1
|
Li Z, Lv Y, Duan X, Liu B, Zhao Y. Highly Uniform DNA Monolayers Generated by Freezing-Directed Assembly on Gold Surfaces Enable Robust Electrochemical Sensing in Whole Blood. Angew Chem Int Ed Engl 2023; 62:e202312975. [PMID: 37726209 DOI: 10.1002/anie.202312975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 09/17/2023] [Accepted: 09/18/2023] [Indexed: 09/21/2023]
Abstract
Assembling DNA on solid surfaces is fundamental to surface-based DNA technology. However, precise control over DNA conformation and organization at solid-liquid interfaces remains a challenge, resulting in limited stability and sensitivity in biosensing applications. We herein communicate a simple and robust method for creating highly uniform DNA monolayers on gold surfaces by a freeze-thawing process. Using Raman spectroscopy, fluorescent imaging, and square wave voltammetry, we demonstrate that thiolated DNA is concentrated and immobilized on gold surfaces with an upright conformation. Moreover, our results reveal that the freezing-induced DNA surfaces are more uniform, leading to improved DNA stability and target recognition. Lastly, we demonstrate the successful detection of a model drug in undiluted whole blood while mitigating the effects of biofouling. Our work not only provides a simple approach to tailor the DNA-gold surface for biosensors but also sheds light on the unique behavior of DNA oligonucleotides upon freezing on the liquid-solid interface.
Collapse
Affiliation(s)
- Zhenglian Li
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yanguan Lv
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Department of Clinical Medical Laboratory, Affiliated Hospital of Yang Zhou University Medical College, Huai'an Maternal and Child Health Care Center, Huai'an, Jiangsu, 223002, P. R. China
| | - Xiaoman Duan
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Biwu Liu
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| | - Yongxi Zhao
- Institute of Analytical Chemistry and Instrument for Life Science, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
- Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi'an, Shaanxi, 710049, P. R. China
| |
Collapse
|
2
|
Detection of breast cancer-related point-mutations using screen-printed and gold-plated electrochemical sensor arrays suitable for point-of-care applications. TALANTA OPEN 2022. [DOI: 10.1016/j.talo.2022.100150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
|
3
|
Su L, Su Y, Liu B. A ratiometric electrochemical strategy based on Fe (III) and Pt (IV) for immobilization-free detection of Escherichia coli. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:2541-2548. [PMID: 35713017 DOI: 10.1039/d2ay00628f] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A new ratiometric electrochemical strategy for immobilization-free detection of Escherichia coli (E. coli) was constructed by using a capture DNA-polyaniline/copper ferrite nanoparticles/graphene oxide (cDNA-PANI/CuFe2O4/GO) composite as capture probes, which has a high specific surface area and good magnetic properties. Then trigger DNA/Au nanoparticles (tDNA/Au NPs) were used as signal amplification labels, and Pt (IV) and Fe (III) were chosen as the signal probes. In the presence of targets, the sandwich format among cDNA-PANI/CuFe2O4/GO, E. coli and auxiliary DNA (aDNA) was realized by using the aptamer recognition system. Then, the tDNA/Au binding could be anchored on the sandwich format due to the principle of base complementation between unpaired aDNA and tDNA. And the unbounded tDNA of tDNA/Au NPs could bind an amount of Pt (IV). After separation using a magnet, a handful of unbound Pt (IV) which remained in the supernatant reacted with a large number of Fe (III) ions, leading to a markedly increased IFe(III)/IPt(IV) value. Oppositely, the sandwich format could not appear in the absence of targets, and even the tDNA/Au could not be immobilized on it. So, the redox reaction between a large amount of Pt (IV) residue in the supernatant and Fe (III) was significantly successful, causing a low IFe(III)/IPt(IV) value. Under optimal conditions, we found that IFe(III)/IPt(IV) was linearly related to the logarithmic E. coli concentration with a low limit of detection (1.862 × 103 cfu mL-1). This devised ratiometric electrochemical method may develop into a powerful and effective means for the detection of E. coli in real samples, which may also be developed as a universal tool for another microorganism.
Collapse
Affiliation(s)
- Lixia Su
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| | - Yonghuan Su
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| | - Bingqian Liu
- Guizhou Engineering Laboratory for Synthetic Drugs (Ministry of Education of Guizhou Province), College of Pharmacy, Guizhou University, Guiyang 550025, China.
| |
Collapse
|
4
|
Shaver A, Arroyo-Currás N. The challenge of long-term stability for nucleic acid-based electrochemical sensors. CURRENT OPINION IN ELECTROCHEMISTRY 2022; 32:100902. [PMID: 36092288 PMCID: PMC9455832 DOI: 10.1016/j.coelec.2021.100902] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Nucleic acid-based electrochemical sensors are a versatile technology enabling affinity-based detection of a great variety of molecular targets, regardless of inherent electrochemical activity or enzymatic reactivity. Additionally, their modular interface and ease of fabrication enable rapid prototyping and sensor development. However, the technology has inhibiting limitations in terms of long-term stability that have precluded translation into clinically valuable platforms like continuous molecular monitors. In this opinion, we discuss published methods to address various aspects of sensor stability, including thiol-based monolayers and anti-biofouling capabilities. We hope the highlighted works will motivate the field to develop innovative strategies for extending the long-term operational life of nucleic acid-based electrochemical sensors.
Collapse
Affiliation(s)
- Alexander Shaver
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Netzahualcóyotl Arroyo-Currás
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21218, USA
- Institute for Nanobiotechnology, Johns Hopkins University, Baltimore, MD, 21218, USA
| |
Collapse
|
5
|
Abstract
Hybridization between nucleic acid strands immobilized on a solid support with partners in solution is widely practiced in bioanalytical technologies and materials science. An important fundamental aspect of understanding these reactions is the role played by immobilization in the dynamics of duplex formation and disassembly. This report reviews and analyzes literature kinetic data to identify commonly observed trends and to correlate them with probable molecular mechanisms. The analysis reveals that while under certain conditions impacts from immobilization are minimal so that surface and solution hybridization kinetics are comparable, it is more typical to observe pronounced offsets between the two scenarios. In the forward (hybridization) direction, rates at the surface commonly decrease by one to two decades relative to solution, while in the reverse direction rates of strand separation at the surface can exceed those in solution by tens of decades. By recasting the deviations in terms of activation barriers, a consensus of how immobilization impacts nucleation, zipping, and strand separation can be conceived within the classical mechanism in which duplex formation is rate limited by preassembly of a nucleus a few base pairs in length, while dehybridization requires the cumulative breakup of base pairs along the length of a duplex. Evidence is considered for how excess interactions encountered on solid supports impact these processes.
Collapse
Affiliation(s)
- Eshan Treasurer
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering, Brooklyn, New York 11201, United States
| |
Collapse
|
6
|
Magnetic Hyperthermia on γ-Fe 2O 3@SiO 2 Core-Shell Nanoparticles for mi-RNA 122 Detection. NANOMATERIALS 2021; 11:nano11010149. [PMID: 33435365 PMCID: PMC7828054 DOI: 10.3390/nano11010149] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 12/30/2020] [Accepted: 01/05/2021] [Indexed: 11/16/2022]
Abstract
Magnetic hyperthermia on core-shell nanoparticles bears promising achievements, especially in biomedical applications. Here, thanks to magnetic hyperthermia, γ-Fe2O3 cores are able to release a DNA target mimicking the liver specific oncotarget miRNA-122. Our silica coated magnetic nanoparticles not only allow the grafting at their surface of a significant number of oligonucleotides but are also shown to be as efficient, by local heating, as 95 °C global heating when submitted to an alternative magnetic field, while keeping the solution at 28 °C, crucial for biological media and energy efficiency. Moreover, a slight modification of the silica coating process revealed an increased heating power, well adapted for the release of small oligonucleotides such as microRNA.
Collapse
|
7
|
Horny MC, Dupuis V, Siaugue JM, Gamby J. Release and Detection of microRNA by Combining Magnetic Hyperthermia and Electrochemistry Modules on a Microfluidic Chip. SENSORS 2020; 21:s21010185. [PMID: 33383936 PMCID: PMC7796339 DOI: 10.3390/s21010185] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 12/23/2020] [Accepted: 12/25/2020] [Indexed: 01/15/2023]
Abstract
The heating of a biologic solution is a crucial part in an amplification process such as the catalytic detection of a biological target. However, in many situations, heating must be limited in microfluidic devices, as high temperatures can cause the denaturation of the chip components. Local heating through magnetic hyperthermia on magnetic nano-objects has opened the doors to numerous improvements, such as for oncology where a reduced heating allows the synergy of chemotherapy and thermotherapy. Here we report on the design and implementation of a lab on chip without global heating of samples. It takes advantage of the extreme efficiency of DNA-modified superparamagnetic core-shell nanoparticles to capture complementary sequences (microRNA-target), uses magnetic hyperthermia to locally release these targets, and detects them through electrochemical techniques using ultra-sensitive channel DNA-modified ultramicroelectrodes. The combination of magnetic hyperthermia and microfluidics coupled with on-chip electrochemistry opens the way to a drastic reduction in the time devoted to the steps of extraction, amplification and nucleic acids detection. The originality comes from the design and microfabrication of the microfluidic chip suitable to its insertion in the millimetric gap of toric inductance with a ferrite core.
Collapse
Affiliation(s)
- Marie-Charlotte Horny
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120 Palaiseau, France;
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France; (V.D.); (J.-M.S.)
- Sorbonne Université, CNRS, Laboratoire Interfaces et Systèmes Electrochimiques, LISE, F-75005 Paris, France
| | - Vincent Dupuis
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France; (V.D.); (J.-M.S.)
| | - Jean-Michel Siaugue
- Sorbonne Université, CNRS, Physico-Chimie des Électrolytes et Nanosystèmes Interfaciaux, PHENIX, F-75005 Paris, France; (V.D.); (J.-M.S.)
| | - Jean Gamby
- Université Paris-Saclay, CNRS, Centre de Nanosciences et de Nanotechnologies, 91120 Palaiseau, France;
- Correspondence: ; Tel.: +33-1-70-27-06-70
| |
Collapse
|
8
|
Ma T, Martens I, Bizzotto D. Thermal Stability of Thiolated DNA SAMs in Buffer: Revealing the Influence of Surface Crystallography and DNA Coverage via In Situ Combinatorial Surface Analysis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2020; 36:14495-14506. [PMID: 33231463 DOI: 10.1021/acs.langmuir.0c01828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The thermal stability of thiol based DNA SAMs prepared on gold surfaces is an important parameter that is correlated to sensor lifetime. The thermal stability of DNA SAMs was evaluated in aqueous buffer through the use of fluorophore labeled DNA, a single crystal gold bead electrode, and microscopy. The stability of different crystallographic regions on the electrode was studied for thermal treatments up to 95 °C for 90 min. Using a in situ combinatorial surface analytical measurement showed that the crystallography of the underlying gold surface played a significant role, with the square or rectangular lattices (e.g., 110, 100, 210) having the highest stability. Surfaces with hexagonal lattices (e.g., 111, 311, 211) were less stable toward thermal treatments. These crystallographic trends were observed for both high and low coverage DNA SAMs. High coverage DNA SAMs were the most stable, with stability decreasing with decreasing coverage on average. Increasing DNA SAM coverage appears to slow the kinetics of thermal desorption, but the coordination to the underlying surface determined their relative stability. Preparing the DNA SAMs under nominally similar conditions were found to create surfaces that were similar at room temperature, but had significantly different thermal stability. Optimal DNA sensing with these surfaces most often requires low coverage DNA SAMs which results in poor thermal stability, which is predictive of a poor shelf life, making optimization of both parameters challenging. Furthermore, the crystallographically specific results should be taken into account when studying the typically used polycrystalline substrates since the underlying surface crystallography maybe different for different samples. It appears that preparing DNA SAMs with low coverage and significant thermal stability will be challenging using the current SAM preparation procedures.
Collapse
Affiliation(s)
- Tianxiao Ma
- Advanced Materials and Process Engineering Laboratory (AMPEL), University of British Columbia, Vancouver V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Isaac Martens
- Advanced Materials and Process Engineering Laboratory (AMPEL), University of British Columbia, Vancouver V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Dan Bizzotto
- Advanced Materials and Process Engineering Laboratory (AMPEL), University of British Columbia, Vancouver V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver V6T 1Z4, Canada
| |
Collapse
|
9
|
Combination of Loop-Mediated Isothermal Amplification and AuNP-Oligoprobe Colourimetric Assay for Pork Authentication in Processed Meat Products. FOOD ANAL METHOD 2020. [DOI: 10.1007/s12161-020-01901-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
AbstractPork adulteration is a major concern for Muslims and Jews whose diets are restricted by religious beliefs, as well as those who are allergic to pork meat and its derivatives. Accurate pork authentication is of great importance to assist this demographic group of people in making decision on their product purchase. The aim of this study was to develop a new analytical method for pork authentication in processed meat products based on a combination of loop-mediated isothermal amplification (LAMP) and AuNP-nanoprobe colourimetric assay. The LAMP conditions were first optimised to obtain the highest yield of amplified DNA products within the shortest time. Oligoprobe-functionalised AuNPs were then hybridised with LAMP-DNA amplicons and subsequently challenged with MgSO4 at a high concentration to induce AuNP aggregation. In the presence of pork DNA, the colloidal AuNP-probe remained unchanged in its red colour, which indicates the dispersion of AuNPs. In contrast, in the absence of pork DNA, the colour was changed to colourless as a result from the aggregation of AuNPs. The LAMP-AuNP-nanoprobe assay offers a high sensitivity with a limit of detection as low as 100 pg of pork DNA. The assay is highly specific to pork content without cross-reactivity with the other meat species tested. The assay developed herein can become a simple, inexpensive, precise, and rapid analytical tool for small laboratories or the general public interested in halal food authentication.
Collapse
|
10
|
Koppert J, Jean-Ruel H, O'Neill D, Harder C, Willmore W, Ianoul A, Albert J. Self-heating tilted fiber Bragg grating device for melt curve analysis of solid-phase DNA hybridization and thermal cycling. Anal Bioanal Chem 2019; 411:6813-6823. [PMID: 31432237 DOI: 10.1007/s00216-019-02072-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 07/11/2019] [Accepted: 08/05/2019] [Indexed: 01/05/2023]
Abstract
We demonstrate a DNA-based optical fiber device that uses an in-fiber grating, a light absorbing coating with surface anchored DNA, and a built-in optical thermometer. This device is used for precisely thermal cycling surface DNA spots bound by a simple UV cross-linking technique. Near-infrared light of wavelengths near 1550 nm and guided power near 300 mW is coupled out of the fiber core by a tilted fiber Bragg grating inscribed in the fiber and absorbed by the coating to increase its temperature to more than 95 °C. A co-propagating broadband light signal (also in the near-infrared region) is used to measure the reflection spectrum of the grating and thus the temperature from the wavelength shifts of the reflection peaks. The device is capable of sensitive DNA melt analysis and can be used for DNA amplification. Graphical abstract.
Collapse
Affiliation(s)
- Jason Koppert
- Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Hubert Jean-Ruel
- Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.,Spartan Biosciences Inc., 2934 Baseline Road #500, Nepean, ON, K2H B2, Canada
| | - Devin O'Neill
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Chris Harder
- Spartan Biosciences Inc., 2934 Baseline Road #500, Nepean, ON, K2H B2, Canada
| | - William Willmore
- Department of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Anatoli Ianoul
- Department of Chemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Jacques Albert
- Department of Electronics, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada.
| |
Collapse
|
11
|
Pinto G, Parisse P, Solano I, Canepa P, Canepa M, Casalis L, Cavalleri O. Functionalizing gold with single strand DNA: novel insight into optical properties via combined spectroscopic ellipsometry and nanolithography measurements. SOFT MATTER 2019; 15:2463-2468. [PMID: 30810150 DOI: 10.1039/c8sm02589d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We have studied the self-assembly of 22-base oligonucleotides bound by a short alkyl thiol linker (C6-ssDNA) on flat Au films. The self-assembled monolayer (SAM) was modified by addition of a spacer (mercaptohexanol, MCH). Molecular depositions were monitored in situ by spectroscopic ellipsometry (SE). SAMs were characterized in a liquid environment by coupling SE (difference spectra method) with Atomic Force Microscope (AFM) measurements. We exploited the biofilm thickness obtained by AFM nanolithography and imaging to solve the refractive index/thickness correlation in optical measurements on ultrathin molecular layers. The combined SE/AFM analysis provided reliable estimates of the thickness and the refractive index of the biofilm in the NIR region (650-1300 nm) and revealed new aspects of DNA molecular organization: exposure to MCH leads to an increase of both film thickness and refractive index, which points to a reorganization of C6-ssDNA film. We show that the contribution of the thiol/Au interface has to be included in the optical model to obtain a more reliable determination of the refractive index of the biofilm in a liquid. The careful, correlative characterization of the mixed C6-ssDNA/MCH SAM represents a key step towards the optimization of a robust detection scheme based on helix-helix hybridization.
Collapse
Affiliation(s)
- Giulia Pinto
- OPTMATLAB, Department of Physics, University of Genova, via Dodecaneso 33, 16146 Genova, Italy.
| | | | | | | | | | | | | |
Collapse
|
12
|
Electrochemical Analysis of Ultrathin Polythiolsiloxane Films for Surface Biomodification. INTERNATIONAL JOURNAL OF ELECTROCHEMISTRY 2018. [DOI: 10.1155/2018/4705031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The ability of different crosslinkers to crosslink nanometer thick films of the polymer poly(mercaptopropyl)methylsiloxane (PMPMS), thus stabilizing these films on solid supports, was investigated. The four crosslinkers included 1,11-bismaleimidotriethyleneglycol (BM(PEG)3), tris-(2-maleimidoethyl)amine (TMEA), bismaleimidohexane (BMH), and 1,1′-(methylenedi-4,1-phenylene) bismaleimide (BMDPM). PMPMS films treated with the four crosslinkers were compared in the effectiveness of achieved crosslinking, continuity and stability of the films to rearrangement at elevated temperatures, and modification with single-stranded DNA. The results of electrochemical analyses show that more hydrophilic crosslinkers had difficulty reacting fully with PMPMS thiols, even in these nanometer thin layers. This observation highlights the critical importance of selecting crosslinkers that are chemically compatible. Optimal selection of crosslinker yielded films in which the polymer film was largely incapable of rearranging, even at elevated temperatures, yielding reproducible and stable layers. These results validate use of these supports for applications such as monitoring thermal denaturation of immobilized DNA duplexes.
Collapse
|
13
|
Ye D, Zuo X, Fan C. DNA Nanotechnology-Enabled Interfacial Engineering for Biosensor Development. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2018; 11:171-195. [PMID: 29490188 DOI: 10.1146/annurev-anchem-061417-010007] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Biosensors represent biomimetic analytical tools for addressing increasing needs in medical diagnosis, environmental monitoring, security, and biodefense. Nevertheless, widespread real-world applications of biosensors remain challenging due to limitations of performance, including sensitivity, specificity, speed, and reproducibility. In this review, we present a DNA nanotechnology-enabled interfacial engineering approach for improving the performance of biosensors. We first introduce the main challenges of the biosensing interfaces, especially under the context of controlling the DNA interfacial assembly. We then summarize recent progress in DNA nanotechnology and efforts to harness DNA nanostructures to engineer various biological interfaces, with a particular focus on the use of framework nucleic acids. We also discuss the implementation of biosensors to detect physiologically relevant nucleic acids, proteins, small molecules, ions, and other biomarkers. This review highlights promising applications of DNA nanotechnology in interfacial engineering for biosensors and related areas.
Collapse
Affiliation(s)
- Dekai Ye
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaolei Zuo
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
- Institute of Molecular Medicine, Renji Hospital, Schools of Medicine and Chemistry and Chemical Engineering, Shanghai Jiao Tong University, Shanghai 200127, China
| | - Chunhai Fan
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility (SSRF), Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China;
| |
Collapse
|
14
|
Radhakrishnan R, Poltronieri P. Fluorescence-Free Biosensor Methods in Detection of Food Pathogens with a Special Focus on Listeria monocytogenes. BIOSENSORS 2017; 7:E63. [PMID: 29261134 PMCID: PMC5746786 DOI: 10.3390/bios7040063] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 12/11/2017] [Accepted: 12/18/2017] [Indexed: 12/16/2022]
Abstract
Food pathogens contaminate food products that allow their growth on the shelf and also under refrigerated conditions. Therefore, it is of utmost importance to lower the limit of detection (LOD) of the method used and to obtain the results within hours to few days. Biosensor methods exploit the available technologies to individuate and provide an approximate quantification of the bacteria present in a sample. The main bottleneck of these methods depends on the aspecific binding to the surfaces and on a change in sensitivity when bacteria are in a complex food matrix with respect to bacteria in a liquid food sample. In this review, we introduce surface plasmon resonance (SPR), new advancements in SPR techniques, and electrochemical impedance spectroscopy (EIS), as fluorescence-free biosensing technologies for detection of L. monocytogenes in foods. The application of the two methods has facilitated L. monocytogenes detection with LOD of 1 log CFU/mL. Further advancements are envisaged through the combination of biosensor methods with immunoseparation of bacteria from larger volumes, application of lab-on-chip technologies, and EIS sensing methods for multiplex pathogen detection. Validation efforts are being conducted to demonstrate the robustness of detection, reproducibility and variability in multi-site installations.
Collapse
|
15
|
Liu S, Wang Y, Zhang S, Wang L. Exonuclease-Catalyzed Methylene Blue Releasing and Enriching onto a Dodecanethiol Monolayer for an Immobilization-Free and Highly Sensitive Electrochemical Nucleic Acid Biosensor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:5099-5107. [PMID: 28478675 DOI: 10.1021/acs.langmuir.6b04671] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Herein, a unique and versatile immobilization-free electrochemical nucleic acid biosensor architecture is proposed for the first time based on the catalyzed release of a methylene blue (MB)-tagged mononucleotide by exonuclease III (Exo III) and the successive enrichment onto a dodecanethiol monolayer, which can be attributed to the hydrophobic force between the alkyl chain of the dodecanethiol monolayer and the hydrophobic part of the MB-tagged mononucleotide. The fabricated biosensor demonstrates considerable advantages including assay simplicity, rapidness, and high sensitivity owing to its immobilization-free and homogenous operation for the biorecognition and amplification process. A low detection limit of approximately 1 pM toward the target DNA could be achieved with an excellent selectivity. The proposed immobilization-free electrochemical biosensing strategy was also extended for the assay of Exo I and III activity. Furthermore, it might be easily extended for the detection of a wide spectrum of targets and thus provide a promising avenue for the development of immobilization-free and sensitive electrochemical biosensors.
Collapse
Affiliation(s)
- Shufeng Liu
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Yanqun Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Shanshan Zhang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| | - Li Wang
- Key Laboratory of Sensor Analysis of Tumor Marker, Ministry of Education, College of Chemistry and Molecular Engineering, Qingdao University of Science and Technology , No. 53, Rd. Zhengzhou, Qingdao, Shandong 266042, China
| |
Collapse
|
16
|
Macedo LJA, Miller EN, Opdahl A. Effect of Probe-Probe Distance on the Stability of DNA Hybrids on Surfaces. Anal Chem 2017; 89:1757-1763. [PMID: 28208255 DOI: 10.1021/acs.analchem.6b04048] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We have used temperature gradient surface plasmon resonance (SPR) measurements to quantitatively evaluate how the stability of different types of hybrids formed with DNA probes on surfaces is affected by probe spacing. SPR sensors with different average surface densities of probes were prepared by coadsorbing probes with lateral spacers strands comprised of phosphorothioated adenine nucleotides (A15*). Increasing the fraction of A15* spacers in the immobilization solution results in larger distances between probes on the sensor, determined here using a combination of SPR and X-ray photoelectron spectroscopy (XPS) measurements. The hybridization activities of probes were simultaneously measured over a temperature range that spanned the denaturation temperature (Tm) of hybrids by applying a spatial temperature gradient across the sensor surface. The resulting temperature profiles of hybridization activity show how the stability of hybrids increases as either the distance between probes or the ionic strength of the hybridization buffer increase. Additionally, hybridization activity profiles sharpen as the spacing between probes increases, indicating more homogeneous hybridization behavior of probes. The results provide quantitative experimental data for testing theoretical models of stability, supporting models that account for both repulsive interactions between DNA strands and local variability in probe surface density.
Collapse
Affiliation(s)
- Lucyano J A Macedo
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse , La Crosse, Wisconsin 54601, United States
| | - Erin N Miller
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse , La Crosse, Wisconsin 54601, United States
| | - Aric Opdahl
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse , La Crosse, Wisconsin 54601, United States
| |
Collapse
|
17
|
Chiang HC, Levicky R. Effects of Chain-Chain Associations on Hybridization in DNA Brushes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:12603-12610. [PMID: 27934512 DOI: 10.1021/acs.langmuir.6b02990] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Hybridization of solution nucleic acids to DNA brushes is widely encountered in diagnostic and materials science applications. Typically, brush chain lengths of ten or more nucleotides are used to provide the needed sequence specificity and binding affinity. At these lengths, coincidental occurrence of complementary regions is expected to lead to associations between the nominally single-stranded brush chains due to intra- or interchain base pairing. This report investigates how these associations impact the brushes' hybridization activity toward complementary "target" sequences. Brushes were prepared from 20-mer chains with four-nucleotide-long "adhesive regions" through which neighboring chains could interact. The affinity and position of the adhesive region along the chain backbone were varied. DNA brushes were exposed to complementary solution targets, and the corresponding melting transitions were measured to estimate free energies of the brush-target hybridization. These results revealed that higher affinity adhesive regions more extensively suppressed brush hybridization relative to hybridization in solution. Associations near the middle of the chains were found to be more penalizing than those at the immobilized or the free end of the chains. Provided that the brush chains were close enough to associate, changes in brush density did not exert a significant effect on hybridization thermodynamics within the investigated coverage window. Comparison of the DNA brush results with those from commercial Affymetrix single-nucleotide-polymorphism (SNP) microarrays revealed agreement in the impact of chain associations on hybridization.
Collapse
Affiliation(s)
- Hao-Chun Chiang
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering , 6 Metrotech Center, Brooklyn, New York 11201, United States
| | - Rastislav Levicky
- Department of Chemical and Biomolecular Engineering, New York University Tandon School of Engineering , 6 Metrotech Center, Brooklyn, New York 11201, United States
| |
Collapse
|
18
|
Qiao W, Chiang HC, Xie H, Levicky R. Surface vs. solution hybridization: effects of salt, temperature, and probe type. Chem Commun (Camb) 2016; 51:17245-8. [PMID: 26459915 DOI: 10.1039/c5cc06674c] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Hybridization thermodynamics on solid supports are compared with those in solution for two types of hybridization probe, DNA and uncharged morpholino oligonucleotides of identical sequences. Trends in hybridization affinity are discussed with respect to ionic strength, temperature, and surface behavior.
Collapse
Affiliation(s)
- Wanqiong Qiao
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hao-Chun Chiang
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Hui Xie
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| | - Rastislav Levicky
- Dept. of Chemical & Biomolecular Engineering, NYU Polytechnic School of Engineering, 6 MetroTech Center, Brooklyn, NY 11201, USA.
| |
Collapse
|
19
|
Das P, Zafar S. Mechanistic Influence of Nanometer Length-Scale Surface Chemistry on DNA Hybridization. ACS NANO 2015; 9:7466-7478. [PMID: 26051361 DOI: 10.1021/acsnano.5b02530] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Hybridization of surface-immobilized oligonucleotides to their complementary counterparts is central to the rational design of novel nanodevices and DNA sensors. In this study, we have adopted a unified approach of combining sensing experiments with molecular dynamics simulations to characterize the hybridization of a 23 nucleotide long single-strand probe DNA tethered to a gold surface. Experiments indicate significant conformational changes of DNA in close vicinity (∼1 nm) of the gold surface upon hybridization and also conformational heterogeneity within hybridized DNA, consistent with simulation results. Simulations show that the conformational heterogeneity on a gold surface arises due to stabilization of surface-adsorbed partial and full duplexes, resulting in impeded hybridization in comparison to what observed on a repulsive surface. Furthermore, these simulations indicate that hybridization could be improved by tuning the nonspecific adsorption on a nanopatterned surface with an optimal patterning length. Simulations were performed on the probe tethered to gold nanodots of varying (2-8 nm) diameter. An improved hybridization of the present probe sequence was only observed for the 6 nm gold dots patterned on a repulsive surface. Results reveal that the 2D nanoconfinement provided by the 6 nm gold dot is optimal for reducing conformational heterogeneity for the specific sequence used in this study. Thus, improved DNA hybridization can be achieved on a gold nanodot patterned repulsive surface, where the optimal dot diameter will depend on the probe length and sequence. In summary, this study provides mechanistic insights onto hybridization on gold and offers a unique method toward improved hybridization on a nanopatterned surface with an optimized patterning length.
Collapse
Affiliation(s)
| | - Sufi Zafar
- ‡IBM Thomas J. Watson Research Center, 1101 Kitchawan Road, Yorktown Heights, New York 10598, United States
| |
Collapse
|
20
|
Wagner CE, Macedo LJA, Opdahl A. Temperature Gradient Approach for Rapidly Assessing Sensor Binding Kinetics and Thermodynamics. Anal Chem 2015; 87:7825-32. [DOI: 10.1021/acs.analchem.5b01518] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Caleb E. Wagner
- Department
of Chemistry and
Biochemistry, University of Wisconsin−La Crosse, La Crosse, Wisconsin 54601, United States
| | - Lucyano J. A. Macedo
- Department
of Chemistry and
Biochemistry, University of Wisconsin−La Crosse, La Crosse, Wisconsin 54601, United States
| | - Aric Opdahl
- Department
of Chemistry and
Biochemistry, University of Wisconsin−La Crosse, La Crosse, Wisconsin 54601, United States
| |
Collapse
|
21
|
Li Z, Weeraman CN, Azam MS, Osman E, Gibbs-Davis JM. The thermal reorganization of DNA immobilized at the silica/buffer interface: a vibrational sum frequency generation investigation. Phys Chem Chem Phys 2015; 17:12452-7. [DOI: 10.1039/c5cp00781j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Vibrational SFG reveals that C–H stretches associated with the nucleobase rather than the phosphate-sugar backbone are most sensitive to DNA duplex “melting” at the silica/buffer interface.
Collapse
Affiliation(s)
- Zhiguo Li
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | | | | | - Eiman Osman
- Department of Chemistry
- University of Alberta
- Edmonton
- Canada
| | | |
Collapse
|
22
|
Petty TJ, Wagner CE, Opdahl A. Influence of attachment strategy on the thermal stability of hybridized DNA on gold surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:15277-15284. [PMID: 25457775 DOI: 10.1021/la504128h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The thermal stabilities of double-stranded DNA hybrids immobilized on gold surfaces are shown to be significantly affected by the conformation of the hybrid. To analyze this behavior, DNA probes were immobilized using attachment strategies where the nucleotides within the strand had varying levels of interactions with the gold substrate. The abilities of these probes to form double-stranded hybrids with solution DNA targets were evaluated by surface plasmon resonance (SPR) over a temperature range 25-60 °C. The measurements were used to construct thermal stability profiles for hybrids in each conformation. We observe that DNA hybrids formed with probe strands that interact extensively with the gold surface have stability profiles that are shifted lower by 5-10 °C compared to hybrids formed with end-tethered probes that have fewer interactions with the surface. The results provide an understanding of the experimental conditions in which these weaker DNA hybrids can form and show the additional complexity of evaluating denaturation profiles generated from DNA on surfaces.
Collapse
Affiliation(s)
- Tyler J Petty
- Department of Chemistry and Biochemistry, University of Wisconsin-La Crosse , La Crosse, Wisconsin 54601, United States
| | | | | |
Collapse
|
23
|
Abstract
AbstractIn addition to its role as a carrier of genetic information, DNA has been recognized as a construction material for the assembly of different objects and structural arrangements with nanoscale features. As a result of DNA’s self-recognition properties (based on the specific base-pairing of G-C and T-A), monolayer films of nucleic acids on solid supports have attracted an escalating attentions. Recently, numerous novel materials based on two-dimensional (2D) and three-dimensional (3D) DNA structures have been reported, which extends their utility to a large number of appliations. This review paper intends to be a new and comprehensive overview of recent strategies to site-specifically immobilized DNA on various materials, including carbonaceous substances, gold, and silica substrate, emphasizing the applications of site-specific DNA nanostructure-based devices for diagnostic, bioanalytical, food safety and environmental monitoring. Additionally, an up-to-date perspective is proposed at the end of this review.
Collapse
|
24
|
Azam MS, Gibbs-Davis JM. Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy. Anal Chem 2013; 85:8031-8. [DOI: 10.1021/ac401009u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Md. Shafiul Azam
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | | |
Collapse
|
25
|
Lee HJ, Jamison AC, Yuan Y, Li CH, Rittikulsittichai S, Rusakova I, Lee TR. Robust carboxylic acid-terminated organic thin films and nanoparticle protectants generated from bidentate alkanethiols. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:10432-10439. [PMID: 23855957 DOI: 10.1021/la4017118] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A new carboxylic acid-terminated alkanethiol having bidentate character, 16-(3,5-bis(mercaptomethyl)phenoxy)hexadecanoic acid (BMPHA), was designed as an absorbate and protectant to form thermally stable carboxylic acid-terminated organic thin films on flat gold and nanoparticles, respectively. The structural features of the organic thin films derived from BMPHA were characterized by ellipsometry, X-ray photoelectron spectroscopy (XPS), and polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), and compared to those derived from mercaptohexadecanoic acid (MHA) and 16-(4-(mercaptomethyl)phenoxy)hexadecanoic acid (MMPHA). This study demonstrates that films derived from BMPHA are less densely packed than films derived from MHA and MMPHA. However, the results of solution-phase thermal desorption tests revealed that the carboxylic acid-terminated films generated from BMPHA exhibit an enhanced thermal stability compared to those generated from MHA and MMPHA. Furthermore, as a nanoparticle protectant, BMPHA can be used to stabilize large gold nanoparticles (~45 nm diameter) in solution, and BMPHA-protected gold nanoparticles exhibited a high thermal stability in solution thermolysis studies.
Collapse
Affiliation(s)
- Han Ju Lee
- Department of Chemistry and the Texas Center for Superconductivity, University of Houston, 4800 Calhoun Road, Houston, Texas 77204-5003, USA
| | | | | | | | | | | | | |
Collapse
|
26
|
Surface-mediated functional gene delivery: An effective strategy for enhancing competitiveness of endothelial cells over smooth muscle cells. Biomaterials 2013; 34:3345-54. [DOI: 10.1016/j.biomaterials.2013.01.065] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 01/15/2013] [Indexed: 12/18/2022]
|
27
|
Belozerova I, Levicky R. Melting thermodynamics of reversible DNA/ligand complexes at interfaces. J Am Chem Soc 2012; 134:18667-76. [PMID: 23046441 PMCID: PMC3498581 DOI: 10.1021/ja3066368] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A variety of solution methods exist for analysis of interactions between small molecule ligands and nucleic acids; however, accomplishing this task economically at the scale of hundreds to thousands of sequences remains challenging. Surface assays offer a prospective solution through array-based multiplexing, capable of mapping out the full sequence context of a DNA/ligand interaction in a single experiment. However, relative to solution assays, accurate quantification of DNA/ligand interactions in a surface format must contend with limited understanding of molecular activities and interactions at a solid-liquid interface. We report a surface adaptation of a solution method in which shifts in duplex stability, induced by ligand binding and quantified from melting transitions, are used for thermodynamic analysis of DNA/ligand interactions. The results are benchmarked against solution calorimetric data. Equilibrium operation is confirmed through superposition of denaturation/hybridization transitions triggered by heating and cooling. The antibiotic compound netropsin, which undergoes electrostatic and sequence-specific minor groove interactions with DNA, is used as a prototypical small molecule. DNA/netropsin interactions are investigated as a function of ionic strength and drug concentration through electrochemical tracing of surface melt transitions. Comparison with solution values finds excellent agreement in free energy, though reliable separation into enthalpic and entropic contributions proves more difficult. The results establish key guidelines for analysis of DNA-ligand interactions via reversible melting denaturation at surfaces.
Collapse
Affiliation(s)
- Irina Belozerova
- Department of Chemical & Biomolecular Engineering, Polytechnic Institute of New York University, Brooklyn, 11201, United States
| | | |
Collapse
|