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Hasoň S, Ostatná V, Fojt L, Fojta M. Arrangements of DNA purine bases on pyrolytic graphite electrode surface. Electrochemical characterization and atomic force microscopy imaging. Electrochim Acta 2022. [DOI: 10.1016/j.electacta.2022.141772] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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2
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In situ electrochemical investigation of the interaction between bacteria Xylella fastidiosa DNA and copper(II) using DNA-electrochemical biosensors. Electrochem commun 2021. [DOI: 10.1016/j.elecom.2021.106975] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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3
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DNA Electrochemical Biosensors for In Situ Probing of Pharmaceutical Drug Oxidative DNA Damage. SENSORS 2021; 21:s21041125. [PMID: 33562790 PMCID: PMC7915242 DOI: 10.3390/s21041125] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 02/01/2021] [Accepted: 02/01/2021] [Indexed: 12/20/2022]
Abstract
Deoxyribonucleic acid (DNA) electrochemical biosensors are devices that incorporate immobilized DNA as a molecular recognition element on the electrode surface, and enable probing in situ the oxidative DNA damage. A wide range of DNA electrochemical biosensor analytical and biotechnological applications in pharmacology are foreseen, due to their ability to determine in situ and in real-time the DNA interaction mechanisms with pharmaceutical drugs, as well as with their degradation products, redox reaction products, and metabolites, and due to their capacity to achieve quantitative electroanalytical evaluation of the drugs, with high sensitivity, short time of analysis, and low cost. This review presents the design and applications of label-free DNA electrochemical biosensors that use DNA direct electrochemical oxidation to detect oxidative DNA damage. The DNA electrochemical biosensor development, from the viewpoint of electrochemical and atomic force microscopy (AFM) characterization, and the bottom-up immobilization of DNA nanostructures at the electrode surface, are described. Applications of DNA electrochemical biosensors that enable the label-free detection of DNA interactions with pharmaceutical compounds, such as acridine derivatives, alkaloids, alkylating agents, alkylphosphocholines, antibiotics, antimetabolites, kinase inhibitors, immunomodulatory agents, metal complexes, nucleoside analogs, and phenolic compounds, which can be used in drug analysis and drug discovery, and may lead to future screening systems, are reviewed.
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Influence of the lengths of thymine, cytosine, and adenine stretches on the two-dimensional condensation of oligodeoxynucleotides at mercury and silver amalgam electrode surfaces. J Electroanal Chem (Lausanne) 2019. [DOI: 10.1016/j.jelechem.2019.113364] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Machini WBS, Fernandes IPG, Oliveira‐Brett AM. Antidiabetic Drug Metformin Oxidation and
in situ
Interaction with dsDNA Using a dsDNA‐electrochemical Biosensor. ELECTROANAL 2019. [DOI: 10.1002/elan.201900162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- W. B. S. Machini
- Department of Chemistry, Faculty of Science and TechnologyUniversity of Coimbra 3004-535 Coimbra Portugal
| | - I. P. G. Fernandes
- Department of Chemistry, Faculty of Science and TechnologyUniversity of Coimbra 3004-535 Coimbra Portugal
| | - A. M. Oliveira‐Brett
- Department of Chemistry, Faculty of Science and TechnologyUniversity of Coimbra 3004-535 Coimbra Portugal
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Song W, Gregory DA, Al-Janabi H, Muthana M, Cai Z, Zhao X. Magnetic-silk/polyethyleneimine core-shell nanoparticles for targeted gene delivery into human breast cancer cells. Int J Pharm 2019; 555:322-336. [PMID: 30448314 DOI: 10.1016/j.ijpharm.2018.11.030] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 11/10/2018] [Accepted: 11/12/2018] [Indexed: 12/19/2022]
Abstract
The lack of efficient and cost-effective methods for gene delivery has significantly hindered the applications of gene therapy. In this paper, a simple one step and cost effective salting-out method has been explored to fabricate silk-PEI nanoparticles (SPPs) and magnetic-silk/PEI core-shell nanoparticles (MSPPs) for targeted delivery of c-myc antisense oligodeoxynucleotides (ODNs) into MDA-MB-231 breast cancer cells. The size and zeta potential of the particles were controlled by adjusting the amount of silk fibroin in particle synthesis. Lower surface charges and reduced cytotoxicity were achieved for MSPPs compared with PEI coated magnetic nanoparticles (MPPs). Both SPPs and MSPPs were capable of delivering the ODNs into MDA-MB-231 cells and significantly inhibited the cell growth. Through magnetofection, high ODN uptake efficiencies (over 70%) were achieved within 20 min using MSPPs as carriers, exhibiting a significantly enhanced uptake effect compared to the same carriers via non-magnetofection. Both SPPs and MSPPs exhibited a significantly higher inhibition effect against MDA-MB-231 breast cancer cells compared to human dermal fibroblast (HDF) cells. Targeted ODN delivery was achieved using MSPPs with the help of a magnet, making them promising candidates for targeted gene therapy applications.
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Affiliation(s)
- Wenxing Song
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK; School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, China
| | - David A Gregory
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Haider Al-Janabi
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Munitta Muthana
- Department of Infection and Immunity, University of Sheffield, Sheffield S10 2RX, UK
| | - Zhiqiang Cai
- School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, China
| | - Xiubo Zhao
- Department of Chemical and Biological Engineering, University of Sheffield, Sheffield S1 3JD, UK; School of Pharmaceutical Engineering and Life Science, Changzhou University, Changzhou 213164, China.
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Ihmels H, Jiang S, Mahmoud MMA, Schönherr H, Wesner D, Zamrik I. Fluorimetric Detection of G-Quadruplex DNA in Solution and Adsorbed on Surfaces with a Selective Trinuclear Cyanine Dye. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:11866-11877. [PMID: 30173518 DOI: 10.1021/acs.langmuir.8b02382] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Quadruplex DNA, which is a relevant target for anticancer therapies, may alter its conformation because of interactions with interfaces. In pursuit of a versatile methodology to probe adsorption-induced conformational changes, the interaction between a fluorescent [2.2.2]heptamethinecyanine dye and quadruplex DNA (G4-DNA) was studied in solution and on surfaces. In solution, the cyanine dye exhibits a strong light-up effect upon the association with G4-DNA without interference from double-stranded DNA. In addition, a terminal π-stacking as a binding mode between the cyanine dye and G4-DNA is concluded using NMR spectroscopy. To unravel the effects of adsorption on the conformation of quadruplex-DNA, G4-DNA, and double-stranded and single-stranded DNA were adsorbed to positively charged poly(allylamine) hydrochloride (PAH) surfaces, both in planar and in constrained 55 nm diameter aluminum oxide nanopore formats. All DNA forms showed a very strong affinity to the PAH surfaces as shown by surface plasmon resonance and reflectometric interference spectroscopy. The significant increase of the fluorescence emission intensity of the cyanine light-up probe observed exclusively for surface immobilized G4-DNA affords evidence for the adsorption of G4-DNA on PAH with retained quadruplex conformation.
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Affiliation(s)
- Heiko Ihmels
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Siyu Jiang
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Mohamed M A Mahmoud
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Holger Schönherr
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Daniel Wesner
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
| | - Imad Zamrik
- Department of Chemistry and Biology , University of Siegen, and Center of Micro- and Nanochemistry and Engineering (Cμ) , Adolf-Reichwein-Str. 2 , 57068 Siegen , Germany
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Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications. J Nucleic Acids 2018; 2018:5307106. [PMID: 29666699 PMCID: PMC5831849 DOI: 10.1155/2018/5307106] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/25/2017] [Accepted: 11/05/2017] [Indexed: 02/06/2023] Open
Abstract
Guanine-rich DNA sequences are able to form G-quadruplexes, being involved in important biological processes and representing smart self-assembling nanomaterials that are increasingly used in DNA nanotechnology and biosensor technology. G-quadruplex electrochemical biosensors have received particular attention, since the electrochemical response is particularly sensitive to the DNA structural changes from single-stranded, double-stranded, or hairpin into a G-quadruplex configuration. Furthermore, the development of an increased number of G-quadruplex aptamers that combine the G-quadruplex stiffness and self-assembling versatility with the aptamer high specificity of binding to a variety of molecular targets allowed the construction of biosensors with increased selectivity and sensitivity. This review discusses the recent advances on the electrochemical characterization, design, and applications of G-quadruplex electrochemical biosensors in the evaluation of metal ions, G-quadruplex ligands, and other small organic molecules, proteins, and cells. The electrochemical and atomic force microscopy characterization of G-quadruplexes is presented. The incubation time and cations concentration dependence in controlling the G-quadruplex folding, stability, and nanostructures formation at carbon electrodes are discussed. Different G-quadruplex electrochemical biosensors design strategies, based on the DNA folding into a G-quadruplex, the use of G-quadruplex aptamers, or the use of hemin/G-quadruplex DNAzymes, are revisited.
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Chiorcea-Paquim AM, Oliveira SCB, Diculescu VC, Oliveira-Brett AM. Applications of DNA-Electrochemical Biosensors in Cancer Research. PAST, PRESENT AND FUTURE CHALLENGES OF BIOSENSORS AND BIOANALYTICAL TOOLS IN ANALYTICAL CHEMISTRY: A TRIBUTE TO PROFESSOR MARCO MASCINI 2017. [DOI: 10.1016/bs.coac.2017.06.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2022]
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DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning. NANOMATERIALS 2016; 6:nano6110196. [PMID: 28335324 PMCID: PMC5245763 DOI: 10.3390/nano6110196] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 10/10/2016] [Accepted: 10/25/2016] [Indexed: 02/04/2023]
Abstract
Although there is a long history of the study of the interaction of DNA with carbon surfaces, limited information exists regarding the interaction of complex DNA-based nanostructures with the important material graphite, which is closely related to graphene. In view of the capacity of DNA to direct the assembly of proteins and optical and electronic nanoparticles, the potential for combining DNA-based materials with graphite, which is an ultra-flat, conductive carbon substrate, requires evaluation. A series of imaging studies utilizing Atomic Force Microscopy has been applied in order to provide a unified picture of this important interaction of structured DNA and graphite. For the test structure examined, we observe a rapid destabilization of the complex DNA origami structure, consistent with a strong interaction of single-stranded DNA with the carbon surface. This destabilizing interaction can be obscured by an intentional or unintentional primary intervening layer of single-stranded DNA. Because the interaction of origami with graphite is not completely dissociative, and because the frustrated, expanded structure is relatively stable over time in solution, it is demonstrated that organized structures of pairs of the model protein streptavidin can be produced on carbon surfaces using DNA origami as the directing material.
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Diculescu VC, Chiorcea-Paquim AM, Oliveira-Brett AM. Applications of a DNA-electrochemical biosensor. Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2016.01.019] [Citation(s) in RCA: 119] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Zhao X, Huang Y, Yang CJ, Mao B. Molecular behavior of the aptamer HJ24 self-assembled on highly oriented pyrolytic graphite (HOPG). Sci China Chem 2015. [DOI: 10.1007/s11426-015-5465-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Chiorcea-Paquim AM, Rodrigues Pontinha AD, Oliveira-Brett AM. Quadruplex-targeting anticancer drug BRACO-19 voltammetric and AFM characterization. Electrochim Acta 2015. [DOI: 10.1016/j.electacta.2015.05.146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Vidláková P, Pivoňková H, Kejnovská I, Trnková L, Vorlíčková M, Fojta M, Havran L. G-quadruplex-based structural transitions in 15-mer DNA oligonucleotides varying in lengths of internal oligo(dG) stretches detected by voltammetric techniques. Anal Bioanal Chem 2015; 407:5817-26. [DOI: 10.1007/s00216-015-8768-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 04/12/2015] [Accepted: 05/06/2015] [Indexed: 10/23/2022]
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Chiorcea-Paquim AM, Pontinha ADR, Eritja R, Lucarelli G, Sparapani S, Neidle S, Oliveira-Brett AM. Atomic Force Microscopy and Voltammetric Investigation of Quadruplex Formation between a Triazole-Acridine Conjugate and Guanine-Containing Repeat DNA Sequences. Anal Chem 2015; 87:6141-9. [DOI: 10.1021/acs.analchem.5b00743] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | | | - Ramon Eritja
- Institute for Research in Biomedicine, IQAC−CSIC, CIBER-BBN
Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona, Spain
| | - Genny Lucarelli
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
| | - Silvia Sparapani
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
| | - Stephen Neidle
- UCL
School of Pharmacy, University College London, London WC1N 1AX, U.K
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Rodrigues Pontinha AD, Chiorcea-Paquim AM, Eritja R, Oliveira-Brett AM. Quadruplex nanostructures of d(TGGGGT): influence of sodium and potassium ions. Anal Chem 2014; 86:5851-7. [PMID: 24794539 DOI: 10.1021/ac500624z] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Tetrahymena telomeric repeat sequence d(TG4T) contains only guanine (G) and thymine (T) bases and has medical and nanotechnological applications because of its ability to self-assemble into stiff tetra-molecular parallel-stranded G-quadruplexes. The hexadeoxynucleotide d(TG4T) was studied using atomic force microscopy (AFM) on the highly oriented pyrolytic graphite surface and differential pulse (DP) voltammetry at a glassy carbon electrode. The d(TG4T) single-strands self-assembled into G-quadruplex structures, very fast in K(+) ions solution and slowly in Na(+) ions containing solution. The G-quadruplex structures were detected in AFM by the adsorption of small spherical aggregates and by DP voltammetry by the G oxidation peak decrease and G-quartets oxidation peak occurrence, in a time and K(+) ions concentration dependent manner. In the presence of Na(+) ions, the d(TG4T) single-strands also slowly self-assembled into higher-order nanostructures, detected by AFM as short nanowires and nanostructured films that were never observed in K(+) ions containing solution.
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