1
|
Ngo LT, Chaudhari P, Wang WK, Tseng YT, Kuo PL, Huang CJ, Chiang CY, Chau LK, Huang TT. Noninvasive Prenatal Genetic Screening of Cell-Free Fetal DNA for Early Prediction of β-Thalassemia Using Fiber Optic Nanogold-Linked Sorbent Assay. ACS Sens 2024. [PMID: 39088458 DOI: 10.1021/acssensors.4c01194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/03/2024]
Abstract
β-Thalassemia is a prevalent type of severe inherited chronic anemia, primarily identified in developing countries. The identification of single nucleotide polymorphisms (SNPs) plays a vital role in the early diagnosis of genetic diseases. Here, we reported the development of an amplification-free fiber optic nanogold-linked sorbent assay method using a fiber optic particle plasmon resonance (FOPPR) biosensor for rapid and ultrasensitive detection of SNPs. Herein, MutS protein was selected as the biorecognition capture probe and immobilized on the sensing region to capture the target mutant DNA, which was hybridized with a single-base mismatched single-stranded DNA labeled by a gold nanoparticle (AuNP). The AuNP acts as a signaling agent to be detected by the FOPPR biosensor when it is bound on the fiber core surface. The method effectively differentiates mismatched double-stranded DNA by MutS protein from perfectly matched/complementary dsDNA. It exhibits an impressively low detection limit for the detection of SNPs at approximately 10-16 M using low-cost sensor chips and devices. By determination of the ratio of mutant DNA to normal DNA in cell-free genomic DNA from blood samples, this method is promising for diagnosing β-thalassemia in fetuses without invasive testing techniques.
Collapse
Affiliation(s)
- Loan Thi Ngo
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pallavi Chaudhari
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Wei-Kai Wang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| | - Yen-Ta Tseng
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Pao-Lin Kuo
- Department of Obstetrics Gynecology, College of Medicine, National Cheng Kung University Hospital, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Obstetrics & Gynecology, E-Da Hospital, 1 Yida Rd., Yanchao District, Kaohsiung City 82445, Taiwan
| | - Chun-Jen Huang
- Department of Chemical and Materials Engineering, National Central University, 300 Zhongda Rd., Zhongli District, Taoyuan City 320, Taiwan
- R&D Center for Membrane Technology, Chung Yuan Christian University, 200 Chung Pei Rd., Chung-Li City 32023, Taiwan
| | - Chang-Yue Chiang
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Lai-Kwan Chau
- Department of Chemistry and Biochemistry, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
- Center for Nano Bio-Detection, National Chung Cheng University, 168 University Rd., Minhsiung, Chiayi 621301, Taiwan
| | - Tze-Ta Huang
- School of Dentistry, Institute of Oral Medicine, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
- Department of Stomatology, College of Medicine and Hospital, National Cheng Kung University, 138 Shengli Rd., North District, Tainan City 704, Taiwan
| |
Collapse
|
2
|
Shang Z, Deng Z, Yi X, Yang M, Nong X, Lin M, Xia F. Construction and bioanalytical applications of poly-adenine-mediated gold nanoparticle-based spherical nucleic acids. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:5564-5576. [PMID: 37861233 DOI: 10.1039/d3ay01618h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
Owing to the versatile photophysical and chemical properties, spherical nucleic acids (SNAs) have been widely used in biosensing. However, traditional SNAs are formed by self-assembly of thiolated DNA on the surface of a gold nanoparticle (AuNP), where it is challenging to precisely control the orientation and surface density of DNA. As a new SNA, a polyadenine (polyA)-mediated SNA using the high binding affinity of consecutive adenines to AuNPs shows controllable surface density and configuration of DNA, which can be used to improve the performance of a biosensor. Herein, we first introduce the properties of polyA-mediated SNAs and fundamental principles regarding the polyA-AuNP interaction. Then, we provide an overview of current representative synthesis methods of polyA-mediated SNAs and their advantages and disadvantages. After that, we summarize the application of polyA-mediated SNAs in biosensing based on fluorescence and colorimetric methods, followed by discussion and an outlook of future challenges in this field.
Collapse
Affiliation(s)
- Zhiwei Shang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Zixuan Deng
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xiaoqing Yi
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Ministry of Education, Gannan Medical University, Ganzhou 341000, China
| | - Mengyu Yang
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Xianliang Nong
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Meihua Lin
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| | - Fan Xia
- State Key Laboratory of Biogeology and Environmental Geology, Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China.
| |
Collapse
|
3
|
Karami A, Hasani M. Methods to functionalize gold nanoparticles with tandem-phosphorothioate DNA: role of physicochemical properties of the phosphorothioate backbone in DNA adsorption to gold nanoparticles. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2023; 15:4104-4113. [PMID: 37551768 DOI: 10.1039/d3ay00960b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
Perception of the differences in the physicochemical properties of phosphorothioate DNA (PS-DNA) and phosphodiester DNA (PO-DNA) greatly aids in understanding the AuNP-DNA binding process. Replacing one non-bridging oxygen atom of the anionic phosphodiester backbone with a sulfur atom leads to a major change in the DNA adsorption mechanism of AuNPs. In this work, we investigated and compared salt-aging, low pH-assisted, and freeze-thaw methods for conjugating phosphorothioate-modified oligonucleotides to AuNPs. The results obtained clearly demonstrate that only the pH-assisted method can successfully bind tandem phosphorothioate DNA to gold nanoparticles and sufficiently maintain the colloidal stability of AuNPs. When a phosphate group is converted to a phosphorothioate group, the negative charge of the phosphate group is located on the sulfur atom. Due to the soft nature of sulfur (a very weak H-bond acceptor), the negative charge on the sulfur atom cannot be shielded even with the gradual addition of salt to increase the ionic strength, so, the pH-assisted based method is the best for the functionalization of AuNPs with tandem-PS DNA.
Collapse
Affiliation(s)
- Abbas Karami
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
| | - Masoumeh Hasani
- Faculty of Chemistry, Bu-Ali Sina University, Hamedan 65174, Iran.
| |
Collapse
|
4
|
Choi DY, Kim S, Oh J, Nam J. Conjugation strategies of
DNA
to gold nanoparticles. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Da Yeon Choi
- Department of Chemistry Seoul National University Seoul South Korea
| | - Suhyun Kim
- Department of Chemistry Hankuk University of Foreign Studies (HUFS) Yongin South Korea
| | - Jeong‐Wook Oh
- Department of Chemistry Hankuk University of Foreign Studies (HUFS) Yongin South Korea
| | - Jwa‐Min Nam
- Department of Chemistry Seoul National University Seoul South Korea
| |
Collapse
|
5
|
Single-Stranded DNA Recognition over Fluorescent Gold-Aryl Nanoparticles. COLLOIDS AND INTERFACES 2022. [DOI: 10.3390/colloids6030042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Fluorescence labeling of gold-aryl nanoparticles, AuNPs-COOH, was achieved by the covalent derivatization with dansyl chloride (DNS-Cl) reagent (5-naphthalene-1-sulfonyl chloride) for potential ssDNA recognition. The fluorescent gold nanoparticles of AuNPs-C6H4-4-COO-dansyl (AuNPs-DNS) of spherical shape and a size of 19.3 ± 8.3 nm were synthesized in a carbonate-bicarbonate buffer (pH = 10.6) at 37 °C. The fluorescence emission at 475 nm was acquired using fluorescence spectroscopy and investigated using time-resolved photoluminescence. The conjugation of ssDNA to AuNPs-DNS using the freeze-thaw and salt-aging methods was confirmed by fluorescence emission quenching, gel electrophoresis separation, and lifetime decrease. Conjugated ssDNA to AuNPs-DNS using the freeze-thaw method was more efficient than the salt-aging method. The purity of ssDNA upon conjugation was measured with optical density, and the obtained A260/A280 ratio was in the range of 1.7–2.0. This research can be applied to other nucleotide recognition and theranostics.
Collapse
|
6
|
Niedzialkowski P, Koterwa A, Olejnik A, Zielinski A, Gornicka K, Brodowski M, Bogdanowicz R, Ryl J. Deciphering the Molecular Mechanism of Substrate-Induced Assembly of Gold Nanocube Arrays toward an Accelerated Electrocatalytic Effect Employing Heterogeneous Diffusion Field Confinement. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:9597-9610. [PMID: 35894869 PMCID: PMC9367014 DOI: 10.1021/acs.langmuir.2c01001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 07/20/2022] [Indexed: 06/15/2023]
Abstract
The complex electrocatalytic performance of gold nanocubes (AuNCs) is the focus of this work. The faceted shapes of AuNCs and the individual assembly processes at the electrode surfaces define the heterogeneous conditions for the purpose of electrocatalytic processes. Topographic and electron imaging demonstrated slightly rounded AuNC (average of 38 nm) assemblies with sizes of ≤1 μm, where the dominating patterns are (111) and (200) crystallographic planes. The AuNCs significantly impact the electrochemical performance of the investigated electrode [indium-tin oxide (ITO), glassy carbon (GC), and bulk gold] systems driven by surface electrons promoting the catalytic effect. Cyclic voltammetry in combination with scanning electrochemical microscopy allowed us to decipher the molecular mechanism of substrate-induced electrostatic assembly of gold nanocube arrays, revealing that the accelerated electrocatalytic effect should be attributed to the confinement of the heterogeneous diffusion fields with tremendous electrochemically active surface area variations. AuNC drop-casting at ITO, GC, and Au led to various mechanisms of heterogeneous charge transfer; only in the case of GC did the decoration significantly increase the electrochemically active surface area (EASA) and ferrocyanide redox kinetics. For ITO and Au substrates, AuNC drop-casting decreases system dimensionality rather than increasing the EASA, where Au-Au self-diffusion was also observed. Interactions of the gold, ITO, and GC surfaces with themselves and with surfactant CTAB and ferrocyanide molecules were investigated using density functional theory.
Collapse
Affiliation(s)
- Pawel Niedzialkowski
- Department
of Analytic Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Adrian Koterwa
- Department
of Analytic Chemistry, University of Gdańsk, Wita Stwosza 63, 80-952 Gdańsk, Poland
| | - Adrian Olejnik
- Department
of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications
and Informatics, Gdańsk University
of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
- Centre
for Plasma and Laser Engineering, The Szewalski Institute of Fluid-Flow
Machinery, Polish Academy of Sciences, Fiszera 14, 80-231 Gdańsk, Poland
| | - Artur Zielinski
- Department
of Electrochemistry, Corrosion and Materials Engineering, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Karolina Gornicka
- Institute
of Nanotechnology and Materials Engineering and Advanced Materials
Center, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Mateusz Brodowski
- Institute
of Nanotechnology and Materials Engineering and Advanced Materials
Center, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| | - Robert Bogdanowicz
- Department
of Metrology and Optoelectronics, Faculty of Electronics, Telecommunications
and Informatics, Gdańsk University
of Technology, Narutowicza
11/12, 80-233 Gdańsk, Poland
| | - Jacek Ryl
- Institute
of Nanotechnology and Materials Engineering and Advanced Materials
Center, Gdańsk University of Technology, Narutowicza 11/12, 80-233 Gdańsk, Poland
| |
Collapse
|
7
|
Yang W, Wang L, Fang M, Sheth V, Zhang Y, Alyssa M. Holden, Donahue ND, Green DE, Frickenstein AN, Mettenbrink EM, Schwemley TA, Francek ER, Haddad M, Hossen MN, Mukherjee S, Wu S, DeAngelis PL, Wilhelm S. Nanoparticle Surface Engineering with Heparosan Polysaccharide Reduces Serum Protein Adsorption and Enhances Cellular Uptake. NANO LETTERS 2022; 22:2103-2111. [PMID: 35166110 PMCID: PMC9540343 DOI: 10.1021/acs.nanolett.2c00349] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Nanoparticle modification with poly(ethylene glycol) (PEG) is a widely used surface engineering strategy in nanomedicine. However, since the artificial PEG polymer may adversely impact nanomedicine safety and efficacy, alternative surface modifications are needed. Here, we explored the "self" polysaccharide heparosan (HEP) to prepare colloidally stable HEP-coated nanoparticles, including gold and silver nanoparticles and liposomes. We found that the HEP-coating reduced the nanoparticle protein corona formation as efficiently as PEG coatings upon serum incubation. Liquid chromatography-mass spectrometry revealed the protein corona profiles. Heparosan-coated nanoparticles exhibited up to 230-fold higher uptake in certain innate immune cells, but not in other tested cell types, than PEGylated nanoparticles. No noticeable cytotoxicity was observed. Serum proteins did not mediate the high cell uptake of HEP-coated nanoparticles. Our work suggests that HEP polymers may be an effective surface modification technology for nanomedicines to safely and efficiently target certain innate immune cells.
Collapse
Affiliation(s)
- Wen Yang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Lin Wang
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Mulin Fang
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Vinit Sheth
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Yushan Zhang
- Department of Pathology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma 73104, USA
| | - Alyssa M. Holden
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Nathan D. Donahue
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Dixy E. Green
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Alex N. Frickenstein
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Evan M. Mettenbrink
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Tyler A. Schwemley
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Emmy R. Francek
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Majood Haddad
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Md Nazir Hossen
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, California Northstate University, Elk Grove, CA, 95757, USA
| | - Shirsha Mukherjee
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
| | - Si Wu
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK, 73019, USA
| | - Paul L. DeAngelis
- Department of Biochemistry and Molecular Biology, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
| | - Stefan Wilhelm
- Stephenson School of Biomedical Engineering, University of Oklahoma, Norman, Oklahoma, 73019, USA
- Stephenson Cancer Center, University of Oklahoma Health Sciences Center, Oklahoma City, Oklahoma, 73104, USA
- Institute for Biomedical Engineering, Science, and Technology (IBEST), University of Oklahoma, Norman, Oklahoma, 73019, USA
| |
Collapse
|
8
|
Huang M, Xiong E, Wang Y, Hu M, Yue H, Tian T, Zhu D, Liu H, Zhou X. Fast microwave heating-based one-step synthesis of DNA and RNA modified gold nanoparticles. Nat Commun 2022; 13:968. [PMID: 35181653 PMCID: PMC8857241 DOI: 10.1038/s41467-022-28627-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 01/25/2022] [Indexed: 12/22/2022] Open
Abstract
DNA/RNA-gold nanoparticle (DNA/RNA-AuNP) nanoprobes have been widely employed for nanobiotechnology applications. Here, we discover that both thiolated and non-thiolated DNA/RNA can be efficiently attached to AuNPs to achieve high-stable spherical nucleic acid (SNA) within minutes under a domestic microwave (MW)-assisted heating-dry circumstance. Further studies show that for non-thiolated DNA/RNA the conjugation is poly (T/U) tag dependent. Spectroscopy, test strip hybridization, and loading counting experiments indicate that low-affinity poly (T/U) tag mediates the formation of a standing-up conformation, which is distributed in the outer layer of SNA structure. In further application studies, CRISPR/Cas9-sgRNA (136 bp), SARS-CoV-2 RNA fragment (1278 bp), and rolling circle amplification (RCA) DNA products (over 1000 bp) can be successfully attached on AuNPs, which overcomes the routine methods in long-chain nucleic acid-AuNP conjugation, exhibiting great promise in biosensing and nucleic acids delivery applications. Current heating-dry strategy has improved traditional DNA/RNA-AuNP conjugation methods in simplicity, rapidity, cost, and universality. Simple methods for attaching polynucleotides to gold nanoparticles are of interest for simplifying conjugation in a range of applications. Here, the authors report a microwave heating-based method for the fast, one-step attachment of a range of thiolated or non-thiolated DNA and RNA to gold nanoparticles.
Collapse
Affiliation(s)
- Mengqi Huang
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Erhu Xiong
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
| | - Yan Wang
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, School of Chemistry, South China Normal University, 510006, Guangzhou, China
| | - Menglu Hu
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Huahua Yue
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Tian Tian
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China
| | - Debin Zhu
- Guangzhou Key Laboratory of Analytical Chemistry for Biomedicine, School of Chemistry, South China Normal University, 510006, Guangzhou, China
| | - Hong Liu
- Key Laboratory of Theoretical Chemistry of Environment Ministry of Education, School of Chemistry, South China Normal University, 510006, Guangzhou, China
| | - Xiaoming Zhou
- School of Life Sciences, South China Normal University, 510631, Guangzhou, China.
| |
Collapse
|
9
|
Huang G, Su C, Wang L, Fei Y, Yang J. The Application of Nucleic Acid Probe-Based Fluorescent Sensing and Imaging in Cancer Diagnosis and Therapy. Front Chem 2021; 9:705458. [PMID: 34141699 PMCID: PMC8204288 DOI: 10.3389/fchem.2021.705458] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/17/2021] [Indexed: 01/27/2023] Open
Abstract
It is well known that cancer incidence and death rates have been growing, but the development of cancer theranostics and therapeutics has been a challenging work. Recently, nucleic acid probe-based fluorescent sensing and imaging have achieved remarkable improvements in a variety of cancer management techniques, credited to their high sensitivity, good tolerance to interference, fast detection, and high versatility. Herein, nucleic acid probe-based fluorescent sensing and imaging are labeled with advanced fluorophores, which are essential for fast and sensitive detection of aberrant nucleic acids and other cancer-relevant molecules, consequently performing cancer early diagnosis and targeted treatment. In this review, we introduce the characteristics of nucleic acid probes, summarize the development of nucleic acid probe-based fluorescent sensing and imaging, and prominently elaborate their applications in cancer diagnosis and treatment. In discussion, some challenges and perspectives are elaborated in the field of nucleic acid probe-based fluorescent sensing and imaging.
Collapse
Affiliation(s)
- Ge Huang
- Department of Medicine, University of South China, Hengyang, China.,Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Chen Su
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Lijuan Wang
- Department of Medicine, University of South China, Hengyang, China.,Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Yanxia Fei
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| | - Jinfeng Yang
- Department of Anesthesiology and Pain Medicine, Hunan Cancer Hospital/The Affiliated Cancer Hospital of Xiangya School of Medicine, Changsha, China
| |
Collapse
|
10
|
Sanchez Barea J, Kang D. Integration of Surface‐enhanced Raman Spectroscopy with
PCR
for Monitoring Single Copy of
KRAS G12D
Mutation. B KOREAN CHEM SOC 2021. [DOI: 10.1002/bkcs.12298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Joel Sanchez Barea
- Department of Chemistry Incheon National University Incheon 22012 Republic of Korea
| | - Dong‐Ku Kang
- Department of Chemistry Incheon National University Incheon 22012 Republic of Korea
- Department of Chemistry Research Institute of Basic Sciences, Incheon National University Incheon 22012 Republic of Korea
| |
Collapse
|
11
|
Zhao J, Lu Z, Wang S, Wei Z, Zhou J, Ren S, Lou X. Nanoscale Affinity Double Layer Overcomes the Poor Antimatrix Interference Capability of Aptamers. Anal Chem 2021; 93:4317-4325. [PMID: 33620193 DOI: 10.1021/acs.analchem.0c05320] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Poor antimatrix interference capability of aptamers is one of the major obstacles preventing their wide applications for real-sample detections. Here, we devise a multiple-function interface, denoted as a nanoscale affinity double layer (NADL), to overcome this bottleneck via in situ simultaneous target enrichment, purification, and detection. The NADL consists of an upper aptamer layer for target purification and sensing and a lower nanoscale solid-phase microextraction (SPME) layer for sample enrichment. The targets flowing through the NADL-functionalized surface are instantly million-fold enriched and purified by the sequential extraction of aptamer and SPME. The formation of the aptamer-target complex is greatly enhanced, enabling ultrasensitive detection of targets with minimized interference from the matrix. Taking the fiber-optic evanescent wave sensor as an example, we demonstrated the feasibility and generality of the NADL. The unprecedented detection of limits of 800, 4.8, 40, and 0.14 fM were, respectively, achieved for three representative small-molecule targets with distinct hydrophobicity (kanamycin A, sulfadimethoxine, and di-(2-ethylhexyl) phthalate) and protein target (human serum albumin), corresponding to 2500 to 3 × 108-fold improvement compared to the sensors without the NADL. Our sensors also showed exceptionally high target specificity (>1000) and tunable dynamic ranges simply by manipulating the SPME layer. With these features comes the ability to directly detect targets in diluted environmental, food, and biological samples at concentrations all well below the tolerance limits.
Collapse
Affiliation(s)
- Jiaxing Zhao
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shuo Wang
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Zhenzhe Wei
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Jianshuo Zhou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Shang Ren
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Xisanhuan North Road 105, Beijing 100048, China
| |
Collapse
|
12
|
An analytical method to control the surface density and stability of DNA-gold nanoparticles for an optimized biosensor. Colloids Surf B Biointerfaces 2020; 187:110650. [DOI: 10.1016/j.colsurfb.2019.110650] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/15/2019] [Accepted: 11/16/2019] [Indexed: 12/17/2022]
|
13
|
Wang L, Wan Y, Xu Q, Lou X. Long-Term Functional Stability of Functional Nucleic Acid-Gold Nanoparticle Conjugates with Different Secondary Structures. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11791-11798. [PMID: 31430429 DOI: 10.1021/acs.langmuir.9b01884] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Thiolated functional nucleic acid-gold nanoparticle conjugates (FNA-AuNPs) are the core recognition elements in biosensors. The long-term functional stability (LTFS) is critical for their practical applications and, however, has been overlooked. Here we report on the huge effects of multiple experimental factors on LTFS, including spacer- and buffer-composition, secondary structures of FNAs, and surface blocking. We quantitatively determined these effects by measuring the relative hybridization capacity (RHC, the relative amount of complementary DNA hybridized with the same amount of conjugates) for linear DNA-AuNP or the relative signal change generated by their function (RSC-F) for molecular beacon (MB) and G-quadruplex (G4)-AuNPs. There is a positive relationship between the spacer affinity [oligoadenine (A10) > oligothymine (T10) > oligoethlyene glycol (EG18)] of the linear DNA probes and the LTFS. The LTFS of linear DNA-AuNP in phosphate buffer (PB) was much better than that in Good's buffers such as HEPES, Tris, and MES. The secondary structure of FNAs also strongly impacted the LTFS, showing the substantially decreased LTFS from G4- to linear DNA- to MB-AuNPs, where EG18 spacer was used for all these conjugates. The surface blocking of FNA-AuNPs greatly improved the LTFS. We experimentally determined that the LTFS of FNA-AuNPs was directly related to the dissociation of DNAs caused by the in situ generated H2O2 due to the oxidase activity of AuNP and thereby oxidation of Au-thiol bonds. The oxidase activity of AuNP was favored at high temperature, low pH, high AuNP concentration, high Good's buffer concentration, and high salt concentration, corresponding well with the positive effects of high affinity spacer, PB, and surface blocking on the LTFS of FNA-AuNPs. Our study has implications on both fundamental surface science and practical applications.
Collapse
Affiliation(s)
- Lei Wang
- Department of Chemistry , Capital Normal University , Xisanhuan North Road 105 , Beijing 100048 , China
| | - Yuan Wan
- Department of Chemistry , Capital Normal University , Xisanhuan North Road 105 , Beijing 100048 , China
| | - Qing Xu
- Department of Chemistry , Capital Normal University , Xisanhuan North Road 105 , Beijing 100048 , China
| | - Xinhui Lou
- Department of Chemistry , Capital Normal University , Xisanhuan North Road 105 , Beijing 100048 , China
| |
Collapse
|
14
|
Caputo TM, Battista E, Netti PA, Causa F. Supramolecular Microgels with Molecular Beacons at the Interface for Ultrasensitive, Amplification-Free, and SNP-Selective miRNA Fluorescence Detection. ACS APPLIED MATERIALS & INTERFACES 2019; 11:17147-17156. [PMID: 31021070 DOI: 10.1021/acsami.8b22635] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, a supramolecular structure with femtomolar biorecognition properties is proposed for use in analytical devices. It is obtained by an innovative interface between synthetic hydrogel polymers and molecular beacon (mb) probes. Supramolecularly structured microgels are synthetized with a core-shell architecture with specific dyes polymerized in a desired compartment. Mb probes are opportunely conjugated at the microgel interface so that their recognition mechanism is preserved and their spatial distribution is optimized to avoid crowding effects. The miR-21, a microRNA involved in various biological processes and usually used as a biomarker in early cancer diagnosis, has been selected as the target. The results demonstrate that by tuning the spatial distribution of molecular probes immobilized on the microgel and/or the amount of microgels, the assay shows scalable sensitivity reaching a limit of detection down to about 10 fM, without amplification steps and with detection time as short as 1 h. The assay results specific toward single mutated targets, and it is stable in the presence of high-interfering oligonucleotides concentrations. The miRNA target is also detected in human serum with performances similar to those observed in PBS buffer because of microgel antifouling properties without the need of any surface treatment. All tests were performed in a low sample volume (20 μL). As a result, mb-microgel represents an innovative biosensor to precisely quantify microRNAs in a direct (mix&read), scalable, and selective way. Such an approach paves the way for creating innovative biosensing interfaces with other probes, such as hairpins, aptamers, and PNA.
Collapse
Affiliation(s)
- Tania M Caputo
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
| | - Edmondo Battista
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Paolo A Netti
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| | - Filippo Causa
- Center for Advanced Biomaterials for Healthcare@CRIB , Istituto Italiano di Tecnologia (IIT) , Largo Barsanti e Matteucci 53 , 80125 Naples , Italy
- InterdisciplinaryResearch Centre on Biomaterials (CRIB) , Università degli Studi di Napoli "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
- Dipartimento di Ingegneria Chimica del Materiali e della Produzione Industriale (DICMAPI) , University "Federico II" , Piazzale Tecchio 80 , 80125 Naples , Italy
| |
Collapse
|
15
|
Liu B, Liu J. Freezing-Driven DNA Adsorption on Gold Nanoparticles: Tolerating Extremely Low Salt Concentration but Requiring High DNA Concentration. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:6476-6482. [PMID: 31008607 DOI: 10.1021/acs.langmuir.9b00746] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Attaching thiolated DNA to gold nanoparticles (AuNPs) is a highly important and useful reaction for many applications. Various methods such as adding salts, acids, polymers, and surfactants have been developed to facilitate the reaction. Recently, it was reported that a very high DNA density can be achieved simply by freezing AuNPs with the DNA without any other reagents. DNA oligonucleotides are also known to stretch and align upon freezing. In this work, a set of experiments were performed with a fluorophore and thiol dual-labeled DNA, and the DNA loading density and colloidal stability of AuNPs were measured. The initial salt concentration was unimportant, and even 0.1 mM Na+ allowed around 100 DNA attached to each 13 nm AuNPs. On the other hand, a high DNA concentration of 3 μM was needed to achieve the high DNA density and good colloidal stability of AuNPs. When the thiolated DNA was forced in stable secondary structures, the attachment was low, and preadsorbed DNA also inhibited the DNA attachment by the freezing method. Overall, nonstructured thiolated DNA strands need to align by freezing and quickly attached through the ends of the DNA. This work illustrates practical experiment design conditions and offers fundamental surface science insights for the DNA attachment by freezing.
Collapse
Affiliation(s)
- Biwu Liu
- 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
|
16
|
Heuer-Jungemann A, Feliu N, Bakaimi I, Hamaly M, Alkilany A, Chakraborty I, Masood A, Casula MF, Kostopoulou A, Oh E, Susumu K, Stewart MH, Medintz IL, Stratakis E, Parak WJ, Kanaras AG. The Role of Ligands in the Chemical Synthesis and Applications of Inorganic Nanoparticles. Chem Rev 2019; 119:4819-4880. [PMID: 30920815 DOI: 10.1021/acs.chemrev.8b00733] [Citation(s) in RCA: 465] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The design of nanoparticles is critical for their efficient use in many applications ranging from biomedicine to sensing and energy. While shape and size are responsible for the properties of the inorganic nanoparticle core, the choice of ligands is of utmost importance for the colloidal stability and function of the nanoparticles. Moreover, the selection of ligands employed in nanoparticle synthesis can determine their final size and shape. Ligands added after nanoparticle synthesis infer both new properties as well as provide enhanced colloidal stability. In this article, we provide a comprehensive review on the role of the ligands with respect to the nanoparticle morphology, stability, and function. We analyze the interaction of nanoparticle surface and ligands with different chemical groups, the types of bonding, the final dispersibility of ligand-coated nanoparticles in complex media, their reactivity, and their performance in biomedicine, photodetectors, photovoltaic devices, light-emitting devices, sensors, memory devices, thermoelectric applications, and catalysis.
Collapse
Affiliation(s)
- Amelie Heuer-Jungemann
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| | - Neus Feliu
- Department of Laboratory Medicine (LABMED) , Karolinska Institutet , Stockholm 171 77 , Sweden.,Fachbereich Physik, CHyN , Universität Hamburg , 22607 Hamburg , Germany
| | - Ioanna Bakaimi
- School of Chemistry, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton SO171BJ , U.K
| | - Majd Hamaly
- King Hussein Cancer Center , P. O. Box 1269, Al-Jubeiha, Amman 11941 , Jordan
| | - Alaaldin Alkilany
- Department of Pharmaceutics & Pharmaceutical Technology, School of Pharmacy , The University of Jordan , Amman 11942 , Jordan.,Fachbereich Physik, CHyN , Universität Hamburg , 22607 Hamburg , Germany
| | | | - Atif Masood
- Fachbereich Physik , Philipps Universität Marburg , 30357 Marburg , Germany
| | - Maria F Casula
- INSTM and Department of Chemical and Geological Sciences , University of Cagliari , 09042 Monserrato , Cagliari , Italy.,Department of Mechanical, Chemical and Materials Engineering , University of Cagliari , Via Marengo 2 , 09123 Cagliari , Italy
| | - Athanasia Kostopoulou
- Institute of Electronic Structure and Laser , Foundation for Research and Technology-Hellas , Heraklion , 71110 Crete , Greece
| | - Eunkeu Oh
- KeyW Corporation , Hanover , Maryland 21076 , United States.,Optical Sciences Division, Code 5600 , U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Kimihiro Susumu
- KeyW Corporation , Hanover , Maryland 21076 , United States.,Optical Sciences Division, Code 5600 , U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Michael H Stewart
- Optical Sciences Division, Code 5600 , U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Igor L Medintz
- Center for Bio/Molecular Science and Engineering, Code 6900 , U.S. Naval Research Laboratory , Washington , D.C. 20375 , United States
| | - Emmanuel Stratakis
- Institute of Electronic Structure and Laser , Foundation for Research and Technology-Hellas , Heraklion , 71110 Crete , Greece
| | - Wolfgang J Parak
- Fachbereich Physik, CHyN , Universität Hamburg , 22607 Hamburg , Germany
| | - Antonios G Kanaras
- School of Physics and Astronomy, Faculty of Engineering and Physical Sciences , University of Southampton , Southampton SO17 1BJ , U.K
| |
Collapse
|
17
|
Liao W, Lin Q, Xu Y, Yang E, Duan Y. Preparation of Au@Ag core-shell nanoparticle decorated silicon nanowires for bacterial capture and sensing combined with laser induced breakdown spectroscopy and surface-enhanced Raman spectroscopy. NANOSCALE 2019; 11:5346-5354. [PMID: 30848272 DOI: 10.1039/c9nr00019d] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Three-dimensional nano-biointerfaces, emerging as significant cell-guiding platforms, have attracted great attention. Nevertheless, complicated chemical modifications and instability of bio-ligands limit their widespread application. In this study, a novel biointerface, based on silicon nanowires (SiNWs) array, was prepared for bacterial capture and sensing. Vertically aligned SiNWs were fabricated via metal assisted chemical etching and decorated with uniform Au@Ag core-shell nanoparticles (Au@Ag NPs). These deposited Au@Ag NPs formed multi-scale topographic structures with nanowires, which provided effective attachment sites for bacterial adhesins. In addition, the Au cores of Au@Ag NPs enhanced the activity of the surface silver atoms and promoted the binding of Au@Ag NPs to bacteria. Thus, the Au@Ag NPs decorated SiNWs (SiNWs-Au@Ag) substrate exhibited high capture capacity for bacteria in drinking water (8.6 and 5.5 × 106 cells per cm2 for E. coli and S. aureus in 40 min, respectively) via physical and chemical effects. Bacteria in drinking water can be sensitively detected by using a combination of laser induced breakdown spectroscopy (LIBS) and label based surface-enhanced Raman spectroscopy (SERS) techniques. Due to the antibacterial activity of Au@Ag NPs and the physical stress exerted on SiNWs, the prepared biointerface also showed high antibacterial rates towards both Gram-positive and Gram-negative bacteria strains. With these excellent properties, the flexible sensing platform might open a new avenue for the prevention and control of microbial hazards in water.
Collapse
Affiliation(s)
- Wenlong Liao
- School of Chemical Engineering, Sichuan University, Chengdu 610065, P. R. China
| | | | | | | | | |
Collapse
|
18
|
Xie YF, Cheng YY, Liu ML, Zou HY, Huang CZ. A single gold nanoprobe for colorimetric detection of silver(i) ions with dark-field microscopy. Analyst 2019; 144:2011-2016. [DOI: 10.1039/c8an02397b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In this work, the formation of C–Ag+–C bonding between cytosines was utilized to induce interparticle coupling of gold nanoparticles modified with single-strand DNA, resulting in a color change as the signal transduction to quantify Ag+ sensitively under dark-field microscopy imaging, while we achieved the quantification of Ag+ could be directly realized in lake water samples and drug samples.
Collapse
Affiliation(s)
- Yi Fen Xie
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Science
- Southwest University
- Chongqing 400715
| | - Yun Ying Cheng
- Key Laboratory of Biomedical Analysis (Southwest University)
- Chongqing Science & Technology Commission
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400716
| | - Meng Li Liu
- Key Laboratory of Biomedical Analysis (Southwest University)
- Chongqing Science & Technology Commission
- College of Chemistry and Chemical Engineering
- Southwest University
- Chongqing 400716
| | - Hong Yan Zou
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Science
- Southwest University
- Chongqing 400715
| | - Cheng Zhi Huang
- Key Laboratory of Luminescent and Real-Time Analytical Chemistry (Southwest University)
- Ministry of Education
- College of Pharmaceutical Science
- Southwest University
- Chongqing 400715
| |
Collapse
|
19
|
Yang Y, Zhong S, Wang K, Huang J. Gold nanoparticle based fluorescent oligonucleotide probes for imaging and therapy in living systems. Analyst 2019; 144:1052-1072. [DOI: 10.1039/c8an02070a] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Gold nanoparticles (AuNPs) with unique physical and chemical properties have become an integral part of research in nanoscience.
Collapse
Affiliation(s)
- Yanjing Yang
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
- State Key Laboratory of Chemo/Biosensing and Chemometrics
| | - Shian Zhong
- College of Chemistry and Chemical Engineering
- Central South University
- Changsha
- PR China
| | - Kemin Wang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| | - Jin Huang
- State Key Laboratory of Chemo/Biosensing and Chemometrics
- College of Chemistry and Chemical Engineering
- Key Laboratory for Bio-Nanotechnology and Molecular Engineering of Hunan Province
- Hunan University
- Changsha 410082
| |
Collapse
|
20
|
Mascini M, Gaggiotti S, Della Pelle F, Wang J, Pingarrón JM, Compagnone D. Hairpin DNA-AuNPs as molecular binding elements for the detection of volatile organic compounds. Biosens Bioelectron 2018; 123:124-130. [PMID: 30054175 DOI: 10.1016/j.bios.2018.07.028] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 07/02/2018] [Accepted: 07/13/2018] [Indexed: 01/02/2023]
Abstract
Hairpin DNA (hpDNA) loops were used for the first time as molecular binding elements in gas analysis. The hpDNA loops sequences of unpaired bases were studied in-silico to evaluate the binding versus four chemical classes (alcohols, aldehydes, esters and ketones) of volatile organic compounds (VOCs). The virtual binding score trend was correlated to the oligonucleotide size and increased of about 25% from tetramer to hexamer. Two tetramer and pentamer and three hexamer loops were selected to test the recognition ability of the DNA motif. The selection was carried out trying to maximize differences among chemical classes in order to evaluate the ability of the sensors to work as an array. All oligonucleotides showed similar trends with best binding scores for alcohols followed by esters, aldehydes and ketones. The seven ssDNA loops (CCAG, TTCT, CCCGA, TAAGT, ATAATC, CATGTC and CTGCAA) were then extended with the same double helix stem of four base pair DNA (GAAG to 5' end and CTTC to 3' end) and covalently bound to gold nanoparticles (AuNPs) using a thiol spacer attached to 5' end of the hpDNA. HpDNA-AuNPs were deposited onto 20 MHz quartz crystal microbalances (QCMs) to form the gas piezoelectric sensors. An estimation of relative binding affinities was obtained using different amounts of eight VOCs (ethanol, 3-methylbutan-1-ol, 1-pentanol, octanal, nonanal, ethyl acetate, ethyl octanoate, and butane-2,3-dione) representative of the four chemical classes. In agreement with the predicted simulation, hexamer DNA loops improved by two orders of magnitude the binding affinity highlighting the key role of the hpDNA loop size. Using the sensors as an array a clear discrimination of VOCs on the basis of molecular weight and functional groups was achieved, analyzing the experimental with principal components analysis (PCA) demonstrating that HpDNA is a promising molecular binding element for analysis of VOCs.
Collapse
Affiliation(s)
- Marcello Mascini
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy; Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093, United States.
| | - Sara Gaggiotti
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Flavio Della Pelle
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy
| | - Joseph Wang
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA 92093, United States
| | - José M Pingarrón
- Department of Analytical Chemistry, Faculty of Chemistry, University Complutense of Madrid, Ciudad Universitaria s/n, 28040 Madrid, Spain
| | - Dario Compagnone
- Faculty of Bioscience and Technology for Food, Agriculture and Environment, University of Teramo, 64100 Teramo, Italy.
| |
Collapse
|
21
|
Bai C, Lu Z, Jiang H, Yang Z, Liu X, Ding H, Li H, Dong J, Huang A, Fang T, Jiang Y, Zhu L, Lou X, Li S, Shao N. Aptamer selection and application in multivalent binding-based electrical impedance detection of inactivated H1N1 virus. Biosens Bioelectron 2018; 110:162-167. [PMID: 29609164 DOI: 10.1016/j.bios.2018.03.047] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Revised: 03/14/2018] [Accepted: 03/21/2018] [Indexed: 12/11/2022]
Abstract
The type A influenza viruses are the most virulent and variable human pathogens with epidemic or even pandemic threat. The development of sensitive, specific and safe field testing methods is in particular need and quite challenging. We report here the selection and practical utilization of the inactivated influenza virus-specific aptamers. The DNA aptamers against inactivated intact H1N1 virus particles were identified through the systematic evolution of ligands by exponential enrichment (SELEX) procedure. The discriminative aptamers and their truncated sequences showed selectively high affinity to inactive H1N1 virus and H3N2 virus with the Kd in the low nanomolar range and collective binding properties. The truncated sequences were first applied in a sandwich enzyme-linked oligonucleotide assay (ELONA) with a H1N1 detection limit (LOD, S/N = 3) of 0.3 ng/μL and then in an electrochemical impedance (EIS) aptasensor with more than 300 times improved LOD (0.9 pg/μL) and the excellent selectivity over other viruses (> 100 times). Therefore the developed aptasensors represent the safer, simpler, and possibly better virus-variation adaptable means of virus diagnostics.
Collapse
Affiliation(s)
- Chenjun Bai
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Zhangwei Lu
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Hua Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Zihua Yang
- Department of Chemistry, Capital Normal University, Beijing, China
| | - Xuemei Liu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Hongmei Ding
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Hui Li
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Jie Dong
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Aixue Huang
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Tao Fang
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Yongqiang Jiang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lingling Zhu
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China
| | - Xinhui Lou
- Department of Chemistry, Capital Normal University, Beijing, China.
| | - Shaohua Li
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China.
| | - Ningsheng Shao
- Department of Biochemistry and Molecular Biology, Beijing Institute of Basic Medical Sciences, Beijing, China.
| |
Collapse
|
22
|
Zhu L, Qing Z, Hou L, Yang S, Zou Z, Cao Z, Yang R. Direct Detection of Nucleic Acid with Minimizing Background and Improving Sensitivity Based on a Conformation-Discriminating Indicator. ACS Sens 2017; 2:1198-1204. [PMID: 28741345 DOI: 10.1021/acssensors.7b00349] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
As is well-known, the nucleic acid indicator-based strategy is one of the major approaches to monitor the nucleic acid hybridization-mediated recognition events in biochemical analysis, displaying obvious advantages including simplicity, low cost, convenience, and generality. However, conventional indicators either hold strong self-fluorescence or can be lighted by both ssDNA and dsDNA, lacking absolute selectivity for a certain conformation, always with high background interference and low sensitivity in sensing; and additional processing (e.g., nanomaterial-mediated background suppression, and enzyme-catalyzed signal amplification) is generally required to improve the detection performance. In this work, a carbazole derivative, EBCB, has been synthesized and screened as a dsDNA-specific fluorescent indicator. Compared with conventional indicators under the same conditions, EBCB displayed a much higher selective coefficient for dsDNA, with little self-fluorescence and negligible effect from ssDNA. Based on its superior capability in DNA conformation-discrimination, high sensitivity with minimizing background interference was demonstrated for direct detection of nucleic acid, and monitoring nucleic acid-based circuitry with good reversibity, resulting in low detection limit and high capability for discriminating base-mismatching. Thus, we expect that this highly specific DNA conformation-discriminating indicator will hold good potential for application in biochemical sensing and molecular logic switching.
Collapse
Affiliation(s)
- Lixuan Zhu
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Zhihe Qing
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
| | - Lina Hou
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Sheng Yang
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Zhen Zou
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Zhong Cao
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
| | - Ronghua Yang
- Hunan
Provincial Key Laboratory of Materials Protection for Electric Power
and Transportation, Hunan Provincial Engineering Research Center for
Food Processing of Aquatic Biotic Resources, School of Chemistry and
Biological Engineering, Changsha University of Science and Technology, Changsha 410114, P. R. China
- State
Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry
and Chemical Engineering, Molecular Science and Biomedicine Laboratory, Hunan University, Changsha 410082, P. R. China
| |
Collapse
|
23
|
Liu B, Liu J. Freezing Directed Construction of Bio/Nano Interfaces: Reagentless Conjugation, Denser Spherical Nucleic Acids, and Better Nanoflares. J Am Chem Soc 2017; 139:9471-9474. [DOI: 10.1021/jacs.7b04885] [Citation(s) in RCA: 200] [Impact Index Per Article: 28.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Biwu Liu
- 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
|