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Feng C, Liu X, Sun YF, Ren CL. Double-Stranded DNA Immobilized in Lying-Flat and Upright Orientation on a PNIPAm-Coated Surface: A Theoretical Study. ACS Macro Lett 2024:105-111. [PMID: 38190547 DOI: 10.1021/acsmacrolett.3c00647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Surface-immobilized double-stranded DNA (dsDNA) in upright orientation plays an important role in optimizing and understanding DNA-based nanosensors and nanodevices. However, it is difficult to regulate the surface density of upright DNA due to the fact that DNA usually stands vertically at a high packing density but may lie down at a low packing density. We herein report dsDNA immobilized in upright orientation on a poly(N-isopropylacrylamide) (PNIPAm)-coated surface in theory. The theoretical results reveal that the angle of upright DNA relative to the surface is larger than that of DNA immobilized on the bare surface caused by the lying-flat DNA under proper PNIPAm surface coverage at 45 °C. The surface density of upright DNA is significantly influenced by DNA concentration and DNA length. It is envisioned that the density-regulated DNA molecules immobilized in upright orientation in the present work are well suited to bottom-up construction of complex DNA-based nanostructures and nanodevices.
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Affiliation(s)
- Chao Feng
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Xiao Liu
- State Key Laboratory of Metastable Materials Science & Technology and Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China
| | - Yang-Feng Sun
- Industrial Technology Center, Chengde Petroleum College, Chengde 067000, China
| | - Chun-Lai Ren
- National Laboratory of Solid State Microstructures and Department of Physics, Nanjing University, Nanjing 210093, China
- Collaborative Innovation Center of Advanced Microstructures, Nanjing University, Nanjing 210093, China
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2
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Highly-selective detection of EGFR mutation gene in lung cancer based on surface enhanced Raman spectroscopy and asymmetric PCR. J Pharm Biomed Anal 2020; 190:113522. [PMID: 32777732 DOI: 10.1016/j.jpba.2020.113522] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 11/23/2022]
Abstract
The evaluation of EGFR mutation genes in circulating tumor DNA (ctDNA) in blood sample is key for patients with lung cancer. Surface-enhanced Raman scattering (SERS) has potential for trace detection of DNA or RNA. The detection rate offered by current methods can not meet clinical demand. By combining asymmetric polymerase chain reaction (PCR) and SERS, a highly-selective detection for EGFR mutation genes in lung cancer was developed. Sea-urchin like Au nanoclusters (AuNCs) were synthesized via Ag seed-mediated growth. AuNCs with a diameter of 120 nm were covered with 79 nanopricks (20 nm). Then, EGFR mutation specific molecular beacons (MBs) labeled with Cy3 were coated on the surface of AuNCs. The loading amount of MBs was calculated as 5720 ± 740 on one AuNCs. These AuNCs probes had good efficiency (equilibrium time: 20 minutes) with high sensitivity (detection limit: 5.8 nM), high specificity (capable of single-base mismatch recognition) and good stability against nucleases. Following this, asymmetric PCR was performed to obtain large numbers of single-stranded DNA (ssDNA, E746-A750del). The ssDNA was incubated with the AuNCs probes and tested quantitatively based on the SERS signals of the AuNCs probes. This combined asymmetric PCR-SERS method had a very high detection threshold (4.24 fM). The asymmetric PCR-SERS method was shown to have an overall sensitivity of 75% and specificity of 100% in a further 15 clinical blood samples. This method is proved to be promising for non-invasive and sensitive detection of EGFR mutations in ctDNA.
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Wittmar J, Meyer S, Sieling T, Kunte J, Smiatek J, Brand I. What Does Ectoine Do to DNA? A Molecular-Scale Picture of Compatible Solute-Biopolymer Interactions. J Phys Chem B 2020; 124:7999-8011. [PMID: 32816487 DOI: 10.1021/acs.jpcb.0c05273] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules such as lipids, proteins, and DNA. The molecular interaction between ectoine and biomolecules, in particular the interaction between ectoine and DNA, is far from being understood. In this paper, we describe molecular aspects of the interaction between ectoine and double-stranded DNA (dsDNA). Two 20 base pairs-long dsDNA fragments were immobilized on a gold surface via a thiol-tether. The interaction between the dsDNA monolayers with diluted and concentrated ectoine solutions was examined by means of X-ray photoelectron and polarization modulation infrared reflection absorption spectroscopies (PM IRRAS). Experimental results indicate that the ability of ectoine to bind water reduces the strength of hydrogen bonds formed to the ribose-phosphate backbone in the dsDNA. In diluted (0.1 M) ectoine solution, DNA interacts predominantly with water molecules. The sugar-phosphate backbone is involved in the formation of strong hydrogen bonds to water, which, over time, leads to a reorientation of the planes of nucleic acid bases. This reorientation destabilizes the strength of hydrogen bonds between the bases and leads to a partial dehybridization of the dsDNA. In concentrated ectoine solution (2.5 M), almost all water molecules interact with ectoine. Under this condition, ectoine is able to interact directly with DNA. Density functional theory (DFT) calculations demonstrate that the direct interaction involves the nitrogen atoms in ectoine and phosphate groups in the DNA molecule. The results of the quantum-chemical calculations show that rearrangements in the ribose-phosphate backbone, caused by a direct interaction with ectoine, facilitates contacts between the O atom in the phosphate group and H atoms in a nucleic acid base. In the PM IRRA spectra, an increase in the number of IR absorption modes in the base pair frequency region proves that the hydrogen bonds between bases become weaker. Thus, a sequence of reorientations caused by interaction with ectoine leads to a breakdown of hydrogen bonds between bases in the double helix.
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Affiliation(s)
- Julia Wittmar
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Susann Meyer
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Thorben Sieling
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
| | - Jörg Kunte
- Biodeterioration and Reference Organisms, Bundesanstalt für Materialforschung und -prüfung BAM, 12205 Berlin, Germany
| | - Jens Smiatek
- Institute for Computational Physics, University of Stuttgart, D-70569 Stuttgart, Germany
| | - Izabella Brand
- Department of Chemistry, Carl von Ossietzky University of Oldenburg, 26111 Oldenburg, Germany
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4
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Goodchild SA, Gao R, Shenton DP, McIntosh AJS, Brown T, Bartlett PN. Direct Detection and Discrimination of Nucleotide Polymorphisms Using Anthraquinone Labeled DNA Probes. Front Chem 2020; 8:381. [PMID: 32478035 PMCID: PMC7235368 DOI: 10.3389/fchem.2020.00381] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 02/04/2023] Open
Abstract
A novel electrochemical detection approach using DNA probes labeled with Anthraquinone (AQ) as a reporter moiety has been successfully exploited as a method for the direct detection of DNA targets. This assay uses simple voltammetry techniques (Differential Pulse Voltammetry) to exploit the unique responsiveness of AQ to its chemical environments within oxygenated aqueous buffers, providing a specific detection mechanism as a result of DNA hybridization. This measurement is based on a cathodic shift of the reduction potential of the AQ tag and the concurrent reduction in peak current upon DNA binding. The further utility of this approach for discrimination of closely related DNA targets is demonstrated using DNA strands specific to B. anthracis and closely related bacillus species. DNA targets were designed to the rpoB gene incorporating nucleotide polymorphisms associated with different bacillus species. This assay was used to demonstrate that the shift in reduction potential is directly related to the homology of the target DNA. The discriminatory mechanism is dependent on the presence of oxygen in the measurement buffer and is strongly linked to the position of the nucleotide polymorphisms; with homology at the terminus carrying the AQ functionalised nucleotide critical to achieving accurate discrimination. This understanding of assay design was used to demonstrate an optimized assay capable of discriminating between Yersinia pestis (the causative agent of plague) and closely related species based on the groEL gene. This method is attractive as it can not only detect DNA binding, but can also discriminate between multiple Single Nucleotide Polymorphisms (SNPs) within that DNA without the need for any additional reagents, reporters, or processes such as melting of DNA strands. This indicates that this approach may have great potential to be exploited within novel biosensors for detection and diagnosis of infectious disease in future Point of Care (PoC) devices.
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Affiliation(s)
- Sarah A Goodchild
- Defence Science and Technology Laboratory, Salisbury, United Kingdom.,University of Southampton, Southampton, United Kingdom
| | - Rachel Gao
- University of Southampton, Southampton, United Kingdom
| | - Daniel P Shenton
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
| | | | - Tom Brown
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Philip N Bartlett
- Defence Science and Technology Laboratory, Salisbury, United Kingdom
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Faria HAM, Zucolotto V. Label-free electrochemical DNA biosensor for zika virus identification. Biosens Bioelectron 2019; 131:149-155. [DOI: 10.1016/j.bios.2019.02.018] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/31/2019] [Accepted: 02/12/2019] [Indexed: 11/29/2022]
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Walper SA, Lasarte Aragonés G, Sapsford KE, Brown CW, Rowland CE, Breger JC, Medintz IL. Detecting Biothreat Agents: From Current Diagnostics to Developing Sensor Technologies. ACS Sens 2018; 3:1894-2024. [PMID: 30080029 DOI: 10.1021/acssensors.8b00420] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although a fundamental understanding of the pathogenicity of most biothreat agents has been elucidated and available treatments have increased substantially over the past decades, they still represent a significant public health threat in this age of (bio)terrorism, indiscriminate warfare, pollution, climate change, unchecked population growth, and globalization. The key step to almost all prevention, protection, prophylaxis, post-exposure treatment, and mitigation of any bioagent is early detection. Here, we review available methods for detecting bioagents including pathogenic bacteria and viruses along with their toxins. An introduction placing this subject in the historical context of previous naturally occurring outbreaks and efforts to weaponize selected agents is first provided along with definitions and relevant considerations. An overview of the detection technologies that find use in this endeavor along with how they provide data or transduce signal within a sensing configuration follows. Current "gold" standards for biothreat detection/diagnostics along with a listing of relevant FDA approved in vitro diagnostic devices is then discussed to provide an overview of the current state of the art. Given the 2014 outbreak of Ebola virus in Western Africa and the recent 2016 spread of Zika virus in the Americas, discussion of what constitutes a public health emergency and how new in vitro diagnostic devices are authorized for emergency use in the U.S. are also included. The majority of the Review is then subdivided around the sensing of bacterial, viral, and toxin biothreats with each including an overview of the major agents in that class, a detailed cross-section of different sensing methods in development based on assay format or analytical technique, and some discussion of related microfluidic lab-on-a-chip/point-of-care devices. Finally, an outlook is given on how this field will develop from the perspective of the biosensing technology itself and the new emerging threats they may face.
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Affiliation(s)
- Scott A. Walper
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Guillermo Lasarte Aragonés
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Kim E. Sapsford
- OMPT/CDRH/OIR/DMD Bacterial Respiratory and Medical Countermeasures Branch, U.S. Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Carl W. Brown
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- College of Science, George Mason University Fairfax, Virginia 22030, United States
| | - Clare E. Rowland
- Center for Bio/Molecular Science and Engineering, Code 6900, U.S. Naval Research Laboratory, Washington, D.C. 20375, United States
- National Research Council, Washington, D.C. 20036, United States
| | - Joyce C. Breger
- Center for Bio/Molecular Science and Engineering, Code 6900, 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
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Ferapontova EE. DNA Electrochemistry and Electrochemical Sensors for Nucleic Acids. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:197-218. [PMID: 29894229 DOI: 10.1146/annurev-anchem-061417-125811] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Sensitive, specific, and fast analysis of nucleic acids (NAs) is strongly needed in medicine, environmental science, biodefence, and agriculture for the study of bacterial contamination of food and beverages and genetically modified organisms. Electrochemistry offers accurate, simple, inexpensive, and robust tools for the development of such analytical platforms that can successfully compete with other approaches for NA detection. Here, electrode reactions of DNA, basic principles of electrochemical NA analysis, and their relevance for practical applications are reviewed and critically discussed.
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Affiliation(s)
- Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, DK-8000 Aarhus C, Denmark;
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Tian Y, Shuai Z, Shen J, Zhang L, Chen S, Song C, Zhao B, Fan Q, Wang L. Plasmonic Heterodimers with Binding Site-Dependent Hot Spot for Surface-Enhanced Raman Scattering. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2018; 14:e1800669. [PMID: 29736956 DOI: 10.1002/smll.201800669] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 03/28/2018] [Indexed: 06/08/2023]
Abstract
A novel plasmonic heterodimer nanostructure with a controllable self-assembled hot spot is fabricated by the conjugation of individual Au@Ag core-shell nanocubes (Au@Ag NCs) and varisized gold nanospheres (GNSs) via the biotin-streptavidin interaction from the ensemble to the single-assembly level. Due to their featured configurations, three types of heterogeneous nanostructures referred to as Vertice, Vicinity, and Middle are proposed and a single hot spot forms between the nanocube and nanosphere, which exhibits distinct diversity in surface plasmon resonance effect. Herein, the calculated surface-enhanced Raman scattering enhancement factors of the three types of heterodimers show a narrow distribution and can be tuned in orders of magnitude by controlling the size of GNSs onto individual Au@Ag NCs. Particularly, the Vertice heterodimer with unique configuration can provide extraordinary enhancement of the electric field for the single hot spot region due to the collaborative interaction of lightning rod effect and interparticle plasmon coupling effect. This established relationship between the architecture and the corresponding optical properties of the heterodimers provides the basis for creating controllable platforms which can be exploited in the applications of plasmonic devices, electronics, and biodetection.
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Affiliation(s)
- Yuanyuan Tian
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Zhenhua Shuai
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Jingjing Shen
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lei Zhang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Shufen Chen
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Chunyuan Song
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Baomin Zhao
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Quli Fan
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
| | - Lianhui Wang
- Key Laboratory for Organic Electronics and Information Displays and Institute of Advanced Materials (IAM), National Jiangsu Synergetic Innovation Center for Advanced Materials (SICAM), Nanjing University of Posts and Telecommunications, 9 Wenyuan Road, Nanjing, 210023, China
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9
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Li X, Yang T, Li CS, Song Y, Lou H, Guan D, Jin L. Surface Enhanced Raman Spectroscopy (SERS) for the Multiplex Detection of Braf, Kras, and Pik3ca Mutations in Plasma of Colorectal Cancer Patients. Am J Cancer Res 2018; 8:1678-1689. [PMID: 29556349 PMCID: PMC5858175 DOI: 10.7150/thno.22502] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 11/24/2017] [Indexed: 12/18/2022] Open
Abstract
In this paper, we discuss the use of a procedure based on polymerase chain reaction (PCR) and surface enhanced Raman spectroscopy (SERS) (PCR-SERS) to detect DNA mutations. Methods: This method was implemented by first amplifying DNA-containing target mutations, then by annealing probes, and finally by applying SERS detection. The obtained SERS spectra were from a mixture of fluorescence tags labeled to complementary sequences on the mutant DNA. Then, the SERS spectra of multiple tags were decomposed to component tag spectra by multiple linear regression (MLR). Results: The detection limit was 10-11 M with a coefficient of determination (R2) of 0.88. To demonstrate the applicability of this process on real samples, the PCR-SERS method was applied on blood plasma taken from 49 colorectal cancer patients to detect six mutations located at the BRAF, KRAS, and PIK3CA genes. The mutation rates obtained by the PCR-SERS method were in concordance with previous research. Fisher's exact test showed that only two detected mutations at BRAF (V600E) and PIK3CA (E542K) were significantly positively correlated with right-sided colon cancer. No other clinical feature such as gender, age, cancer stage, or differentiation was correlated with mutation (V600E at BRAF, G12C, G12D, G12V, G13D at KRAS, and E542K at PIK3CA). Visually, a dendrogram drawn through hierarchical clustering analysis (HCA) supported the results of Fisher's exact test. The clusters drawn by all six mutations did not conform to the distributions of cancer stages, differentiation or cancer positions. However, the cluster drawn by the two mutations of V600E and E542K showed that all samples with those mutations belonged to the right-sided colon cancer group. Conclusion: The suggested PCR-SERS method is multiplexed, flexible in probe design, easy to incorporate into existing PCR conditions, and was sensitive enough to detect mutations in blood plasma.
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Affiliation(s)
- Emil Paleček
- Biophysical Chemistry and Molecular Oncology; Institute of Biophysics AS CR, v.v.i.; Kralovopolska 135 612 65 Brno Czech Republic
| | - Martin Bartošík
- Regional Centre for Applied Molecular Oncology; Masaryk Memorial Cancer Institute; Zluty kopec 7 656 53 Brno Czech Republic
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Choi N, Lee J, Ko J, Jeon JH, Rhie GE, deMello AJ, Choo J. Integrated SERS-Based Microdroplet Platform for the Automated Immunoassay of F1 Antigens in Yersinia pestis. Anal Chem 2017; 89:8413-8420. [PMID: 28737374 DOI: 10.1021/acs.analchem.7b01822] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The development of surface-enhanced Raman scattering (SERS)-based microfluidic platforms has attracted significant recent attention in the biological sciences. SERS is a highly sensitive detection modality, with microfluidic platforms providing many advantages over microscale methods, including high analytical throughput, facile automation, and reduced sample requirements. Accordingly, the integration of SERS with microfluidic platforms offers significant utility in chemical and biological experimentation. Herein, we report a fully integrated SERS-based microdroplet platform for the automatic immunoassay of specific antigen fraction 1 (F1) in Yersinia pestis. Specifically, highly efficient and rapid immunoreactions are achieved through sequential droplet generation, transport, and merging, while wash-free immunodetection is realized through droplet-splitting. Such integration affords a novel multifunctional platform capable of performing complex multistep immunoassays in nL-volume droplets. The limit of detection of the F1 antigen for Yersinia pestis using the integrated SERS-based microdroplet platform is 59.6 pg/mL, a value approximately 2 orders of magnitude more sensitive than conventional enzyme-linked immunosorbent assays. This assay system has additional advantages including reduced sample consumption (less than 100 μL), rapid assay times (less than 10 min), and fully automated fluid control. We anticipate that this integrated SERS-based microdroplet device will provide new insights in the development of facile assay platforms for various hazardous materials.
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Affiliation(s)
- Namhyun Choi
- Department of Bionano Technology, Hanyang University , Ansan 15588, South Korea
| | - Jiyoung Lee
- Department of Bionano Technology, Hanyang University , Ansan 15588, South Korea
| | - Juhui Ko
- Department of Bionano Technology, Hanyang University , Ansan 15588, South Korea
| | - Jun Ho Jeon
- Division of High-risk Pathogen Research, Center for Infectious Diseases, National Institute of Health , Cheongju 28159, South Korea
| | - Gi-Eun Rhie
- Division of High-risk Pathogen Research, Center for Infectious Diseases, National Institute of Health , Cheongju 28159, South Korea
| | - Andrew J deMello
- Department of Chemistry and Applied Biosciences, Institute of Chemical and Bioengineering, ETH Zürich , Vladimir Prelog Weg 1, 8093 Zürich, Switzerland
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University , Ansan 15588, South Korea
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12
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Kékedy-Nagy L, Ferapontova EE, Brand I. Submolecular Structure and Orientation of Oligonucleotide Duplexes Tethered to Gold Electrodes Probed by Infrared Reflection Absorption Spectroscopy: Effect of the Electrode Potentials. J Phys Chem B 2017; 121:1552-1565. [PMID: 28177253 DOI: 10.1021/acs.jpcb.6b12363] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Unique electronic and ligand recognition properties of the DNA double helix provide basis for DNA applications in biomolecular electronic and biosensor devices. However, the relation between the structure of DNA at electrified interfaces and its electronic properties is still not well understood. Here, potential-driven changes in the submolecular structure of DNA double helices composed of either adenine-thymine (dAdT)25 or cytosine-guanine (dGdC)20 base pairs tethered to the gold electrodes are for the first time analyzed by in situ polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) performed under the electrochemical control. It is shown that the conformation of the DNA duplexes tethered to gold electrodes via the C6 alkanethiol linker strongly depends on the nucleic acid sequence composition. The tilt of purine and pyrimidine rings of the complementary base pairs (dAdT and dGdC) depends on the potential applied to the electrode. By contrast, neither the conformation nor orientation of the ionic in character phosphate-sugar backbone is affected by the electrode potentials. At potentials more positive than the potential of zero charge (pzc), a gradual tilting of the double helix is observed. In this tilted orientation, the planes of the complementary purine and pyrimidine rings lie ideally parallel to each other. These potentials do not affect the integral stability of the DNA double helix at the charged interface. At potentials more negative than the pzc, DNA helices adopt a vertical to the gold surface orientation. Tilt of the purine and pyrimidine rings depends on the composition of the double helix. In monolayers composed of (dAdT)25 molecules the rings of the complementary base pairs lie parallel to each other. By contrast, the tilt of purine and pyrimidine rings in (dGdC)20 helices depends on the potential applied to the electrode. Such potential-induced mobility of the complementary base pairs can destabilize the helix structure at a submolecular level. These pioneer results on the potential-driven changes in the submolecular structure of double stranded DNA adsorbed on conductive supports contribute to further understanding of the potential-driven sequence-specific electronic properties of surface-tethered oligonucleotides.
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Affiliation(s)
- László Kékedy-Nagy
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Elena E Ferapontova
- Interdisciplinary Nanoscience Center (iNANO) and Center for DNA Nanotechnology (CDNA), Science and Technology, Aarhus University , Gustav Wieds Vej 14, DK-8000 Aarhus-C, Denmark
| | - Izabella Brand
- Department of Chemistry, University of Oldenburg , 26111 Oldenburg, Germany
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13
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14
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Affiliation(s)
- Hana Černocká
- Institute of Biophysics of the CAS, v. v. i.; Královopolská 135 612 65 Brno Czech Republic
| | - Emil Paleček
- Institute of Biophysics of the CAS, v. v. i.; Královopolská 135 612 65 Brno Czech Republic
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15
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Papadopoulou E, Gale N, Thompson JF, Fleming TA, Brown T, Bartlett PN. Specifically horizontally tethered DNA probes on Au surfaces allow labelled and label-free DNA detection using SERS and electrochemically driven melting. Chem Sci 2015; 7:386-393. [PMID: 29861989 PMCID: PMC5952265 DOI: 10.1039/c5sc03185k] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 10/08/2015] [Indexed: 11/21/2022] Open
Abstract
Controlled covalent attachment of dsDNA horizontally orientated on a gold surface is achieved through the use of a single surface-linker located approximately half way along the attached DNA probe strand.
Controlled covalent attachment of dsDNA horizontally orientated on a gold surface is achieved through the use of a single surface-linker located approximately half way along the attached DNA probe strand. We show that horizontally oriented dsDNA on a gold surface can undergo melting and re-hybridization to target strand in solution and thus can be used for the detection of specific target DNA sequences using surface-enhanced Raman spectroscopy (SERS). We show that a range of lengths of target DNA sequences from ∼30-bases to 78-bases can be specifically hybridized to the short immobilized DNA probe sequence and adopt a horizontal orientation on the gold surface. Following thermal or electrochemically driven melting of the immobilized dsDNA, the target DNA strand diffuses away while the probe strand remains attached to the surface allowing the functionalized surfaces to be reused. The melting of the horizontally orientated immobilized dsDNA can be monitored using SERS either by employing a dye label covalently attached on the DNA target strand or by employing a binding agent selective for dsDNA. This approach of covalently immobilizing the DNA probe strand through a linker located at approximately the middle of the strand has great potential to improve the sensitivity and specificity of molecular assays that employ DNA arrays on solid surfaces.
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Affiliation(s)
- E Papadopoulou
- Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK .
| | - N Gale
- ATDBio Ltd , Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK
| | - J F Thompson
- Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK .
| | - T A Fleming
- Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK .
| | - T Brown
- Department of Chemistry , University of Oxford , Chemistry Research Laboratory , 12 Mansfield Rd , Oxford OX1 3TA , UK
| | - P N Bartlett
- Chemistry , University of Southampton , Highfield , Southampton , SO17 1BJ , UK .
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Papadopoulou E, Meneghello M, Marafini P, Johnson RP, Brown T, Bartlett PN. The effect of temperature on electrochemically driven denaturation monitored by SERS. Bioelectrochemistry 2015; 106:353-8. [PMID: 26145815 DOI: 10.1016/j.bioelechem.2015.06.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 05/11/2015] [Accepted: 06/21/2015] [Indexed: 10/23/2022]
Abstract
Scanning the electrochemical potential negative results in the gradual denaturation of dsDNA immobilised at a nanostructure gold electrode, the DNA melting is monitored by SERS. We demonstrate the effect of the experimental temperature on the electrochemically driven melting (E-melting) by carrying out experiments between 10 and 28 °C using two DNA duplexes (20 and 21 base pairs). Significant temperature dependence for both the melting potentials, Em, and the steepness of the melting curves was found over the range 10 to 18 °C. Above 18 °C the results were found to be independent of temperature. The relative temperature insensitivity of the melting potentials above 18 °C is advantageous for the application of the electrochemically driven melting technique because precise temperature control is not necessary for measurements that are carried out around room temperature. Conversely temperature dependence below 18 °C offers a way to improve discrimination for highly similar DNA sequences.
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Affiliation(s)
| | - Marta Meneghello
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Pietro Marafini
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Robert P Johnson
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK
| | - Tom Brown
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Oxford OX1 3TA, UK
| | - Philip N Bartlett
- Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, UK.
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