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Karoń S, Drozd M, Malinowska E. A Careful Insight into DDI-Type Receptor Layers on the Way to Improvement of Click-Biology-Based Immunosensors. BIOSENSORS 2024; 14:136. [PMID: 38534243 DOI: 10.3390/bios14030136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Revised: 02/26/2024] [Accepted: 03/02/2024] [Indexed: 03/28/2024]
Abstract
Protein-based microarrays are important tools for high-throughput medical diagnostics, offering versatile platforms for multiplex immunodetection. However, challenges arise in protein microarrays due to the heterogeneous nature of proteins and, thus, differences in their immobilization conditions. This article advocates DNA-directed immobilization (DDI) as a solution, emphasizing its rapid and cost-effective fabrication of biosensing platforms. Thiolated single-stranded DNA and its analogues, such as ZNA® and PNA probes, were used to immobilize model proteins (anti-CRP antibodies and SARS-CoV nucleoprotein). The study explores factors influencing DDI-based immunosensor performance, including the purity of protein-DNA conjugates and the stability of their duplexes with DNA and analogues. It also provides insight into backfilling agent type and probe surface density. The research reveals that single-component monolayers lack protection against protein adsorption, while mixing the probes with long-chain ligands may hinder DNA-protein conjugate anchoring. Conventional DNA probes offer slightly higher surface density, while ZNA® probes exhibit better binding efficiency. Despite no enhanced stability in different ionic strength media, the cost-effectiveness of DNA probes led to their preference. The findings contribute to advancing microarray technology, paving the way for new generations of DDI-based multiplex platforms for rapid and robust diagnostics.
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Affiliation(s)
- Sylwia Karoń
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Marcin Drozd
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
| | - Elżbieta Malinowska
- Department of Medical Diagnostics, Centre for Advanced Materials and Technologies CEZAMAT, Warsaw University of Technology, Poleczki 19, 02-822 Warsaw, Poland
- Chair of Medical Biotechnology, Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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2
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Lai Q, Chen W, Zhang Y, Liu Z. Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors. Analyst 2021; 146:5822-5835. [PMID: 34581324 DOI: 10.1039/d1an00765c] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.
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Affiliation(s)
- Qingteng Lai
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Wei Chen
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China. .,Department of Clinical Laboratory, Xiangya Hospital of Central South University, Changsha 410008, China
| | - Yanke Zhang
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
| | - Zhengchun Liu
- Hunan Key Laboratory of Super Microstructure and Ultrafast Process, School of Physics and Electronics, Central South University, Changsha 410083, China.
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Moazzenzade T, Huskens J, Lemay SG. Stochastic electrochemistry at ultralow concentrations: the case for digital sensors. Analyst 2020; 145:750-758. [PMID: 31808469 DOI: 10.1039/c9an01832h] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There is increasing demand, in particular from the medical field, for assays capable of detecting sub-pM macromolecular concentrations with high specificity. Methods for detecting single bio/macromolecules have already been developed based on a variety of transduction mechanisms, which represents the ultimate limit of mass sensitivity. Due to limitations imposed by mass transport and binding kinetics, however, achieving high concentration sensitivity additionally requires the massive parallelization of these single-molecule methods. This leads to a new sort of 'digital' assay based on large numbers of parallel, time-resolved measurements aimed at detecting, identifying and counting discrete macromolecular events instead of reading out an average response. In this Tutorial Review we first discuss the challenges inherent to trace-level detection and the motivations for developing digital assays. We then focus on the potential of recently developed single-entity impact electrochemistry methods for use in digital sensors. These have the inherent advantage of relying on purely electrical signals. They can thus in principle be implemented using integrated circuits to provide the parallelization, readout and analysis capabilities required for digital sensors.
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Affiliation(s)
- Taghi Moazzenzade
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
| | - Jurriaan Huskens
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
| | - Serge G Lemay
- MESA+ Institute for Nanotechnology, University of Twente, P.O. Box 217, 7500 AE Enschede, The Netherlands.
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Sun C, Chen T, Ruan W, Zhao B, Cong Q. Controlling the orientation of probe molecules on surface-enhanced Raman scattering substrates: A novel strategy to improve sensitivity. Anal Chim Acta 2017; 994:65-72. [DOI: 10.1016/j.aca.2017.10.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Revised: 09/02/2017] [Accepted: 10/04/2017] [Indexed: 10/18/2022]
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5
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Lee E, Mari C, Gel M, Gardiner J, Gasser G, Haylock D. Immobilisation of Multiple Ligands Using Peptide Nucleic Acids: A Strategy to Prepare the Microenvironment for Cell Culture. ChemistrySelect 2017. [DOI: 10.1002/slct.201700541] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Eun‐ju Lee
- Manufacturing Commonwealth Scientific and Industrial Research Organisation Ian Wark Laboratory Bayview Avenue Clayton, Victoria 3168 Australia
| | - Cristina Mari
- Department of Chemistry University of Zurich Winterthurerstrasse 190 CH-8057 Zurich Switzerland
| | - Murat Gel
- Manufacturing Commonwealth Scientific and Industrial Research Organisation Ian Wark Laboratory Bayview Avenue Clayton, Victoria 3168 Australia
| | - James Gardiner
- Manufacturing Commonwealth Scientific and Industrial Research Organisation Ian Wark Laboratory Bayview Avenue Clayton, Victoria 3168 Australia
| | - Gilles Gasser
- Chimie ParisTech PSL Research University Laboratory for Inorganic Chemical Biology F-75005 Paris France
| | - David Haylock
- Manufacturing Commonwealth Scientific and Industrial Research Organisation Ian Wark Laboratory Bayview Avenue Clayton, Victoria 3168 Australia
- Australian Regenerative Medicine Institute Monash University Clayton, Victoria 3168 Australia
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Pinto B, Rusciano G, D'Errico S, Borbone N, Sasso A, Piccialli V, Mayol L, Oliviero G, Piccialli G. Synthesis and label free characterization of a bimolecular PNA homo quadruplex. Biochim Biophys Acta Gen Subj 2016; 1861:1222-1228. [PMID: 27913190 DOI: 10.1016/j.bbagen.2016.11.037] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 12/31/2022]
Abstract
BACKGROUND G-quadruplex DNA is involved in many physiological and pathological processes. Both clinical and experimental studies on DNA G-quadruplexes are slowed down by their enzymatic instability. In this frame, more stable chemically modified analogs are needed. METHODS The bis-end-linked-(gggt)2 PNA molecule (BEL-PNA) was synthesized using in solution and solid phase synthetic approaches. Quadruplex formation was assessed by circular dichroism (CD) and surface enhanced Raman scattering (SERS). RESULTS An unprecedented bimolecular PNA homo quadruplex is here reported. To achieve this goal, we developed a bifunctional linker that once functionalized with gggt PNA strands and annealed in K+ buffer allowed the obtainment of a PNA homo quadruplex. The identification of the strong SERS band at ~1481cm-1, attributable to vibrations involving the quadruplex diagnostic Hoogsteen type hydrogen bonds, confirmed the formation of the PNA homo quadruplex. CONCLUSIONS By tethering two G-rich PNA strands to the two ends of a suitable bifunctional linker it is possible to obtain bimolecular PNA homo quadruplexes after annealing in K+-containing buffers. The formation of such CD-unfriendly complexes can be monitored, even at low concentrations, by using the SERS technique. GENERAL SIGNIFICANCE Given the importance of DNA G-quadruplexes in medicine and nanotechnology, the obtainment of G-quadruplex analogs provided with enhanced enzymatic stability, and their monitoring by highly sensitive label-free techniques are of the highest importance. This article is part of a Special Issue entitled "G-quadruplex" Guest Editor: Dr. Concetta Giancola and Dr. Daniela Montesarchio.
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Affiliation(s)
- Brunella Pinto
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giulia Rusciano
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Stefano D'Errico
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Nicola Borbone
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Antonio Sasso
- Dipartimento di Scienze Fisiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Vincenzo Piccialli
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, 80126 Napoli, Italy
| | - Luciano Mayol
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy
| | - Giorgia Oliviero
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy.
| | - Gennaro Piccialli
- Dipartimento di Farmacia, Università degli Studi di Napoli Federico II, 80131 Napoli, Italy; CNR, Institute of Protein Biochemistry, 80131 Napoli, Italy.
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7
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García-Sacristán A, Moreno M, Ariza-Mateos A, López-Camacho E, Jáudenes RM, Vázquez L, Gómez J, Martín-Gago JÁ, Briones C. A magnesium-induced RNA conformational switch at the internal ribosome entry site of hepatitis C virus genome visualized by atomic force microscopy. Nucleic Acids Res 2014; 43:565-80. [PMID: 25510496 PMCID: PMC4288189 DOI: 10.1093/nar/gku1299] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 5' untranslated region of hepatitis C virus (HCV) genomic RNA contains an internal ribosome entry site (IRES) element, composed of domains II-IV, which is required for cap-independent translation initiation. Little information on the 3D structure of the whole functional HCV IRES is still available. Here, we use atomic force microscopy to visualize the HCV IRES conformation in its natural sequence context, which includes the upstream domain I and the essential, downstream domains V and VI. The 574 nt-long molecule analyzed underwent an unexpected, Mg(2+)-induced switch between two alternative conformations: from 'open', elongated morphologies at 0-2 mM Mg(2+) concentration to a 'closed', comma-shaped conformation at 4-6 mM Mg(2+). This sharp transition, confirmed by gel-shift analysis and partial RNase T1 cleavage, was hindered by the microRNA miR-122. The comma-shaped IRES-574 molecules visualized at 4-6 mM Mg(2+) in the absence of miR-122 showed two arms. Our data support that the first arm would contain domain III, while the second one would be composed of domains (I-II)+(V-VI) thanks to a long-range RNA interaction between the I-II spacer and the basal region of domain VI. This reinforces the previously described structural continuity between the HCV IRES and its flanking domains I, V and VI.
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Affiliation(s)
- Ana García-Sacristán
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
| | - Miguel Moreno
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Ascensión Ariza-Mateos
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - Elena López-Camacho
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Rosa M Jáudenes
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain
| | - Luis Vázquez
- Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Jordi Gómez
- Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina 'López-Neyra' (CSIC), Parque Tecnológico Ciencias de la Salud, Armilla, Granada 18016, Spain
| | - José Ángel Martín-Gago
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Instituto de Ciencia de Materiales de Madrid (CSIC), Cantoblanco, Madrid 28049, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid 28850, Spain Centro de Investigaciones Biomédicas en Red de Enfermedades Hepáticas y Digestivas, (CIBERehd), Spain
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8
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Deng H, Shen W, Ren Y, Gao Z. A highly sensitive microRNA biosensor based on hybridized microRNA-guided deposition of polyaniline. Biosens Bioelectron 2014; 60:195-200. [DOI: 10.1016/j.bios.2014.04.023] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 04/04/2014] [Accepted: 04/15/2014] [Indexed: 11/26/2022]
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9
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Hu Q, Hu W, Kong J, Zhang X. PNA-based DNA assay with attomolar detection limit based on polygalacturonic acid mediated in-situ deposition of metallic silver on a gold electrode. Mikrochim Acta 2014. [DOI: 10.1007/s00604-014-1351-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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10
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Arroyo-Hernández M, Svec M, Rogero C, Briones C, Martín-Gago JA, Costa-Krämer JL. Structural modifications of gold thin films produced by thiol-derivatized single-stranded DNA immobilization. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2014; 26:055010. [PMID: 24440831 DOI: 10.1088/0953-8984/26/5/055010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Recent experiments have reported an opposite sign of the differential surface stress produced on gold-coated cantilevers by a thiol-derivatized single-stranded DNA (SH-DNA) immobilization process. The sign of the surface stress depends on the method used to evaporate the gold thin film, being compressive (negative) or tensile (positive) for e-beam or resistively deposited gold, respectively. This study investigates the origin of this effect by means of a combination of x-ray diffraction and x-ray photoelectron spectroscopy. Both e-beam and resistively grown gold thin films are characterized to find the subtle differences responsible for this intriguing stress behaviour. Somewhat remarkably, these studies show a tight relation between the surface structure of the gold overlayer and the SH-DNA immobilization efficiency. The average grain size variation seems to correlate well with the differential surface stress triggered by the SH-DNA immobilization previously reported. These results suggest that the relation of the probe molecules with the surface structure must be considered to understand surface stress changes.
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Affiliation(s)
- María Arroyo-Hernández
- IMM-Instituto de Microelectrónica de Madrid (CNM-CSIC), Isaac Newton 8, PTM, E-28760 Tres Cantos, Madrid, Spain
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11
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Ghosh S, Mishra S, Mukhopadhyay R. Enhancing sensitivity in a piezoresistive cantilever-based label-free DNA detection assay using ssPNA sensor probes. J Mater Chem B 2014; 2:960-970. [DOI: 10.1039/c3tb21392g] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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12
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Ruiz-Mirazo K, Briones C, de la Escosura A. Prebiotic Systems Chemistry: New Perspectives for the Origins of Life. Chem Rev 2013; 114:285-366. [DOI: 10.1021/cr2004844] [Citation(s) in RCA: 563] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Kepa Ruiz-Mirazo
- Biophysics
Unit (CSIC-UPV/EHU), Leioa, and Department of Logic and Philosophy
of Science, University of the Basque Country, Avenida de Tolosa 70, 20080 Donostia−San Sebastián, Spain
| | - Carlos Briones
- Department
of Molecular Evolution, Centro de Astrobiología (CSIC−INTA, associated to the NASA Astrobiology Institute), Carretera de Ajalvir, Km 4, 28850 Torrejón de Ardoz, Madrid, Spain
| | - Andrés de la Escosura
- Organic
Chemistry Department, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
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13
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Ghosh S, Mishra S, Mukhopadhyay R. Enhancing on-surface mismatch discrimination capability of PNA probes by AuNP modification of gold(111) surface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:11982-90. [PMID: 23978256 DOI: 10.1021/la4019579] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Unambiguous identification of single base mismatches in nucleic acid sequences is of great importance in nucleic acid detection assays. However, ambiguities are often encountered with, and therefore, a strategy for attaining substantially large enhancement of mismatch discrimination has been worked upon in this study. Short single-stranded peptide nucleic acid (PNA) and deoxyribonucleic acid (DNA) sensor probes that are immobilized onto gold nanoparticle (AuNP) modified Au(111) surface have been applied for target DNA detection. It will be shown that while both PNA and the analogous DNA probes exhibit generally better target detection abilities on the AuNP-modified Au(111) surface (elicited from fluorescence-based measurement of on-surface Tm values), compared to the bare Au(111) surface, PNA supersedes DNA, for all sizes of AuNPs (10, 50, and 90 nm) applied, with the difference being quite drastic in the case of the smallest 10 nm AuNP. It is found that while the AuNP curvature plays a pivotal role in target detection abilities of the PNA probes, the changes in the surface roughness caused by AuNP treatment do not exert any significant influence. This study also presents a means for preparing PNA-AuNP hybrids without altering PNA functionality and without AuNP aggregation by working with the surface-affixed AuNPs.
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Affiliation(s)
- Srabani Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science , Jadavpur, Kolkata-700 032, India
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14
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Ghosh S, Mishra S, Banerjee T, Mukhopadhyay R. Facilitating mismatch discrimination by surface-affixed PNA probes via ionic regulation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:3370-3379. [PMID: 23414328 DOI: 10.1021/la400125x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
There has been a search for alternative nucleic acids that can be more effectively used in nucleic acid detection technologies compared to the DNA probes. Peptide nucleic acid (PNA), which contains a non-ionic peptidic backbone, offers such possibilities since it is nuclease-resistant, it binds to DNA with high affinity, and it can be readily self-assembled onto solid substrates, e.g., gold(111), with a molecular backbone orientation away from the substrate. Although application of PNA as a sensor probe has been exemplified, so far there is little or no account of the ionic modulation of single base mismatch discrimination capacity of surface-tethered PNA probes. Herein, we report "on-surface" melting temperatures of PNA-DNA duplexes formed on gold(111) surface, as obtained from fluorescence measurements. We show that surface-tethered PNA forms a stabler duplex than DNA, and is more effective in single base mismatch discrimination than DNA. Importantly, although PNA backbone is non-ionic, variation in the ionic components in hybridization buffer, i.e., varying concentration of monovalent sodium ion, and the nature of anion and the cation, exhibits clear effects on the mismatch discrimination capacity of PNA probes. In general, with decreasing cation concentration, PNA-DNA duplexes are stabilized and mismatch discrimination capacity of the PNA probes is enhanced. The stabilizing/destabilizing effects of anions are found to follow the Hofmeister series, emphasizing the importance of hydrophobic interaction between nucleobases for stability of the PNA-DNA duplexes. Interestingly, the nature of ionic dependence of "on-surface" mismatch detection ability of PNA probes differs significantly from the "solution" behavior of these probes.
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Affiliation(s)
- Srabani Ghosh
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
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15
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Watson SMD, Hedley JH, Galindo MA, Al-Said SAF, Wright NG, Connolly BA, Horrocks BR, Houlton A. Synthesis, Characterisation and Electrical Properties of Supramolecular DNA-Templated Polymer Nanowires of 2,5-(Bis-2-thienyl)-pyrrole. Chemistry 2012; 18:12008-19. [DOI: 10.1002/chem.201201495] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Indexed: 01/16/2023]
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Bonifazi D, Carloni LE, Corvaglia V, Delforge A. Peptide nucleic acids in materials science. ARTIFICIAL DNA, PNA & XNA 2012; 3:112-22. [PMID: 22925824 PMCID: PMC3581510 DOI: 10.4161/adna.21941] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
This review highlights the recent methods to prepare PNA-based materials through a combination of self-assembly and self-organization processes. The use of these methods allows easy and versatile preparation of structured hybrid materials showing specific recognition properties and unique physicochemical properties at the nano- and micro-scale levels displaying potential applications in several directions, ranging from sensors and microarrays to nanostructured devices for biochips.
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Affiliation(s)
- Davide Bonifazi
- Namur Research College, Department of Chemistry, University of Namur, Namur, Belgium.
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17
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Applications of peptide nucleic acids (PNAs) and locked nucleic acids (LNAs) in biosensor development. Anal Bioanal Chem 2012; 402:3071-89. [PMID: 22297860 DOI: 10.1007/s00216-012-5742-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Accepted: 01/12/2012] [Indexed: 01/06/2023]
Abstract
Nucleic acid biosensors have a growing number of applications in genetics and biomedicine. This contribution is a critical review of the current state of the art concerning the use of nucleic acid analogues, in particular peptide nucleic acids (PNA) and locked nucleic acids (LNA), for the development of high-performance affinity biosensors. Both PNA and LNA have outstanding affinity for natural nucleic acids, and the destabilizing effect of base mismatches in PNA- or LNA-containing heterodimers is much higher than in double-stranded DNA or RNA. Therefore, PNA- and LNA-based biosensors have unprecedented sensitivity and specificity, with special applicability in DNA genotyping. Herein, the most relevant PNA- and LNA-based biosensors are presented, and their advantages and their current limitations are discussed. Some of the reviewed technology, while promising, still needs to bridge the gap between experimental status and the harder reality of biotechnological or biomedical applications.
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Mishra S, Ghosh S, Mukhopadhyay R. Ordered self-assembled locked nucleic acid (LNA) structures on gold(111) surface with enhanced single base mismatch recognition capability. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2012; 28:4325-4333. [PMID: 22309111 DOI: 10.1021/la204026j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Locked nucleic acid (LNA) is a conformationally restricted nucleic acid analogue, which is potentially a better alternative than DNA for application in the nucleic acid based biosensor technologies, due to its efficient and sequence-specific DNA/RNA detection capability and lack of molecule-surface interaction on solid surfaces, compared to DNA. We report, for the first time, a straightforward way (based on simple immersion method) of generating an ordered self-assembled LNA monolayer, which is bioactive, onto a gold(111) surface. This layer is capable of giving rise to a stronger DNA recognition signal (4-4.5 times) than its DNA counterpart, and importantly, it can differentiate between a fully complementary DNA target and that having a single base mismatch, where the mismatch discrimination ratio is almost two times compared to the ratio relevant in case of DNA-based detection. We have presented high-resolution atomic force microscopy (AFM) topographs of the well-defined one-dimensional LNA molecular ordering (few hundred nanometers long) and of the two-dimensional ordered assembly formed over a large area (7 μm × 7 μm) due to parallel positioning of the one-dimensional ordered arrangements. The effects of different parameters such as LNA concentration and incubation time on LNA self-assembly have been investigated. Further, reflection absorption infrared (RAIR) spectroscopy has been applied to obtain information about the orientation of the surface-immobilized LNA molecules for the first time. It has been found that the LNA molecules undergo an orientational transition from the "lying down" to the "upright" configuration in a time scale of few hours.
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Affiliation(s)
- Sourav Mishra
- Department of Biological Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Kolkata, India
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Rahaie M, Kazemi S. Lectin-based Biosensors: As Powerful Tools in Bioanalytical Applications. ACTA ACUST UNITED AC 2010. [DOI: 10.3923/biotech.2010.428.443] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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20
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Hassanien R, Al-Hinai M, Farha Al-Said SA, Little R, Siller L, Wright NG, Houlton A, Horrocks BR. Preparation and characterization of conductive and photoluminescent DNA-templated polyindole nanowires. ACS NANO 2010; 4:2149-59. [PMID: 20218665 DOI: 10.1021/nn9014533] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Polyindole (PIn) nanowires were formed on a lambda-DNA template by chemical oxidation of indole using aqueous FeCl3. The resulting nanowires are smooth, regular, conductive and had diameters in the range of 5-30 nm. These features allow them to be aligned by molecular combing and studied by scanned conductance microscopy, conductive AFM, and two-terminal I-V measurements. Using this combination of measurements, we find that the conductivity of PIn/DNA nanowires is between 2.5 and 40 S cm(-1) at room temperature, which is substantially greater than that in previous reports on the bulk polyindole conductivity (typically 10(-2)-10(-1) S cm(-1)). The conductance at zero bias shows an Arrhenius-type of dependence on temperature over the range of 233 to 373 K, and the values observed upon heating and cooling are repeatable within 5%; this behavior is consistent with a hopping mechanism of conductivity.
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Affiliation(s)
- Reda Hassanien
- Chemical Nanoscience Laboratories, School of Chemistry, Bedson Building, Engineering and Advanced Materials, Newcastle University, Newcastle Upon Tyne NE1 7RU, United Kingdom
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21
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An overview of foodborne pathogen detection: In the perspective of biosensors. Biotechnol Adv 2010; 28:232-54. [DOI: 10.1016/j.biotechadv.2009.12.004] [Citation(s) in RCA: 805] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2008] [Revised: 12/03/2009] [Accepted: 12/04/2009] [Indexed: 12/12/2022]
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22
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Hejazi MS, Pournaghi-Azar MH, Ahour F. Electrochemical detection of short sequences of hepatitis C 3a virus using a peptide nucleic acid-assembled gold electrode. Anal Biochem 2009; 399:118-24. [PMID: 19931215 DOI: 10.1016/j.ab.2009.11.019] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2009] [Revised: 11/15/2009] [Accepted: 11/16/2009] [Indexed: 12/12/2022]
Abstract
Development of an electrochemical DNA biosensor, using a gold electrode modified with a self-assembled monolayer composed of a peptide nucleic acid (PNA) probe and 6-mercapto-1-hexanol, is described. The sensor relies on covalent attachment of the 14-mer PNA probe related to the hepatitis C virus genotype 3a (pHCV3a) core/E1 region on the electrode. Covalently self-assembled PNA could selectively hybridize with a complementary sequence in solution to form double-stranded PNA-DNA on the surface. The increase of peak current of methylene blue (MB), upon hybridization of the self-assembled probe with the target DNA in the solution, was observed and used to detect the target DNA sequence. Some hybridization experiments with noncomplementary oligonucleotides were carried out to assess whether the suggested DNA sensor responds selectively to the target. Diagnostic performance of the biosensor is described and the detection limit was found to be 5.7 x 10(-11)M with a relative standard deviation of 1.4% in phosphate buffer solution, pH 7.0. This sensor exhibits high reproducibility and could be used for detection of the target DNA for seven times after the regeneration process.
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Affiliation(s)
- M S Hejazi
- Faculty of Pharmacy, Tabriz University of Medical Sciences, Tabriz, Iran.
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Arroyo-Hernández M, Tamayo J, Costa-Krämer JL. Stress and DNA assembly differences on cantilevers gold coated by resistive and e-beam evaporation techniques. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:10633-10638. [PMID: 19694416 DOI: 10.1021/la900696f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Changes in the sign of differential surface stress of gold-coated cantilevers produced by thiol-derivatized single-stranded DNA immobilization are observed, depending on the method used to deposit the gold. While the DNA immobilization on e-beam gold-coated cantilevers produces a compressive differential surface stress in the metallic layer, the opposite is observed for resistively coated cantilevers under the same immobilization conditions. The gold films exhibit quite a similar morphology, and the immobilization differences seem to be related to the charge state of the metallic layer surface. This in turn produces a different distribution of the orientation of the DNA strands on the gold layer. A tentative explanation for the observed effect is proposed.
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Affiliation(s)
- M Arroyo-Hernández
- Instituto de Microelectrónica de Madrid, IMM-CNM-CSIC, Isaac Newton 8, PTM, 28760 Tres Cantos, Madrid, Spain.
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Mateo-Martí E, Briones C, Rogero C, Gomez-Navarro C, Methivier C, Pradier C, Martín-Gago J. Nucleic acid interactions with pyrite surfaces. Chem Phys 2008. [DOI: 10.1016/j.chemphys.2008.05.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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25
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Zhang GJ, Zhang G, Chua JH, Chee RE, Wong EH, Agarwal A, Buddharaju KD, Singh N, Gao Z, Balasubramanian N. DNA sensing by silicon nanowire: charge layer distance dependence. NANO LETTERS 2008; 8:1066-1070. [PMID: 18311939 DOI: 10.1021/nl072991l] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
To provide a comprehensive understanding of the field effect in silicon nanowire (SiNW) sensors, we take a systematic approach to fine tune the distance of a charge layer by controlling the hybridization sites of DNA to the SiNW preimmobilized with peptide nucleic acid (PNA) capture probes. Six target DNAs of the same length, but differentiated successively by three bases in the complementary segment, are hybridized to the PNA. Fluorescent images show that the hybridization occurs exclusively on the SiNW surface between the target DNAs and the PNA. However, the field-effect response of the SiNW sensor decreases as the DNA (charge layer) moves away from the SiNW surface. Theoretical analysis shows that the field effect of the SiNW sensor relies primarily on the location of the charge layer. A maximum of 102% change in resistance is estimated based on the shortest distance of the DNA charge layer (4.7 A) to the SiNW surface.
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Affiliation(s)
- Guo-Jun Zhang
- Institute of Microelectronics, Agency for Science, Technology and Research, 11 Science Park Road, Singapore 117685.
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26
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Pita M, Abad JM, Vaz-Dominguez C, Briones C, Mateo-Martí E, Martín-Gago JA, Morales MDP, Fernández VM. Synthesis of cobalt ferrite core/metallic shell nanoparticles for the development of a specific PNA/DNA biosensor. J Colloid Interface Sci 2008; 321:484-92. [PMID: 18329659 DOI: 10.1016/j.jcis.2008.02.010] [Citation(s) in RCA: 113] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2008] [Accepted: 02/06/2008] [Indexed: 11/28/2022]
Abstract
Controlled synthesis of cobalt ferrite superparamagnetic nanoparticles covered with a gold shell has been achieved by an affinity and trap strategy. Magnetic nanoparticles are functionalized with a mixture of amino and thiol groups that facilitate the electrostatic attraction and further chemisorption of gold nanoparticles, respectively. Using these nanoparticles as seeds, a complete coating shell is achieved by gold salt-iterative reduction leading to monodisperse water-soluble gold-covered magnetic nanoparticles, with an average diameter ranging from 21 to 29 nm. These constitute a versatile platform for immobilization of biomolecules via thiol chemistry, which is exemplified by the immobilization of peptide nucleic acid (PNA) oligomers that specifically hybridize with complementary DNA molecules in solution. Hybridation with DNA probes has been measured using Rhodamine 6G fluorescence marker and the detection of a single nucleotide mutation has been achieved. These results suggest the PNA-nanoparticles application as a biosensor for DNA genotyping avoiding commonly time-consuming procedures employed.
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Affiliation(s)
- Marcos Pita
- Instituto de Catálisis y Petroleoquímica, CSIC, C/Marie Curie 2, 28049 Cantoblanco, Madrid, Spain.
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Jedlicka SS, Little KM, Nivens DE, Zemlyanov D, Rickus JL. Peptide ormosils as cellular substrates. ACTA ACUST UNITED AC 2007. [DOI: 10.1039/b705393b] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Mateo-Martí E, Briones C, Pradier CM, Martín-Gago JA. A DNA biosensor based on peptide nucleic acids on gold surfaces. Biosens Bioelectron 2006; 22:1926-32. [PMID: 16996729 DOI: 10.1016/j.bios.2006.08.012] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2006] [Revised: 07/28/2006] [Accepted: 08/09/2006] [Indexed: 10/24/2022]
Abstract
We present a DNA biosensor based on self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) molecules adsorbed on gold surfaces. Previous works have shown that PNA molecules at an optimal concentration can be self-assembled with their molecular axes normal to the surface. In such structural configuration BioSAMs of PNAs maintain their capability for recognizing complementary DNA. We describe the combined use of PM-RAIRS and synchrotron radiation XPS for the detection and spectroscopic characterization of PNA-DNA hybridization process on gold surfaces. RAIRS and XPS are powerful techniques for surface characterization and molecular detection, which do not require a fluorescence labeling of the target. We present a characterization of the spectroscopic IR and XPS features, some of them associated to the phosphate groups of the DNA backbone, as an unambiguous signature of the PNA-DNA heteroduplex formation. The N(1s) XPS core level peak after DNA hybridization is decomposed in curves components, and every component assigned to different chemical species. Therefore, the results obtained by means of two complementary structural characterization techniques encourage the use of PNA-based biosensors for the detection of DNA molecules on natural samples.
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Selhuber C, Blümmel J, Czerwinski F, Spatz JP. Tuning surface energies with nanopatterned substrates. NANO LETTERS 2006; 6:267-70. [PMID: 16464048 DOI: 10.1021/nl052256e] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
A novel approach to varying the surface energy of biofunctional substrates has been developed, where surface energies are controlled by utilizing tunable nanopatterned substrates. In this study we functionalized the nanopattern with streptavidin, providing an adhesive interface for biotinylated probes. To obtain the surface energies, we applied the Johnson-Kendall-Roberts model to the adhesion-induced deformation of elastic beads. The results reveal a linear relationship between surface energy and ligand density, demonstrating the capability of this technique to adjust surface energy.
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Affiliation(s)
- Christine Selhuber
- Max-Planck-Institute for Metals Research, Department New Materials and Biosystems, Heisenbergstr. 3, D - 70 569 Stuttgart, Germany
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31
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Mateo-Martí E, Briones C, Román E, Briand E, Pradier CM, Martín-Gago JA. Self-assembled monolayers of peptide nucleic acids on gold surfaces: a spectroscopic study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2005; 21:9510-7. [PMID: 16207029 DOI: 10.1021/la050366v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
We have characterized self-assembled monolayers (SAMs) of thiol-derivatized peptide nucleic acid (PNA) chains adsorbed on gold surfaces by using reflection absorption infrared spectroscopy (RAIRS) and X-ray photoemission spectroscopy (XPS) techniques. We have found that the molecular orientation of PNAs strongly depends on surface coverage. At low coverage, PNA chains lie flat on the surface, while at high coverage, PNA molecules realign their molecular axes with the surface normal and form SAMs without the need of co-immobilization of spacers or other adjuvant molecules. The change in the molecular orientation has been studied by infrared spectroscopy and it has been confirmed by atomic force microscopy (AFM). PNA immobilization has been followed by analyzing the N(1s) XPS core-level peak. We show that the fine line shape of the N(1s) core-level peak at optimal concentration for biosensing is due to a chemical shift. A combination of the above-mentioned techniques allow us to affirm that the structure of the SAMs is stabilized by molecule-molecule interactions through noncomplementary adjacent nucleic bases.
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Affiliation(s)
- E Mateo-Martí
- Centro de Astrobiología (CSIC-INTA), Ctra. Ajalvir, Km. 4, 28850 Torrejón de Ardoz, Madrid, Spain
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