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Wang W, Wang W, Chen Y, Lin M, Chen YR, Zeng R, He T, Shen Z, Wu ZS. Superlarge, Rigidified DNA Tetrahedron with a Y-Shaped Backbone for Organizing Biomolecules Spatially and Maintaining Their Full Bioactivity. ACS NANO 2024; 18:18257-18281. [PMID: 38973121 DOI: 10.1021/acsnano.3c13189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
A major impediment to the clinical translation of DNA tiling nanostructures is a technical bottleneck for the programmable assembly of DNA architectures with well-defined local geometry due to the inability to achieve both sufficient structural rigidity and a large framework. In this work, a Y-backbone was inserted into each face to construct a superlarge, sufficiently rigidified tetrahedral DNA nanostructure (called RDT) with extremely high efficiency. In RDT, the spatial size increased by 6.86-fold, and the structural rigidity was enhanced at least 4-fold, contributing to an ∼350-fold improvement in the resistance to nucleolytic degradation even without a protective coating. RDT can be mounted onto an artificial lipid-bilayer membrane with molecular-level precision and well-defined spatial orientation that can be validated using the fluorescence resonance energy transfer (FRET) assay. The spatial orientation of Y-shaped backbone-rigidified RDT is unachievable for conventional DNA polyhedrons and ensures a high level of precision in the geometric positioning of diverse biomolecules with an approximately homogeneous environment. In tests of RDT, surface-confined horseradish peroxidase (HRP) exhibited nearly 100% catalytic activity and targeting aptamer-immobilized gold nanoparticles showed 5.3-fold enhanced cellular internalization. Significantly, RDT exhibited a 27.5-fold enhanced structural stability in a bodily environment and did not induce detectable systemic toxicity.
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Affiliation(s)
- Weijun Wang
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
- College of Chemistry and Food Science, Nanchang Normal University, Nanchang 330032, China
| | - Wenqing Wang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yaxin Chen
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Mengling Lin
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Yan-Ru Chen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Ruijin Zeng
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Tenghang He
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zhifa Shen
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
| | - Zai-Sheng Wu
- Key Laboratory of Laboratory Medicine of the Ministry of Education, Zhejiang Provincial Key Laboratory of Medicine Genetics, School of Laboratory Medicine and Life Sciences, Institute of Functional Nucleic Acids and Personalized Cancer Theranostics, Wenzhou Medical University, Wenzhou 325035, China
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 350108, China
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Ebersole JL, Hasturk H, Huber M, Gellibolian R, Markaryan A, Zhang XD, Miller CS. Realizing the clinical utility of saliva for monitoring oral diseases. Periodontol 2000 2024. [PMID: 39010260 DOI: 10.1111/prd.12581] [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: 03/18/2024] [Revised: 05/01/2024] [Accepted: 05/16/2024] [Indexed: 07/17/2024]
Abstract
In the era of personalized/precision health care, additional effort is being expended to understand the biology and molecular mechanisms of disease processes. How these mechanisms are affected by individual genetics, environmental exposures, and behavioral choices will encompass an expanding role in the future of optimally preventing and treating diseases. Considering saliva as an important biological fluid for analysis to inform oral disease detection/description continues to expand. This review provides an overview of saliva as a diagnostic fluid and the features of various biomarkers that have been reported. We emphasize the use of salivary biomarkers in periodontitis and transport the reader through extant literature, gaps in knowledge, and a structured approach toward validating and determine the utility of biomarkers in periodontitis. A summation of the findings support the likelihood that a panel of biomarkers including both host molecules and specific microorganisms will be required to most effectively identify risk for early transition to disease, ongoing disease activity, progression, and likelihood of response to standard periodontal therapy. The goals would be to develop predictive algorithms that serve as adjunctive diagnostic tools which provide the clinician and patient important information for making informed clinical decisions.
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Affiliation(s)
- Jeffrey L Ebersole
- Department of Biomedical Sciences, School of Dental Medicine, University of Nevada Las Vegas, Las Vegas, Nevada, USA
| | - Hatice Hasturk
- Immunology and Inflammation, Center for Clinical and Translational Research, The ADA Forsyth Institute, Cambridge, Massachusetts, USA
| | - Michaell Huber
- Department of Comprehensive Dentistry, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | | | | | - Xiaohua D Zhang
- Department of Biostatistics, College of Public Health, University of Kentucky, Lexington, Kentucky, USA
| | - Craig S Miller
- Department of Oral Health Practice, College of Dentistry, University of Kentucky, Lexington, Kentucky, USA
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Li D, Huang Q, Wang K. Exonuclease III-propelled DNAzyme walker: an electrochemical strategy for microRNA diagnostics. Mikrochim Acta 2024; 191:173. [PMID: 38436735 DOI: 10.1007/s00604-024-06208-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 01/09/2024] [Indexed: 03/05/2024]
Abstract
MicroRNA detection is crucial for early infectious disease diagnosis and rapid cancer screening. However, conventional techniques like reverse transcription-quantitative polymerase chain reaction, requiring specialized training and intricate procedures, are less suitable for point-of-care analyses. To address this, we've developed a straightforward amplifier based on an exonuclease III (exo III)-propelled DNAzyme walker for sensitive and selective microRNA detection. This amplifier employs a specially designed hairpin probe with two exposed segments for strand recognition. Once the target microRNA is identified by the hairpin's extended single-strand DNA, exo III initiates its digestion, allowing microRNA regeneration and subsequent hairpin probe digestion cycles. This cyclical process produces a significant amount of DNAzyme, leading to a marked reduction in electrochemical signals. The biosensor exhibits a detection range from 10 fM to 100 pM and achieves a detection limit of 5 fM (3σ criterion). Importantly, by integrating an "And logic gate," our system gains the capacity for simultaneous diagnosis of multiple microRNAs, enhancing its applicability in RNA-based disease diagnostics.
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Affiliation(s)
- Dengke Li
- Department of Rehabilitation Medicine, the Affiliated Huaian No.1 People's Hospital of Nanjing Medical University, Huaian, 223300, China.
| | - Qiuyan Huang
- Department of Chemistry, New York University, New York, NY, 10003, USA
| | - Kun Wang
- Department of Physics, New York University, New York, NY, 10003, USA
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Mohammadi A, Chiang S, Li F, Wei F, Lau CS, Aziz M, Ibarrondo FJ, Fulcher JA, Yang OO, Chia D, Kim Y, Wong DT. Direct Detection of 4-Dimensions of SARS-CoV-2: Infection (vRNA), Infectivity (Antigen), Binding Antibody, and Functional Neutralizing Antibody in Saliva. RESEARCH SQUARE 2023:rs.3.rs-3745787. [PMID: 38234820 PMCID: PMC10793499 DOI: 10.21203/rs.3.rs-3745787/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
We developed a 4-parameter clinical assay using Electric Field Induced Release and Measurement (EFIRM) technology to simultaneously assess SARS-CoV-2 RNA (vRNA), nucleocapsid antigen, host binding (BAb) and neutralizing antibody (NAb) levels from a drop of saliva with performance that equals or surpasses current EUA-approved tests. The vRNA and antigen assays achieved lower limit of detection (LOD) of 100 copies/reaction and 3.5 TCID₅₀/mL, respectively. The vRNA assay differentiated between acutely infected (n=10) and infection-naïve patients (n=33) with an AUC of 0.9818, sensitivity of 90%, and specificity of 100%. The antigen assay similarly differentiated these patient populations with an AUC of 1.000. The BAb assay detected BAbs with an LOD of 39 pg/mL and distinguished acutely infected (n=35), vaccinated with prior infection (n=13), and vaccinated infection-naïve patients (n=13) from control (n=81) with AUC of 0.9481, 1.000, and 0.9962, respectively. The NAb assay detected NAbs with an LOD of 31.6 Unit/mL and differentiated between COVID-19 recovered or vaccinated patients (n=31) and pre-pandemic controls (n=60) with an AUC 0.923, sensitivity of 87.10%, and specificity of 86.67%. Our multiparameter assay represents a significant technological advancement to simultaneously address SARS-CoV-2 infection and immunity, and it lays the foundation for tackling potential future pandemics.
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Affiliation(s)
- Aida Mohammadi
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Samantha Chiang
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Feng Li
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Fang Wei
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Mohammad Aziz
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Francisco J. Ibarrondo
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Jennifer A. Fulcher
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Otto O. Yang
- Division of Infectious Diseases, Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - David Chia
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - Yong Kim
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
| | - David T.W. Wong
- School of Dentistry, University of California Los Angeles, Los Angeles, CA, USA
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5
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Nonaka T, Wong DTW. Saliva diagnostics: Salivaomics, saliva exosomics, and saliva liquid biopsy. J Am Dent Assoc 2023; 154:696-704. [PMID: 37500232 PMCID: PMC11390004 DOI: 10.1016/j.adaj.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Revised: 04/12/2023] [Accepted: 05/11/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Each day, humans produce approximately 0.5 through 1.5 liters of saliva, a biofluid that is rich in biological omic constituents. Our lack of understanding how omic biomarkers migrate from diseased tissue to the saliva has impeded the clinical translation of saliva testing. Although such biomarkers must be conveyed via the vascular and lymphatic systems to the salivary glands, the molecular mechanisms that underlie this transport remain unclear. Although COVID-19 highlighted the need for rapid and reliable testing for infectious diseases, it represents only one of the many health conditions that potentially can be diagnosed using a saliva sample. TYPES OF STUDIES REVIEWED The authors discuss salivaomics, saliva exosomics, and the mechanisms on which saliva diagnostics are based and introduce a novel electrochemical sensing technology that may be exploited for saliva liquid biopsy. RESULTS The utility of saliva for screening for lung cancer is under investigation. Saliva testing may be used to stratify patients, monitor treatment response, and detect disease recurrence. The authors also highlight the landscapes of saliva-based SARS-CoV-2 testing and ultrashort cell-free DNA and outline how these fields are likely to evolve in the near future. PRACTICAL IMPLICATIONS Breakthroughs in the study of saliva research, therefore, will facilitate clinical deployment of saliva-based testing.
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Allegra A, Petrarca C, Di Gioacchino M, Mirabile G, Gangemi S. Electrochemical Biosensors in the Diagnosis of Acute and Chronic Leukemias. Cancers (Basel) 2022; 15:cancers15010146. [PMID: 36612142 PMCID: PMC9817807 DOI: 10.3390/cancers15010146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Until now, morphological assessment with an optical or electronic microscope, fluorescence in situ hybridization, DNA sequencing, flow cytometry, polymerase chain reactions, and immunohistochemistry have been employed for leukemia identification. Nevertheless, despite their numerous different vantages, it is difficult to recognize leukemic cells correctly. Recently, the electrochemical evaluation with a nano-sensing interface seems an attractive alternative. Electrochemical biosensors measure the modification in the electrical characteristics of the nano-sensing interface, which is modified by the contact between a biological recognition element and the analyte objective. The implementation of nanosensors is founded not on single nanomaterials but rather on compilating these components efficiently. Biosensors able to identify the molecules of deoxyribonucleic acid are defined as DNA biosensors. Our review aimed to evaluate the literature on the possible use of electrochemical biosensors for identifying hematological neoplasms such as acute promyelocytic leukemia, acute lymphoblastic leukemia, and chronic myeloid leukemia. In particular, we focus our attention on using DNA electrochemical biosensors to evaluate leukemias.
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Affiliation(s)
- Alessandro Allegra
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
| | - Claudia Petrarca
- Department of Medicine and Aging Sciences, G. D’Annunzio University, 66100 Chieti, Italy
- Center for Advanced Studies and Technology, G. D’Annunzio University, 66100 Chieti, Italy
- Correspondence:
| | - Mario Di Gioacchino
- Institute for Clinical Immunotherapy and Advanced Biological Treatments, 65100 Pescara, Italy
| | - Giuseppe Mirabile
- Division of Hematology, Department of Human Pathology in Adulthood and Childhood “Gaetano Barresi”, University of Messina, 98125 Messina, Italy
| | - Sebastiano Gangemi
- Unit of Allergy and Clinical Immunology, Department of Clinical and Experimental Medicine, School of Allergy and Clinical Immunology, University of Messina, 98125 Messina, Italy
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Markandan K, Tiong YW, Sankaran R, Subramanian S, Markandan UD, Chaudhary V, Numan A, Khalid M, Walvekar R. Emergence of infectious diseases and role of advanced nanomaterials in point-of-care diagnostics: a review. Biotechnol Genet Eng Rev 2022:1-89. [PMID: 36243900 DOI: 10.1080/02648725.2022.2127070] [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: 06/08/2022] [Accepted: 09/12/2022] [Indexed: 11/09/2022]
Abstract
Infectious outbreaks are the foremost global public health concern, challenging the current healthcare system, which claims millions of lives annually. The most crucial way to control an infectious outbreak is by early detection through point-of-care (POC) diagnostics. POC diagnostics are highly advantageous owing to the prompt diagnosis, which is economical, simple and highly efficient with remote access capabilities. In particular, utilization of nanomaterials to architect POC devices has enabled highly integrated and portable (compact) devices with enhanced efficiency. As such, this review will detail the factors influencing the emergence of infectious diseases and methods for fast and accurate detection, thus elucidating the underlying factors of these infections. Furthermore, it comprehensively highlights the importance of different nanomaterials in POCs to detect nucleic acid, whole pathogens, proteins and antibody detection systems. Finally, we summarize findings reported on nanomaterials based on advanced POCs such as lab-on-chip, lab-on-disc-devices, point-of-action and hospital-on-chip. To this end, we discuss the challenges, potential solutions, prospects of integrating internet-of-things, artificial intelligence, 5G communications and data clouding to achieve intelligent POCs.
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Affiliation(s)
- Kalaimani Markandan
- Temasek Laboratories, Nanyang Technological University, Nanyang Drive, Singapore
- Faculty of Engineering, Technology and Built Environment, UCSI University, Kuala Lumpur, Malaysia
| | - Yong Wei Tiong
- NUS Environmental Research Institute, National University of Singapore, Engineering Drive, Singapore
| | - Revathy Sankaran
- Graduate School, University of Nottingham Malaysia Campus, Semenyih, Selangor, Malaysia
| | - Sakthinathan Subramanian
- Department of Materials & Mineral Resources Engineering, National Taipei University of Technology (NTUT), Taipei, Taiwan
| | | | - Vishal Chaudhary
- Research Cell & Department of Physics, Bhagini Nivedita College, University of Delhi, New Delhi, India
| | - Arshid Numan
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, Petaling Jaya, Selangor, Malaysia
- Sunway Materials Smart Science & Engineering (SMS2E) Research Cluster School of Engineering and Technology, Sunway University, Selangor, Malaysia
| | - Mohammad Khalid
- Graphene & Advanced 2D Materials Research Group (GAMRG), School of Engineering and Technology, Sunway University, Petaling Jaya, Selangor, Malaysia
- Sunway Materials Smart Science & Engineering (SMS2E) Research Cluster School of Engineering and Technology, Sunway University, Selangor, Malaysia
| | - Rashmi Walvekar
- Department of Chemical Engineering, School of Energy and Chemical Engineering, Xiamen University Malaysia, Sepang, Selangor, Malaysia
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Abstract
Cancer remains one of the leading causes of death, and early detection of this disease is crucial for increasing survival rates. Although cancer can be diagnosed following tissue biopsy, the biopsy procedure is invasive; liquid biopsy provides an alternative that is more comfortable for the patient. While blood, urine, and cerebral spinal fluid can all be used as a source of liquid biopsy, saliva is an ideal source of body fluid that is readily available and easily collected in the most noninvasive manner. Characterization of salivary constituents in the disease setting provides critical data for understanding pathophysiology and the evaluation of diagnostic potential. The aim of saliva diagnostics is therefore to develop a rapid and noninvasive detection of oral and systemic diseases that could be used together with compact analysis systems in the clinic to facilitate point-of-care diagnostics.
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Affiliation(s)
- Taichiro Nonaka
- Department of Cellular Biology and Anatomy, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA;
| | - David T W Wong
- Division of Oral Biology and Medicine, School of Dentistry, University of California, Los Angeles, California;
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Zheng Q, Ji C, Liu R, Xu J, Wang Y, Yang A, Zheng W, Cao J. Detection of soybean transgenic event GTS-40-3-2 using electric field-induced release and measurement (EFIRM). Anal Bioanal Chem 2021; 413:6671-6676. [PMID: 34523013 DOI: 10.1007/s00216-021-03634-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 08/19/2021] [Accepted: 08/23/2021] [Indexed: 01/01/2023]
Abstract
Polymerase chain reaction (PCR) technology has become a standard technique for the detection of genetically modified organisms (GMOs). However, this method requires a PCR amplification process which is both expensive and time-consuming. Herein, we propose electric field-induced release and measurement (EFIRM) technology as an alternative method for GMO screening. The specificity and sensitivity of the EFIRM assay were proven to be comparable to those of the real-time PCR method for detecting genetically modified soybeans. After all the parameters had been evaluated, the actual evaluation of soybean samples from soybean cargoes was performed. An actual EFIRM screening was performed on 157 soybean cargo samples, which had 102 transgenic soybean samples containing the GTS-40-3-2 gene, through a blind trial at the Dalian port of China. Our results showed that 101 transgenic soybean samples were correctly detected, with only one false-negative case, and 55 non-transgenic soybean samples were detected as negative; this demonstrates that the EFIRM assay is an effective, accurate, simple, and economical novel method for detecting transgenic products, which may have a positive impact on the development of rapid on-site GMO monitoring platforms.
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Affiliation(s)
- Qiuyue Zheng
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, 116600, China
| | - Chao Ji
- Laboratory for Quality Control and Traceability of Food, Tianjin Normal University, Tianjin, 300387, People's Republic of China
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, People's Republic of China
| | - Ran Liu
- Technology Center of Dalian Customs District, Dalian, 116001, People's Republic of China
| | - Junyi Xu
- Technology Center of Dalian Customs District, Dalian, 116001, People's Republic of China
| | - Yong Wang
- Tianjin Academy of Agricultural Sciences, Tianjin, 300192, People's Republic of China
| | - Aifu Yang
- Technology Center of Dalian Customs District, Dalian, 116001, People's Republic of China
| | - Wenjie Zheng
- Laboratory for Quality Control and Traceability of Food, Tianjin Normal University, Tianjin, 300387, People's Republic of China.
| | - Jijuan Cao
- Key Laboratory of Biotechnology and Bioresources Utilization of Ministry of Education, College of Life Science, Dalian Minzu University, Dalian, 116600, China.
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10
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Wang GA, Xu J, Traynor SM, Chen H, Eljabu F, Wu X, Yan H, Li F. DNA Balance for Native Characterization of Chemically Modified DNA. J Am Chem Soc 2021; 143:13655-13663. [PMID: 34404208 DOI: 10.1021/jacs.1c05236] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Chemical modification is a powerful approach to expand the chemical diversity and functionality of natural DNA. However, when chemically modified oligonucleotides are employed in DNA-based reactions or structures, it becomes quite difficult to predict, understand, and control their kinetics and thermodynamics. To address this challenge, we introduce a rationally designed DNA balance capable of measuring critical thermodynamic and kinetic properties of chemically modified DNA in their native environment. Our DNA balance is operated using the principle of toehold-exchange, where a panel of weight probes were designed by tuning the lengths of forward and reverse toeholds. Once placed on the DNA balance, the chemical modification will be interrogated using the weight probes to determine changes in both Gibbs free energy and hybridization rate constant. Using cyclic-azobenzene (cAB)-modified DNA as a model system, we demonstrated that our DNA balance could not only measure stable chemical modifications, but also solve more challenging issues where unstable chemical modifications and transient isomerization reactions were involved. We anticipate that our DNA balance will find wide uses for measuring important thermodynamic and kinetic parameters for DNA carrying various chemical modifications, as well as for probing transient chemical changes in DNA.
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Affiliation(s)
- Guan Alex Wang
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Junpeng Xu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Sarah M Traynor
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Haodi Chen
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Fatma Eljabu
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Xinghong Wu
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China
| | - Hongbin Yan
- Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
| | - Feng Li
- Key Laboratory of Green Chemistry and Technology of Ministry of Education, College of Chemistry, Sichuan University, Chengdu, Sichuan 610064, P. R. China.,Department of Chemistry, Centre for Biotechnology, Brock University, St. Catharines, Ontario L2S 3A1, Canada
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11
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Abstract
Pancreatic cancer is the fourth leading cause of cancer death in the United States. Pancreatic cancer presents dismal clinical outcomes in patients, and the incidence of pancreatic cancer has continuously increased to likely become the second most common cause of cancer-related deaths by as early as 2030. One of main reasons for the high mortality rate of pancreatic cancer is the lack of tools for early-stage detection. Current practice in detecting and monitoring therapeutic response in pancreatic cancer relies on imaging analysis and invasive endoscopic examination. Liquid biopsy-based analysis of genetic alterations in biofluids has become a fundamental component in the diagnosis and management of cancers. There is an urgent need for scientific and technological advancement to detect pancreatic cancer early and to develop effective therapies. The development of a highly sensitive and specific liquid biopsy tool will require extensive understanding on the characteristics of circulating tumor DNA in biofluids. Here, we have reviewed the current status of liquid biopsy in detecting and monitoring pancreatic cancers and our understanding of circulating tumor DNA that should be considered for the development of a liquid biopsy tool, which will greatly aid in the diagnosis and healthcare of people at risk.
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12
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Tu M, Wong MY, Sun X, Dai M, Huang R, Chen Y, Lin X, Yang A, Zheng Q, Liao W. Rapid PCR-free meat species mitochondrial DNA identification using Electric Field Induced Release and Measurement (EFIRM®). Anal Chim Acta 2020; 1099:68-74. [PMID: 31986279 DOI: 10.1016/j.aca.2019.11.051] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 11/17/2022]
Abstract
This work details the usage of EFIRM® (Electric Field Induced Release and Measurement) for PCR-free rapid electrochemical detection of mitochondrial DNA. EFIRM® was able to perform highly sensitive detection of animal species for meat contamination testing without multistep sample lysis, DNA extraction, or PCR amplification steps, demonstrating the capability to detect the presence of foreign meat species that only constituted 0.1% of the total mass of a food sample (achieving sensitivity equivalent to that of PCR). The EFIRM® strategy utilizes surface immobilized nucleic acid probes that complement to mitochondrial sequence of Ovis Aries, Sus Scrofa, and Bos Taurus and are immobilized in a polypyrrole matrix on a 96-electrode array. Quantification was performed through amperometric measurement of oxidation-reduction reactions on a streptavidin-peroxidase enzyme chain that completes the nucleic acid complex. All electrochemical procedures were performed using a high-throughput potentiostat system that allows parallelized electrochemical measurement and interfacing to the 96-electrode array.
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Affiliation(s)
- Michael Tu
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Man Yee Wong
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Xiaoxia Sun
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Minxian Dai
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Renping Huang
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Ying Chen
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Xiaoyan Lin
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA
| | - Aifu Yang
- DaLian Customs District, Dalian, 116001, China
| | | | - Wei Liao
- EZLife Bio Inc, 21250 Califa St, #101, Woodland Hills, CA, 91367, USA.
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13
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Kaczor-Urbanowicz KE, Wei F, Rao SL, Kim J, Shin H, Cheng J, Tu M, Wong DTW, Kim Y. Clinical validity of saliva and novel technology for cancer detection. Biochim Biophys Acta Rev Cancer 2019; 1872:49-59. [PMID: 31152821 PMCID: PMC6692231 DOI: 10.1016/j.bbcan.2019.05.007] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 04/05/2019] [Accepted: 05/14/2019] [Indexed: 12/17/2022]
Abstract
Cancer, a local disease at an early stage, systemically evolves as it progresses by triggering alterations in surrounding microenvironment, disturbing immune surveillance and further disseminating its molecular contents into circulation. This pathogenic characteristic of cancer makes the use of biofluids such as blood/serum/plasma, urine, tear and cerebrospinal fluids credible surrogates harboring tumor tissue-derived molecular alterations for the detection of cancer. Most importantly, a number of recent reports have credentialed the clinical validity of saliva for the detection of systemic diseases including cancers. In this review, we discussed the validity of saliva as credible biofluid and clinical sample type for the detection of cancers. We have presented the molecular constituents of saliva that could mirror the systemic status of our body and recent findings of salivaomics associated with cancers. Recently, liquid biopsy to detect cancer-derived circulating tumor DNA has emerged as a credible cancer-detection tool with potential benefits in screening, diagnosis and also risk management of cancers. We have further presented the clinical validity of saliva for liquid biopsy of cancers and a new technology platform based on electrochemical detection of cancer-derived ctDNA in saliva with superior sensitivity and point-of-care potential. The clinical utilities of saliva for the detection of cancers have been evidenced, but biological underpinning on the existence of molecular signatures of cancer-origin in saliva, such as via exosomal distribution, should be addressed in detail.
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Affiliation(s)
- Karolina Elżbieta Kaczor-Urbanowicz
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Section of Orthodontics, UCLA School of Dentistry, University of California at Los Angeles, United States of America
| | - Fang Wei
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Shannon Liu Rao
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Jinseok Kim
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Heebum Shin
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Jordan Cheng
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America
| | - Michael Tu
- EZLife Bio Inc., 21250 Califa St #101, Woodland Hills, CA 9367, United States of America
| | - David T W Wong
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Jonsson Comprehensive Cancer Center, United States of America.
| | - Yong Kim
- Center for Oral and Head/Neck Oncology Research, School of Dentistry, University of California at Los Angeles, United States of America; UCLA's Jonsson Comprehensive Cancer Center, United States of America.
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14
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Eftekhari A, Hasanzadeh M, Sharifi S, Dizaj SM, Khalilov R, Ahmadian E. Bioassay of saliva proteins: The best alternative for conventional methods in non-invasive diagnosis of cancer. Int J Biol Macromol 2018; 124:1246-1255. [PMID: 30513307 DOI: 10.1016/j.ijbiomac.2018.11.277] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 11/28/2018] [Accepted: 11/30/2018] [Indexed: 12/29/2022]
Abstract
Non-invasive diagnosis of cancer is often the key to effective treatment and patient survival. Saliva as a multi-constituent oral fluid comprises various disease signaling biomarkers, holds great potential for early-stage cancer diagnostics with cost-effective and easy collection, storage, transport and processing. Therefore, detection of biomarkers and proteins in the saliva samples is highly demand. The current review was performed using reliable internet database (mainly PubMed) to provide an overview of the most recent developments on non-invasive diagnosis of cancers in saliva and highlights main challenges and future prospects in sensing of the salivary biomarkers. The conventional detection methods of cancer biomarkers in saliva is discussed in the paper, however, the main focus is on non-invasive diagnosis of cancers in saliva using immunosensing (electrochemical, optical, piezoelectric), DNA based sensors, aptasensors and peptide based bio-assays The reviewed literature revealed that non-invasive cancer detection methods using the mentioned biosensors and without any processing of saliva sample offers a quick, sensitive, specific and cost effective analytical tool. Besides, salivary based detection methods can be used for simultaneous detection of panels of disease specific biomarkers in a real time manner or as home testing kits in near future.
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Affiliation(s)
- Aziz Eftekhari
- Pharmacology and Toxicology Department, Maragheh University of Medical Sciences, Maragheh, Iran
| | - Mohammad Hasanzadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 51664, Iran.
| | - Simin Sharifi
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Solmaz Maleki Dizaj
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Rovshan Khalilov
- Joint Ukrainian-Azerbaijan International Research and Education Center of Nanobiotechnology and Functional Nanosystems, Drohobych Ukraine & Baku, Azerbaijan, Institute of Radiation Problems of NAS Azerbaijan, Baku, Azerbaijan
| | - Elham Ahmadian
- Dental and Periodontal Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Students' Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.
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15
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Koo B, Yorita AM, Schmidt JJ, Monbouquette HG. Amplification-free, sequence-specific 16S rRNA detection at 1 aM. LAB ON A CHIP 2018; 18:2291-2299. [PMID: 29987290 DOI: 10.1039/c8lc00452h] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
A nucleic acid amplification-free, optics-free platform has been demonstrated for sequence-specific detection of Escherichia coli (E. coli) 16S rRNA at 1 aM (10-18 M) against a 106-fold (1 pM) background of Pseudomonas putida (P. putida) RNA. This work was driven by the need for simple, rapid, and low cost means for species-specific bacterial detection at low concentration. Our simple, conductometric sensing device functioned by detecting blockage of a nanopore fabricated in a sub-micron-thick glass membrane. Upon sequence-specific binding of target 16S rRNA, otherwise charge-neutral, PNA oligonucleotide probe-polystyrene bead conjugates become electrophoretically mobile and are driven to the glass nanopore of lesser diameter, which is blocked, thereby generating a large, sustained and readily observable step decrease in ionic current. No false positive signals were observed with P. putida RNA when this device was configured to detect E. coli 16S rRNA. Also, when a universal PNA probe complementary to the 16S rRNA of both E. coli and P. putida was conjugated to beads, a positive response to rRNA of both bacterial species was observed. Finally, the device readily detected E. coli at 10 CFU mL-1 in a 1 mL sample, also against a million-fold background of viable P. putida. These results suggest that this new device may serve as the basis for small, portable, low power, and low-cost systems for rapid detection of specific bacterial species in clinical samples, food, and water.
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Affiliation(s)
- Bonhye Koo
- Chemical and Biomolecular Engineering Department, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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16
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Gao X, Wang X, Li Y, He J, Yu HZ. Exonuclease I-Hydrolysis Assisted Electrochemical Quantitation of Surface-Immobilized DNA Hairpins and Improved HIV-1 Gene Detection. Anal Chem 2018; 90:8147-8153. [DOI: 10.1021/acs.analchem.8b01445] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Xiaoyi Gao
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - Xinglin Wang
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yunchao Li
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Jiale He
- Department of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Hua-Zhong Yu
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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17
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Wang X, Lai W, Man T, Qu X, Li L, Chandrasekaran AR, Pei H. Bio-surface engineering with DNA scaffolds for theranostic applications. NANOFABRICATION 2018. [DOI: 10.1515/nanofab-2018-0001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Biosensor design is important to bioanalysis yet challenged by the restricted target accessibility at the biomolecule-surface (bio-surface). The last two decades have witnessed the appearance of various “art-like” DNA nanostructures in one, two, or three dimensions, and DNA nanostructures have attracted tremendous attention for applications in diagnosis and therapy due to their unique properties (e.g., mechanical flexibility, programmable control over their shape and size, easy and high-yield preparation, precise spatial addressability and biocompatibility). DNA nanotechnology is capable of providing an effective approach to control the surface functionality, thereby increasing the molecular recognition ability at the biosurface. Herein, we present a critical review of recent progress in the development of DNA nanostructures in one, two and three dimensions and highlight their biological applications including diagnostics and therapeutics. We hope that this review provides a guideline for bio-surface engineering with DNA nanostructures.
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18
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Yang F, Zuo X, Fan C, Zhang XE. Biomacromolecular nanostructures-based interfacial engineering: from precise assembly to precision biosensing. Natl Sci Rev 2018. [DOI: 10.1093/nsr/nwx134] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Abstract
Biosensors are a type of important biodevice that integrate biological recognition elements, such as enzyme, antibody and DNA, and physical or chemical transducers, which have revolutionized clinical diagnosis especially under the context of point-of-care tests. Since the performance of a biosensor depends largely on the bio–solid interface, design and engineering of the interface play a pivotal role in developing quality biosensors. Along this line, a number of strategies have been developed to improve the homogeneity of the interface or the precision in regulating the interactions between biomolecules and the interface. Especially, intense efforts have been devoted to controlling the surface chemistry, orientation of immobilization, molecular conformation and packing density of surface-confined biomolecular probes (proteins and nucleic acids). By finely tuning these surface properties, through either gene manipulation or self-assembly, one may reduce the heterogeneity of self-assembled monolayers, increase the accessibility of target molecules and decrease the binding energy barrier to realize high sensitivity and specificity. In this review, we summarize recent progress in interfacial engineering of biosensors with particular focus on the use of protein and DNA nanostructures. These biomacromolecular nanostructures with atomistic precision lead to highly regulated interfacial assemblies at the nanoscale. We further describe the potential use of the high-performance biosensors for precision diagnostics.
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Affiliation(s)
- Fan Yang
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
- School of Laboratory Medicine, Hubei University of Chinese Medicine, Wuhan 430065, China
| | - Xiaolei Zuo
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chunhai Fan
- Division of Physical Biology & Bioimaging Center, Shanghai Synchrotron Radiation Facility, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xian-En Zhang
- National Key Laboratory of Biomacromolecules, CAS Excellence Center for Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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19
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Abstract
Although the type and amount of salivary components are influenced by many factors, due to easy, quick, cheap, and noninvasive sampling method alongside with the existence of the vast majority of the substances found in peripheral blood and urine in it, in recent years saliva has been considered as an ideal biofluid for disease research. Salivary circular RNA (circRNA), as an endogenous RNA molecule with a great variety of regulatory potency, is becoming a novel focus for detecting wide range of local or systemic diseases. Expectantly, with characterization of many more circRNAs in saliva, their motifs, and target sites, they can be used routinely in personalized medicine.
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Affiliation(s)
- Farinaz Jafari Ghods
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey.
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20
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Hasanzadeh M, Shadjou N, de la Guardia M. Non-invasive diagnosis of oral cancer: The role of electro-analytical methods and nanomaterials. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.04.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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21
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Pu Q, Li J, Qiu J, Yang X, Li Y, Yin D, Zhang X, Tao Y, Sheng S, Xie G. Universal ratiometric electrochemical biosensing platform based on mesoporous platinum nanocomposite and nicking endonuclease assisted DNA walking strategy. Biosens Bioelectron 2017; 94:719-727. [PMID: 28395255 DOI: 10.1016/j.bios.2017.03.062] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 03/19/2017] [Accepted: 03/30/2017] [Indexed: 01/21/2023]
Abstract
The occurrence and development of many complex diseases are associated with various molecules, whose contents are rarely in the early stage of the disease. Thus a universal platform for the ultrasensitive detection of multilevel biomarkers should be developed. In this study, we introduced an electrochemical biosensing system based on nicking endonuclease (Nt.BbvCI) assisted DNA walking strategy. We successfully constructed a universal signal-off-on ratiometric electrochemical biosensor for various biomolecules, including small molecules, nucleic acids, and proteins, by progressively optimizing the schematics (schemes 1, 2, and 3). The MB-hairpin probes (MB-HPs) acted as a signal-off probe, and nanocomposites (MPNs@DOX@DNA2) acted as a conventional signal-on probe (scheme 3). With the aid of the MPNs@DOX@DNA2 and Nt.BbvCI assisted DNA walking mechanism, the designed ratiometric electrochemical biosensor showed a high sensitivity and broad detection range. In addition, the proposed method can be utilized to detect diverse targets quantitatively by changing the sequence of aptamers under optimum experimental conditions. Furthermore, it has been widely proved to realize well-accepted signal response in identifying complex samples, thereby resulting in an wide prospect for bioanalysis and clinical diagnosis.
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Affiliation(s)
- Qinli Pu
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Junlong Li
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Juhui Qiu
- State Key Laboratory of Membrane Biology, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, PR China
| | - Xuanhua Yang
- Department of Gastrointestinal Surgery, Second Clinical Medical Institution of North Sichuan Medical College. Nanchong Central Hospital, Nanchong, Sichuan 637000, PR China
| | - Yi Li
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Dan Yin
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Xinyuan Zhang
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Yiyi Tao
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China
| | - Shangchun Sheng
- The No.2 Peoples' Hospital of Yibin, Sichuan 644000, PR China
| | - Guoming Xie
- Key Laboratory of Laboratory Medical Diagnostics of Education, Department of Laboratory Medicine, Chongqing Medical University, Chongqing 400016, PR China.
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22
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Campuzano S, Yánez-Sedeño P, Pingarrón JM. Electrochemical bioaffinity sensors for salivary biomarkers detection. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2016.10.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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23
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Esfandiari L, Wang S, Wang S, Banda A, Lorenzini M, Kocharyan G, Monbouquette HG, Schmidt JJ. PCR-Independent Detection of Bacterial Species-Specific 16S rRNA at 10 fM by a Pore-Blockage Sensor. BIOSENSORS-BASEL 2016; 6:bios6030037. [PMID: 27455337 PMCID: PMC5039656 DOI: 10.3390/bios6030037] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 07/08/2016] [Accepted: 07/15/2016] [Indexed: 11/16/2022]
Abstract
A PCR-free, optics-free device is used for the detection of Escherichia coli (E. coli) 16S rRNA at 10 fM, which corresponds to ~100-1000 colony forming units/mL (CFU/mL) depending on cellular rRNA levels. The development of a rapid, sensitive, and cost-effective nucleic acid detection platform is sought for the detection of pathogenic microbes in food, water and body fluids. Since 16S rRNA sequences are species specific and are present at high copy number in viable cells, these nucleic acids offer an attractive target for microbial pathogen detection schemes. Here, target 16S rRNA of E. coli at 10 fM concentration was detected against a total RNA background using a conceptually simple approach based on electromechanical signal transduction, whereby a step change reduction in ionic current through a pore indicates blockage by an electrophoretically mobilized bead-peptide nucleic acid probe conjugate hybridized to target nucleic acid. We investigated the concentration detection limit for bacterial species-specific 16S rRNA at 1 pM to 1 fM and found a limit of detection of 10 fM for our device, which is consistent with our previous finding with single-stranded DNA of similar length. In addition, no false positive responses were obtained with control RNA and no false negatives with target 16S rRNA present down to the limit of detection (LOD) of 10 fM. Thus, this detection scheme shows promise for integration into portable, low-cost systems for rapid detection of pathogenic microbes in food, water and body fluids.
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Affiliation(s)
- Leyla Esfandiari
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
| | - Siqing Wang
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA 90095, USA.
| | - Siqi Wang
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| | - Anisha Banda
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
| | - Michael Lorenzini
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
| | - Gayane Kocharyan
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
| | - Harold G Monbouquette
- Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA 90095, USA.
| | - Jacob J Schmidt
- Department of Bioengineering, University of California, Los Angeles, CA 90095, USA.
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24
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Li C, Wu D, Hu X, Xiang Y, Shu Y, Li G. One-Step Modification of Electrode Surface for Ultrasensitive and Highly Selective Detection of Nucleic Acids with Practical Applications. Anal Chem 2016; 88:7583-90. [DOI: 10.1021/acs.analchem.6b01250] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Chao Li
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Dan Wu
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Xiaolu Hu
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Yang Xiang
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
| | - Yongqian Shu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing 210029, P. R. China
| | - Genxi Li
- State Key Laboratory
of Pharmaceutical Biotechnology and Collaborative Innovation Center
of Chemistry for Life Sciences, Department of Biochemistry, Nanjing University, Nanjing 210093, P. R. China
- Laboratory of Biosensing Technology, School
of Life Sciences, Shanghai University, Shanghai, 200444, China
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25
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Torrente-Rodríguez RM, Campuzano S, Ruiz-Valdepeñas Montiel V, Gamella M, Pingarrón JM. Electrochemical bioplatforms for the simultaneous determination of interleukin (IL)-8 mRNA and IL-8 protein oral cancer biomarkers in raw saliva. Biosens Bioelectron 2015; 77:543-8. [PMID: 26474095 DOI: 10.1016/j.bios.2015.10.016] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Revised: 09/11/2015] [Accepted: 10/05/2015] [Indexed: 10/22/2022]
Abstract
The development of electrochemical magnetobiosensors for the simultaneous determination of two biomarkers associated with salivary oral cancer, protein IL-8 and its messenger RNA (IL-8 mRNA) associated, in undiluted human saliva samples is reported in this work. The implemented methodology involves the use of functionalized magnetic beads, specific antibodies against IL-8 protein, a specific hairpin DNA sequence for IL-8 mRNA and amperometric detection at disposable dual screen printed carbon electrodes. This methodology exhibits high sensitivity and selectivity for the target analytes providing detection limits of 0.21 nM for IL-8 mRNA and 72.4 pgmL(-1) (far below the clinical established cut-off of 600 pgmL(-1)) for IL-8 protein in undiluted saliva samples. The dual amperometric magnetobiosensor was applied to the direct determination of both biomarkers in spiked raw saliva samples and to determine the endogenous content of IL-8 protein in saliva samples from 7 healthy individuals. The obtained results were statistically in agreement with those provided by a commercial ELISA kit.
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Affiliation(s)
- R M Torrente-Rodríguez
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - S Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - V Ruiz-Valdepeñas Montiel
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - M Gamella
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
| | - J M Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas, Universidad Complutense de Madrid, E-28040 Madrid, Spain.
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26
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Zhu X, Li J, He H, Huang M, Zhang X, Wang S. Application of nanomaterials in the bioanalytical detection of disease-related genes. Biosens Bioelectron 2015; 74:113-33. [PMID: 26134290 DOI: 10.1016/j.bios.2015.04.069] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Revised: 04/09/2015] [Accepted: 04/21/2015] [Indexed: 12/15/2022]
Abstract
In the diagnosis of genetic diseases and disorders, nanomaterials-based gene detection systems have significant advantages over conventional diagnostic systems in terms of simplicity, sensitivity, specificity, and portability. In this review, we describe the application of nanomaterials for disease-related genes detection in different methods excluding PCR-related method, such as colorimetry, fluorescence-based methods, electrochemistry, microarray methods, surface-enhanced Raman spectroscopy (SERS), quartz crystal microbalance (QCM) methods, and dynamic light scattering (DLS). The most commonly used nanomaterials are gold, silver, carbon and semiconducting nanoparticles. Various nanomaterials-based gene detection methods are introduced, their respective advantages are discussed, and selected examples are provided to illustrate the properties of these nanomaterials and their emerging applications for the detection of specific nucleic acid sequences.
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Affiliation(s)
- Xiaoqian Zhu
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Jiao Li
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Hanping He
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China.
| | - Min Huang
- Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Xiuhua Zhang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
| | - Shengfu Wang
- Hubei Collaborative Innovation Center for Advanced Organic Chemical Materials, Ministry of Education Key Laboratory for the Synthesis and Application of Organic Functional Molecules, College of Chemistry and Chemical Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China; Ministry-of-Education Key Laboratory for the Green Preparation and Application of Functional Materials, College of Materials Science and Engineering, Hubei University, Youyi Road 368, Wuchang, Wuhan, Hubei 430062, PR China
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27
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Majem B, Rigau M, Reventós J, Wong DT. Non-coding RNAs in saliva: emerging biomarkers for molecular diagnostics. Int J Mol Sci 2015; 16:8676-98. [PMID: 25898412 PMCID: PMC4425103 DOI: 10.3390/ijms16048676] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 04/02/2015] [Accepted: 04/08/2015] [Indexed: 01/05/2023] Open
Abstract
Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, which are extensively supplied by blood. Therefore, molecules such as proteins, DNA, RNA, etc., present in plasma could be also present in saliva. Many studies have reported that saliva body fluid can be useful for discriminating several oral diseases, but also systemic diseases including cancer. Most of these studies revealed messenger RNA (mRNA) and proteomic biomarker signatures rather than specific non-coding RNA (ncRNA) profiles. NcRNAs are emerging as new regulators of diverse biological functions, playing an important role in oncogenesis and tumor progression. Indeed, the small size of these molecules makes them very stable in different body fluids and not as susceptible as mRNAs to degradation by ribonucleases (RNases). Therefore, the development of a non-invasive salivary test, based on ncRNAs profiles, could have a significant applicability to clinical practice, not only by reducing the cost of the health system, but also by benefitting the patient. Here, we summarize the current status and clinical implications of the ncRNAs present in human saliva as a source of biological information.
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Affiliation(s)
- Blanca Majem
- Research Unit in Biomedicine and Translational Oncology, Lab 209, Collserola Building, Vall Hebron Research Institute (VHIR) and University Hospital, Pg. Vall Hebron 119-129, 08035 Barcelona, Spain.
| | - Marina Rigau
- Research Unit in Biomedicine and Translational Oncology, Lab 209, Collserola Building, Vall Hebron Research Institute (VHIR) and University Hospital, Pg. Vall Hebron 119-129, 08035 Barcelona, Spain.
| | - Jaume Reventós
- Research Unit in Biomedicine and Translational Oncology, Lab 209, Collserola Building, Vall Hebron Research Institute (VHIR) and University Hospital, Pg. Vall Hebron 119-129, 08035 Barcelona, Spain.
- IDIBELL-Bellvitge Biomedical Research Institute & Universitat Internacional de Catalunya, 08908 Barcelona, Spain.
| | - David T Wong
- Center for Oral/Head & Neck Oncology Research, University of California, Los Angeles, CA 90095, USA.
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Wong DTW. Salivary extracellular noncoding RNA: emerging biomarkers for molecular diagnostics. Clin Ther 2015; 37:540-51. [PMID: 25795433 DOI: 10.1016/j.clinthera.2015.02.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/17/2015] [Indexed: 01/05/2023]
Abstract
Saliva is a complex body fluid that comprises secretions from the major and minor salivary glands, nourished by body's vasculature. Although many circulatory molecules (DNA, RNA, and proteins) can also be present in saliva, saliva harbors unique molecular constituents that can be discriminatory for oral and systemic disease screening and detection. Many studies have reported that salivary constituents can discriminate oral diseases (oral cancer and Sjögren's syndrome) and also systemic diseases (lung cancer, breast cancer, pancreatic cancer, and ovarian cancer). Noncoding RNAs (ncRNAs) are emerging new regulators of diverse biological functions, playing important roles in oncogenesis and tumor progression. Indeed, the short size of these molecules makes them stable in different body fluids such as urine, blood, and saliva, being not as susceptible as mRNAs to degradation by RNases. Here, the current status and clinical implications of the ncRNAs present in human saliva are reviewed for translational applications and basic biological research. The development of noninvasive salivary test (based on ncRNAs profiles) for disease detection could have effective applications into the clinical context with a translational significance as emerging molecular biomarkers for non-invasively disease detection, not only by reducing the cost to the health care system but also by benefitting patients.
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Affiliation(s)
- David T W Wong
- Division of Oral Biology, School of Dentistry; Jonnson Comprehensive Cancer Center, Department of Head and Neck Surgery, David Geffen School of Medicine; School of Engineering, University of California Los Angeles, Los Angeles, California.
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Yang Y, Li C, Yin L, Liu M, Wang Z, Shu Y, Li G. Enhanced charge transfer by gold nanoparticle at DNA modified electrode and its application to label-free DNA detection. ACS APPLIED MATERIALS & INTERFACES 2014; 6:7579-7584. [PMID: 24734899 DOI: 10.1021/am500912m] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Rational utilization of nanomaterials to construct electrochemical nucleic acid sensors has attracted large attention in recent years. In this work, we systematically interrogate the interaction between gold nanoparticles (GNPs) and single-strand DNA (ssDNA) immobilized on an electrode surface and then take advantage of the ultrahigh charge-transfer efficiency of GNPs to develop a novel DNA sensing method. Specifically, ssDNA modified gold electrode can adsorb GNPs because of the interaction between gold and nitrogen-containing bases; thus, the negative electrochemical species [Fe(CN)6](3-/4-) may transfer electrons to electrode through adsorbed GNPs. In the presence of target DNA, the formed double-strand DNA (dsDNA) cannot capture GNPs onto the electrode surface and the dsDNA may result in a large charge-transfer resistance owing to the negatively charged phosphate backbones of DNA. So a simple but sensitive method for the detection of target DNA can be developed by using GNPs without any requirement of modification. Experimental results demonstrate that the electrochemical method we have proposed in this work can detect as low as 1 pM breast cancer gene BRCA1 in a 10 μL sample volume without any signal amplification process or the involvement of other synthesized complex, which may provide an alternative for cancer DNA detection. This method may also be generalized for detecting a spectrum of targets using functional DNA (aptamer, metal-specific oligonucleotide, or DNAzyme) in the future.
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Affiliation(s)
- Yucai Yang
- Department of Oncology, The Second Affiliated Hospital of Nanjing Medical University , Nanjing 210011, P. R. China
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Jin B, Wang P, Mao H, Hu B, Zhang H, Cheng Z, Wu Z, Bian X, Jia C, Jing F, Jin Q, Zhao J. Multi-nanomaterial electrochemical biosensor based on label-free graphene for detecting cancer biomarkers. Biosens Bioelectron 2014; 55:464-9. [DOI: 10.1016/j.bios.2013.12.025] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 12/03/2013] [Accepted: 12/10/2013] [Indexed: 10/01/2022]
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Pei H, Zuo X, Zhu D, Huang Q, Fan C. Functional DNA nanostructures for theranostic applications. Acc Chem Res 2014; 47:550-9. [PMID: 24380626 DOI: 10.1021/ar400195t] [Citation(s) in RCA: 301] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
There has been tremendous interest in constructing nanostructures by exploiting the unparalleled ability of DNA molecules in self-assembly. We have seen the appearance of many fantastic, "art-like" DNA nanostructures in one, two, or three dimensions during the last two decades. More recently, much attention has been directed to the use of these elegant nanoobjects for applications in a wide range of areas. Among them, diagnosis and therapy (i.e., theranostics) are of particular interest given the biological nature of DNA. One of the major barricades for the biosensor design lies in the restricted target accessibility at the solid-water interface. DNA nanotechnology provides a convenient approach to well control the biomolecule-confined surface to increase the ability of molecular recognition at the biosensing interface. For example, tetrahedral DNA nanostructures with thiol modifications can be self-assembled at the gold surface with high reproducibility. Since DNA tetrahedra are highly rigid and well-defined structures with atomic precision and versatile functionality, they provide scaffolds for anchoring of a variety of biomolecular probes (DNA, aptamers, peptides, and proteins) for biosensing. Significantly, this DNA nanostructure-based biosensing platform greatly increases target accessibility and improves the sensitivity for various types of molecular targets (DNA, RNA, proteins, and small molecules) by several orders of magnitude. In an alternative approach, DNA nanostructures provide a framework for the development of dynamic nanosensors that can function inside the cell. DNA tetrahedra are found to be facilely cell permeable and can sense and image specific molecules in cells. More importantly, these DNA nanostructures can be efficient drug delivery nanocarriers. Since they are DNA molecules by themselves, they have shown excellent cellular biocompatibility with minimal cytotoxicity. As an example, DNA tetrahedra tailored with CpG oligonucleotide drugs have shown greatly improved immunostimulatory effects that makes them a highly promising nanomedicine. By taking them together, we believe these functionalized DNA nanostructures can be a type of intelligent theranostic nanodevice for simultaneous sensing, diagnosis, and therapy inside the cell.
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Affiliation(s)
- Hao Pei
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Xiaolei Zuo
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Dan Zhu
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Qing Huang
- Division of Physical Biology, and Bioimaging Center, Shanghai Synchrotron Radiation Facility, CAS Key Laboratory of Microscale 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 Laboratory of Microscale Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Quadratic isothermal amplification for the detection of microRNA. Nat Protoc 2014; 9:597-607. [DOI: 10.1038/nprot.2014.036] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Ge J, Huang ZM, Xi Q, Yu RQ, Jiang JH, Chu X. A novel graphene oxide based fluorescent nanosensing strategy with hybridization chain reaction signal amplification for highly sensitive biothiol detection. Chem Commun (Camb) 2014; 50:11879-82. [DOI: 10.1039/c4cc05309e] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A novel fluorescent nanosensor was developed for detecting biothiols via coupling graphene based fluorescence quenching with T–Hg(ii)–T controlled hybridization chain reaction.
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Affiliation(s)
- Jia Ge
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Zhi-Mei Huang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Qiang Xi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Ru-Qin Yu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Jian-Hui Jiang
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
| | - Xia Chu
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Hunan University
- Changsha, P. R. China
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Ma C, Han D, Shi C. A new isothermal nucleic acid detection strategy mediated by a double-nicked beacon. Chem Commun (Camb) 2014; 50:3799-801. [DOI: 10.1039/c3cc49841g] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Fábryová H, Celec P. On the origin and diagnostic use of salivary RNA. Oral Dis 2013; 20:146-52. [PMID: 23517132 DOI: 10.1111/odi.12098] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2012] [Revised: 02/23/2013] [Accepted: 02/24/2013] [Indexed: 01/09/2023]
Abstract
Saliva as a diagnostic fluid enables non-invasive sampling, which can be performed even by an untrained person. Saliva is, thus, particularly useful for large population screenings, for children, elderly and whenever repeated samplings are needed. Saliva is a plasma filtrate actively modified by the salivary glands. Saliva could replace some routine blood tests in the future. The sources of salivary RNA include oral epithelial cells and oral micro-organisms. Recent developments suggest that using known salivary RNA markers, it is possible to diagnose diseases such as oral carcinoma and other diseases will be added soon. Salivary RNA can be used to identify oral bacteria and to determine the expression of specific genes. On a systemic level, it provides information about the whole oral transcriptome and microbiome. Despite the small amount of salivary RNA, the issues with its isolation have been overcome. Saliva, thus, contains RNA of sufficient quality and quantity for sensitive and specific analyses. Salivary RNA can provide medically relevant information about oral microbiome, oral carcinoma, but also breast and pancreatic cancer and is, thus, a promising tool for future research and clinical diagnostics.
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Affiliation(s)
- H Fábryová
- Institute of Molecular Biomedicine, Comenius University, Bratislava, Slovakia
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Duan R, Zuo X, Wang S, Quan X, Chen D, Chen Z, Jiang L, Fan C, Xia F. Lab in a Tube: Ultrasensitive Detection of MicroRNAs at the Single-Cell Level and in Breast Cancer Patients Using Quadratic Isothermal Amplification. J Am Chem Soc 2013; 135:4604-7. [DOI: 10.1021/ja311313b] [Citation(s) in RCA: 298] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ruixue Duan
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Xiaolei Zuo
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Shutao Wang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Xiyun Quan
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Dongliang Chen
- The Pathology Department of Zhuzhou No. 1 Hospital, Hunan 412000, China
| | - Zhifei Chen
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
| | - Lei Jiang
- Beijing National Laboratory for
Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute
of Chemistry, Chinese Academy of Sciences, Beijing 100190, China
| | - Chunhai Fan
- Laboratory of Physical Biology,
Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Fan Xia
- School of
Chemistry and Chemical
Engineering, Huazhong University of Science and Technology, Wuhan 430074, China
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Labib M, Berezovski MV. Electrochemical aptasensors for microbial and viral pathogens. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2013; 140:155-81. [PMID: 23917779 DOI: 10.1007/10_2013_229] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Aptamers are DNA and RNA oligonucleotides that can bind to a variety of nonnucleic acid targets with high affinity and specificity. Pathogen detection is a promising area in aptamer research. One of its major advantages is the ability of the aptamers to target and specifically differentiate microbial and viral strains without previous knowledge of the membrane-associated antigenic determinants or molecular biomarkers present in that particular microorganism. Electrochemical sensors emerged as a promising field in the area of aptamer research and pathogen detection. An electrochemical sensor is a device that combines a recognition element and an electrochemical transduction unit, where aptamers represent the latest addition to the large catalog of recognition elements. This chapter summarizes and evaluates recent developments of electrochemical aptamer-based sensors for microbial and viral pathogen detection, viability assessment of microorganisms, bacterial typing, identification of epitope-specific aptamers, affinity measurement between aptamers and their respective targets, and estimation of the degree of aptamer protection of oncolytic viruses for therapeutic purposes.
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Affiliation(s)
- Mahmoud Labib
- Department of Chemistry, University of Ottawa, 10 Marie Curie, Ottawa, ON K1N 6N5, Canada
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Olasagasti F, Ruiz de Gordoa JC. Miniaturized technology for protein and nucleic acid point-of-care testing. Transl Res 2012; 160:332-45. [PMID: 22683416 PMCID: PMC7104926 DOI: 10.1016/j.trsl.2012.02.012] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/29/2011] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 01/26/2023]
Abstract
The field of point-of-care (POC) testing technology is developing quickly and producing instruments that are increasingly reliable, while their size is being gradually reduced. Proteins are a common target for POC analyses and the detection of protein markers typically involves immunoassays aimed at detecting different groups of proteins such as tumor markers, inflammation proteins, and cardiac markers; but other techniques can also be used to analyze plasma proteins. In the case of nucleic acids, hybridization and amplification strategies can be used to record electromagnetic or electric signals. These techniques allow for the identification of specific viral or bacterial infections as well as specific cancers. In this review, we consider some of the latest advances in the analysis of specific nucleic acid and protein biomarkers, taking into account their trend toward miniaturization and paying special attention to the technology that can be implemented in future applications, such as lab-on-a-chip instruments.
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Key Words
- poc, point-of-care
- lfi, lateral flow immunochromatography
- psa, prostate-specific antigen
- hcg, human chorionic gonadotropin
- tsh, thyroid-stimulating hormone
- seb, staphylococcal enterotixin b
- fret, förster resonance energy transfer
- mmp, matrix metalloproteinase 9
- bnp, b-type natriuretic peptide
- crp, c-reactive protein
- pdms, polydimethylsiloxane
- ig, immunoglobulin
- hb a1c, hemoglobin a1c
- ag, antigen
- ab, antibody
- tnfα, tumor necrosis factor α
- pct, procalcitonin
- il, interleukin
- pcr, polymerase chain reaction
- ca, cancer antigen
- cea, carcinoembryonic antigen
- nmp, nuclear matrix protein
- s100β, s100 calcium binding protein beta
- elisa, enzyme-linked immunosorbent assay
- vegf, vascular endothelial growth factor
- pmma, methyl methacrylate
- ctni, cardiac troponin i
- egf, epidermal growth factor
- ip, interferon-inducible
- mcp, monocyte chemoattractant protein
- timp-1, tissue inhibitor of matrix metalloproteinase-1
- rantes, regulated upon activation, normal t cell expressed and secreted
- mip-1 β, macrophage inflammatory protein-beta
- ctnt, cardiac troponin t
- hrp, horseradish peroxidase
- si-fet, silicon field-effect-transistor
- afp, alpha fetoprotein
- act, antichymotrypsin
- mia, magnetic immunoassay
- apc, allophycocyanin
- he4, human epididymis protein 4
- tmb, 3,3',5,5'-tetramethylbenzidine
- hp, hairpin
- lamp, loop-mediated isothermal amplification
- mrsa, methicillin resistant staphylococcus aureus
- fmdv, foot-and-mouth disease virus
- mμlamp, multiplex microfluidic lamp
- had, helicase-dependent amplification
- nasba, nucleic acid sequence based amplification
- lfm, lateral flow chromatography microarrays
- hsp, heat shock proteins
- spr, surface plasmon resonance
- mems, micro-electro-mechanical systems
- mimed, magnetic integrated microfluidic electrochemical detectors
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Affiliation(s)
- Felix Olasagasti
- Department of Biochemistry and Molecular Biology, Farmazia Fakultatea/Facultad de Farmacia, UPV-EHU, Gasteiz, Spain.
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Wei F, Cheng S, Korin Y, Reed EF, Gjertson D, Ho CM, Gritsch HA, Veale J. Serum creatinine detection by a conducting-polymer-based electrochemical sensor to identify allograft dysfunction. Anal Chem 2012; 84:7933-7. [PMID: 22881369 PMCID: PMC4364383 DOI: 10.1021/ac3016888] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Kidney transplant recipients who have abnormally high creatinine levels in their blood often have allograft dysfunction secondary to rejection. Creatinine has become the preferred marker for renal dysfunction and is readily available in hospital clinical settings. We developed a rapid and accurate polymer-based electrochemical point-of-care (POC) assay for creatinine detection from whole blood to identify allograft dysfunction. The creatinine concentrations of 19 blood samples from transplant recipients were measured directly from clinical serum samples by the conducting polymer-based electrochemical (EC) sensor arrays. These measurements were compared to the traditional clinical laboratory assay. The time required for detection was <5 min from sample loading. Sensitivity of the detection was found to be 0.46 mg/dL of creatinine with only 40 μL sample in the creatinine concentration range of 0 mg/dL to 11.33 mg/dL. Signal levels that were detected electrochemically correlated closely with the creatinine blood concentration detected by the UCLA Ronald Reagan Medical Center traditional clinical laboratory assay (correlation coefficient = 0.94). This work is encouraging for the development of a rapid and accurate POC device for measuring creatinine levels in whole blood.
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Affiliation(s)
- Fang Wei
- School of Dentistry, Dental Research Institute, University of California, Los Angeles, CA
| | - Scott Cheng
- Keck School of Medicine, Department of Family Medicine, University of Southern California
| | - Yael Korin
- UCLA Immunogenetics Center, Department of Patholgy and Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Elaine F. Reed
- UCLA Immunogenetics Center, Department of Patholgy and Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - David Gjertson
- UCLA Immunogenetics Center, Department of Patholgy and Laboratory Medicine, David Geffen School of Medicine, UCLA
| | - Chih-ming Ho
- Keck School of Medicine, Department of Family Medicine, University of Southern California
| | | | - Jeffrey Veale
- Department of Urology, David Geffen School of Medicine at UCLA
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Affiliation(s)
- Emil Paleček
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
| | - Martin Bartošík
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, 612
65 Brno, Czech Republic
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Lin L, Liu Q, Wang L, Liu A, Weng S, Lei Y, Chen W, Lin X, Chen Y. Enzyme-amplified electrochemical biosensor for detection of PML-RARα fusion gene based on hairpin LNA probe. Biosens Bioelectron 2011; 28:277-83. [PMID: 21840703 DOI: 10.1016/j.bios.2011.07.032] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2011] [Revised: 07/14/2011] [Accepted: 07/14/2011] [Indexed: 01/18/2023]
Abstract
In this study, an enzyme-amplified electrochemical biosensor was developed for detection of the promyelocytic leukemia/retinoic acid receptor alpha (PML/RARα) fusion gene in acute promyelocytic leukemia (APL). This new sensor employs a hairpin locked nucleic acids (LNAs) probe dually labeled with biotin and carboxyfluorescein molecule (FAM). The probe is immobilized at a streptavidin-modified electrode surface via the biotin-streptavidin bridge, and FAM serves as an affinity tag for the peroxidase conjugate binding. Initially, the immobilized hairpin probe was in the "closed" state in the absence of the target, which shielded FAM from being approached by the bulky anti-FAM-HRP conjugate due to the steric effect. Target binding opens the hairpin structure of the probe, the probe undergoes a significant conformational change, forcing FAM away from the electrode. As a result, the FAM label becomes accessible by the anti-FAM-HRP, and the target hybridization event can be sensitively transduced via the enzymatically amplified electrochemical current signal. This new biosensor demonstrates its excellent specificity for single-base mismatch and able to detect as little as 83 fM target DNA even in the presence of human serum. We also employed this sensor to directly detect PCR real sample with satisfactory results.
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Affiliation(s)
- Liqing Lin
- Department of Pharmaceutical Analysis, Faculty of Pharmacy, Fujian Medical University, Fuzhou 350004, China
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Deoxyribonucleic Acid Molecular Design for Electrochemical Biosensors. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2011. [DOI: 10.1016/s1872-2040(10)60449-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Chen J, Zhang J, Guo Y, Li J, Fu F, Yang HH, Chen G. An ultrasensitive electrochemical biosensor for detection of DNA species related to oral cancer based on nuclease-assisted target recycling and amplification of DNAzyme. Chem Commun (Camb) 2011; 47:8004-6. [DOI: 10.1039/c1cc11929j] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Lillehoj PB, Wei F, Ho CM. A self-pumping lab-on-a-chip for rapid detection of botulinum toxin. LAB ON A CHIP 2010; 10:2265-70. [PMID: 20596556 DOI: 10.1039/c004885b] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
A robust poly(dimethylsiloxane) (PDMS) surface treatment was utilized for the development of a self-pumping lab-on-a-chip (LOC) to rapidly detect minute quantities of toxic substances. One such toxin, botulinum neurotoxin (BoNT), is an extremely lethal substance, which has the potential to cause hundreds of thousands of fatalities if as little as a few grams are released into the environment. To prevent such an outcome, a quick (<45 min) and sensitive detection format is needed. We have developed a self-pumping LOC that can sense down to 1 pg of BoNT type A (in a 1 microL sample) within 15 min in an autonomous manner. The key technologies enabling for such a device are a sensitive electrochemical sensor, an optimized fluidic network and a robust hydrophilic PDMS coating, thereby facilitating autonomous delivery of liquid samples for rapid detection. The stability, simplicity and portability of this device make possible for a storable and distributable system for monitoring bioterrorist attacks.
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Affiliation(s)
- Peter B Lillehoj
- Mechanical and Aerospace Engineering department, University of California, Los Angeles, CA, USA
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Hsieh K, Xiao Y, Soh HT. Electrochemical DNA detection via exonuclease and target-catalyzed transformation of surface-bound probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10392-10396. [PMID: 20232926 PMCID: PMC2883016 DOI: 10.1021/la100227s] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
We report a single-step, single-reagent, label-free, isothermal electrochemical DNA sensor based on the phenomenon of target recycling. The sensor exploits strand-specific exonuclease activity to achieve the selective enzymatic digestion of target/probe duplexes. This results in a permanent change in the probe structure that yields an increased faradaic current and liberates the intact target molecule to interact with additional detection probes to achieve further signal amplification. Using this architecture, we achieve an improved detection limit in comparison to hybridization-based sensors without amplification. We also demonstrate a 16-fold signal amplification factor at low target concentrations. Combined with the advantages of electrochemical detection and its ready integration with microelectronics, our approach may represent a promising path toward direct DNA detection at the point of care.
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Affiliation(s)
- Kuangwen Hsieh
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
| | - Yi Xiao
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Materials Department, University of California, Santa Barbara, CA 93106
| | - H. Tom Soh
- Department of Mechanical Engineering, University of California, Santa Barbara, CA 93106
- Materials Department, University of California, Santa Barbara, CA 93106
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Abstract
The detection of mismatched base pairs in DNA plays a crucial role in the diagnosis of genetic-related diseases and conditions, especially for early stage treatment. Among the various biosensors that have been used for DNA detection, EC sensors show great promise because they are capable of precise DNA recognition and efficient signal transduction. Advancements in micro- and nanotechnologies, specifically fabrication techniques and new nanomaterials, have enabled for the development of highly sensitive, highly specific sensors making them attractive for the detection of small sequence variations. Furthermore, the integration of sensors with sample preparation and fluidic processes enables for rapid, multiplexed DNA detection essential for POC clinical diagnostics.
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Affiliation(s)
- Fang Wei
- Mechanical and Aerospace Engineering Department, School of Engineering and Applied Science, University of California, Los Angeles, California 90095, USA
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50
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Zuo X, Xia F, Xiao Y, Plaxco KW. Sensitive and Selective Amplified Fluorescence DNA Detection Based on Exonuclease III-Aided Target Recycling. J Am Chem Soc 2010; 132:1816-8. [DOI: 10.1021/ja909551b] [Citation(s) in RCA: 446] [Impact Index Per Article: 31.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaolei Zuo
- Department of Chemistry and Biochemistry, Department of Physics, Materials Department, Department of Mechanical Engineering, and Program in BioMolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - Fan Xia
- Department of Chemistry and Biochemistry, Department of Physics, Materials Department, Department of Mechanical Engineering, and Program in BioMolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - Yi Xiao
- Department of Chemistry and Biochemistry, Department of Physics, Materials Department, Department of Mechanical Engineering, and Program in BioMolecular Science and Engineering, University of California, Santa Barbara, California 93106
| | - Kevin W. Plaxco
- Department of Chemistry and Biochemistry, Department of Physics, Materials Department, Department of Mechanical Engineering, and Program in BioMolecular Science and Engineering, University of California, Santa Barbara, California 93106
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