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Jia Z, Tu K, Xu Q, Gao W, Liu C, Fang B, Zhang M. A novel disease-associated nucleic acid sensing platform based on split DNA-scaffolded sliver nanocluster. Anal Chim Acta 2021; 1175:338734. [PMID: 34330446 DOI: 10.1016/j.aca.2021.338734] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/01/2021] [Accepted: 06/01/2021] [Indexed: 12/18/2022]
Abstract
Disease-associated nucleic acids, such as DNAs and miRNAs, are important biomarkers for the diagnosis, prognosis and treatment guidance of human diseases. Therefore, the accurate and sensitive detection of nucleic acid is of great significance for the early diagnosis of diseases. DNA-scaffolded silver nanocluster (DNA-Ag NC) is a new type of probe with good photostability and low toxicity that has been widely used in biomedical analysis. In this work, a new universal sensing platform based on target triggered labeling luminescent DNA-Ag NC for disease-related nucleic acids detection was constructed. The assembled split DNA fragment pair (C4AC4T and C3GT4) could be used as a template to develop a bright green fluorescent Ag NC. According to this phenomenon, we devised two probe sequences DNA 1 and DNA 2, which could hybridize to the same one target and contained a different split fragment of Ag NC' scaffold. The target compelled the split fragments close to each other through base pairing with DNA 1 and DNA 2, thus quantification of the target could be achieved through measuring green fluorescence of Ag NC that produced by assembled scaffold in ternary hybrid products. We applied this platform successfully for miR-362, a potential biomarker of inflammatory bowel diseases (IBD), or HIV-related DNA (hDNA) detection, achieving the detection limits of 6.5 nM and 1.7 nM, respectively. Both of the assays showed excellent reproducibility, selectivity and potential applications in human serum samples. In summary, an economic and convenient universal platform was developed for disease-associated nucleic acid detection.
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Affiliation(s)
- Zhenzhen Jia
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Kangsheng Tu
- Department of Hepatobiliary Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China
| | - Qiuran Xu
- The Key Laboratory of Tumor Molecular Diagnosis and Individualized Medicine of Zhejiang Province, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, 310014, China
| | - Wenhui Gao
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Cui Liu
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China
| | - Biyun Fang
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China.
| | - Mingzhen Zhang
- School of Basic Medical Sciences, Xi'an Key Laboratory of Immune Related Diseases, Xi'an Jiaotong University, Xi'an, Shaanxi, 710061, China; Key Laboratory of Environment and Genes Related to Diseases, Xi'an Jiaotong University, Ministry of Education, Xi'an, Shaanxi, 710061, China.
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Tran HV, Piro B. Recent trends in application of nanomaterials for the development of electrochemical microRNA biosensors. Mikrochim Acta 2021; 188:128. [PMID: 33740140 DOI: 10.1007/s00604-021-04784-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Accepted: 03/10/2021] [Indexed: 01/10/2023]
Abstract
The biology of the late twentieth century was marked by the discovery in 1993 of a new class of small non-coding ribonucleic acids (RNAs) which play major roles in regulating the translation and degradation of messenger RNAs. These small RNAs (18-25 nucleotides), called microRNAs (miRNAs), are implied in several biological processes such as differentiation, metabolic homeostasis, or cellular apoptosis and proliferation. The discovery in 2008 that the presence of miRNAs in body fluids could be correlated with cancer (prostate, breast, colon, lung, etc.) or other diseases (diabetes, heart diseases, etc.) has made them new key players as biomarkers. Therefore, miRNA detection is of considerable significance in both disease diagnosis and in the study of miRNA function. Until these days, more than 1200 miRNAs have been identified. However, traditional methods developed for conventional DNA does not apply satisfactorily for miRNA, in particular due to the low expression level of these miRNA in biofluids, and because they are very short strands. Electrochemical biosensors can provide this sensitivity and also offer the advantages of mass fabrication, low-cost, and potential decentralized analysis, which has wide application for microRNAs sensing, with many promising results already reported. The present review summarizes some newly developed electrochemical miRNA detection methods.
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Affiliation(s)
- Hoang Vinh Tran
- School of Chemical Engineering, Hanoi University of Science and Technology (HUST), 1st Dai Co Viet Road, Hanoi, Vietnam.
| | - Benoit Piro
- ITODYS, CNRS, Université de Paris, F-75006, Paris, France
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Vishnubhotla R, Montgomery CB, Steffens KL, Semancik S. Conformational Changes of Immobilized Polythymine due to External Stressors Studied with Temperature-Controlled Electrochemical Microdevices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:2607-2618. [PMID: 33595321 PMCID: PMC9278808 DOI: 10.1021/acs.langmuir.0c03219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Conformational changes of single-stranded DNA (ssDNA) play an important role in a DNA strand's ability to bind to target ligands. A variety of factors can influence conformation, including temperature, ionic strength, pH, buffer cation valency, strand length, and sequence. To better understand the effects of these factors on immobilized DNA structures, we employ temperature-controlled electrochemical microsensors to study the effects of salt concentration and temperature variation on the conformation and motion of polythymine (polyT) strands of varying lengths (10, 20, 50 nucleotides). PolyT strands were tethered to a gold working electrode at the proximal end through a thiol linker via covalent bonding between the Au electrode and sulfur link, which can tend to decompose between a temperature range of 60 and 90 °C. The strands were also modified with an electrochemically active methylene blue (MB) moiety at the distal end. Electron transfer (eT) was measured by square wave voltammetry (SWV) and used to infer information pertaining to the average distance between the MB and the working electrode. We observe changes in DNA flexibility due to varying ionic strength, while the effects of increased DNA thermal motion are tracked for elevated temperatures. This work elucidates the behavior of ssDNA in the presence of a phosphate-buffered saline at NaCl concentrations ranging from 20 to 1000 mmol/L through a temperature range of 10-50 °C in 1° increments, well below the decomposition temperature range. The results lay the groundwork for studies on more complex DNA strands in conjunction with different chemical and physical conditions.
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Opportunities, Challenges, and Prospects in Electrochemical Biosensing of Circulating Tumor DNA and its Specific Features. SENSORS 2019; 19:s19173762. [PMID: 31480367 PMCID: PMC6749466 DOI: 10.3390/s19173762] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 08/24/2019] [Accepted: 08/25/2019] [Indexed: 12/19/2022]
Abstract
Nowadays, analyzing circulating tumor DNA (ctDNA), a very small part of circulating free DNA (cfDNA) carried by blood, is considered to be an interesting alternative to conventional single-site tumor tissue biopsies, both to assess tumor burden and provide a more comprehensive snapshot of the time-related and spatial heterogeneity of cancer genetic/epigenetic scenery. The determination of ctDNA and/or mapping its characteristic features, including tumor-specific mutations, chromosomal aberrations, microsatellite alterations, and epigenetic changes, are minimally invasive, powerful and credible biomarkers for early diagnosis, follow-up, prediction of therapy response/resistance, relapse monitoring, and tracking the rise of new mutant subclones, leading to improved cancer outcomes This review provides an outline of advances published in the last five years in electrochemical biosensing of ctDNA and surrogate markers. It emphasizes those strategies that have been successfully applied to real clinical samples. It highlights the unique opportunities they offer to shift the focus of cancer patient management methods from actual decision making, based on clinic-pathological features, to biomarker-driven treatment strategies, based on genotypes and customized targeted therapies. Also highlighted are the unmet hurdles and future key points to guide these devices in the development of liquid biopsy cornerstone tools in routine clinical practice for the diagnosis, prognosis, and therapy response monitoring in cancer patients.
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Fang CS, Kim KS, Yu B, Jon S, Kim MS, Yang H. Ultrasensitive Electrochemical Detection of miRNA-21 Using a Zinc Finger Protein Specific to DNA-RNA Hybrids. Anal Chem 2017; 89:2024-2031. [PMID: 28208259 DOI: 10.1021/acs.analchem.6b04609] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Both high sensitivity and high specificity are crucial for detection of miRNAs that have emerged as important clinical biomarkers. Just Another Zinc finger proteins (JAZ, ZNF346) bind preferably (but nonsequence-specifically) to DNA-RNA hybrids over single-stranded RNAs, single-stranded DNAs, and double-stranded DNAs. We present an ultrasensitive and highly specific electrochemical method for miRNA-21 detection based on the selective binding of JAZ to the DNA-RNA hybrid formed between a DNA capture probe and a target miRNA-21. This enables us to use chemically stable DNA as a capture probe instead of RNA as well as to apply a standard sandwich-type assay format to miRNA detection. High signal amplification is obtained by (i) enzymatic amplification by alkaline phosphatase (ALP) coupled with (ii) electrochemical-chemical-chemical (ECC) redox cycling involving an ALP product (hydroquinone). Low nonspecific adsorption of ALP-conjugated JAZ is obtained using a polymeric self-assembled-monolayer-modified and casein-treated indium-tin oxide electrode. The detection method can discriminate between target miRNA-21 and nontarget nucleic acids (DNA-DNA hybrid, single-stranded DNA, miRNA-125b, miRNA-155, single-base mismatched miRNA, and three-base mismatched miRNA). The detection limits for miRNA-21 in buffer and 10-fold diluted serum are approximately 2 and 30 fM, respectively, indicating that the detection method is ultrasensitive. This detection method can be readily extended to multiplex detection of miRNAs with only one ALP-conjugated JAZ probe due to its nonsequence-specific binding character. We also believe that the method could offer a promising solution for point-of-care testing of miRNAs in body fluids.
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Affiliation(s)
- Chiew San Fang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University , Busan 46241, Korea
| | - Kwang-Sun Kim
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University , Busan 46241, Korea
| | - Byeongjun Yu
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
| | - Sangyong Jon
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST) , Daejeon 34141, Korea
| | - Moon-Soo Kim
- Department of Chemistry, Western Kentucky University , Bowling Green, Kentucky 42101, United States
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials, Pusan National University , Busan 46241, Korea
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Bettazzi F, Marrazza G, Minunni M, Palchetti I, Scarano S. Biosensors and Related Bioanalytical Tools. PAST, PRESENT AND FUTURE CHALLENGES OF BIOSENSORS AND BIOANALYTICAL TOOLS IN ANALYTICAL CHEMISTRY: A TRIBUTE TO PROFESSOR MARCO MASCINI 2017. [DOI: 10.1016/bs.coac.2017.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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Voccia D, Sosnowska M, Bettazzi F, Roscigno G, Fratini E, De Franciscis V, Condorelli G, Chitta R, D’Souza F, Kutner W, Palchetti I. Direct determination of small RNAs using a biotinylated polythiophene impedimetric genosensor. Biosens Bioelectron 2017; 87:1012-1019. [DOI: 10.1016/j.bios.2016.09.058] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Revised: 09/02/2016] [Accepted: 09/16/2016] [Indexed: 12/14/2022]
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