Atomic force microscopy and voltammetric characterisation of synthetic homo-oligodeoxynucleotides

Chiorcea-Paquim, Ana-Maria; Santos, Paulina V. F.; Oliveira-Brett, Ana Maria

doi:10.1016/j.electacta.2013.03.103

Cited by 22 publications

(19 citation statements)

References 28 publications

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“…Secondly, and more compelling, is the appearance of holes or deep (1–1.5 nm) pores in the layer that reach down to the graphite surface. This apparent monolayer coverage is consistent with an excellent study that revealed the growth of a dense, porous mat structure, resulting from dosing the HOPG surface with single-stranded DNA homopolymers that were 10 mers in length [37]. …”

Section: Resultssupporting

confidence: 86%

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

et al. 2016

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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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Section: Resultssupporting

confidence: 86%

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

et al. 2016

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“…The presence of K + ions strongly stabilizes and accelerates the G4 formation. For increased d(G) 10 concentrations, long G-nanowires were formed, demonstrating the potential of G-rich DNA sequences as a scaffold for nanotechnological applications [19,32,39,40].…”

Section: G4 Electrochemistrymentioning

confidence: 99%

“…The influence of the ODN sequence and concentration, pH (Figure 1), the presence of monovalent cations, Na + vs. K + (Figure 2A,C), and incubation time ( Figure 2B,C) was determined [19,32,39,40]. The formation of G4 structures and higher-order nanostructures, due to the presence of a long contiguous G region, and the influence of the thymine residues at the 5 1 and 3 1 molecular ends in d(TG 9 ) and d(TG 8 T) were clarified.…”

Section: G4 Electrochemistrymentioning

confidence: 99%

Guanine Quadruplex Electrochemical Aptasensors

Chiorcea-Paquim

Oliveira-Brett

2016

Chemosensors

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Guanine-rich nucleic acids are able to self-assemble into G-quadruplex four-stranded secondary structures, which are found at the level of telomeric regions of chromosomes, oncogene promoter sequences and other biologically-relevant regions of the genome. Due to their extraordinary stiffness and biological role, G-quadruples become relevant in areas ranging from structural biology to medicinal chemistry, supra-molecular chemistry, nanotechnology and biosensor technology. In addition to classical methodologies, such as circular dichroism, nuclear magnetic resonance or crystallography, electrochemical methods have been successfully used for the rapid detection of the conformational changes from single-strand to G-quadruplex. This review presents recent advances on the G-quadruplex electrochemical characterization and on the design and applications of G-quadruplex electrochemical biosensors, with special emphasis on the G-quadruplex aptasensors and hemin/G-quadruplex peroxidase-mimicking DNAzyme biosensors.

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“…However, DNA can be found in a variety of other conformations, such as double-helixes with different types of loops (bulge, internal, hairpin, junction, knotted loops, etc. ), single-strands, triplex-helixes, or four-stranded secondary structures (e.g., i -motifs and G-quadruplexes (GQs)) [ 11 – 13 ].…”

Section: Introductionmentioning

confidence: 99%

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications

Chiorcea-Paquim

Eritja

Oliveira‐Brett

2018

Journal of Nucleic Acids

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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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Atomic force microscopy and voltammetric characterisation of synthetic homo-oligodeoxynucleotides

Cited by 22 publications

References 28 publications

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

DNA Origami Reorganizes upon Interaction with Graphite: Implications for High-Resolution DNA Directed Protein Patterning

Guanine Quadruplex Electrochemical Aptasensors

Electrochemical and AFM Characterization of G-Quadruplex Electrochemical Biosensors and Applications

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