1
|
Li Q, Gao C, Shen X, Xing D. Graphene oxide-functionalized molecular beacon for real-time interference-free detection of Ki-67 mRNA in living cells. Talanta 2024; 278:126538. [PMID: 39002264 DOI: 10.1016/j.talanta.2024.126538] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 06/08/2024] [Accepted: 07/09/2024] [Indexed: 07/15/2024]
Abstract
Molecular beacons (MBs) based on hairpin-shaped oligonucleotides are captivating owing to their capability to enable effective real-time detection of cytosolic mRNA in living cells. However, DNase in the nucleus and lysosome could induce the degradation of oligonucleotides in MBs, leading to the generation of false-positive signals. Herein, a graphene oxide (GO) nanosheet was applied as a nanocarrier for MBs to greatly enhance the anti-interference of the easily designed nanoprobe. Advantageously, the absorption capacity of GO for MBs increased with the decrease in pH values, providing the MB-GO nanoprobe with the ability to detect the expression of cytosolic Ki-67 mRNA without interference from DNase Ⅱ in lysosomes. Moreover, the size of GO nanosheets was considerably higher than that of the nuclear pore complex (NPC), which prevented nanoprobes from transition through the NPCs, thereby avoiding the generation of false-positive signals in the nucleus. Altogether, the present work affords a convenient approach for the successful detection of Ki-67 mRNA expression in the cytosol without interference from DNase Ⅰ/Ⅱ in the nucleus/lysosome, which may be potentially further applied for the detection of other cytosolic RNAs.
Collapse
Affiliation(s)
- Qian Li
- Cancer Institute, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China; Qingdao Cancer Institute, Qingdao, 266071, China.
| | - Chihao Gao
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; Institute of High Performance Polymers, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Xin Shen
- State Key Laboratory Base of Eco-chemical Engineering, College of Chemical Engineering, Qingdao University of Science and Technology, Qingdao, 266042, China; Institute of High Performance Polymers, Qingdao University of Science and Technology, Qingdao, 266042, China
| | - Dongming Xing
- Cancer Institute, the Affiliated Hospital of Qingdao University, Qingdao University, Qingdao, 266071, China; Qingdao Cancer Institute, Qingdao, 266071, China; School of Life Sciences, Tsinghua University, Beijing, 100084, China
| |
Collapse
|
2
|
Wang Z, Wang Y, Tong Y, Niu W. Enzyme-aided amplification strategy for sensitive detection of methamphetamine based on fluorescence aptamer sensor. ANAL SCI 2024:10.1007/s44211-024-00648-x. [PMID: 39150484 DOI: 10.1007/s44211-024-00648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 08/04/2024] [Indexed: 08/17/2024]
Abstract
Methamphetamine (METH) abuse poses a serious risk to human health and social stability. It is critical to develop sensitive and selective methods for detecting METH. Here, we develop a fluorescence aptamer sensor to detect METH based on DNA exonuclease III (Exo III), graphene oxide (GO), and FAM-labeled aptamer. First, the sensor used GO's strong binding capacity to adsorb and quench the fluorescence of the aptamer attached to GO surface. When METH was added to the system, the formation of stable complex for aptamer and METH dissociated from the surface of GO, leading to a fluorescence restoration. Then, the fluorescence signal was further amplified by using Exo III to liberate target METH for cyclic hybridization. And the gel electrophoresis experiment further verified the reliability of this strategy. This aptamer sensor exhibited a low detection limit (0.52 nM) and excellent selectivity under optimal conditions. Notably, this sensor has been successfully validated in the detection of METH in urine and saliva samples, exhibited commendable recovery (94.00-104.65%). Its benefits include facile, sensitive, and rapid. Expected to be used in practical METH detection.
Collapse
Affiliation(s)
- Zheyu Wang
- School of Forensic Medicine, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yandan Wang
- School of Forensic Medicine, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Yishuo Tong
- School of Forensic Medicine, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China
| | - Weifen Niu
- School of Forensic Medicine, Key Laboratory of Forensic Toxicology of Ministry of Public Security, Shanxi Medical University, Jinzhong, 030600, Shanxi, People's Republic of China.
| |
Collapse
|
3
|
Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
Collapse
Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| |
Collapse
|
4
|
Xing Y, Zhang Y, Zhu X, Wang C, Zhang T, Cheng F, Qu J, Peijnenburg WJGM. A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 906:167615. [PMID: 37806581 DOI: 10.1016/j.scitotenv.2023.167615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/03/2023] [Accepted: 10/04/2023] [Indexed: 10/10/2023]
Abstract
Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.
Collapse
Affiliation(s)
- Yi Xing
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Yanan Zhang
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Xiaolin Zhu
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Chengzhi Wang
- Center for Water Research, Beijing Normal University, Beijing 100875, China
| | - Tingting Zhang
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Fangyuan Cheng
- School of Environment, Northeast Normal University, Changchun 130117, China
| | - Jiao Qu
- School of Environment, Northeast Normal University, Changchun 130117, China.
| | - Willie J G M Peijnenburg
- Institute of Environmental Sciences, Leiden University, Leiden, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Bilthoven, the Netherlands
| |
Collapse
|
5
|
Jiang Y, Qian X, Zheng M, Deng K, Li C. Enhancement and inactivation effect of CRISPR/Cas12a via extending hairpin activators for detection of transcription factors. Mikrochim Acta 2023; 191:43. [PMID: 38114763 DOI: 10.1007/s00604-023-06123-0] [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: 07/24/2023] [Accepted: 11/23/2023] [Indexed: 12/21/2023]
Abstract
An enhancement effect for the activation of CRISPR/Cas12a (CRISPR = clustered regularly interspaced short palindromic repeats; Cas = CRISPR-associated) was discovered. That was, a hairpin model with dangling 5' end complementary to crRNA (CRISPR RNA) greatly improved the activity of CRISPR/Cas12a after extention of two random sequences. But, the corresponding intact hairpin without PAM (protospacer adjacent motif) or suboptimal PAM sequences was completely inactive to CRISPR/Cas12a because of the superhigh stability of intact hairpin. According to the finding, a CRISPR/Cas12a-based strategy coupled with a signal reported system was designed for transcription factors detection. By using mono-labeled ssDNA (single-stranded DNA) as reporter and two newly synthesized N-C (nitrogen-doped carbon) nanosheets as scavenger to eliminate the fluorescent background, the strategy realized the detection of NF-ĸB p50 (p50 subunit of nuclear factor kappa-B) with a linear detection range of 0.8 - 2000.0 pM and a LOD of 0.5 pM. The discovery of "enhancement and inactivation effect" not only deepened insight into CRISPR/Cas12a but also broadened the practical application of CRISPR/Cas systems for the molecular detection and disease diagnostics.
Collapse
Affiliation(s)
- Yu Jiang
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Xinmei Qian
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China
| | - Mingyu Zheng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China
| | - Keqin Deng
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China.
| | - Chunxiang Li
- Key Laboratory of Theoretical Organic Chemistry and Function Molecule, Ministry of Education, Hunan University of Science and Technology, Xiangtan, 411201, People's Republic of China.
- Hunan Province College Key Laboratory of Molecular Design and Green Chemistry, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan, 411201, China.
| |
Collapse
|
6
|
Abstract
DNA has excellent molecular recognition properties. At the same time, DNA has a programmable structure, high stability, and can be easily modified, making DNA attractive for biosensor design. To convert DNA hybridization or aptamer binding events to physically detectable signals, various nanomaterials have been extensively exploited to take advantage of their optical and surface properties. A popular sensing scheme is through the adsorption of a fluorescently-labeled DNA probe, where detection is achieved by target-induced probe desorption and fluorescence recovery. Another method is to use DNA to protect the colloidal stability of nanomaterials, where subsequent target binding can decrease the protection ability and induce aggregation; this method has mainly been used for gold nanoparticles. This Perspective summarizes some of our work in examining the sensing mechanisms, and we articulate the importance of the understanding of DNA/surface and target/surface interactions for the development of practical DNA-based biosensors.
Collapse
Affiliation(s)
- Stefen Stangherlin
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, Waterloo, ON, N2L 3G1, Canada.
| |
Collapse
|
7
|
Li K, Liu Y, Lou B, Tan Y, Chen L, Liu Z. DNA-directed assembly of nanomaterials and their biomedical applications. Int J Biol Macromol 2023:125551. [PMID: 37356694 DOI: 10.1016/j.ijbiomac.2023.125551] [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: 03/24/2023] [Revised: 06/15/2023] [Accepted: 06/22/2023] [Indexed: 06/27/2023]
Abstract
In the past decades, DNA has been widely used in the field of nanostructures due to its unique programmable properties. Besides being used to form its own diverse structures such as the assembly of DNA origami, DNA can also be used for the assembly of nanostructures with other materials. In this review, different strategies for the functionalization of DNA on nanoparticle surfaces are listed, and the roles of DNA in the assembly of nanostructures as well as the influencing factors are discussed. Finally, the biomedical applications of DNA-assembled nanostructures were summarized. This review provided new insight into the application of DNA in nanostructure assembly.
Collapse
Affiliation(s)
- Ke Li
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yanfei Liu
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Beibei Lou
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China
| | - Yifu Tan
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Liwei Chen
- Department of Pharmaceutical Engineering, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, Hunan Province, PR China
| | - Zhenbao Liu
- Department of Pharmaceutics, Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, Hunan Province, PR China; Molecular Imaging Research Center of Central South University, Changsha 410008, Hunan Province, PR China.
| |
Collapse
|
8
|
Toader GA, Nitu FR, Ionita M. Graphene Oxide/Nitrocellulose Non-Covalent Hybrid as Solid Phase for Oligo-DNA Extraction from Complex Medium. Molecules 2023; 28:4599. [PMID: 37375154 DOI: 10.3390/molecules28124599] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/31/2023] [Accepted: 06/03/2023] [Indexed: 06/29/2023] Open
Abstract
A nitrocellulose-graphene oxide hybrid that consists of a commercially nitrocellulose (NC) membrane non-covalently modified with graphene oxide (GO) microparticles was successfully prepared for oligonucleotide extraction. The modification of NC membrane was confirmed by Fourier Transform Infrared Spectroscopy (FTIR), which highlighted the principal absorption bands of both the NC membrane at 1641, 1276, and 835 cm-1 (NO2) and of GO in the range of 3450 cm-1 (CH2-OH). The SEM analysis underlined the well-dispersed and uniform coverage of NC membrane with GO, which displayed thin spider web morphology. The wettability assay indicated that the NC-GO hybrid membrane exhibited slightly lower hydrophilic behavior, with a water contact angle of 26.7°, compared to the 15° contact angle of the NC control membrane. The NC-GO hybrid membranes were used to separate oligonucleotides that had fewer than 50 nucleotides (nt) from complex solutions. The features of the NC-GO hybrid membranes were tested for extraction periods of 30, 45, and 60 min in three different complex solutions, i.e., an aqueous medium, an α-Minimum Essential Medium (αMEM), and an αMEM supplemented with fetal bovine serum (FBS). The oligonucleotides were desorbed from the surface of the NC-GO hybrid membrane using Tris-HCl buffer with a pH of 8.0. Out of the three media utilized, the best results were achieved after 60 min incubation of the NC-GO membranes in αMEM, as evidenced by the highest fluorescence emission of 294 relative fluorescence units (r.f.u.). This value corresponded to the extraction of approximately 330-370 pg (≈7%) of the total oligo-DNA. This method is an efficient and effortless way to purify short oligonucleotides from complex solutions.
Collapse
Affiliation(s)
- Georgian A Toader
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
| | - Florentin R Nitu
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
- Genetic Lab, Str. Milcov, nr. 5, Sector 1, 012273 Bucuresti, Romania
| | - Mariana Ionita
- Faculty of Medical Engineering, University Politehnica of Bucharest, Gh Polizu 1-7, 011061 Bucharest, Romania
- Advanced Polymer Materials Group, University Politehnica of Bucharest, Gheorghe Polizu 1-7, 011061 Bucharest, Romania
- eBio-Hub Research Centre, University Politehnica of Bucharest-Campus, Iuliu Maniu 6, 061344 Bucharest, Romania
| |
Collapse
|
9
|
Wu L, Manchanda A, Gupta V, Paull B. Graphene Oxide-Functionalized Thread-Based Electrofluidic Approach for DNA Hybridization. ACS OMEGA 2023; 8:13569-13577. [PMID: 37091394 PMCID: PMC10116522 DOI: 10.1021/acsomega.2c06228] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 03/28/2023] [Indexed: 05/03/2023]
Abstract
A novel, low-cost, and disposable thread-based electrofluidic analytical method employing isotachophoresis (ITP) was developed for demonstrating surface DNA hybridization. This approach was based on graphene oxide (GO) surface-functionalized zones on nylon threads as a binding platform to trap a fluorescently labeled isotachophoretically focused single-stranded DNA (ssDNA) band, resulting in quenching of the fluorescence, which signaled quantitative trapping. In the event of an isotachophoretically focused complementary DNA (cDNA) band passing over the GO-trapped ssDNA zone, surface hybridization of the ssDNA and cDNA to form double-stranded DNA (dsDNA) band occurred, which is released from the GO-coated zones, resulting in restoration of the fluorescent signal as it exits the GO band and migrates further along the thread. This controllable process demonstrates the potential of the GO-functionalized thread-based microfluidic analytical approach for DNA hybridization and its visualization, which could be adapted into point-of-care (POC) diagnostic devices for real-world applications.
Collapse
|
10
|
Zhou J, Sun Y, Zhang J, Luo F, Ma H, Guan M, Feng J, Dong X. Dumbbell Aptamer Sensor Based on Dual Biomarkers for Early Detection of Alzheimer's Disease. ACS APPLIED MATERIALS & INTERFACES 2023; 15:16394-16407. [PMID: 36951764 DOI: 10.1021/acsami.2c21379] [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: 06/18/2023]
Abstract
Finding a timely, sensitive, and noninvasive detection method has become an urgent need for asymptomatic early diagnosis of Alzheimer's disease (AD). MicroRNA-193b (miR-193b) and Aβ42 oligomers (AβO42) in neurogenic exosomes were confirmed to reflect pathological changes in the AD early stage. The combination of two biomarkers is promising for the earlier detection of AD. In this study, a detection system based on the principle of the entropy-driven strand displacement reaction (ESDR) was developed, including a dumbbell detection probe (H), an indicator probe (R), and graphene oxide (GO). In the detection system, the two hairpins of H were opened by the interaction of miR-193b (T1) and AβO42 (T2) with the aptamer. Then R hybridized with H and began to displace T, initiating the next round of ESDR to achieve sensitive detection of T. GO specifically adsorbed free R and quenched the fluorescence, further reducing the intensity of the background signal. Both of these points provided the system with a more sensitive analytical performance. The detection limit of miR-193b was 77 pM and the detection limit of AβO42 was 53 pM. This sensor detected the change of "one increase (AβO42) and one decrease (miR-193b)" in the exosome sample. Additionally, results showed that this detection system could distinguish the model of early AD from the non-AD control, which was sufficient for earlier and more sensitive detection of AD. This strategy has strong specificity, high sensitivity, and easy operation, which provides broad prospects for the early diagnosis of AD.
Collapse
Affiliation(s)
- Jie Zhou
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Yiwen Sun
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jin Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Fusui Luo
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Huili Ma
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Min Guan
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Junfen Feng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xiaomeng Dong
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| |
Collapse
|
11
|
Recent advance in nucleic acid amplification-integrated methods for DNA methyltransferase assay. Trends Analyt Chem 2023. [DOI: 10.1016/j.trac.2023.116998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
|
12
|
Kadhim MM, Rheima AM, Abbas ZS, Jlood HH, Hachim SK, Kadhum WR, kianfar E. Evaluation of a biosensor-based graphene oxide-DNA nanohybrid for lung cancer. RSC Adv 2023; 13:2487-2500. [PMID: 36741187 PMCID: PMC9843741 DOI: 10.1039/d2ra05808a] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/05/2023] [Indexed: 01/18/2023] Open
Abstract
Lung cancer is nowadays among the most prevalent diseases worldwide and features the highest mortality rate among various cancers, indicating that early diagnosis of the disease is of paramount importance. Given that the conventional methods of cancer detection are expensive and time-consuming, special attention has been paid to the provision of less expensive and faster techniques. In recent years, the dramatic advances in nanotechnology and the development of various nanomaterials have led to activities in this context. Recent studies indicate that the graphene oxide (GO) nanomaterial has high potential in the design of nano biosensors for lung cancer detection owing to its unique properties. In the current article, a nano biosensor based on a DNA-GO nanohybrid is introduced to detect deletion mutations causing lung cancer. In this method, mutations were detected using a FAM-labeled DNA probe with fluorescence spectrometry. GO was synthesized according to Hummers' method and examined and confirmed using Fourier Transform Infrared (FT-IR) Spectrometry and UV-vis spectrometry methods and Transmission Electron Microscopy (TEM) images.
Collapse
Affiliation(s)
- Mustafa M. Kadhim
- Medical Laboratory Techniques Department, Al-Farahidi UniversityBaghdad 10022Iraq
| | - Ahmed Mahdi Rheima
- Department of Chemistry, College of Science, Mustansiriyah UniversityBaghdadIraq
| | | | | | - Safa K. Hachim
- College of Technical Engineering, The Islamic UniversityNajafIraq,Medical Laboratory Techniques Department, Al-Turath University CollegeIraqBaghdad
| | - Wesam R. Kadhum
- Department of Pharmacy, Kut University CollegeKut 52001WasitIraq
| | - Ehsan kianfar
- Istanbul Medeniyet UniversityIstanbulTurkey+90 917-744-1049,Department of Chemical Engineering, Islamic Azad UniversityArak BranchArakIran,Young Researchers and Elite Club, Islamic Azad UniversityGachsaran BranchGachsaranIran,Department of Chemistry, Islamic Azad UniversitySousangerd BranchSousangerdIran
| |
Collapse
|
13
|
Environmental Health and Safety of Engineered Nanomaterials. Nanomedicine (Lond) 2023. [DOI: 10.1007/978-981-16-8984-0_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
|
14
|
Sugar Moiety Driven Adsorption of Nucleic Acid on Graphene Quantum Dots: Photophysical, Thermodynamic and Theoretical Evidence. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
|
15
|
Light-emitting crystals of aptamer-hybrid organic semiconductor signaling on human cells expressing EpCAM. J IND ENG CHEM 2022. [DOI: 10.1016/j.jiec.2022.09.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
16
|
Yang L, Yi Z, Zeng X, Huang X, Zhong F, Zhou J, Qiu Z. Sensitive Fluorescent Determination of Chloramphenicol Based upon Graphdiyne and RecJ f Exonuclease-Assisted Signal Amplification. ANAL LETT 2022. [DOI: 10.1080/00032719.2022.2073364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- Lixia Yang
- Changsha Institute for Food and Drug Control, Changsha, Hunan, China
| | - Zi Yi
- Food Safety Production Engineering Research Center of Hunan Province, Changsha, Hunan, China
| | - Xike Zeng
- Changsha Institute for Food and Drug Control, Changsha, Hunan, China
| | - Xiaobei Huang
- National Alcohol Products Quality Supervision and Inspection Center, Changsha, Hunan, China
| | - Feifei Zhong
- Changsha Institute for Food and Drug Control, Changsha, Hunan, China
| | - Jinsha Zhou
- Changsha Institute for Food and Drug Control, Changsha, Hunan, China
| | - Zhipeng Qiu
- Changsha Institute for Food and Drug Control, Changsha, Hunan, China
| |
Collapse
|
17
|
Liang Y, Ang WL, Lim RRX, Bonanni A. Exploring graphene oxide intrinsic electroactivity to elucidate the non-covalent interactions with DNA oligonucleotides. Chem Commun (Camb) 2022; 58:2662-2665. [PMID: 35107450 DOI: 10.1039/d1cc06657a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We show here how the electrochemical reduction signal of graphene oxide nanocolloids is inhibited upon the formation of non-covalent interactions with single stranded DNA oligonucleotides. The drop in the reduction current intensity is strongly influenced by the nucleobase sequence, and can therefore be directly correlated to the specific DNA homo-oligonucleotide.
Collapse
Affiliation(s)
- Yaquan Liang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Wei Li Ang
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Rachel Rui Xia Lim
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| | - Alessandra Bonanni
- Division of Chemistry & Biological Chemistry, School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371, Singapore.
| |
Collapse
|
18
|
Detachment-Independent Cationic-Dipeptide Beacons: Reduced False-Negative Signal and Accelerated Fluorescent Lighting in Cell Imaging. JOURNAL OF ANALYSIS AND TESTING 2022. [DOI: 10.1007/s41664-021-00207-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
19
|
Faikhruea K, Choopara I, Somboonna N, Assavalapsakul W, Kim BH, Vilaivan T. Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects. ACS APPLIED BIO MATERIALS 2022; 5:789-800. [PMID: 35119822 DOI: 10.1021/acsabm.1c01177] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.
Collapse
Affiliation(s)
- Kriangsak Faikhruea
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Ilada Choopara
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Naraporn Somboonna
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Wanchai Assavalapsakul
- Department of Microbiology, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| | - Byeang Hyean Kim
- Department of Chemistry, Division of Advanced Materials Science, Pohang University of Science and Technology (POSTECH), Pohang 37673, Republic of Korea
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Pathumwan, Bangkok 10330, Thailand
| |
Collapse
|
20
|
Zahra QUA, Fang X, Luo Z, Ullah S, Fatima S, Batool S, Qiu B, Shahzad F. Graphene Based Nanohybrid Aptasensors in Environmental Monitoring: Concepts, Design and Future Outlook. Crit Rev Anal Chem 2022; 53:1433-1454. [PMID: 35085047 DOI: 10.1080/10408347.2022.2025758] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
In view of ever-increasing environmental pollution, there is an immediate requirement to promote cheap, multiplexed, sensitive and fast biosensing systems to monitor these pollutants or contaminants. Aptamers have shown numerous advantages in being used as molecular recognition elements in various biosensing devices. Graphene and graphene-based materials/nanohybrids combined with several detection methods exhibit great potential owing to their exceptional optical, electronic and physicochemical properties which can be employed extensively to monitor environmental contaminants. For environmental monitoring applications, aptamers have been successfully combined with graphene-based nanohybrids to produce a wide range of innovative methodologies. Aptamers are immobilized at the surface of graphene based nanohybrids via covalent and non-covalent strategies. This review highlights the design, working principle, recent developmental advances and applications of graphene based nanohybrid aptasensors (GNH-Apts) (since January 2014 to September 2021) with a special emphasis on two major signal-transduction methods, i.e., optical and electrochemical for the monitoring of pesticides, heavy metals, bacteria, antibiotics, and organic compounds from different environmental samples (e.g., water, soil and related). Lastly, the challenges confronted by scientists and the possible future outlook have also been addressed. It is expected that high-performance graphene-based nanohybrid aptasensors would find broad applications in the field of environmental monitoring.
Collapse
Affiliation(s)
- Qurat Ul Ain Zahra
- Biomedical Imaging Center, University of Science and Technology of China, Hefei, Anhui, China
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Xiaona Fang
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Zhaofeng Luo
- The Key Laboratory of Zhejiang Province for Aptamers and Theranostics, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, China
| | - Salim Ullah
- School of Nano-Tech and Nano-Bionics, University of Science and Technology of China, Hefei, China
- CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou, China
| | - Shazia Fatima
- Nuclear Medicine, Oncology & Radiotherapy Institute (NORI), Islamabad, Pakistan
| | - Sadaf Batool
- Nuclear Medicine, Oncology & Radiotherapy Institute (NORI), Islamabad, Pakistan
| | - Bensheng Qiu
- Biomedical Imaging Center, University of Science and Technology of China, Hefei, Anhui, China
| | - Faisal Shahzad
- Department of Metallurgy and Materials Engineering, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| |
Collapse
|
21
|
Environmental Health and Safety of Engineered Nanomaterials. Nanomedicine (Lond) 2022. [DOI: 10.1007/978-981-13-9374-7_23-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
|
22
|
Bhai S, Ganguly B. Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study. Phys Chem Chem Phys 2021; 24:829-841. [PMID: 34928284 DOI: 10.1039/d1cp04009j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.
Collapse
Affiliation(s)
- Surjit Bhai
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
| | - Bishwajit Ganguly
- Computational and Simulation Unit (Analytical and Environment Science Division and Centralized Instrument Facility) CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar, Gujarat, 364002, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.,CSIR-CSMCRI, Bhavnagar-364002, Gujarat, India
| |
Collapse
|
23
|
Jouha J, Xiong H. DNAzyme-Functionalized Nanomaterials: Recent Preparation, Current Applications, and Future Challenges. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2021; 17:e2105439. [PMID: 34802181 DOI: 10.1002/smll.202105439] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 10/14/2021] [Indexed: 06/13/2023]
Abstract
DNAzyme-nanomaterial bioconjugates are a popular hybrid and have received major attention for diverse biomedical applications, such as bioimaging, biosensor development, cancer therapy, and drug delivery. Therefore, significant efforts are made to develop different strategies for the preparation of inorganic and organic nanoparticles (NPs) with specific morphologies and properties. DNAzymes functionalized with metal-organic frameworks (MOFs), gold nanoparticles (AuNPs), graphene oxide (GO), and molybdenum disulfide (MoS2 ) are introduced and summarized in detail in this review. Moreover, the focus is on representative examples of applications of DNAzyme-nanomaterials over recent years, especially in bioimaging, biosensing, phototherapy, and stimulation response delivery in living systems, with their several advantages and drawbacks. Finally, the perspective regarding the future directions of research addressing these challenges is also discussed and highlighted.
Collapse
Affiliation(s)
- Jabrane Jouha
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
- College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China
| | - Hai Xiong
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, China
| |
Collapse
|
24
|
Gosai A, Khondakar KR, Ma X, Ali MA. Application of Functionalized Graphene Oxide Based Biosensors for Health Monitoring: Simple Graphene Derivatives to 3D Printed Platforms. BIOSENSORS 2021; 11:384. [PMID: 34677340 PMCID: PMC8533804 DOI: 10.3390/bios11100384] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/06/2021] [Accepted: 10/08/2021] [Indexed: 01/01/2023]
Abstract
Biosensors hold great potential for revolutionizing personalized medicine and environmental monitoring. Their construction is the key factor which depends on either manufacturing techniques or robust sensing materials to improve efficacy of the device. Functional graphene is an attractive choice for transducing material due to its various advantages in interfacing with biorecognition elements. Graphene and its derivatives such as graphene oxide (GO) are thus being used extensively for biosensors for monitoring of diseases. In addition, graphene can be patterned to a variety of structures and is incorporated into biosensor devices such as microfluidic devices and electrochemical and plasmonic sensors. Among biosensing materials, GO is gaining much attention due to its easy synthesis process and patternable features, high functionality, and high electron transfer properties with a large surface area leading to sensitive point-of-use applications. Considering demand and recent challenges, this perspective review is an attempt to describe state-of-the-art biosensors based on functional graphene. Special emphasis is given to elucidating the mechanism of sensing while discussing different applications. Further, we describe the future prospects of functional GO-based biosensors for health care and environmental monitoring with a focus on additive manufacturing such as 3D printing.
Collapse
Affiliation(s)
- Agnivo Gosai
- Corning Inc., Science & Technology, Painted Post, NY 14870, USA;
| | - Kamil Reza Khondakar
- Department of Electrical and Computer Engineering, Florida International University, Miami, FL 33174, USA;
| | - Xiao Ma
- Department of Biomedical Engineering, New York University, Brooklyn, NY 11201, USA
| | - Md. Azahar Ali
- Department of Mechanical Engineering, Carnegie Mellon University, Pittsburgh, PA 15235, USA
| |
Collapse
|
25
|
Gao Y, Yu H, Tian J, Xiao B. Nonenzymatic DNA-Based Fluorescence Biosensor Combining Carbon Dots and Graphene Oxide with Target-Induced DNA Strand Displacement for microRNA Detection. NANOMATERIALS (BASEL, SWITZERLAND) 2021; 11:2608. [PMID: 34685049 PMCID: PMC8537593 DOI: 10.3390/nano11102608] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 09/24/2021] [Accepted: 09/30/2021] [Indexed: 12/18/2022]
Abstract
Based on a fluorescence "on-off-on" strategy, we fabricated a simple and highly sensitive DNA-based fluorescence biosensor for the detection of micro (mi)RNA from carbon dots (CDs) and graphene oxide (GO) without complicated and time-consuming operations. CDs were successfully synthesized and conjugated to the end of a single-stranded fuel DNA that was adsorbed onto the surface of GO through π-π stacking, resulting in fluorescence quenching. In the presence of the target miRNA let-7a, the fuel DNA was desorbed from the GO surface, and fluorescence was restored through two successive toehold-mediated strand displacement reactions on double-stranded DNA-modified gold nanoparticles. The target miRNA let-7a was recycled, leading to signal amplification. The concentration of let-7a was proportional to the degree of fluorescence recovery. Under optimal conditions, there was a good linear relationship between the relative fluorescence intensity and let-7a concentration in the range of 0.01-1 nM, with a detection limit of 7.8 pM. With its advantages of signal amplification and high biocompatibility, this fluorescence sensing strategy can be applied to the detection of a variety of target miRNAs and can guide the design of novel biosensors with improved properties.
Collapse
Affiliation(s)
- Yuanyuan Gao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.G.); (H.Y.)
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Material Science and Engineering, Hainan University, Haikou 570228, China;
| | - Hong Yu
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.G.); (H.Y.)
| | - Jingjing Tian
- State Key Laboratory of Marine Resource Utilization in South China Sea, School of Material Science and Engineering, Hainan University, Haikou 570228, China;
- Key Laboratory of Emergency and Trauma of Ministry of Education & Research Unit of Island Emergency Medicine of Chinese Academy of Medical Sciences, Hainan Medical University, Haikou 571199, China
| | - Botao Xiao
- Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; (Y.G.); (H.Y.)
- Joint International Research Laboratory of Synthetic Biology and Medicine, School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| |
Collapse
|
26
|
Intrinsically conductive polymers hybrid bilayer films for the fluorescence molecular diagnosis of the Zika virus. Colloids Surf B Biointerfaces 2021; 208:112120. [PMID: 34597940 DOI: 10.1016/j.colsurfb.2021.112120] [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: 06/04/2021] [Revised: 09/09/2021] [Accepted: 09/13/2021] [Indexed: 11/20/2022]
Abstract
In 2016, the Zika virus (ZIKV) infection became a major public health problem, after the discovery that an alarming increase in the number of Brazilian newborns with microcephaly could be associated with the occurrence of this viral disease during the pregnancy of their mothers. The urgent need for simple diagnostic methods that allow rapid screening of suspected cases has stimulated the search for low-cost devices capable of detecting specific sequences of nucleic acids. The present work describes the development of nanostructured films formed by bilayers of conjugated polymers for rapid detection of the presence of Zika virus DNA, via fluorescence methods. For this, we initially deposited alternating layers of polyaniline (PANI) and polypyrrole (PPY) on the surface of polyethylene terephthalate (PET) sheets. The films obtained were then characterized by SEM, UV-Vis, ATR-FTIR, and contact angle measurements. For their use as quenchers for the diagnosis of Zika, a single DNA strand-specific for ZIKV was labeled with a fluorophore (FAM-ssDNA). We determined the time required for the saturation of the interaction between probe FAM-ssDNA and the film (180 min) and the time for the maximal hybridization between FAM-ssDNA and target DNA to occur (60 min). The detection limits were estimated as 345 pM and 278 pM for the PET/PPY-PANI and PET/PANI-PPY hybrid films, respectively. The simplicity of the procedure, coupled with the fact that a positive/negative response can be obtained in less than 60 min, suggests that the proposal of using these polymeric bilayer films is a promising methodology for the development of rapid molecular diagnostic tests.
Collapse
|
27
|
Yim Y, Shin H, Ahn SM, Min DH. Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery. Chem Commun (Camb) 2021; 57:9820-9833. [PMID: 34494621 DOI: 10.1039/d1cc02157e] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.
Collapse
Affiliation(s)
- Yeajee Yim
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Hojeong Shin
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Seong Min Ahn
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea.
| | - Dal-Hee Min
- Department of Chemistry, Seoul National University, Seoul 08826, Republic of Korea. .,Department of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.,Institute of Biotherapeutics Convergence Technology, Lemonex Inc., Seoul 06683, Republic of Korea
| |
Collapse
|
28
|
Ghosh T, Mondal A, Vamsi Bharadwaj SV, Mishra S. A naturally fluorescent protein C-phycoerythrin and graphene oxide bio-composite as a selective fluorescence 'turn off/on' probe for DNA quantification and characterization. Int J Biol Macromol 2021; 185:644-653. [PMID: 34217741 DOI: 10.1016/j.ijbiomac.2021.06.201] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 10/21/2022]
Abstract
Highly specific graphene-DNA interactions have been at the forefront of graphene-based sensor design for various analytes, including DNA itself. However, in addition to its detection, DNA also needs to be characterized according to its size and concentration in a sample, which is an additional analytical step. Designing a highly sensitive and selective DNA sensing and characterization platform is, thus, of great interest. The present study demonstrates that a bio-derived, naturally fluorescent protein C-phycoerythrin (CPE) - graphene oxide (GO) bio-composite can be used to detect dsDNA in nanomolar quantities efficiently via fluorescent "turn off/on" mechanism. Interaction with GO temporarily quenches CPE fluorescence in a dose-dependent manner. Analytical characterization indicates an indirect charge transfer with a corresponding loss of crystalline GO structure. The fluorescence is regained with the addition of DNA, while other biomolecules do not pose any hinderance in the detection process. The extent of regain is DNA length dependent, and the corresponding calibration curve successfully quantifies the size of an unknown DNA. The incubation time for detection is ~3-5 min. The bio-composite platform also works successfully in a complex biomolecule matrix and cell lysate. However, the presence of serum albumin poses a hinderance in the serum sample. Particle size analysis proves that CPE displacement from GO surface by the incoming DNA is the reason for the 'turn on' response, and that the sensing process is exclusive to dsDNA. This new platform could be an exciting and rapid DNA sensing and characterization tool.
Collapse
Affiliation(s)
- Tonmoy Ghosh
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| | - Aniruddha Mondal
- Inorganic Materials and Catalysis Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - S V Vamsi Bharadwaj
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India
| | - Sandhya Mishra
- Applied Phycology and Biotechnology Division, CSIR - Central Salt and Marine Chemicals Research Institute, Gijubhai Badheka Marg, Bhavnagar 364002, Gujarat, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, Uttar Pradesh, India.
| |
Collapse
|
29
|
Choi MH, Lee J, Seo YJ. Combined recombinase polymerase amplification/rkDNA-graphene oxide probing system for detection of SARS-CoV-2. Anal Chim Acta 2021; 1158:338390. [PMID: 33863409 PMCID: PMC7973912 DOI: 10.1016/j.aca.2021.338390] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/18/2021] [Accepted: 03/08/2021] [Indexed: 01/07/2023]
Abstract
The development of rapid, highly sensitive, and selective methods for the diagnosis of infection by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) should help to prevent the spread of this pandemic virus. In this study, we combined recombinase polymerase amplification (RPA), as a means of isothermal DNA amplification, with an rkDNA-graphene oxide (GO) probe system to allow the rapid detection of SARS-CoV-2 with high sensitivity and selectivity. We used in situ enzymatic synthesis to prepare an rkDNA probe that was complementary to an RPA-amplified sequence of the target N-gene of SARS-CoV-2. The fluorescence of this rkDNA was perfectly quenched in the presence of GO. When the quenched rkDNA-GO system was added to the RPA-amplified sequence of the target SARS-CoV-2, the fluorescence recovered dramatically. The combined RPA/rkDNA-GO system exhibited extremely high selectivity (discrimination factor: 17.2) and sensitivity (LOD = 6.0 aM) for the detection of SARS-CoV-2. The total processing time was only 1.6 h. This combined RPA/rkDNA-GO system appears to be a very efficient and simple method for the point-of-care detection of SARS-CoV-2.
Collapse
Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea
| | - Jaehyeon Lee
- Department of Laborotory Medicine, Jeonbuk National University Medical School and Hospital, Jeonju, 54896, South Korea
| | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju, 54896, South Korea.
| |
Collapse
|
30
|
Tunable graphdiyne for DNA surface adsorption: affinities, displacement, and applications for fluorescence sensing. Anal Bioanal Chem 2021; 413:3847-3859. [PMID: 33934191 DOI: 10.1007/s00216-021-03355-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 04/12/2021] [Accepted: 04/15/2021] [Indexed: 02/01/2023]
Abstract
Graphdiyne (GDY) adsorbed DNA probes have been used as a fluorescent sensing platform, but topics including DNA adsorption affinities, DNA probe displacement, and fluorescence quenching ability were rarely researched. Herein, the adsorption affinity of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) on a tremella-like GDY was tuned by modulating the surface chemistry of GDY. The fluorescence quenching ability of GDY with different oxidation degrees was compared. The nonspecific displacement of DNA probes on GDY was studied. Under the same concentrations, GDY with low oxidation degree exhibited stronger adsorption affinity and higher adsorption capacity to both ssDNA and dsDNA than highly oxidized GDY. DNA adsorbed on low-oxidized GDY was more resistant to displacement by other DNAs. Protein showed strong interaction with different GDY and could displace DNA probes on GDY. Based on these findings, an ideal GDY with proper oxidation degree, exhibiting high surface affinity for ssDNA and low affinity for dsDNA, was used as scavenger of redundant ssDNA fluorescent probe in an enzyme-assisted amplification system for sensitive ochratoxin (OTA) detection. This study has enhanced our fundamental understanding of DNA adsorption by GDY. It also provided a rational way to apply GDY for fluorescence sensing in a complicated system.
Collapse
|
31
|
Wei Z, Yu Y, Hu S, Yi X, Wang J. Bifunctional Diblock DNA-Mediated Synthesis of Nanoflower-Shaped Photothermal Nanozymes for a Highly Sensitive Colorimetric Assay of Cancer Cells. ACS APPLIED MATERIALS & INTERFACES 2021; 13:16801-16811. [PMID: 33788550 DOI: 10.1021/acsami.0c21109] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The activity of a nanozyme is closely related to its surface area-to-volume ratio and the surrounding temperature. To acquire highly active nanozymes, one-pot metallization-like synthesis of novel nanoflower-shaped photothermal nanostructures was conducted using polyadenine-containing diblock DNA as the scaffold. The nanoflower-shaped structures with a high surface area-to-volume ratio and photothermal performance exhibited excellent peroxidase-mimicking activity, and the biorecognition capability was retained by the capping agent of diblock DNA. The functionalized nanostructures were used for a proof-of-concept colorimetric assay of cancer cells in vitro. Upon incorporation of 808 nm laser irradiation, high sensitivity and selectivity for the cancer cell assay were achieved with the lowest detection level of 10 cells/mL. Relative to spherical gold nanostructures, the nanoflower-shaped photothermal nanozyme exhibited higher assay sensitivity, paving the way for the construction of nanozyme-based colorimetric sensors for point-of-care testing.
Collapse
Affiliation(s)
- Zhaohui Wei
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Yuefan Yu
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Xinyao Yi
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| | - Jianxiu Wang
- Hunan Provincial Key Laboratory of Micro & Nano Materials Interface Science, College of Chemistry and Chemical Engineering, Central South University, Changsha 410083, P. R. China
| |
Collapse
|
32
|
Karachevtsev MV, Valeev VA, Karachevtsev VA. Interaction of double-stranded polynucleotide poly(A:U) with graphene/graphene oxide. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2021; 44:24. [PMID: 33686498 DOI: 10.1140/epje/s10189-021-00030-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Hybrids formed by DNA/RNA and graphene family nanomaterials are considered as potentially useful multifunctional agents in biosensing and nanomedicine. In this work, we study the noncovalent interaction between double-stranded (ds) RNA, polyadenylic:polyuridylic acids (poly(A:U)) and graphene oxide/graphene (GO/Gr) using UV absorption spectroscopy and molecular dynamics (MD) simulations. RNA melting showed that relatively long ds-RNA is adsorbed onto GO (at an ionic strength of [Formula: see text]) at that a large fraction of RNA maintains the duplex structure. It was revealed that this fraction decreases over long time (during a few days), indicating a slow adsorption process of the long polymer. MD simulations showed that the adsorption of duplex (rA)[Formula: see text]: (rU)[Formula: see text] or (rA)[Formula: see text]: (rU)[Formula: see text] on graphene starts with the interaction between [Formula: see text]-systems of graphene and base pairs located at a duplex tail. In contrast to relatively long duplex (rA)[Formula: see text]: (rU)[Formula: see text] which keeps parallel arrangement along the graphene surface, the shorter one ((rA)[Formula: see text]: (rU)[Formula: see text]) always adopts a perpendicular orientation relative to graphene even in case of the initial parallel orientation. It was found out that (rA)[Formula: see text]: (rU)[Formula: see text] forms the stable hybrid with graphene keeping essential fraction of the duplex, while (rA)[Formula: see text]: (rU)[Formula: see text] demonstrates the duplex unzipping into two single strands with time. The interaction energies between adenine/uracil stacked with graphene as well between nucleotides in water environment were determined.
Collapse
Affiliation(s)
- Maksym V Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine.
| | - Vladimir A Valeev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
| | - Victor A Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, 47, Nauky Ave., Kharkiv, 61103, Ukraine
| |
Collapse
|
33
|
Yukhet P, Buddhachat K, Vilaivan T, Suparpprom C. Isothermal Detection of Canine Blood Parasite ( Ehrlichia canis) Utilizing Recombinase Polymerase Amplification Coupled with Graphene Oxide Quenching-Based Pyrrolidinyl Peptide Nucleic Acid. Bioconjug Chem 2021; 32:523-532. [PMID: 33651604 DOI: 10.1021/acs.bioconjchem.0c00639] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Canine monocytic ehrlichiosis (CME), caused by transmitted Ehrlichia canis infection, is a major disease in dogs with worldwide distribution. Herein, a nucleic acid assay was established for the identification of E. canis infection employing a fluorescently labeled conformationally constrained pyrrolidinyl PNA probe (Flu-acpcPNA) designed to sequence-specifically target the 16S rRNA gene. The sensing principle is based on the excellent quenching ability of graphene oxide (GO) of the free PNA probe, that was diminished upon binding to the DNA target. The addition of DNase I improved the performance of the detection system by eliminating the nonspecific quenching capability of long-chain dsDNA and thus enhancing the fluorescence signaling. The assay was coupled with a recombinase polymerase amplification (RPA) technique, which could be performed under isothermal conditions (37 °C) without DNA denaturation and purification steps. The established method is simple to set up and execute, proving a rapid, specific, and sensitive detection of 16S rRNA gene of E. canis with a limit of detection at least 11.1 pM. This technique shows good potential for the visual detection of double-stranded DNA targets without the need for PCR or complicated instruments, which shows great promise for practical usage in resource limited areas.
Collapse
Affiliation(s)
- Phanomsak Yukhet
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
| | - Kittisak Buddhachat
- Department of Biology, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand.,Excellence Center in Veterinary Bioscience, Chiang Mai University, Chiang Mai, 50200, Thailand
| | - Tirayut Vilaivan
- Organic Synthesis Research Unit, Department of Chemistry, Faculty of Science, Chulalongkorn University, Phayathai Road, Patumwan, Bangkok 10330, Thailand
| | - Chaturong Suparpprom
- Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Naresuan University, Tah-Poe District, Muang, Phitsanulok 65000, Thailand
| |
Collapse
|
34
|
Meng Y, Chen Y, Zhu J, Qi Y, Ding J, Zhou W. Polarity control of DNA adsorption enabling the surface functionalization of CuO nanozymes for targeted tumor therapy. MATERIALS HORIZONS 2021; 8:972-986. [PMID: 34821328 DOI: 10.1039/d0mh01372b] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanomaterials with intrinsic catalytic activities (nanozyme) have drawn broad attention for various biomedical applications, with peroxidase-mimic nanozymes particularly attractive for cancer therapy due to their capability to catalyze the conversion of tumor-abundant H2O2 into more toxic hydroxyl radicals (˙OH) for effective tumor ablation. However, the facile surface modification of nanozymes for tumor-targeted delivery while retaining their catalytic activity remains a challenge. Here, we report an approach to functionalize the CuO nanozyme with DNA to enable targeted delivery and selective tumor destruction. We systematically studied the adsorption of DNA on the CuO surface, with special attention paid to the catalytic activity and DNA adsorption stability in the presence of various biological ligands. After gaining a fundamental understanding, a di-block DNA sequence was designed for adsorption on to the CuO surface, which allowed stable adsorption during in vivo circulation, passive accumulation into the tumor tissue, and the specific recognition of tumor cells, resulting in significant nanocatalytic tumor suppression in tumor xenograft mice models with no noticeable cytotoxicity. This work paves a way for the rational design of DNA-modified nanozymes for catalytic tumor therapy, and fundamentally, provides a new insight into the biointerface chemistry of CuO with DNA.
Collapse
Affiliation(s)
- Yingcai Meng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, Hunan 410013, China.
| | | | | | | | | | | |
Collapse
|
35
|
Lee J, Kim WK. PEGylated graphene oxide-based colorimetric sensor for recording temperature. J IND ENG CHEM 2021. [DOI: 10.1016/j.jiec.2020.11.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
36
|
Lopez A, Liu J. Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide. Anal Chem 2021; 93:3018-3025. [PMID: 33513006 DOI: 10.1021/acs.analchem.0c05062] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO2, ZnO, NiO, Fe3O4, and TiO2, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.
Collapse
Affiliation(s)
- Anand Lopez
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
37
|
Xiong X, Dang W, Luo R, Long Y, Tong C, Yuan L, Liu B. A graphene-based fluorescent nanoprobe for simultaneous imaging of dual miRNAs in living cells. Talanta 2020; 225:121947. [PMID: 33592702 DOI: 10.1016/j.talanta.2020.121947] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/19/2020] [Accepted: 11/30/2020] [Indexed: 02/06/2023]
Abstract
MicroRNAs (miRNAs) are regarded as important biomarkers for disease diagnostics and therapeutics due to their significant regulatory roles in physiologic and pathologic processes. Herein, a versatile nanoprobe based on reduced graphene oxide (rGO) and nucleic acid (DNA) probe was prepared for simultaneously visualize miR-451a and miR-214-3p in living cells. In vitro experiments demonstrated that the nanoprobe exhibits excellent selectivity and outstanding sensitivity as low as 1 nM towards miR-451a and miR-214-3p. Moreover, the detection signals of miRNAs have good linearity in their respective concentration ranges (miR-451a: 1-100 nM, Y1 = 9.3062X1+114.85 (R2 = 0.9965). miR-214-3p: 1-200 nM, Y2 = 1.4424X2+91.312 (R2 = 0.9961)). Finally, simultaneous dual-color imaging of miR-451a and miR-214-3p in human breast cancer cells (MDA-MB-231) was realized by exploiting the P1&P2@rGO nanoprobe. In summary, this simple and effective strategy provides a general sensing platform for highly sensitive detection and simultaneous imaging of dual miRNAs in living cells.
Collapse
Affiliation(s)
- Xiang Xiong
- Department of General Surgery, Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China
| | - Wenya Dang
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ruxin Luo
- College of Biology, Hunan University, Changsha, 410082, China
| | - Ying Long
- College of Biology, Hunan University, Changsha, 410082, China
| | - Chunyi Tong
- College of Biology, Hunan University, Changsha, 410082, China
| | - Liqin Yuan
- Department of General Surgery, Department of Burn and Plastic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, 410011, China.
| | - Bin Liu
- College of Biology, Hunan University, Changsha, 410082, China.
| |
Collapse
|
38
|
Huang Z, Zhao Y, Liu B, Guan S, Liu J. Stronger Adsorption of Phosphorothioate DNA Oligonucleotides on Graphene Oxide by van der Waals Forces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:13708-13715. [PMID: 33161721 DOI: 10.1021/acs.langmuir.0c02761] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Finding DNA sequences that can adsorb strongly on nanomaterials is critical for bioconjugate and biointerface chemistry. In most previous work, unmodified DNA with a phosphodiester backbone (PO DNA) were screened or selected for adsorption on inorganic surfaces. In this work, the adsorption of phosphorothioate (PS)-modified DNA (PS DNA) on graphene oxide (GO) is studied. By use of fluorescently labeled oligonucleotides as probes, all the tested PS DNA strands are adsorbed more strongly on GO compared to the PO DNA of the same sequence. The adsorption mechanism is probed by washing the adsorbed DNA with proteins, surfactants, and urea. Molecular dynamics simulations show that van der Waals forces are responsible for the tighter adsorption of PS DNA. Polycytosine (poly-C) DNA, in general, has a high affinity for the GO surface, and PS poly-C DNA can adsorb even stronger, making it an ideal anchoring sequence on GO. With this knowledge, noncovalent functionalization of GO with a diblock DNA is demonstrated, where a PS poly-C block is used to anchor on the surface. This conjugate achieves better hybridization than the PO DNA of the same sequence for hybridization with the complementary DNA.
Collapse
Affiliation(s)
- Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Yu Zhao
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Shaokang Guan
- School of Materials Science and Engineering, Zhengzhou University, Zhengzhou 450001, China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| |
Collapse
|
39
|
Ghosh T, Mondal A, Vyas A, Mishra S. A ‘one–tube’ synthesis of a selective fluorescence ‘turn off/on’ DNA probe based on a C-phycocyanin-graphene oxide (CPC-GO) bio composite. Int J Biol Macromol 2020; 163:977-984. [DOI: 10.1016/j.ijbiomac.2020.06.286] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 06/26/2020] [Accepted: 06/28/2020] [Indexed: 01/10/2023]
|
40
|
Moccia M, Antonacci A, Saviano M, Caratelli V, Arduini F, Scognamiglio V. Emerging technologies in the design of peptide nucleic acids (PNAs) based biosensors. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2020.116062] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
41
|
Krsihna BV, Ravi S, Prakash MD. Recent developments in graphene based field effect transistors. MATERIALS TODAY. PROCEEDINGS 2020; 45:S2214-7853(20)35804-1. [PMID: 32983908 PMCID: PMC7505095 DOI: 10.1016/j.matpr.2020.07.678] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 12/25/2022]
Abstract
This paper presents a comprehensive survey on the recent developments in Graphene Field Effect Transistor (G-FET), considering various aspects such as fabrication, modelling and simulation tools and applications especially in sensors, highlighting the future directions. Complying with the Moore's law, to increase the transistor density of an Integrated Circuit, new alternate materials for fabrication have been tried, instead of silicon due to its limitations in reducing transistor dimensions. Graphene, one such material, proves to be a suitable alternate for silicon due to the factors like superior carrier mobility and very high trans-conductance gain, etc and G-FET is becoming the most suitable choice for high-speed analog VLSI, RF, and bio- sensor circuits.
Collapse
Affiliation(s)
- B Vamsi Krsihna
- Department of Electronics and Communication Engineering, Koneru Lakshmaiah Education Foundation, Guntur 522502, Andhra Pradesh, India
| | - S Ravi
- Department of Electronics and Communication Engineering, Gudlavalleru Engineering College, Gudlavalleru 521356, Andhra Pradesh, India
| | - M Durga Prakash
- Department of Electronics and Communication Engineering, Koneru Lakshmaiah Education Foundation, Guntur 522502, Andhra Pradesh, India
- Department of Electronics and Communication Engineering, Velagapudi Ramakrishna Siddhartha Engineering College, Vijayawada 520 007, Andhra Pradesh, India
| |
Collapse
|
42
|
Fatema K, Liu Y, Cho KY, Oh WC. Comparative Study of Electrochemical Biosensors Based on Highly Efficient Mesoporous ZrO 2-Ag-G-SiO 2 and In 2O 3-G-SiO 2 for Rapid Recognition of E. coli O157:H7. ACS OMEGA 2020; 5:22719-22730. [PMID: 32954119 PMCID: PMC7495462 DOI: 10.1021/acsomega.0c00895] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 06/01/2020] [Indexed: 05/05/2023]
Abstract
Here, we reported an innovative and electrochemical biosensor for the rapid detection of Escherichia coli O157:H7. We fabricated the mesoporous ZrO2-Ag-G-SiO2 (ZAGS) and In2O3-G-SiO2 (IGS) sensors, and cyclic voltammetry (CV) was employed to detect the bacteria. The development of these portable sensors addresses the challenges of conventional time-consuming and more expensive laboratory-based analyses. Hence, the biosensors were highly selective to detect E. coli. The sensor could recognize an individual E. coli cell in 1 μL of sample volume within 30 s. E. coli live cells tied down on sample nanoparticles worked toward the definite acquirement of E. coli. The high thickness of negative charge on the surface of E. coli cells effectively regulated the concentration of dominant part charge carriers in the mesoporous channel, allowing a continuous check of E. coli concentration in a known sample. The signal current decreased linearly, while the E. coli concentration increased from 1.0 × 101 to 1.0 × 1010 CFU/mL. ZAGS and IGS biosensors could detect E. coli in the range from 101 to 1010 CFU/mL. ZAGS and IGS biosensors in this investigation showed great specificity, reproducibility, stability, and selectivity and are expected to have a great impact on applications in the detection of foodborne pathogens.
Collapse
Affiliation(s)
- Kamrun
Nahar Fatema
- Department
of Advanced Materials Science & Engineering, Hanseo University, Seosan-si, Chungnam 356-706, South Korea
| | - Yin Liu
- College
of Materials Science and Engineering, Anhui
University of Science & Technology, Huainan 232001, P. R. China
| | - Kwang Youn Cho
- Korea Institute
of
Ceramic Engineering and Technology, Soho-ro, Jinju-si, Gyeongsangnam-do 153801, South Korea
| | - Won-Chun Oh
- Department
of Advanced Materials Science & Engineering, Hanseo University, Seosan-si, Chungnam 356-706, South Korea
- College
of Materials Science and Engineering, Anhui
University of Science & Technology, Huainan 232001, P. R. China
| |
Collapse
|
43
|
Choi MH, Ravi Kumara GS, Seo YJ. rkDNA-graphene oxide as a simple probe for the rapid detection of miRNA21. Bioorg Med Chem Lett 2020; 30:127398. [PMID: 32738995 DOI: 10.1016/j.bmcl.2020.127398] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 01/10/2023]
Abstract
In this study we developed a novel diagnostic tool for the detection of miRNA21, based on the fluorescent nucleotide morpholine naphthalimide deoxyuridine (dUrkTP). We incorporated dUrkTP into DNA through primer extension to obtain rkDNA displaying high fluorescence. We then used lambda exonuclease, a specific nuclease for 3́-monophosphate-containing DNA, to separate rkDNA from its complementary sequence. The fluorescence of the free rkDNA was quenched dramatically upon interacting with graphene oxide (GO). Our rkDNA-GO fluorescence probing system exhibited high sensitivity and selectivity for the detection of miRNA21. This inexpensive probing system, employing simple primer extension and exonuclease degradation, required only 30 min to detect its target miRNA. This strategy appears suitable for the detection of diverse types of miRNA.
Collapse
Affiliation(s)
- Moon Hyeok Choi
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea
| | | | - Young Jun Seo
- Department of Chemistry, Jeonbuk National University, Jeonju 54896, South Korea.
| |
Collapse
|
44
|
Roy E, Nagar A, Chaudhary S, Pal S. Advanced Properties and Applications of AIEgens-Inspired Smart Materials. Ind Eng Chem Res 2020. [DOI: 10.1021/acs.iecr.0c01869] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ekta Roy
- Department of Chemistry, Government Engineering College Jhalawar, Jhalawar, Rajasthan 326023, India
| | - Achala Nagar
- Department of Chemistry, Government Engineering College Jhalawar, Jhalawar, Rajasthan 326023, India
| | - Sandeep Chaudhary
- Laboratory of Organic and Medicinal Chemistry, Department of Chemistry, Malaviya National Institute of Technology, Jaipur, Rajasthan 302017, India
| | - Souvik Pal
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan 11677, R.O.C
| |
Collapse
|
45
|
Ma H, Xu Z, Fang H, Lei X. Unexpected sequence adsorption features of polynucleotide ssDNA on graphene oxide. Phys Chem Chem Phys 2020; 22:11740-11746. [PMID: 32409813 DOI: 10.1039/d0cp01066a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The sequence features of single-stranded DNA (ssDNA) adsorbed on a graphene oxide (GO) surface are important for applications of the DNA/GO functional structure in biosensors, biomedicine, and materials science. In this study, molecular dynamics (MD) simulations were used to examine the adsorption of polynucleotide ssDNAs (A12, C12, G12, and T12) and single nucleotides (A, C, G, and T) on the GO surface. For the latter case, the nucleotide-GO interaction energy followed the trend G > A > C > T, even though it was influenced by specific adsorption sites. In the case of polynucleotides, unexpectedly polythymidine (T12) had the strongest interaction with the GO surface. The angle distributions of the adsorbed nucleobases indicated that T12 was more likely to form a quasi-parallel structure with GO compared to A12, C12, or G12. This was attributed to the weakest π-stacking interactions of thymine. Weaker intra-molecular base-stacking interactions made it easier to break the structures of pyrimidine bases relative to those of purine bases. Weaker inter-molecular base-stacking interactions between T12 and the GO surface enabled T12 to adjust its structure easily to a more stable one by slipping on the surface. This result provides a new understanding of polynucleotide ssDNA adsorption on GO surfaces, which will help in the design of functional DNA/GO structure-based platforms.
Collapse
Affiliation(s)
- Huishu Ma
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, P.O. Box 800-204, Shanghai, 201800, China
| | | | | | | |
Collapse
|
46
|
Du H, Chen J, Zhang J, Zhou R, Yang P, Hou X, Cheng N. Toehold-regulated competitive assembly to accelerate the kinetics of graphene oxide-based biosensors. J Mater Chem B 2020; 8:3683-3689. [PMID: 32108844 DOI: 10.1039/c9tb02454a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
With effective adsorption and quenching efficiency, graphene oxide (GO) can be utilized for sensing biomolecules such as nucleic acids and proteins. In these assays, the fluorophore-labeled nucleic acid (reporter) is usually adsorbed by GO first, followed by adding the target molecules to bind the reporter, thus restoring the fluorescence signal. However, the kinetics of fluorescence recovery is usually very slow because the target is probably adsorbed by GO and compromises the binding of the target and the reporter. Herein, we proposed a toehold-regulated strand displacement strategy to accelerate the kinetics of GO-based biosensing. In this strategy, the toehold of the duplex mediated a competitive assembly with the aim of eliminating the adsorption of the target by GO, facilitating the binding of the target and the reporter. While the duplex with the toehold of the target-blocker DNA or reporter-blocker DNA was formed, the rigid structure of the duplex weakened the adsorption of the target by GO and enhanced the recognition of the target by the reporter. This strategy achieved up to 2.6-fold enhancement in fluorescence signal restoration for nucleic acid detection, while there was 3.2-fold enhancement in fluorescence signal restoration for thrombin detection. It has also been demonstrated that this strategy can be used for the determination of DNA and thrombin in diluted serum with excellent specificity.
Collapse
Affiliation(s)
- Huan Du
- Analytical & Testing Center, Sichuan University, Chengdu, Sichuan 610064, China.
| | | | | | | | | | | | | |
Collapse
|
47
|
Oligonucleotide Detection and Optical Measurement with Graphene Oxide in the Presence of Bovine Serum Albumin Enabled by Use of Surfactants and Salts. COATINGS 2020. [DOI: 10.3390/coatings10040420] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
As graphene oxide-based oligonucleotide biosensors improve, there is a growing need to explore their ability to retain high sensitivity for low target concentrations in the context of biological fluids. Therefore, we innovatively combined assay milieu factors that could influence the key performance parameters of DNA hybridization and graphene oxide (GO) colloid dispersion, verifying their suitability to enhance oligonucleotide–GO interactions and biosensor performance. As a model system, we tested single-strand (ss) DNA detection in a complex solution containing bovine serum albumin (BSA) and salts with surfactants. A fluorescein conjugated 30-mer oligonucleotide ssDNA probe was combined with its complementary cDNA target, together with solute dispersed GO and either non-ionic (Triton X-100 and Tween-20) or anionic sodium dodecyl sulfate (SDS) surfactants. In this context, we compared the effect of divalent Mg2+ or monovalent Na+ salts on GO binding for the quench-based detection of specific target–probe DNA hybridization. GO biosensor strategies for quench-based DNA detection include a “turn on” enhancement of fluorescence upon target–probe interaction versus a “turn off” decreased fluorescence for the GO-bound probe. We found that the sensitive and specific detection of low concentrations of oligonucleotide target was best achieved using a strategy that involved target–probe DNA hybridization in the solution with a subsequent modified “turn-off” GO capture and the quenching of the unhybridized probe. Using carefully formulated assay procedures that prevented GO aggregation, the preferential binding and quenching of the unhybridized probe were both achieved using 0.1% BSA, 0.065% SDS and 6 mM NaCl. This resulted in the sensitive measurement of the specific target–probe complexes remaining in the solution. The fluorescein-conjugated single stranded probe (FAM–ssDNA) exhibited linearity to cDNA hybridization with concentrations in the range of 1–8 nM, with a limit of detection equivalent to 0.1 pmoles of target in 100 µL of assay mix. We highlight a general approach that may be adopted for oligonucleotide target detection within complex solutions.
Collapse
|
48
|
Traeger JC, Schwartz DK. Interplay of electrostatic repulsion and surface grafting density on surface-mediated DNA hybridization. J Colloid Interface Sci 2020; 566:369-374. [DOI: 10.1016/j.jcis.2020.01.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 12/14/2022]
|
49
|
Bhai S, Ganguly B. Probing the Interaction of Nucleobases and Fluorophore‐Tagged Nucleobases with Graphene Surface: Adsorption and Fluorescence Studies. ChemistrySelect 2020. [DOI: 10.1002/slct.201904442] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Surjit Bhai
- Academy of Scientific and Innovative ResearchComputation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility) CSIR-CSMCRI, Bhavnagar- 364002 Gujarat India
| | - Bishwajit Ganguly
- Computation and Simulation Unit (Analytical Discipline and Centralized Instrument Facility)CSIR-Central Salt & Marine Chemicals Research Institute, Bhavnagar Gujarat India- 364 002
| |
Collapse
|
50
|
Chang Y, Liu B, Huang Z, Liu Y, Liu M, Liu J. Yttrium Oxide as a Strongly Adsorbing but Nonquenching Surface for DNA Oligonucleotides. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:1034-1042. [PMID: 31935105 DOI: 10.1021/acs.langmuir.9b02743] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
A large number of nanomaterials can strongly adsorb DNA and quench fluorescence, such as graphene oxide, gold nanoparticles, and most metal oxides. On the other hand, noncationic nanomaterials that adsorb DNA but cannot quench fluorescence are less known. These materials are attractive for studying the mechanism of DNA-based surface reactions. Y2O3 was found to have this property. Herein, we used fluorescently labeled oligonucleotides as probes to study the mechanism of DNA adsorption. The fluorescence was quenched at low concentrations of Y2O3 and then recovered and even enhanced with higher Y2O3 concentrations. The reason was attributed to the intermolecular quenching by the DNA bases of the neighboring strands. The fluorescence enhancement was due to breaking of the intramolecular fluorophore/DNA interactions, and the most enhancement was observed with a Cy3-labeled DNA. DNA adsorption followed the Langmuir isotherm on Y2O3. Desorption experiments suggested that DNA was adsorbed through the phosphate backbone, with FAM-G15 and FAM-C15 adsorbed more strongly than the other two DNA homopolymers. With a high salt concentration, no fluorescence change was observed, suggesting that the DNA adsorbed in a folded state reducing intermolecular quenching. Overall, Y2O3 might be useful as a model surface for investigating DNA hybridization on a surface.
Collapse
Affiliation(s)
- Yangyang Chang
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Biwu Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Zhicheng Huang
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Yibo Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| | - Meng Liu
- School of Environmental Science and Technology, Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) , Dalian University of Technology , Dalian 116024 , China
| | - Juewen Liu
- Department of Chemistry, Waterloo Institute for Nanotechnology , University of Waterloo , Waterloo , Ontario N2L 3G1 , Canada
| |
Collapse
|