Electrostatic repulsion and steric hindrance effects of surface probe density on deoxyribonucleic acid (DNA)/peptide nucleic acid (PNA) hybridization

Xu, Fang; Pellino, August M.; Knoll, Wolfgang

doi:10.1016/j.tsf.2008.06.067

Cited by 37 publications

(35 citation statements)

References 28 publications

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“…Although an exact comparison is difficult because of the different experimental parameters and different NAs used but the k on , k off , and K d obtained in this study are in agreement with the range of data previously reported for PNA-NA hybridization on planar surfaces. 40,42,[54][55][56][57][58][59] It is important to note that under the experimental conditions used only the miRNA bound to the sensing zone of the nanopore influences the potential signal and therefore the unbound target strands in the sample bulk do not need to be removed. This is a clear advantage of the proposed potentiometric label-free sensing principle compared with conventional heterogeneous phase hybridization assays based on labels and end-point detection.…”

Section: Resultsmentioning

confidence: 99%

Potentiometric sensing of nucleic acids using chemically modified nanopores

et al. 2017

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Unlike the overwhelming majority of nanopore sensors that are based on the measurement of a transpore ionic current, here we introduce a potentiometric sensing scheme and demonstrate its application for the selective detection of nucleic acids. The sensing concept uses the charge inversion that occurs in the sensing zone of a nanopore upon binding of negatively charged microRNA strands to positively charged peptide-nucleic acid (PNA) modified nanopores. The initial anionic permselectivity of PNA-modified nanopores is thus gradually changed to cationic permselectivity, which can be detected simply by measuring the nanoporous membrane potential. A quantitative theoretical treatment of the potentiometric microRNA response is provided based on the Nernst-Planck/Poisson model for the nanopore system assuming first order kinetics for the nucleic acid hybridization. An excellent correlation between the theoretical and experimental results was observed, which revealed that the binding process is focused at the nanopore entrance with contributions from both in pore and out of pore sections of the nanoporous membrane. The theoretical treatment is able to give clear guidelines for further optimization of potentiometric nanopore-based nucleic acid sensors by predicting the effect of the most important experimental parameters on the potential response.

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Section: Resultsmentioning

confidence: 99%

Potentiometric sensing of nucleic acids using chemically modified nanopores

et al. 2017

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“…1:0 and 1:0.25), they are also, on average, separated further apart from the neighboring probes by the T9 spacer. This reduces steric hindrances and results in an increased accessibility of the target cDNA to hybridize [37][38][39], as well as for NcDNA to interact with the aligned probes. The negative S/N values seen at ratio 1:0 and 1:0.25 are due to the negative current change caused by interaction with NcDNA, Fig.…”

Section: Resultsmentioning

confidence: 99%

Ternary DNA chip based on a novel thymine spacer group chemistry

Yang¹,

Yıldız²,

Peh³

et al. 2015

Colloids and Surfaces B: Biointerfaces

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“…However, this means that the very low concentration of target DNA in actual samples will yield very low signals as well. In addition, even if there is enough target DNA, the surface density is limited by the electrostatic charges of the negatively‐charged DNA probes attached . To address this issue on sensitivity, the signal can be improved through nucleic acid self‐assembly processes wherein additional probes are designed to create DNA nanostructures that will lead to an increase in the signal.…”

Section: Immobilized Electrochemical Dna Biosensorsmentioning

confidence: 99%

Rational Design of Electrochemical DNA Biosensors for Point‐of‐Care Applications

Maslova

Hsing

2017

ChemElectroChem

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Electrochemical DNA biosensors show great potential for the sensitive and sequence‐specific detection of disease pathogens. To date, although there are a large number of published articles showing various sensing strategies of an electrochemical biosensor, only a few of those studies actually reach the commercialization phase, because addressing one technical issue would usually be at the expense of another. Moreover, there are various adoptable formats in electrochemical biosensors. Current approaches may or may not use enzymes, immobilize DNA probes, label the sensing substrates with an electroactive reporter molecule, or any combination of these. Although much has been paid to individual advantages and disadvantages, there are a very limited number Review articles studying and analyzing the synergistic aspects of various detection strategies when combined with each other. It is the aim of this Review to highlight the hotspots for innovation when these strategies are used in tandem, in order to create more streamlined improvements in making a versatile biosensor platform that can be administered at point of care.

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Electrostatic repulsion and steric hindrance effects of surface probe density on deoxyribonucleic acid (DNA)/peptide nucleic acid (PNA) hybridization

Cited by 37 publications

References 28 publications

Potentiometric sensing of nucleic acids using chemically modified nanopores

Potentiometric sensing of nucleic acids using chemically modified nanopores

Ternary DNA chip based on a novel thymine spacer group chemistry

Rational Design of Electrochemical DNA Biosensors for Point‐of‐Care Applications

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