1
|
Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. Charge Transfer Mechanism in Guanine-Based Self-Assembled Monolayers on a Gold Surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:15129-15139. [PMID: 38984413 PMCID: PMC11270990 DOI: 10.1021/acs.langmuir.4c01512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/11/2024]
Abstract
In this work, we have theoretically determined the one-electron oxidation potentials and charge transfer mechanisms in complex systems based on a self-assembled monolayer of guanine molecules adsorbed on a gold surface through different organic linkers. Classical molecular dynamics simulations were carried out to sample the conformational space of both the neutral and the cationic species. Thus, the redox potentials were determined for the ensembles of geometries through multiscale quantum-mechanics/molecular-mechanics/continuum solvation model calculations in the framework of the Marcus theory and in combination with an additive scheme previously developed. In this context, conformational sampling, description of the environment, and effects caused by the linker have been considered. Applying this methodology, we unravel the phenomena of electric current transport by evaluating the different stages in which charge transfer could occur. The results revealed how the positive charge migrates from the organic layer to the gold surface. Specifically, the transport mechanism seems to take place mainly along a single ligand and driven with the help of the electrostatic interactions of the surrounding molecules. Aside, several self-assembled monolayers with different linkers have been analyzed to understand how the nature of that moiety can tune the redox properties and the efficiency of the transport. We have found that the conjugation between the guanine and the linker, at the same time conjugated to the gold surface, gives rise to a more efficient transport. In conclusion, the established computational protocol sheds light on the mechanism behind charge transport in electrochemical DNA-based biosensor nanodevices.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
2
|
Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Modeling One-Electron Oxidation Potentials and Hole Delocalization in Double-Stranded DNA by Multilayer and Dynamic Approaches. J Chem Inf Model 2024; 64:4802-4810. [PMID: 38856665 PMCID: PMC11200263 DOI: 10.1021/acs.jcim.4c00528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/27/2024] [Accepted: 05/28/2024] [Indexed: 06/11/2024]
Abstract
The number of innovative applications for DNA nowadays is growing quickly. Its use as a nanowire or electrochemical biosensor leads to the need for a deep understanding of the charge-transfer process along the strand, as well as its redox properties. These features are computationally simulated and analyzed in detail throughout this work by combining molecular dynamics, multilayer schemes, and the Marcus theory. One-electron oxidation potential and hole delocalization have been analyzed for six DNA double strands that cover all possible binary combinations of nucleotides. The results have revealed that the one-electron oxidation potential decreases with respect to the single-stranded DNA, giving evidence that the greater rigidity of a double helix induces an increase in the capacity of storing the positive charge generated upon oxidation. In addition, the hole is mainly stored in nucleobases with large reducer character, i.e., purines, especially when those are arranged in a stacked configuration in the same strand. From the computational point of view, the sampling needed to describe biological systems implies a significant computational cost. Here, we show that a small number of representative conformations generated by clustering analysis provides accurate results when compared with those obtained from sampling, reducing considerably the computational cost.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, 28049 Madrid, Spain
- Institute
for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
3
|
Shan CW, Chen Z, Han GC, Feng XZ, Kraatz HB. Electrochemical immuno-biosensors for the detection of the tumor marker alpha-fetoprotein: A review. Talanta 2024; 271:125638. [PMID: 38237279 DOI: 10.1016/j.talanta.2024.125638] [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: 11/18/2023] [Revised: 11/27/2023] [Accepted: 01/05/2024] [Indexed: 02/24/2024]
Abstract
Alpha-fetoprotein (AFP) is a glycoprotein that has many important physiological functions, including transportation, immunosuppression, and induction of apoptosis by T lymphocytes. AFP is closely related to the development of hepatocellular carcinoma and many kinds of tumors, all of which can show high concentrations, so it is used as a positive test indicator for many kinds of tumors. This paper reviews recent advances in the detection of the tumor marker AFP based on three immuno-biosensors: electrochemical (EC), photoelectrochemical (PEC), and electrochemical luminescence (ECL). The electrodes are modified by different materials or homemade composites, different signaling molecules are selected as single probes or dual probes for the detection of AFP. The detection limit was as low as 3 fg/mL, which indicated that the AFP immunosensor had achieved highly sensitive detection. In addition, we also reviewed and summarized the current development status and application prospect of AFP immunoelectrochemical sensors. There are not too many researches on immunosensors based on dual-signal ratios, and the commonly used probes are methylene blue (MB) and ferrocene (Fc). It would be more innovative to have more novel signaling molecules as probes to prepare dual-signal ratio sensors.
Collapse
Affiliation(s)
- Chen-Wei Shan
- School of Life and Environmental Sciences, Guangxi Human Physiological Information Non Invasive Detection Engineering Technology Research Center, Guangxi Colleges and Universities Key Laboratory of Biomedical Sensors and Intelligent Instruments, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Zhencheng Chen
- School of Life and Environmental Sciences, Guangxi Human Physiological Information Non Invasive Detection Engineering Technology Research Center, Guangxi Colleges and Universities Key Laboratory of Biomedical Sensors and Intelligent Instruments, Guilin University of Electronic Technology, Guilin, 541004, PR China
| | - Guo-Cheng Han
- School of Life and Environmental Sciences, Guangxi Human Physiological Information Non Invasive Detection Engineering Technology Research Center, Guangxi Colleges and Universities Key Laboratory of Biomedical Sensors and Intelligent Instruments, Guilin University of Electronic Technology, Guilin, 541004, PR China.
| | - Xiao-Zhen Feng
- School of Life and Environmental Sciences, Guangxi Human Physiological Information Non Invasive Detection Engineering Technology Research Center, Guangxi Colleges and Universities Key Laboratory of Biomedical Sensors and Intelligent Instruments, Guilin University of Electronic Technology, Guilin, 541004, PR China.
| | - Heinz-Bernhard Kraatz
- Department of Physical and Environmental Sciences, University of Toronto Scarborough, 1065 Military Trail, Toronto, Ontario, M1C 1A4, Canada.
| |
Collapse
|
4
|
Ganganboina AB, Park EY. Signal-Amplified Nanobiosensors for Virus Detection Using Advanced Nanomaterials. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2024; 187:381-412. [PMID: 38337075 DOI: 10.1007/10_2023_244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/12/2024]
Abstract
Rapid diagnosis and treatment of infectious illnesses are crucial for clinical outcomes and public health. Biosensing developments enhance diagnostics at the point of care. This is superior to traditional procedures, which need centralized lab facilities, specialized personnel, and large equipment. The emerging coronavirus epidemic threatens global health and economic security. Increasing viral surveillance and regulatory actions against disease transmission necessitate rapid, sensitive testing tools for viruses. Due to their sensitivity and specificity, biosensors offer a possible reliable and quantifiable viral detection method. Current advances in genetic engineering, such as genetic alteration and material engineering, have provided several opportunities to enhance biosensors' sensitivity, selectivity, and recognition efficiency. This chapter explains biosensing techniques, biosensor varieties, and signal amplification technologies. Challenges and potential developments for viral microorganisms based on biosensors and signal amplification were also investigated.
Collapse
Affiliation(s)
- Akhilesh Babu Ganganboina
- International Center for Young Scientists ICYS-NAMIKI, National Institute for Materials Science, Ibaraki, Japan.
| | - Enoch Y Park
- Research Institute of Green Science and Technology, Shizuoka University, Shizuoka, Japan.
| |
Collapse
|
5
|
Lucia-Tamudo J, Alcamí M, Díaz-Tendero S, Nogueira JJ. One-Electron Oxidation Potentials and Hole Delocalization in Heterogeneous Single-Stranded DNA. Biochemistry 2023; 62:3312-3322. [PMID: 37923303 PMCID: PMC10666269 DOI: 10.1021/acs.biochem.3c00324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/07/2023]
Abstract
The study of DNA processes is essential to understand not only its intrinsic biological functions but also its role in many innovative applications. The use of DNA as a nanowire or electrochemical biosensor leads to the need for a deep investigation of the charge transfer process along the strand as well as of the redox properties. In this contribution, the one-electron oxidation potential and the charge delocalization of the hole formed after oxidation are computationally investigated for different heterogeneous single-stranded DNA strands. We have established a two-step protocol: (i) molecular dynamics simulations in the frame of quantum mechanics/molecular mechanics (QM/MM) were performed to sample the conformational space; (ii) energetic properties were then obtained within a QM1/QM2/continuum approach in combination with the Marcus theory over an ensemble of selected geometries. The results reveal that the one-electron oxidation potential in the heterogeneous strands can be seen as a linear combination of that property within the homogeneous strands. In addition, the hole delocalization between different nucleobases is, in general, small, supporting the conclusion of a hopping mechanism for charge transport along the strands. However, charge delocalization becomes more important, and so does the tunneling mechanism contribution, when the reducing power of the nucleobases forming the strand is similar. Moreover, charge delocalization is slightly enhanced when there is a correlation between pairs of some of the interbase coordinates of the strand: twist/shift, twist/slide, shift/slide, and rise/tilt. However, the internal structure of the strand is not the predominant factor for hole delocalization but the specific sequence of nucleotides that compose the strand.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
| | - Manuel Alcamí
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Sergio Díaz-Tendero
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
- Condensed
Matter Physics Center (IFIMAC), Universidad
Autónoma de Madrid, Madrid 28049, Spain
| | - Juan J. Nogueira
- Department
of Chemistry, Universidad Autónoma
de Madrid, Madrid 28049, Spain
- Institute
for Advanced Research in Chemical Sciences (IAdChem), Universidad Autónoma de Madrid, Madrid 28049, Spain
| |
Collapse
|
6
|
Karimi-Maleh H, Erk N. Gemcitabine drug intercalation with ds-DNA at surface of ds-DNA/Pt-ZnO/SWCNTs/GCE biosensor: A DNA-biosensor for gemcitabine monitoring confirmed by molecular docking study. CHEMOSPHERE 2023; 336:139268. [PMID: 37343636 DOI: 10.1016/j.chemosphere.2023.139268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/01/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]
Abstract
Herein, a facile and highly sensitive electroanalytical tool for monitoring and quantifying the antineoplastic drug gemcitabine in real sample was provided. In this regard, a novel DNA-biosensor based on Pt-doped ZnO decorated single walled carbon nanotubes (Pt-ZnO/SWCNTs) hybrid nanomaterial modification of glassy carbon electrode (GCE) was fabricated. Ds-DNA (Calf Thymus), as a biological recognition element, was decorated onto nanomaterial-modified GCE via layer-by-layer fabrication strategy to attain ultimate biosensor ds-DNA/Pt-ZnO/SWCNTs/GCE. The characterizations confirmed the successful fabrication of hybrid nanomaterial, as well as the modification of electrode surface by fabricated nanomaterial. The electrochemical impedance spectroscopy (EIS) analysis revealed that the nanomaterial modification of GCE surface enhanced the electrical conductivity thanks to the synergistic effects of Pt-ZnO and SWCNTs structures, thereby boosted the electrocatalytic activity of the resultant biosensor. The electrochemical characterization results showed that the suggested biosensor is capable of detecting gemcitabine in a wide concentration range of 0.01-30.0 μM, with a detection limit of 5.0 nM. The intercalation binding mode of Gemcitabine inside guanine and cytosine rich region of DNA receptor was approved by molecular docking study. The results of the experimental data were well congruent with the molecular docking analysis, which showed that the binding mode of gemcitabine drug with ds-DNA was intercalation.
Collapse
Affiliation(s)
- Hassan Karimi-Maleh
- The Quzhou Affiliated Hospital of Wenzhou Medical University, Quzhou People's Hospital, Quzhou, 324000, China; School of Resources and Environment, University of Electronic Science and Technology of China, P.O. Box 611731, Xiyuan Ave, Chengdu, PR China.
| | - Nevin Erk
- Ankara University, Faculty of Pharmacy, Department of Analytical Chemistry, Ankara, Turkey.
| |
Collapse
|
7
|
Yuwen L, Zhang S, Chao J. Recent Advances in DNA Nanotechnology-Enabled Biosensors for Virus Detection. BIOSENSORS 2023; 13:822. [PMID: 37622908 PMCID: PMC10452139 DOI: 10.3390/bios13080822] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/05/2023] [Accepted: 08/12/2023] [Indexed: 08/26/2023]
Abstract
Virus-related infectious diseases are serious threats to humans, which makes virus detection of great importance. Traditional virus-detection methods usually suffer from low sensitivity and specificity, are time-consuming, have a high cost, etc. Recently, DNA biosensors based on DNA nanotechnology have shown great potential in virus detection. DNA nanotechnology, specifically DNA tiles and DNA aptamers, has achieved atomic precision in nanostructure construction. Exploiting the programmable nature of DNA nanostructures, researchers have developed DNA nanobiosensors that outperform traditional virus-detection methods. This paper reviews the history of DNA tiles and DNA aptamers, and it briefly describes the Baltimore classification of virology. Moreover, the advance of virus detection by using DNA nanobiosensors is discussed in detail and compared with traditional virus-detection methods. Finally, challenges faced by DNA nanobiosensors in virus detection are summarized, and a perspective on the future development of DNA nanobiosensors in virus detection is also provided.
Collapse
Affiliation(s)
- Lihui Yuwen
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Shifeng Zhang
- State Key Laboratory of Organic Electronics and Information Displays, Jiangsu Key Laboratory for Biosensors, Institute of Advanced Materials (IAM), Nanjing University of Posts and Telecommunications, Nanjing 210023, China; (L.Y.); (S.Z.)
| | - Jie Chao
- School of Geography and Biological Information, Nanjing University of Posts and Telecommunications, Nanjing 210023, China
| |
Collapse
|
8
|
Lucia-Tamudo J, Díaz-Tendero S, Nogueira JJ. Intramolecular and intermolecular hole delocalization rules the reducer character of isolated nucleobases and homogeneous single-stranded DNA. Phys Chem Chem Phys 2023; 25:14578-14589. [PMID: 37191244 DOI: 10.1039/d3cp00884c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of DNA strands as nanowires or electrochemical biosensors requires a deep understanding of charge transfer processes along the strand, as well as of the redox properties. These properties are computationally assessed in detail throughout this study. By applying molecular dynamics and hybrid QM/continuum and QM/QM/continuum schemes, the vertical ionization energies, adiabatic ionization energies, vertical attachment energies, one-electron oxidation potentials, and delocalization of the hole generated upon oxidation have been determined for nucleobases in their free form and as part of a pure single-stranded DNA. We show that the reducer ability of the isolated nucleobases is explained by the intramolecular delocalization of the positively charged hole, while the enhancement of the reducer character when going from aqueous solution to the strand correlates very well with the intermolecular hole delocalization. Our simulations suggest that the redox properties of DNA strands can be tuned by playing with the balance between intramolecular and intermolecular charge delocalization.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
9
|
Lucia-Tamudo J, Nogueira JJ, Díaz-Tendero S. An Efficient Multilayer Approach to Model DNA-Based Nanobiosensors. J Phys Chem B 2023; 127:1513-1525. [PMID: 36779932 PMCID: PMC9969517 DOI: 10.1021/acs.jpcb.2c07225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
In this work, we present a full computational protocol to successfully obtain the one-electron reduction potential of nanobiosensors based on a self-assembled monolayer of DNA nucleobases linked to a gold substrate. The model is able to account for conformational sampling and environmental effects at a quantum mechanical (QM) level efficiently, by combining molecular mechanics (MM) molecular dynamics and multilayer QM/MM/continuum calculations within the framework of Marcus theory. The theoretical model shows that a guanine-based biosensor is more prone to be oxidized than the isolated nucleobase in water due to the electrostatic interactions between the assembled guanine molecules. In addition, the redox properties of the biosensor can be tuned by modifying the nature of the linker that anchor the nucleobases to the metal support.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049, Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
10
|
Eksin E, Erdem A. Recent Progress on Optical Biosensors Developed for Nucleic Acid Detection Related to Infectious Viral Diseases. MICROMACHINES 2023; 14:mi14020295. [PMID: 36837995 PMCID: PMC9966969 DOI: 10.3390/mi14020295] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 05/28/2023]
Abstract
Optical biosensors have many advantages over traditional analytical methods. They enable the identification of several biological and chemical compounds directly, instantly, and without the need of labels. Their benefits include excellent specificity, sensitivity, compact size, and low cost. In this review, the main focus is placed on the nucleic acid-based optical biosensor technologies, including colorimetric, fluorescence, surface plasmon resonance (SPR), Evanescent-Wave Optical, Fiber optic and bioluminescent optical fibre. The fundamentals of each type of biosensor are briefly explained, and particular emphasis has been placed on the achievements which have been gained in the last decade on the field of diagnosis of infectious viral diseases. Concluding remarks concerning the perspectives of further developments are discussed.
Collapse
Affiliation(s)
- Ece Eksin
- Biomedical Device Technology Program, Vocational School of Health Services, Izmir Democracy University, 35290 Izmir, Turkey
| | - Arzum Erdem
- Department of Analytical Chemistry, Faculty of Pharmacy, Ege University, 35100 Izmir, Turkey
| |
Collapse
|
11
|
Lucia-Tamudo J, Cárdenas G, Anguita-Ortiz N, Díaz-Tendero S, Nogueira JJ. Computation of Oxidation Potentials of Solvated Nucleobases by Static and Dynamic Multilayer Approaches. J Chem Inf Model 2022; 62:3365-3380. [PMID: 35771991 PMCID: PMC9326891 DOI: 10.1021/acs.jcim.2c00234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The determination
of the redox properties of nucleobases is of
paramount importance to get insight into the charge-transfer processes
in which they are involved, such as those occurring in DNA-inspired
biosensors. Although many theoretical and experimental studies have
been conducted, the value of the one-electron oxidation potentials
of nucleobases is not well-defined. Moreover, the most appropriate
theoretical protocol to model the redox properties has not been established
yet. In this work, we have implemented and evaluated different static
and dynamic approaches to compute the one-electron oxidation potentials
of solvated nucleobases. In the static framework, two thermodynamic
cycles have been tested to assess their accuracy against the direct
determination of oxidation potentials from the adiabatic ionization
energies. Then, the introduction of vibrational sampling, the effect
of implicit and explicit solvation models, and the application of
the Marcus theory have been analyzed through dynamic methods. The
results revealed that the static direct determination provides more
accurate results than thermodynamic cycles. Moreover, the effect of
sampling has not shown to be relevant, and the results are improved
within the dynamic framework when the Marcus theory is applied, especially
in explicit solvent, with respect to the direct approach. Finally,
the presence of different tautomers in water does not affect significantly
the one-electron oxidation potentials.
Collapse
Affiliation(s)
- Jesús Lucia-Tamudo
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Gustavo Cárdenas
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Nuria Anguita-Ortiz
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Sergio Díaz-Tendero
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Juan J Nogueira
- Department of Chemistry, Universidad Autónoma de Madrid, 28049 Madrid, Spain.,Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
12
|
Magriñá I, Ortiz M, Simonova A, Hocek M, O’ Sullivan CK, Forster RJ. Ferrocene-Containing DNA Monolayers: Influence of Electrostatics on the Electron Transfer Dynamics. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:3359-3369. [PMID: 33705153 PMCID: PMC8819689 DOI: 10.1021/acs.langmuir.0c03485] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 03/01/2021] [Indexed: 06/12/2023]
Abstract
A 153-mer target DNA was amplified using ethynyl ferrocene dATP and a tailed forward primer resulting in a duplex with a single-stranded DNA tail for hybridization to a surface-tethered probe. A thiolated probe containing the sequence complementary to the tail as well as a 15 polythimine vertical spacer with a (CH2)6 spacer was immobilized on the surface of a gold electrode and hybridized to the ferrocene-modified complementary strand. Potential step chronoamperometry and cyclic voltammetry were used to probe the potential of zero charge, PZC, and the rate of heterogeneous electron transfer between the electrode and the immobilized ferrocene moieties. Chronoamperometry gives three, well-resolved exponential current-time decays corresponding to ferrocene centers located within 13 Å (4 bases) along the duplex. Significantly, the apparent standard heterogeneous electron transfer rate constant, kappo, observed depends on the initial potential, i.e., the rate of electron transfer at zero driving force is not the same for oxidation and reduction of the ferrocene labels. Moreover, the presence of ions, such as Sr2+, that strongly ion pair with the negatively charged DNA backbone modulates the electron transfer rate significantly. Specifically, kappo = 246 ± 23.5 and 14 ± 1.2 s-1 for reduction and oxidation, respectively, where the Sr2+ concentration is 10 mM, but the corresponding values in 1 M Sr2+ are 8 ± 0.8 and 150 ± 12 s-1. While other factors may be involved, these results are consistent with a model in which a low Sr2+ concentration and an initial potential that is negative of the PZC lead to electrostatic repulsion of the negatively charged DNA backbone and the negatively charged electrode. This leads to the DNA adopting an extended configuration (concertina open), resulting in a slow rate of heterogeneous electron transfer. In contrast, for ferrocene reduction, the initial potential is positive of PZC and the negatively charged DNA is electrostatically attracted to the electrode (concertina closed), giving a shorter electron transfer distance and a higher rate of heterogeneous electron transfer. When the Sr2+ concentration is high, the charge on the DNA backbone is compensated by the electrolyte and the charge on the electrode dominates the electron transfer dynamics and the opposite potential dependence is observed. These results open up the possibility of electromechanical switching using DNA superstructures.
Collapse
Affiliation(s)
- Ivan Magriñá
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
| | - Mayreli Ortiz
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
| | - Anna Simonova
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
| | - Michal Hocek
- Institute
of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610 Prague, Czech Republic
- Department
of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843 Prague 2, Czech Republic
| | - Ciara K. O’ Sullivan
- Departament
d’Enginyeria Química, Universitat
Rovira i Virgili, 26
Països Catalans, 43007 Tarragona, Spain
- Institució
Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010 Barcelona, Spain
| | - Robert J. Forster
- School
of Chemical Sciences, FutureNeuro SFI Research Centre, National Centre
for Sensor Research, Dublin City University, Dublin D09 V209, Ireland
| |
Collapse
|
13
|
Aydin S, Tanik NA, Aykut Y. Guanine oxidation signal amplification in single strand DNA molecules with heat‐treated polyacrylonitrile/sulfuric acid micro/nanofibrous system. POLYM ADVAN TECHNOL 2021. [DOI: 10.1002/pat.5114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Seval Aydin
- Textile Engineering Graduate School of Natural and Applied Sciences, Bursa Uludag University Bursa
| | - Nilay A. Tanik
- Textile Engineering Graduate School of Natural and Applied Sciences, Bursa Uludag University Bursa
| | - Yakup Aykut
- Textile Engineering Graduate School of Natural and Applied Sciences, Bursa Uludag University Bursa
- Textile Engineering Department Engineering Faculty, Bursa Uludag University Bursa Turkey
| |
Collapse
|
14
|
Rani R, Singh G, Batra K, Minakshi P. Bioengineered Polymer/Composites as Advanced Biological Detection of Sorbitol: An Application in Healthcare Sector. Curr Top Med Chem 2021; 20:963-981. [PMID: 32141419 DOI: 10.2174/1568026620666200306131416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 01/20/2020] [Accepted: 01/31/2020] [Indexed: 12/23/2022]
Abstract
Bioengineered polymers and nanomaterials have emerged as promising and advanced materials for the fabrication and development of novel biosensors. Nanotechnology-enabled biosensor methods have high sensitivity, selectivity and more rapid detection of an analyte. Biosensor based methods are more rapid and simple with higher sensitivity and selectivity and can be developed for point-of-care diagnostic testing. Development of a simple, sensitive and rapid method for sorbitol detection is of considerable significance to efficient monitoring of diabetes-associated disorders like cataract, neuropathy, and nephropathy at initial stages. This issue encourages us to write a review that highlights recent advancements in the field of sorbitol detection as no such reports have been published till the date. The first section of this review will be dedicated to the conventional approaches or methods that had been playing a role in detection. The second part focused on the emerging field i.e. biosensors with optical, electrochemical, piezoelectric, etc. approaches for sorbitol detection and the importance of its detection in healthcare application. It is expected that this review will be very helpful for readers to know the different conventional and recent detection techniques for sorbitol at a glance.
Collapse
Affiliation(s)
- Ruma Rani
- ICAR-National Research Centre on Equines, Hisar-125001, India
| | - Geeta Singh
- Deenbandhu Chhotu Ram University of Science and Technology, Murthal-131027, Sonipat, India
| | - Kanisht Batra
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, India
| | - Prasad Minakshi
- Department of Animal Biotechnology, LLR University of Veterinary and Animal Sciences, Hisar-125001, Haryana, India
| |
Collapse
|
15
|
The importance of the assembling of DNA strands on the performance of electrochemical genosensors. Microchem J 2020. [DOI: 10.1016/j.microc.2020.105358] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
|
16
|
Liu YL, Zhu J, Weng GJ, Li JJ, Zhao JW. Gold nanotubes: synthesis, properties and biomedical applications. Mikrochim Acta 2020; 187:612. [PMID: 33064202 DOI: 10.1007/s00604-020-04460-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 07/16/2020] [Indexed: 11/25/2022]
Abstract
This review (with 106 references) summarizes the latest progress in the synthesis, properties and biomedical applications of gold nanotubes (AuNTs). Following an introduction into the field, a first large section covers two popular AuNTs synthesis methods. The hard template method introduces anodic alumina oxide template (AAO) and track-etched membranes (TeMs), while the sacrificial template method based on galvanic replacement introduces bimetallic, trimetallic AuNTs and AuNT-semiconductor hybrid materials. Then, the factors affecting the morphology of AuNTs are discussed. The next section covers their unique surface plasmon resonance (SPR), surface-enhanced Raman scattering (SERS) and their catalytic properties. This is followed by overviews on the applications of AuNTs in biosensors, protein transportation, photothermal therapy and imaging. Several tables are presented that give an overview on the wealth of synthetic methods, morphology factors and biological application. A concluding section summarizes the current status, addresses current challenges and gives an outlook on potential applications of AuNTs in biochemical detection and drug delivery.Graphical abstract.
Collapse
Affiliation(s)
- Yan-Ling Liu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jian Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| | - Guo-Jun Weng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jian-Jun Li
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China
| | - Jun-Wu Zhao
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, 710049, People's Republic of China.
| |
Collapse
|
17
|
Ahmadi M, Ahour F. An electrochemical biosensor based on a graphene oxide modified pencil graphite electrode for direct detection and discrimination of double-stranded DNA sequences. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2020; 12:4541-4550. [PMID: 32869790 DOI: 10.1039/d0ay01128b] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
The ability to directly recognize double-stranded DNA (ds-DNA) is a major challenge in disease diagnosis and gene therapy because DNA is naturally double-stranded. Herein, a novel electrochemical biosensor for the sequence-specific recognition of ds-DNA using a peptide nucleic acid (PNA) probe and graphene oxide (GO) modified pencil graphite electrode is reported and applied for the direct detection of the desired sequence in plasmid samples. For this purpose, GO was assembled onto the pencil graphite electrode surface (GO/PGE) by a simple casting method and applied for PNA probe immobilization (PNA-GO/PGE). Upon addition of ds-DNA, the interaction of the PNA probe with ds-DNA induces probe detachment from the electrode surface which results in a guanine oxidation signal decrease. Under optimized conditions, the guanine oxidation signal decreased linearly with the ds-DNA concentration increasing in the range from 30 pM to 10 nM, with a detection limit of 1.3 pM. Moreover, the proposed biosensor was applied for the sensitive and selective detection of double-stranded target DNA in plasmid samples. This proposed method could be used as a platform for direct detection of various sequences in double-stranded genomic DNA.
Collapse
Affiliation(s)
- Mehran Ahmadi
- Nanotechnology Research Center, Faculty of Science, Urmia University, Urmia, Iran.
| | | |
Collapse
|
18
|
Debia NP, Rodríguez JJ, da Silveira CH, Chaves OA, Iglesias BA, Rodembusch FS, Lüdtke DS. Synthesis and photophysics of benzazole based triazoles with amino acid-derived pendant units. Multiparametric optical sensors for BSA and CT-DNA in solution. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113092] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
19
|
MVF Sensor Enables Analysis of Nucleic Acids with Stable Secondary Structures. ELECTROANAL 2020. [DOI: 10.1002/elan.201900690] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
20
|
Sarkar S, Singh PC. Alteration of the groove width of DNA induced by the multimodal hydrogen bonding of denaturants with DNA bases in its grooves affects their stability. Biochim Biophys Acta Gen Subj 2020; 1864:129498. [DOI: 10.1016/j.bbagen.2019.129498] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023]
|
21
|
Rani A, Donovan N, Mantri N. Review: The future of plant pathogen diagnostics in a nursery production system. Biosens Bioelectron 2019; 145:111631. [DOI: 10.1016/j.bios.2019.111631] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/14/2019] [Accepted: 08/22/2019] [Indexed: 12/13/2022]
|
22
|
Boguszewska K, Szewczuk M, Urbaniak S, Karwowski BT. Review: immunoassays in DNA damage and instability detection. Cell Mol Life Sci 2019; 76:4689-4704. [PMID: 31342119 PMCID: PMC6858475 DOI: 10.1007/s00018-019-03239-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 06/30/2019] [Accepted: 07/18/2019] [Indexed: 02/03/2023]
Abstract
The review includes information on the current state of knowledge of immunometric methods with emphasis on the possibility of deoxyribonucleic acid (DNA) damage detection. Beginning with basic immunoassay enzyme-linked immunosorbent assay (ELISA), this review describes methods such as tyramide signal amplification (TSA), enhanced polymer one-step staining (EPOS), and time resolved amplified cryptate emission (TRACE) as improvements of ELISA's developed over time to obtain more accurate results. In the second part of the review, surface plasmon resonance (SPR) and quantum dots (QDs) are presented as the newest outlooks in the context of immunoanalysis of biological material and molecular studies. The aim of this review is to briefly present immunoassays with emphasis on DNA damage detection; therefore, the types of methods are listed and described, types of signal indicators, basic definitions such as antigen and antibody are given. Every method is considered with an exemplary application focusing on DNA studies, DNA damage and instability detection.
Collapse
Affiliation(s)
- Karolina Boguszewska
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151, Lodz, Poland.
| | - Michał Szewczuk
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151, Lodz, Poland
| | - Sandra Urbaniak
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151, Lodz, Poland
| | - Bolesław T Karwowski
- DNA Damage Laboratory of Food Science Department, Faculty of Pharmacy, Medical University of Lodz, ul. Muszynskiego 1, 90-151, Lodz, Poland.
| |
Collapse
|
23
|
Mohammadniaei M, Park C, Min J, Sohn H, Lee T. Fabrication of Electrochemical-Based Bioelectronic Device and Biosensor Composed of Biomaterial-Nanomaterial Hybrid. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1064:263-296. [PMID: 30471039 PMCID: PMC7120487 DOI: 10.1007/978-981-13-0445-3_17] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The field of bioelectronics has paved the way for the development of biochips, biomedical devices, biosensors and biocomputation devices. Various biosensors and biomedical devices have been developed to commercialize laboratory products and transform them into industry products in the clinical, pharmaceutical, environmental fields. Recently, the electrochemical bioelectronic devices that mimicked the functionality of living organisms in nature were applied to the use of bioelectronics device and biosensors. In particular, the electrochemical-based bioelectronic devices and biosensors composed of biomolecule-nanoparticle hybrids have been proposed to generate new functionality as alternatives to silicon-based electronic computation devices, such as information storage, process, computations and detection. In this chapter, we described the recent progress of bioelectronic devices and biosensors based on biomaterial-nanomaterial hybrid.
Collapse
Affiliation(s)
- Mohsen Mohammadniaei
- Department of Chemical and Biomolecular Engineering, Sogang University, Seoul, South Korea
| | - Chulhwan Park
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea
| | - Junhong Min
- School of Integrative Engineering Chung-Ang University, Seoul, South Korea
| | - Hiesang Sohn
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| | - Taek Lee
- Department of Chemical Engineering, Kwangwoon University, Seoul, South Korea.
| |
Collapse
|
24
|
Lahiri H, Mishra S, Mukhopadhyay R. Nanoscale Nucleic Acid Recognition at the Solid-Liquid Interface Using Xeno Nucleic Acid Probes. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8875-8888. [PMID: 30398876 DOI: 10.1021/acs.langmuir.8b02770] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Challenges in reliable nucleic acid detection are manifold. The major ones are related to false positive or negative signals due to a lack of target specificity in detection and to low sensitivity, especially when a plethora of background sequences are present that can mask the specific recognition signal. Utilizing designed synthetic nucleic acids that are commonly called xeno nucleic acids could offer potential routes to meeting such challenges. In this article, we present the general framework of nucleic acid detection, especially for nanoscale applications, and discuss how and why the xeno nucleic acids could be truly an alternative to the DNA probes. Two specific cases, locked nucleic acid (LNA) and peptide nucleic acid (PNA), which are nuclease-resistant and can form thermally stable duplexes with DNA, are addressed. It is shown that the relative ease of the conformationally rigid LNA probe to be oriented upright on the substrate surface and of the nonionic PNA probe to result into high probe density assists in their use in nanoscale nucleic acid recognition. It is anticipated that success with these probes may lead to important developments such as PCR-independent approaches where the major aim is to detect a small number of target sequences present in the analyte medium.
Collapse
Affiliation(s)
- Hiya Lahiri
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Sourav Mishra
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| | - Rupa Mukhopadhyay
- School of Biological Sciences , Indian Association for the Cultivation of Science , Jadavpur, Kolkata 700 032 , India
| |
Collapse
|
25
|
Jung I, Ih S, Jung S, Yoo S, Park S. Tricomponent Multiblock Nanorods for Fourier Transform Surface Plasmon Resonance and Its Chemical Sensing. Anal Chem 2019; 91:5494-5498. [PMID: 30994330 DOI: 10.1021/acs.analchem.9b00466] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this study, we report a new mode of chemical sensing using Fourier transform surface plasmon resonance with tricomponent nanorods (Au, Ni, and Pt). By applying an external magnetic field, magnetically responsive multiblock nanorods fluctuate periodically, producing sigmoidal optical responses that are represented as a dominant frequency peak after Fourier transform conversion. Adding H2O2 to the solution under an external magnetic field perturbed the periodic nanorod rotation due to a catalytic reaction between the Pt segment and H2O2, which produces catalytic random fluctuation states. The target chemicals were detected by measuring the frequency domain recovery time between two competing states, the magnetic dominant state and the catalytic random state. These two states can be controlled and maximized by nanorod block design, demonstrating the effectiveness of our chemical sensing design using Fourier transform surface plasmon resonance.
Collapse
Affiliation(s)
- Insub Jung
- Department of Chemistry , Sungkyunkwan University , Suwon , Gyeonggi 16419 South Korea
| | - Seongkeun Ih
- Department of Chemistry , Sungkyunkwan University , Suwon , Gyeonggi 16419 South Korea
| | - Sangbaek Jung
- Department of Chemistry , Sungkyunkwan University , Suwon , Gyeonggi 16419 South Korea
| | - Sungjae Yoo
- Department of Chemistry , Sungkyunkwan University , Suwon , Gyeonggi 16419 South Korea
| | - Sungho Park
- Department of Chemistry , Sungkyunkwan University , Suwon , Gyeonggi 16419 South Korea
| |
Collapse
|
26
|
Abstract
A novel disposable electrochemical biosensor based on immobilized calf thymus double-stranded DNA (dsDNA) on the carbon-based screen-printed electrode (SPE) is developed for rapid biorecognition of carrageenan by using methylene blue (MB) redox indicator. The biosensor protocol for the detection of carrageenan is based on the concept of competitive binding of positively charged MB to the negatively charged dsDNA and carrageenan. The decrement in the MB cathodic peak current (ipc) signal as a result of the released MB from the immobilized dsDNA, and attracted to the carrageenan can be monitored via differential pulse voltammetry (DPV). The biosensor showed high sensitivity and selectivity to carrageenan at low concentration without interference from other polyanions such as alginate, gum arabic and starch. Calibration of the biosensor with carrageenan exhibited an excellent linear dependence from 1–10 mg L−1 (R2 = 0.98) with a detection limit of 0.08 mg L−1. The DNA-based carrageenan biosensor showed satisfactory reproducibility with 5.6–6.9% (n = 3) relative standard deviations (RSD), and possessing several advantages such as simplicity, fast and direct application to real sample analysis without any prior extensive sample treatments, particularly for seaweeds and food analyses.
Collapse
|
27
|
Magriñá I, Toldrà A, Campàs M, Ortiz M, Simonova A, Katakis I, Hocek M, O'Sullivan CK. Electrochemical genosensor for the direct detection of tailed PCR amplicons incorporating ferrocene labelled dATP. Biosens Bioelectron 2019; 134:76-82. [PMID: 30954929 DOI: 10.1016/j.bios.2019.03.060] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Revised: 03/26/2019] [Accepted: 03/27/2019] [Indexed: 01/09/2023]
Abstract
An electrochemical genosensor for the detection and quantification of Karlodinium armiger is presented. The genosensor exploits tailed primers and ferrocene labelled dATP analogue to produce PCR products that can be directly hybridised on a gold electrode array and quantitatively measured using square wave voltammetry. Tailed primers consist of a sequence specific for the target, followed by a carbon spacer and a sequence specifically designed not to bind to genomic DNA, resulting in a duplex flanked by single stranded binding primers. The incorporation of the 7-(ferrocenylethynyl)-7-deaza-2'-deoxyadenosine triphosphate was optimised in terms of a compromise between maximum PCR efficiency and the limit of detection and sensitivity attainable using electrochemical detection via hybridisation of the tailed, ferrocene labelled PCR product. A limit of detection of 277aM with a linear range from 315aM to 10 fM starting DNA concentration and a sensitivity of 122 nA decade-1 was achieved. The system was successfully applied to the detection of genomic DNA in real seawater samples.
Collapse
Affiliation(s)
- Ivan Magriñá
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Anna Toldrà
- IRTA, Ctra. Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - Mònica Campàs
- IRTA, Ctra. Poble Nou, km 5.5, 43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - Mayreli Ortiz
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610, Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic
| | - Ioanis Katakis
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nám. 2, CZ-16610, Prague, Czech Republic; Department of Organic Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, CZ-12843, Prague 2, Czech Republic.
| | - Ciara K O'Sullivan
- Departament d'Enginyeria Química, Universitat Rovira i Virgili, 26 Països Catalans, 43007, Tarragona, Spain; Institució Catalana de Recerca i Estudis Avançats, Passeig Lluís Companys, 23, 08010, Barcelona, Spain.
| |
Collapse
|
28
|
Balahura LR, Stefan-Van Staden RI, Van Staden JF, Aboul-Enein HY. Advances in immunosensors for clinical applications. J Immunoassay Immunochem 2018; 40:40-51. [DOI: 10.1080/15321819.2018.1543704] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Liliana-Roxana Balahura
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, Bucharest, Romania
| | - Raluca-Ioana Stefan-Van Staden
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, Bucharest, Romania
| | - Jacobus Frederick Van Staden
- Laboratory of Electrochemistry and PATLAB, National Institute of Research for Electrochemistry and Condensed Matter, Bucharest, Romania
| | - Hassan Y. Aboul-Enein
- Pharmaceutical and Medicinal Chemistry Department, The Pharmaceutical and Drug Industries Research Division, National Research Centre, Cairo, Egypt
| |
Collapse
|
29
|
Zhang Q, Scigliano A, Biver T, Pucci A, Swager TM. Interfacial bioconjugation on emulsion droplet for biosensors. Bioorg Med Chem 2018; 26:5307-5313. [PMID: 29691155 DOI: 10.1016/j.bmc.2018.04.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2018] [Revised: 04/06/2018] [Accepted: 04/07/2018] [Indexed: 10/17/2022]
Abstract
Interfacial bioconjugation methods are developed for intact liquid emulsion droplets. Complex emulsion droplets having internal hydrocarbon and fluorocarbon immiscible structured phases maintain a dynamic interface for controlled interfacial reactivity. The internal morphological change after binding to biomolecules is readily visualized and detected by light transmission, which provides a platform for the formation of inexpensive and portable bio-sensing assays for enzymes, antibodies, nucleic acids and carbohydrates.
Collapse
Affiliation(s)
- Qifan Zhang
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States
| | - Anita Scigliano
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, I-56124 Pisa, Italy
| | - Tarita Biver
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, I-56124 Pisa, Italy
| | - Andrea Pucci
- Department of Chemistry and Industrial Chemistry, University of Pisa, Via Moruzzi 13, I-56124 Pisa, Italy
| | - Timothy M Swager
- Department of Chemistry and Institute for Soldier Nanotechnologies, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.
| |
Collapse
|
30
|
Zhou Y, Wang Y, Wang X, Lu J. Polystyrene Microspheres Coupled with Hybridization Chain Reaction for Dual-Amplified Chemiluminescence Detection of Specific DNA Sequences. JOURNAL OF ANALYSIS AND TESTING 2017. [DOI: 10.1007/s41664-017-0042-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
31
|
Cam E, Aladag Tanik N, Cerkez I, Demirkan E, Aykut Y. Guanine oxidation signal enhancement in single strand DNA with polyacrylonitrile/polyaniline (PAN/PAni) hybrid nanofibers. J Appl Polym Sci 2017. [DOI: 10.1002/app.45567] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ezginur Cam
- Textile Engineering Department, Engineering Faculty; Uludag University; Gorukle Bursa 16059 Turkey
| | - Nilay Aladag Tanik
- Biology Department, Faculty of Science and Art; Uludag University; Gorukle Bursa 16059 Turkey
| | - Idris Cerkez
- Department of Fiber and Polymer Engineering; Bursa Technical University; Yildirim Bursa 16310 Turkey
| | - Elif Demirkan
- Biology Department, Faculty of Science and Art; Uludag University; Gorukle Bursa 16059 Turkey
| | - Yakup Aykut
- Textile Engineering Department, Engineering Faculty; Uludag University; Gorukle Bursa 16059 Turkey
| |
Collapse
|
32
|
Liu LS, Wu C, Zhang S. Ultrasensitive Detection of DNA and Ramos Cell Using In Situ Selective Crystallization Based Quartz Crystal Microbalance. Anal Chem 2017; 89:4309-4313. [DOI: 10.1021/acs.analchem.7b00411] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Li-shang Liu
- Shandong Province
Key Laboratory of Detection Technology of Tumor Markers, School of
Chemistry and Chemical Engineering,, Linyi University, Linyi 276005, China
| | - Congcong Wu
- Shandong Province
Key Laboratory of Detection Technology of Tumor Markers, School of
Chemistry and Chemical Engineering,, Linyi University, Linyi 276005, China
- Collaborative Innovation
Center of Functionalized Probes for Chemical Imaging in Universities
of Shandong, Shandong Normal University, Jinan 250014, China
| | - Shusheng Zhang
- Shandong Province
Key Laboratory of Detection Technology of Tumor Markers, School of
Chemistry and Chemical Engineering,, Linyi University, Linyi 276005, China
| |
Collapse
|
33
|
Ben-Yoav H, Dykstra PH, Bentley WE, Ghodssi R. Microfluidic Arrayed Lab-On-A-Chip for Electrochemical Capacitive Detection of DNA Hybridization Events. Methods Mol Biol 2017; 1572:71-88. [PMID: 28299682 DOI: 10.1007/978-1-4939-6911-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A microfluidic electrochemical lab-on-a-chip (LOC) device for DNA hybridization detection has been developed. The device comprises a 3 × 3 array of microelectrodes integrated with a dual layer microfluidic valved manipulation system that provides controlled and automated capabilities for high throughput analysis of microliter volume samples. The surface of the microelectrodes is functionalized with single-stranded DNA (ssDNA) probes which enable specific detection of complementary ssDNA targets. These targets are detected by a capacitive technique which measures dielectric variation at the microelectrode-electrolyte interface due to DNA hybridization events. A quantitative analysis of the hybridization events is carried out based on a sensing modeling that includes detailed analysis of energy storage and dissipation components. By calculating these components during hybridization events the device is able to demonstrate specific and dose response sensing characteristics. The developed microfluidic LOC for DNA hybridization detection offers a technology for real-time and label-free assessment of genetic markers outside of laboratory settings, such as at the point-of-care or in-field environmental monitoring.
Collapse
Affiliation(s)
- Hadar Ben-Yoav
- Department of Biomedical Engineering, Ben-Gurion University of the Negev, Beer Sheva, 8410501, Israel.
| | - Peter H Dykstra
- MEMS Sensors and Actuators Laboratory (MSAL), Department of Electrical and Computer Engineering, Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - William E Bentley
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| | - Reza Ghodssi
- MEMS Sensors and Actuators Laboratory (MSAL), Department of Electrical and Computer Engineering, Institute for Systems Research, University of Maryland, College Park, MD, 20742, USA
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, 20742, USA
| |
Collapse
|
34
|
Hassan SHA, Van Ginkel SW, Hussein MAM, Abskharon R, Oh SE. Toxicity assessment using different bioassays and microbial biosensors. ENVIRONMENT INTERNATIONAL 2016; 92-93:106-18. [PMID: 27071051 DOI: 10.1016/j.envint.2016.03.003] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 03/05/2016] [Accepted: 03/05/2016] [Indexed: 05/23/2023]
Abstract
Toxicity assessment of water streams, wastewater, and contaminated sediments, is a very important part of environmental pollution monitoring. Evaluation of biological effects using a rapid, sensitive and cost effective method can indicate specific information on ecotoxicity assessment. Recently, different biological assays for toxicity assessment based on higher and lower organisms such as fish, invertebrates, plants and algal cells, and microbial bioassays have been used. This review focuses on microbial biosensors as an analytical device for environmental, food, and biomedical applications. Different techniques which are commonly used in microbial biosensing include amperometry, potentiometry, conductometry, voltammetry, microbial fuel cells, fluorescence, bioluminescence, and colorimetry. Examples of the use of different microbial biosensors in assessing a variety of environments are summarized.
Collapse
Affiliation(s)
- Sedky H A Hassan
- Botany Department, Faculty of Science, Assiut University, New Valley Branch, 72511 Al-Kharja, Egypt
| | - Steven W Van Ginkel
- School of Civil and Environmental Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | | | - Romany Abskharon
- National Institute of Oceanography and Fisheries (NIFO), 11516 Cairo, Egypt
| | - Sang-Eun Oh
- Department of Biological Environment, Kangwon National University, 200-701 Chuncheon, Kangwon-do, South Korea.
| |
Collapse
|
35
|
Liang G, Luo Z, Liu K, Wang Y, Dai J, Duan Y. Fiber Optic Surface Plasmon Resonance–Based Biosensor Technique: Fabrication, Advancement, and Application. Crit Rev Anal Chem 2015; 46:213-23. [DOI: 10.1080/10408347.2015.1045119] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Gaoling Liang
- College of Chemistry, Sichuan University, Chengdu, China
| | - Zewei Luo
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Sichuan University, Chengdu, China
| | - Kunping Liu
- College of Chemistry, Sichuan University, Chengdu, China
- Faculty of Biotechnology Industry, Chengdu University, Chengdu, China
| | - Yimin Wang
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Sichuan University, Chengdu, China
| | - Jianxiong Dai
- Analytical and Testing Center, Sichuan University, Chengdu, China
| | - Yixiang Duan
- Research Center of Analytical Instrumentation, Key Laboratory of Bio-resource and Eco-environment, Sichuan University, Chengdu, China
| |
Collapse
|
36
|
Bilgic T, Klok HA. Oligonucleotide Immobilization and Hybridization on Aldehyde-Functionalized Poly(2-hydroxyethyl methacrylate) Brushes. Biomacromolecules 2015; 16:3657-65. [PMID: 26441148 DOI: 10.1021/acs.biomac.5b01116] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
DNA biosensing requires high oligonucleotide binding capacity interface chemistries that can be tuned to maximize probe presentation as well as hybridization efficiency. This contribution investigates the feasibility of aldehyde-functionalized poly(2-hydroxyethyl methacrylate) (PHEMA) brush-based interfaces for oligonucleotide binding and hybridization. These polymer brushes, which allow covalent immobilization of oligonucleotides, are prepared by surface-initiated atom transfer radical polymerization (SI-ATRP) of HEMA followed by a postpolymerization oxidation step to generate side chain aldehyde groups. A series of polymer brushes covering a range of film thicknesses and grafting densities was investigated with regard to their oligonucleotide binding capacity as well as their ability to support oligonucleotide hybridization. Densely grafted brushes were found to have probe oligonucleotide binding capacities of up to ∼30 pmol/cm(2). Increasing the thickness of these densely grafted brush films, however, resulted in a decrease in the oligonucleotide binding capacity. Less densely grafted brushes possess binding capacities of ∼10 pmol/cm(2), which did not significantly depend on film thickness. The oligonucleotide hybridization efficiencies, however, were highest (93%) on those brushes that present the lowest surface concentration of the probe oligonucleotide. These results highlight the importance of optimizing the probe oligonucleotide surface concentration and binding interface chemistry. The versatility and tunability of the PHEMA-based brushes presented herein makes these films a very attractive platform for the immobilization and hybridization of oligonucleotides.
Collapse
Affiliation(s)
- Tugba Bilgic
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| | - Harm-Anton Klok
- Institut des Matériaux and Institut des Sciences et Ingénierie Chimiques, Laboratoire des Polymères, Ecole Polytechnique Fédérale de Lausanne (EPFL) , Bâtiment MXD, Station 12, CH-1015 Lausanne, Switzerland
| |
Collapse
|
37
|
Gulur Srinivas AR, Barker D, Travas-Sejdic J. ‘Switch-on’ DNA sensor based on poly (p-phenylene vinylenes) bound tentacle probes. PURE APPL CHEM 2015. [DOI: 10.1515/pac-2014-1114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
AbstractThe development of highly sensitive and selective DNA sensors has fuelled applications in a wide range of fields including medical diagnostics, forensics, biodefense, food contamination and environment monitoring. We demonstrate a novel superquenching based DNA sensor with “switch-on” readout using poly(p-phenylenevinylene) (PPV) coated magnetic beads (PPV-MagSi) and quencher functionalized tentacle probes (TP). The sensor design utilizes signal amplification properties of PPV and cooperativity of TPs to monitor hybridization of target oligonucleotides (ONs). The switch-on sensor exhibits excellent sensitivity and selectively discriminates mismatches in the target DNA sequence. Two novel anionic PPVs – poly (6,6′-((2-methyl-5-((E)-4-((E)-prop-1-en-1-yl)styryl)-1,4-phenylene)-bis(oxy) dihexanoic acid) (PMDH) and poly (6,6′-((2-((E)-2,5-bis(2-methoxyethoxy)-4-((E)-prop-1-en-1-yl)styryl)-5-methyl-1,4-phenylene)-bis-(oxy)) di-hexanoic acid) (PDMonoG) were tested and compared against each other as part of the sensor design. The employed hairpin TPs possess further advantages of avoiding labelling of target ON, increased selectivity and sensitivity; faster assay time, and capability of magnetically controlled deployment and separation of PPV-MagSi beads.
Collapse
Affiliation(s)
- Anupama R. Gulur Srinivas
- 1Polymer Electronics Research Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | - David Barker
- 1Polymer Electronics Research Centre, School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland, New Zealand
| | | |
Collapse
|
38
|
DNA-Based Nanobiosensors as an Emerging Platform for Detection of Disease. SENSORS 2015; 15:14539-68. [PMID: 26102488 PMCID: PMC4507582 DOI: 10.3390/s150614539] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Revised: 05/19/2015] [Accepted: 05/22/2015] [Indexed: 11/17/2022]
Abstract
Detection of disease at an early stage is one of the biggest challenges in medicine. Different disciplines of science are working together in this regard. The goal of nanodiagnostics is to provide more accurate tools for earlier diagnosis, to reduce cost and to simplify healthcare delivery of effective and personalized medicine, especially with regard to chronic diseases (e.g., diabetes and cardiovascular diseases) that have high healthcare costs. Up-to-date results suggest that DNA-based nanobiosensors could be used effectively to provide simple, fast, cost-effective, sensitive and specific detection of some genetic, cancer, and infectious diseases. In addition, they could potentially be used as a platform to detect immunodeficiency, and neurological and other diseases. This review examines different types of DNA-based nanobiosensors, the basic principles upon which they are based and their advantages and potential in diagnosis of acute and chronic diseases. We discuss recent trends and applications of new strategies for DNA-based nanobiosensors, and emphasize the challenges in translating basic research to the clinical laboratory.
Collapse
|
39
|
|
40
|
Wang R, Xiang Y, Zhou X, Liu LH, Shi H. A reusable aptamer-based evanescent wave all-fiber biosensor for highly sensitive detection of Ochratoxin A. Biosens Bioelectron 2014; 66:11-8. [PMID: 25460875 DOI: 10.1016/j.bios.2014.10.079] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2014] [Revised: 10/23/2014] [Accepted: 10/31/2014] [Indexed: 12/24/2022]
Abstract
Although aptamer-based biosensors have attracted ever-increasing attentions and found potential applications in a wide range of areas, they usually adopted the assay protocol of immobilizing DNA probe (e.g., aptamer, aptamer-complementary oligonucleotides) on a solid sensing surface, making it critical and challengeable to keep the integration of nucleic acid surface during the regeneration and the restoration to its original DNA probe form after repeated uses. In order to address the issue, we report a novel aptamer-based biosensing strategy based on an evanescent wave all-fiber (EWA) platform. In a simple target capturing step using aptamer-functionalized magnetic microbeads, signal probes conjugated with streptavidin are released and further detected by a EWA biosensor via a facial dethiobiotin-streptavidin recognition. Apart from the inherent advantages of aptamer-based evanescent wave biosensors (e.g. target versatility, sensitivity, selectivity and portability), the proposed strategy exhibits a high stability and remarkable reusability over other aptasensors. Under the optimized conditions, the typical calibration curve obtained for Ochratoxin A has a detection limit of 3nM with a linear response ranging from 6nM to 500nM. The dethiobiotin-streptavidin sensing surface instead of the traditional nucleic acid one can be reused for over 300 times without losing sensitivity.
Collapse
Affiliation(s)
- Ruoyu Wang
- School of environment, Tsinghua University, Beijing 100084, China
| | - Yu Xiang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaohong Zhou
- School of environment, Tsinghua University, Beijing 100084, China.
| | - Lan-Hua Liu
- School of environment, Tsinghua University, Beijing 100084, China
| | - Hanchang Shi
- School of environment, Tsinghua University, Beijing 100084, China
| |
Collapse
|
41
|
Gheerardijn V, Van den Begin J, Madder A. Versatile synthesis of amino acid functionalized nucleosides via a domino carboxamidation reaction. Beilstein J Org Chem 2014; 10:2566-72. [PMID: 25383128 PMCID: PMC4222392 DOI: 10.3762/bjoc.10.268] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 10/23/2014] [Indexed: 12/23/2022] Open
Abstract
Functionalized oligonucleotides have recently gained increased attention for incorporation in modified nucleic acid structures both for the design of aptamers with enhanced binding properties as well as the construction of catalytic DNA and RNA. As a shortcut alternative to the incorporation of multiple modified residues, each bearing one extra functional group, we present here a straightforward method for direct linking of functionalized amino acids to the nucleoside base, thus equipping the nucleoside with two extra functionalities at once. As a proof of principle, we have introduced three amino acids with functional groups frequently used as key-intermediates in DNA- and RNAzymes via an efficient and straightforward domino carboxamidation reaction.
Collapse
Affiliation(s)
- Vicky Gheerardijn
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Jos Van den Begin
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| | - Annemieke Madder
- Department of Organic and Macromolecular Chemistry, Organic and Biomimetic Chemistry Research Group, Ghent University, Krijgslaan 281 S4, 9000 Ghent, Belgium
| |
Collapse
|
42
|
Oliveira ON, Iost RM, Siqueira JR, Crespilho FN, Caseli L. Nanomaterials for diagnosis: challenges and applications in smart devices based on molecular recognition. ACS APPLIED MATERIALS & INTERFACES 2014; 6:14745-66. [PMID: 24968359 DOI: 10.1021/am5015056] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Clinical diagnosis has always been dependent on the efficient immobilization of biomolecules in solid matrices with preserved activity, but significant developments have taken place in recent years with the increasing control of molecular architecture in organized films. Of particular importance is the synergy achieved with distinct materials such as nanoparticles, antibodies, enzymes, and other nanostructures, forming structures organized on the nanoscale. In this review, emphasis will be placed on nanomaterials for biosensing based on molecular recognition, where the recognition element may be an enzyme, DNA, RNA, catalytic antibody, aptamer, and labeled biomolecule. All of these elements may be assembled in nanostructured films, whose layer-by-layer nature is essential for combining different properties in the same device. Sensing can be done with a number of optical, electrical, and electrochemical methods, which may also rely on nanostructures for enhanced performance, as is the case of reporting nanoparticles in bioelectronics devices. The successful design of such devices requires investigation of interface properties of functionalized surfaces, for which a variety of experimental and theoretical methods have been used. Because diagnosis involves the acquisition of large amounts of data, statistical and computational methods are now in widespread use, and one may envisage an integrated expert system where information from different sources may be mined to generate the diagnostics.
Collapse
Affiliation(s)
- Osvaldo N Oliveira
- São Carlos Institute of Physics, University of São Paulo , CP 369, 13560-970 São Carlos, São Paulo, Brazil
| | | | | | | | | |
Collapse
|
43
|
Silva RR, Avelino KYPS, Ribeiro KL, Franco OL, Oliveira MDL, Andrade CAS. Optical and dielectric sensors based on antimicrobial peptides for microorganism diagnosis. Front Microbiol 2014; 5:443. [PMID: 25191319 PMCID: PMC4138613 DOI: 10.3389/fmicb.2014.00443] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 08/04/2014] [Indexed: 12/24/2022] Open
Abstract
Antimicrobial peptides (AMPs) are natural compounds isolated from a wide variety of organisms that include microorganisms, insects, amphibians, plants, and humans. These biomolecules are considered as part of the innate immune system and are known as natural antibiotics, presenting a broad spectrum of activities against bacteria, fungi, and/or viruses. Technological innovations have enabled AMPs to be utilized for the development of novel biodetection devices. Advances in nanotechnology, such as the synthesis of nanocomposites, nanoparticles, and nanotubes have permitted the development of nanostructured platforms with biocompatibility and greater surface areas for the immobilization of biocomponents, arising as additional tools for obtaining more efficient biosensors. Diverse AMPs have been used as biological recognition elements for obtaining biosensors with more specificity and lower detection limits, whose analytical response can be evaluated through electrochemical impedance and fluorescence spectroscopies. AMP-based biosensors have shown potential for applications such as supplementary tools for conventional diagnosis methods of microorganisms. In this review, conventional methods for microorganism diagnosis as well new strategies using AMPs for the development of impedimetric and fluorescent biosensors are highlighted. AMP-based biosensors show promise as methods for diagnosing infections and bacterial contaminations as well as applications in quality control for clinical analyses and microbiological laboratories.
Collapse
Affiliation(s)
- Rafael R Silva
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco Recife, Brasil
| | - Karen Y P S Avelino
- Departamento de Bioquímica, Universidade Federal de Pernambuco Recife, Brasil
| | - Kalline L Ribeiro
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco Recife, Brasil
| | - Octavio L Franco
- Centro de Análises Proteômicas e Bioquímicas, Universidade Católica de Brasília Brasília-DF, Brasil
| | - Maria D L Oliveira
- Departamento de Bioquímica, Universidade Federal de Pernambuco Recife, Brasil
| | - Cesar A S Andrade
- Programa de Pós-Graduação em Inovação Terapêutica, Universidade Federal de Pernambuco Recife, Brasil ; Departamento de Bioquímica, Universidade Federal de Pernambuco Recife, Brasil
| |
Collapse
|
44
|
Jarczewska M, Kierzkowska E, Ziółkowski R, Górski L, Malinowska E. Electrochemical oligonucleotide-based biosensor for the determination of lead ion. Bioelectrochemistry 2014; 101:35-41. [PMID: 25042900 DOI: 10.1016/j.bioelechem.2014.06.013] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/30/2014] [Accepted: 06/30/2014] [Indexed: 01/25/2023]
Abstract
The possibility of utilization of gold electrodes modified with short guanine-rich ssDNA probes for determination of Pb(2+) was examined. Interaction between guanine residues and lead ion followed by formation of G-quadruplex structures was confirmed by electrochemical impedance spectroscopy investigations. An external cationic redox label, methylene blue, was employed in voltammetric measurements for analytical signal generation. It was shown that due to the G-quadruplex formation, the oligonucleotides in the recognition layer fold, which enhances the electron transfer between methylene blue and the electrode surface. The MB current signal rises proportionally to the lead ion concentration in the range from 0.05 to 1μmol/L. The developed biosensor demonstrated high selectivity towards Pb(2+) ion, with only minor response towards interfering metal cations. The calculated limit of detection was of 34.7nmol/L. The utilization of the biosensor for Pb(2+) determination in real samples of water was also tested.
Collapse
Affiliation(s)
- Marta Jarczewska
- Institute of Biotechnology, Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Ewa Kierzkowska
- Institute of Biotechnology, Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Robert Ziółkowski
- Institute of Biotechnology, Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Lukasz Górski
- Institute of Biotechnology, Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland.
| | - Elżbieta Malinowska
- Institute of Biotechnology, Department of Microbioanalytics, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| |
Collapse
|
45
|
Fusco V, Quero GM. Culture-Dependent and Culture-Independent Nucleic-Acid-Based Methods Used in the Microbial Safety Assessment of Milk and Dairy Products. Compr Rev Food Sci Food Saf 2014; 13:493-537. [DOI: 10.1111/1541-4337.12074] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2014] [Accepted: 03/08/2014] [Indexed: 12/12/2022]
Affiliation(s)
- Vincenzina Fusco
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| | - Grazia Marina Quero
- Nal. Research Council of Italy; Inst. of Sciences of Food Production (CNR-ISPA); Bari Italy
| |
Collapse
|
46
|
Sengupta E, Yan Y, Wang X, Munechika K, Ginger DS. Dynamic force spectroscopy of photoswitch-modified DNA. ACS NANO 2014; 8:2625-2631. [PMID: 24502655 DOI: 10.1021/nn406334b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
We apply a combination of photoswitch-modified DNA and AFM-based pulling measurements to study the force-induced melting of double-stranded DNA in the unzipping geometry. We measure the differences in peak rupture force for azobenzene-modified DNA, as the incorporated azobenzenes are photoswitched reversibly between the trans and the cis form. Fitting our rupture force versus loading rate data, we obtain off rate (koff) at zero force values in the range of ∼10 s(-1). We show that the change in peak rupture force and koff induced by destabilizing the DNA duplex depends on the position of the destabilizing azobenzene photoswitch relative to the force-loading site. When the azobenzenes are proximal to the unzipping end, the decrease in peak force and koff upon azobenzene photoisomerization is significantly larger than when the azobenzene is distal to the site of force loading. We interpret these results as experimental evidence supporting the picture that the destabilization of a double-stranded DNA by a photoswitch isomerization is localized to a small bubble around the photoswitch.
Collapse
Affiliation(s)
- Esha Sengupta
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | | | | | | | | |
Collapse
|
47
|
Nakano SI, Miyoshi D, Sugimoto N. Effects of molecular crowding on the structures, interactions, and functions of nucleic acids. Chem Rev 2013; 114:2733-58. [PMID: 24364729 DOI: 10.1021/cr400113m] [Citation(s) in RCA: 369] [Impact Index Per Article: 33.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Shu-ichi Nakano
- Department of Nanobiochemistry, Faculty of Frontiers of Innovative Research in Science and Technology (FIRST) and Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University , 7-1-20 Minatojima-minamimachi, Chuo-ku, Kobe 650-0047, Japan
| | | | | |
Collapse
|
48
|
Wang X, Lau C, Kai M, Lu J. Hybridization chain reaction-based instantaneous derivatization technology for chemiluminescence detection of specific DNA sequences. Analyst 2013; 138:2691-7. [PMID: 23515350 DOI: 10.1039/c3an36885h] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We propose here a new amplifying strategy that uses hybridization chain reaction (HCR) to detect specific sequences of DNA, where stable DNA monomers assemble on the magnetic beads only upon exposure to a target DNA. Briefly, in the HCR process, two complementary stable species of hairpins coexist in solution until the introduction of initiator reporter strands triggers a cascade of hybridization events that yield nicked double helices analogous to alternating copolymers. Moreover, a "sandwich-type" detection strategy is employed in our design. Magnetic beads, which are functionalized with capture DNA, are reacted with the target, and sandwiched with the above nicked double helices. Then, chemiluminescence (CL) detection proceeds via an instantaneous derivatization reaction between a specific CL reagent, 3,4,5-trimethoxylphenylglyoxal (TMPG), and the guanine nucleotides within the target DNA, reporter strands and DNA monomers for the generation of light. Our results clearly show that the amplification detection of specific sequences of DNA achieves a better performance (e.g. wide linear response range, low detection limit, and high specificity) as compared to the traditional sandwich type (capture/target/reporter) assays. Upon modification, the approach presented could be extended to detect other types of targets. We believe that this simple technique is promising for improving medical diagnosis and treatment.
Collapse
Affiliation(s)
- Xin Wang
- School of Pharmacy, Fudan University, 826 Zhangheng Road, Shanghai 201203, China
| | | | | | | |
Collapse
|
49
|
Poh HL, Bonanni A, Pumera M. Nanoporous carbon as a sensing platform for DNA detection: The use of impedance spectroscopy for hairpin-DNA based assay. RSC Adv 2012. [DOI: 10.1039/c1ra00812a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
|
50
|
Xu X, Ying Y. Microbial Biosensors for Environmental Monitoring and Food Analysis. FOOD REVIEWS INTERNATIONAL 2011. [DOI: 10.1080/87559129.2011.563393] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|