Electrochemical nucleic acid-based biosensors: Concepts, terms, and methodology (IUPAC Technical Report)

Labuda, Ján; Oliveira-Brett, Ana Maria; Evtugyn, Gennady; Fojta, Miroslav; Mascini, Marco; Ozsoz, Mehmet; Palchetti, Ilaria; Paleček, Emil; Wang, Joseph

doi:10.1351/pac-rep-09-08-16

Cited by 209 publications

(118 citation statements)

References 51 publications

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“…[1][2][3][4][5][6][7][8] . A comprehensive analysis of the properties of these systems could be very useful for designing highly biocompatible materials and specific biosensors [9][10][11][12][13][14] . DNA-based biosensors, for example, can consist of probes attached to functionalized substrates with the capability of recognizing and capturing specific DNA targets.…”

Section: Introductionmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

112

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Computational spectroscopy techniques have become in the last years effective means to analyze and assign infrared (IR) spectra for molecular systems of increasing dimensions and in different environments. However, transition from compilations of harmonic data to full anharmonic simulations of spectra is still under way. The most promising results for large systems have been obtained, in our opinion, by perturbative vibrational approaches based on potential energy surfaces computed by hybrid (especially B3LYP) density functionals and medium size (e.g. SNSD) basis sets. In this framework, we are actively developing a comprehensive and robust computational protocol aimed to a quantitative reproduction of the spectra of nucleic acid bases complexes and their adsorption on solid supports (organic/inorganic). In this contribution we report the essential results of the first step devoted to isolated monomers and dimers. It is well known that in order to model the vibrational spectra of weakly bound molecular complexes dispersion interactions should be taken into proper account. In this work, we have chosen two popular and inexpensive approaches to model dispersion interaction, namely the semi-empirical dispersion correction (D3) and pseudopotential based (DCP) methodologies both in conjunction with the B3LYP functional. These have been used for simulating fully anharmonic IR spectra of nucleobases and their dimers through generalized second order vibrational perturbation theory (GVPT2). We have studied, in particular, isolated adenine, hypoxanthine, uracil, thymine and cytosine, the hydrogen-bonded and stacked adenine and uracil dimers, and the stacked adenine-naphthalene heterodimer. Anharmonic frequencies are compared with standard B3LYP results and experimental findings, while the computed interaction energies and structures of complexes are compared to the best available theoretical estimates.

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Section: Introductionmentioning

confidence: 99%

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Fornaro

Biczysko

Monti

et al. 2014

Phys. Chem. Chem. Phys.

112

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“…but it lends itself also for providing analytical information on the structure and chemical and mineralogical composition of solid materials of various kinds, e.g., metals and alloys, films in electrochemical biosensors [5,6], conducting polymers, and materials used in nanotechnology (redox-active nanomaterials, catalyst nanocomposites, metallic nanoparticles, etc.) [7].…”

Section: Introductionmentioning

confidence: 99%

Electroanalytical chemistry for the analysis of solids: Characterization and classification (IUPAC Technical Report)

Doménech‐Carbó

Labuda

Scholz

2012

Pure and Applied Chemistry

Self Cite

151

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Solid state electroanalytical chemistry (SSEAC) deals with studies of the processes, materials, and methods specifically aimed to obtain analytical information (quantitative elemental composition, phase composition, structure information, and reactivity) on solid materials by means of electrochemical methods. The electrochemical characterization of solids is not only crucial for electrochemical applications of materials (e.g., in batteries, fuel cells, corrosion protection, electrochemical machining, etc.) but it lends itself also for providing analytical information on the structure and chemical and mineralogical composition of solid materials of all kinds such as metals and alloys, various films, conducting polymers, and materials used in nanotechnology. The present report concerns the relationships between molecular electrochemistry (i.e., solution electrochemistry) and solid state electrochemistry as applied to analysis. Special attention is focused on a critical evaluation of the different types of analytical information that are accessible by SSEAC.

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“…Their main characteristic is high specificity and selectivity against the target molecule. Moreover constantly decreasing costs of producing synthetic nucleic acid sequences makes such sensors highly attractive to develop and implement [78,79].…”

Section: Biocompatibility and Implantable Biosensorsmentioning

confidence: 99%

Biosensor Design with Molecular Engineering and Nanotechnology

Johnson

Trzebinski

et al. 2014

Body Sensor Networks

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The concept of a biosensor is well established and the idea of integrating a molecular recognition layer with a base sensor, such that analyte binding or reaction at the former results in a measureable change (in current or voltage) in the latter has seen many ingenious embodiments. Despite this and the huge amount of research worldwide in biosensors, as outlined in Chap. 2, many challenges still remain in building reliable, long-lived biosensors, especially in the hostile environment of the human body. The enormous potential for in vivo sensing of pathophysiological molecules over time and space has led to many attempts to achieve this and the rewards, both in terms of clinical benefit and improved understanding, cannot be underestimated. As new tools for producing biosensors become available, they are rapidly recruited. In recent years, developments in two areas of science and engineering have provided new opportunities to look again at how biosensors are built and deployed. These developments were not driven by the needs of those building and using biosensors but by much broader scientific and technological trends, which nonetheless have found ready applicability in this area.One of the trends is an increasing knowledge of the structural factors that determine function in biological macromolecules and the other is the appreciation that the properties of materials with a characteristic length scale from 1 to 100 nm are not those expected from dividing macroscopic materials into smaller pieces nor those expected from adding atoms or molecules together. The first of these trends is sometimes referred to as biomolecular engineering and the second as nanotechnology.There are many drivers for the use of molecular engineering and nanotechnology in the design and application of biosensors and the past decade has seen these tools

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Electrochemical nucleic acid-based biosensors: Concepts, terms, and methodology (IUPAC Technical Report)

Cited by 209 publications

References 51 publications

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Dispersion corrected DFT approaches for anharmonic vibrational frequency calculations: nucleobases and their dimers

Electroanalytical chemistry for the analysis of solids: Characterization and classification (IUPAC Technical Report)

Biosensor Design with Molecular Engineering and Nanotechnology

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