan, 430079, P. R. China
| | - Ji-Ming Hu
- The Centre of Analysis and Measurement of Wuhan University, Wuhan University, Wuhan, 430072, P. R. China
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan, 430072, P. R. China
| | - Matt Trau
- Centre for Personalized Nanomedicine, Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, 4072, Australia
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