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Gerdan Z, Saylan Y, Denizli A. Biosensing Platforms for Cardiac Biomarker Detection. ACS OMEGA 2024; 9:9946-9960. [PMID: 38463295 PMCID: PMC10918812 DOI: 10.1021/acsomega.3c06571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 01/24/2024] [Accepted: 01/30/2024] [Indexed: 03/12/2024]
Abstract
Myocardial infarction (MI) is a cardiovascular disease that occurs when there is an elevated demand for myocardial oxygen as a result of the rupture or erosion of atherosclerotic plaques. Globally, the mortality rates associated with MI are steadily on the rise. Traditional diagnostic biomarkers employed in clinical settings for MI diagnosis have various drawbacks, prompting researchers to investigate fast, precise, and highly sensitive biosensor platforms and technologies. Biosensors are analytical devices that combine biological elements with physicochemical transducers to detect and quantify specific compounds or analytes. These devices play a crucial role in various fields including healthcare, environmental monitoring, food safety, and biotechnology. Biosensors developed for the detection of cardiac biomarkers are typically electrochemical, mass, and optical biosensors. Nanomaterials have emerged as revolutionary components in the field of biosensing, offering unique properties that significantly enhance the sensitivity and specificity of the detection systems. This review provides a comprehensive overview of the advancements and applications of nanomaterial-based biosensing systems. Beginning with an exploration of the fundamental principles governing nanomaterials, we delve into their diverse properties, including but not limited to electrical, optical, magnetic, and thermal characteristics. The integration of these nanomaterials as transducers in biosensors has paved the way for unprecedented developments in analytical techniques. Moreover, the principles and types of biosensors and their applications in cardiovascular disease diagnosis are explained in detail. The current biosensors for cardiac biomarker detection are also discussed, with an elaboration of the pros and cons of existing platforms and concluding with future perspectives.
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Affiliation(s)
- Zeynep Gerdan
- Department
of Biomedical Engineering, Istanbul Beykent
University, Istanbul 34398, Turkey
| | - Yeşeren Saylan
- Department
of Chemistry, Hacettepe University, Ankara 06800, Turkey
| | - Adil Denizli
- Department
of Chemistry, Hacettepe University, Ankara 06800, Turkey
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2
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Domljanovic I, Ianiro A, Rüegg C, Mayer M, Taskova M. Natural and Modified Oligonucleotide Sequences Show Distinct Strand Displacement Kinetics and These Are Affected Further by Molecular Crowders. Biomolecules 2022; 12:1249. [PMID: 36139087 PMCID: PMC9496266 DOI: 10.3390/biom12091249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/02/2022] [Accepted: 09/04/2022] [Indexed: 11/25/2022] Open
Abstract
DNA and RNA strand exchange is a process of fundamental importance in biology. Herein, we used a FRET-based assay to investigate, for the first time, the stand exchange kinetics of natural DNA, natural RNA, and locked nucleic acid (LNA)-modified DNA sequences in vitro in PBS in the absence or presence of molecular additives and macromolecular crowders such as diethylene glycol dimethyl ether (deg), polyethylene glycol (peg), and polyvinylpyrrolidone (pvp). The results show that the kinetics of strand exchange mediated by DNA, RNA, and LNA-DNA oligonucleotide sequences are different. Different molecular crowders further affect the strand displacement kinetics, highlighting the complexity of the process of nucleic acid strand exchange as it occurs in vivo. In a peg-containing buffer, the rate constant of displacement was slightly increased for the DNA displacement strand, while it was slightly decreased for the RNA and the LNA-DNA strands compared with displacement in pure PBS. When we used a deg-containing buffer, the rate constants of displacement for all three sequences were drastically increased compared with displacement in PBS. Overall, we show that interactions of the additives with the duplex strands have a significant effect on the strand displacement kinetics and this effect can exceed the one exerted by the chemical nature of the displacement strand itself.
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Affiliation(s)
- Ivana Domljanovic
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
| | - Alessandro Ianiro
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
| | - Curzio Rüegg
- Laboratory of Experimental and Translational Oncology, Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Chemin du Musée 18, PER17, 1700 Fribourg, Switzerland
| | - Michael Mayer
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
| | - Maria Taskova
- BioPhysics, Adolphe Merkle Institute, University of Fribourg, Chemin des Verdiers 4, PER 18, 1700 Fribourg, Switzerland
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Ferreira I, Slott S, Astakhova K, Weber G. Complete Mesoscopic Parameterization of Single LNA Modifications in DNA Applied to Oncogene Probe Design. J Chem Inf Model 2021; 61:3615-3624. [PMID: 34251211 DOI: 10.1021/acs.jcim.1c00470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of mesoscopic models to describe the thermodynamic properties of locked nucleic acid (LNA)-modified nucleotides can provide useful insights into their properties, such as hydrogen-bonding and stacking interactions. In addition, the mesoscopic parameters can be used to optimize LNA insertion in probes, to achieve accurate melting temperature predictions, and to obtain duplex opening profiles at the base-pair level. Here, we applied this type of model to parameterize a large set of melting temperatures for LNA-modified sequences, from published sources, covering all possible nearest-neighbor configurations. We have found a very large increase in Morse potentials, which indicates very strong hydrogen bonding as the main cause of improved LNA thermodynamic stability. LNA-modified adenine-thymine (AT) was found to have similar hydrogen bonding to unmodified cytosine-guanine (CG) base pairs, while for LNA CG, we found exceptionally large hydrogen bonding. In contrast, stacking interactions, which were thought to be behind the stability of LNA, were similar to unmodified DNA in most cases. We applied the new LNA parameters to the design of BRAF, KRAS, and EGFR oncogene variants by testing all possible LNA modifications. Selected sequences were then synthesized and had their hybridization temperatures measured, achieving a prediction accuracy within 1 °C. We performed a detailed base-pair opening analysis to discuss specific aspects of these probe hybridizations that may be relevant for probe design.
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Affiliation(s)
- Izabela Ferreira
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil.,Programa Interunidades de Pós-Graduação em Bioinformática, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
| | - Sofie Slott
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark
| | - Kira Astakhova
- Department of Chemistry, Technical University of Denmark, Kemitorvet, Bygning 207, 2800 Kgs. Lyngby, Denmark
| | - Gerald Weber
- Departamento de Física, Universidade Federal de Minas Gerais, 31270-901 Belo Horizonte, MG, Brazil
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4
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Optical and theoretical study of strand recognition by nucleic acid probes. Commun Chem 2020; 3:111. [PMID: 36703315 PMCID: PMC9814704 DOI: 10.1038/s42004-020-00362-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 07/23/2020] [Indexed: 01/29/2023] Open
Abstract
Detection of nucleic acids is crucial to the study of their basic properties and consequently to applying this knowledge to the determination of pathologies such as cancer. In this work, our goal is to determine new trends for creating diagnostic tools for cancer driver mutations. Herein, we study a library of natural and modified oligonucleotide duplexes by a combination of optical and theoretical methods. We report a profound effect of additives on the duplexes, including nucleic acids as an active crowder. Unpredictably and inconsistent with DNA+LNA/RNA duplexes, locked nucleic acids contribute poorly to mismatch discrimination in the DNA+LNA/DNA duplexes. We develop a theoretical framework that explains poor mismatch discrimination in KRAS oncogene. We implement our findings in a bead-bait genotyping assay to detect mutated human cancer RNA. The performance of rationally designed probes in this assay is superior to the LNA-primer polymerase chain reaction, and it agrees with sequencing data.
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5
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Kim Y, Lee H. Balanced Detection Method Using Optical Affinity Sensors for Quick Measurement of Biomolecule Concentrations. Anal Chem 2020; 92:6189-6193. [PMID: 32298099 DOI: 10.1021/acs.analchem.0c00637] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
To determine the concentration of biomolecules using a label-free optical biosensor, it is necessary to measure the serial signal from the reaction starting point, which is inconvenient for practical applications. Here, we propose an alternative detection method for determining the concentration of a biomolecule. The method, which is derived from the fraction bound equation of the Langmuir adsorption model, determines the concentration relative to a reference sample with required accuracy, with a single measurement at any point in time. We also experimentally demonstrated the method and its accuracy by detecting streptavidin-biotin complexes using on-chip optical sensors based on active disk resonators integrated with microfluidic circuits. By performing the proposed method in a simultaneous parallel measurement scheme, signal fluctuations evenly induced in the detectors by external perturbations could be automatically suppressed, similar to the balanced detection method. We expect our approach to be applicable to practical applications where fast and accurate detection responses are needed.
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Affiliation(s)
- Yeseul Kim
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Hansuek Lee
- Department of Physics, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Graduate School of Nanoscience and Technology, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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Sreeramareddygari M, Somasundrum M, Surareungchai W. In situ polymerization and covalent functionalisation of trithiocyanuric acid by MoS2 nanosheets resulting in a novel nanozyme with enhanced peroxidase activity. NEW J CHEM 2020. [DOI: 10.1039/c9nj04527a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
MoS2 catalysed the polymerisation of trithiocyanuric acid, resulting in a network exhibiting peroxidase activity via a ping-pong mechanism.
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Affiliation(s)
| | - Mithran Somasundrum
- Biochemical Engineering and Pilot Plant Research and Development Unit
- National Center for Genetic Engineering and Biotechnology
- National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi
- Thailand
| | - Werasak Surareungchai
- Pilot Plant Development and Training Institute
- King Mongkut's University of Technology Thonburi
- Bangkok 10150
- Thailand
- School of Bioresources and Technology
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Ngo HT, Freedman E, Odion RA, Strobbia P, De Silva Indrasekara AS, Vohra P, Taylor SM, Vo-Dinh T. Direct Detection of Unamplified Pathogen RNA in Blood Lysate using an Integrated Lab-in-a-Stick Device and Ultrabright SERS Nanorattles. Sci Rep 2018; 8:4075. [PMID: 29511216 PMCID: PMC5840326 DOI: 10.1038/s41598-018-21615-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/23/2018] [Indexed: 12/19/2022] Open
Abstract
Direct detection of genetic biomarkers in body fluid lysate without target amplification will revolutionize nucleic acid-based diagnostics. However, the low concentration of target sequences makes this goal challenging. We report a method for direct detection of pathogen RNA in blood lysate using a bioassay using surface-enhanced Raman spectroscopy (SERS)-based detection integrated in a "lab-in-a-stick" portable device. Two levels of signal enhancement were employed to achieve the sensitivity required for direct detection. Each target sequence was tagged with an ultrabright SERS-encoded nanorattle with ultrahigh SERS signals, and these tagged target sequences were concentrated into a focused spot for detection using hybridization sandwiches with magnetic microbeads. Furthermore, the washing process was automated by integration into a "lab-in-a-stick" portable device. We could directly detect synthetic target with a limit of detection of 200 fM. More importantly, we detected plasmodium falciparum malaria parasite RNA directly in infected red blood cells lysate. To our knowledge, this is the first report of SERS-based direct detection of pathogen nucleic acid in blood lysate without nucleic acid extraction or target amplification. The results show the potential of our integrated bioassay for field use and point-of-care diagnostics.
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Affiliation(s)
- Hoan T Ngo
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Biomedical Engineering Department, International University, Vietnam National University-Ho Chi Minh City (VNU-HCMC), Ho Chi Minh City, Vietnam
| | - Elizabeth Freedman
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Medicine & Duke Global Health Institute, Duke University, Durham, NC, 27708, USA
| | - Ren Abelard Odion
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Pietro Strobbia
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Agampodi Swarnapali De Silva Indrasekara
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
| | - Priya Vohra
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA
- Division of Head and Neck Surgery and Communication Sciences, Duke University, Durham, NC, 27708, USA
| | - Steve M Taylor
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA
- Department of Medicine & Duke Global Health Institute, Duke University, Durham, NC, 27708, USA
| | - Tuan Vo-Dinh
- Fitzpatrick Institute for Photonics, Duke University, Durham, NC, 27708, USA.
- Department of Biomedical Engineering, Duke University, Durham, NC, 27708, USA.
- Department of Chemistry, Duke University, Durham, NC, 27708, USA.
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Junager NPL, Kongsted J, Astakhova K. Revealing Nucleic Acid Mutations Using Förster Resonance Energy Transfer-Based Probes. SENSORS (BASEL, SWITZERLAND) 2016; 16:E1173. [PMID: 27472344 PMCID: PMC5017339 DOI: 10.3390/s16081173] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2016] [Revised: 07/18/2016] [Accepted: 07/19/2016] [Indexed: 01/08/2023]
Abstract
Nucleic acid mutations are of tremendous importance in modern clinical work, biotechnology and in fundamental studies of nucleic acids. Therefore, rapid, cost-effective and reliable detection of mutations is an object of extensive research. Today, Förster resonance energy transfer (FRET) probes are among the most often used tools for the detection of nucleic acids and in particular, for the detection of mutations. However, multiple parameters must be taken into account in order to create efficient FRET probes that are sensitive to nucleic acid mutations. In this review; we focus on the design principles for such probes and available computational methods that allow for their rational design. Applications of advanced, rationally designed FRET probes range from new insights into cellular heterogeneity to gaining new knowledge of nucleic acid structures directly in living cells.
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Affiliation(s)
- Nina P L Junager
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kira Astakhova
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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