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Sequence-Specific Recognition of DNA Oligomer Using Peptide Nucleic Acid (PNA)-Modified Synthetic Ion Channels: PNA/DNA Hybridization in Nanoconfined Environment

Ali, Mubarak and Neumann, Reinhard and Ensinger, Wolfgang :
Sequence-Specific Recognition of DNA Oligomer Using Peptide Nucleic Acid (PNA)-Modified Synthetic Ion Channels: PNA/DNA Hybridization in Nanoconfined Environment.
[Online-Edition: http://dx.doi.org/10.1021/nn102119q]
In: ACS Nano, 4 (12) pp. 7267-7274.
[Article] , (2010)

Official URL: http://dx.doi.org/10.1021/nn102119q

Abstract

Here we demonstrate the design and construction of a simple, highly sensitive and selective nanofluidic sensing device, based on a single synthetic conical nanochannel for the sequence specific detection of single-stranded DNA oligonucleotides. The biosensing performance of the device depends sensitively on the surface charge and chemical groups incorporated on the inner channel wall that act as binding sites for different analytes. Uncharged peptide nucleic acid (PNA) probes are covalently immobilized on the channel surface through carbodiimide coupling chemistry. This diminishes the channel surface charge, leading to a significant decrease in the rectified ion current flowing through the channel. The PNA-modified channel acts as a highly specific and selective device for the detection of a complementary single-stranded DNA sequence. Upon PNA/DNA hybridization, the channel surface charge density increased due to the presence of the negatively charged DNA strand. The changes in the surface charge-dependent current-voltage (I-V) curves and rectification ratio of the channel confirm the success of immobilization and PNA/DNA hybridization within a confined space at the nanoscale. In addition, a control experiment indicated that the biosensor exhibits remarkable specificity toward a cDNA strand and also has the ability to discriminate single-base mismatch DNA sequences on the basis of rectified ion flux through the nanochannel. In this context, we envision that the single conical nanochannels functionalized with a PNA probe will provide a biosensing platform for the detection and discrimination of short single-stranded DNA oligomer of unknown sequence.

Item Type: Article
Erschienen: 2010
Creators: Ali, Mubarak and Neumann, Reinhard and Ensinger, Wolfgang
Title: Sequence-Specific Recognition of DNA Oligomer Using Peptide Nucleic Acid (PNA)-Modified Synthetic Ion Channels: PNA/DNA Hybridization in Nanoconfined Environment
Language: English
Abstract:

Here we demonstrate the design and construction of a simple, highly sensitive and selective nanofluidic sensing device, based on a single synthetic conical nanochannel for the sequence specific detection of single-stranded DNA oligonucleotides. The biosensing performance of the device depends sensitively on the surface charge and chemical groups incorporated on the inner channel wall that act as binding sites for different analytes. Uncharged peptide nucleic acid (PNA) probes are covalently immobilized on the channel surface through carbodiimide coupling chemistry. This diminishes the channel surface charge, leading to a significant decrease in the rectified ion current flowing through the channel. The PNA-modified channel acts as a highly specific and selective device for the detection of a complementary single-stranded DNA sequence. Upon PNA/DNA hybridization, the channel surface charge density increased due to the presence of the negatively charged DNA strand. The changes in the surface charge-dependent current-voltage (I-V) curves and rectification ratio of the channel confirm the success of immobilization and PNA/DNA hybridization within a confined space at the nanoscale. In addition, a control experiment indicated that the biosensor exhibits remarkable specificity toward a cDNA strand and also has the ability to discriminate single-base mismatch DNA sequences on the basis of rectified ion flux through the nanochannel. In this context, we envision that the single conical nanochannels functionalized with a PNA probe will provide a biosensing platform for the detection and discrimination of short single-stranded DNA oligomer of unknown sequence.

Journal or Publication Title: ACS Nano
Volume: 4
Number: 12
Publisher: ACS Publications
Uncontrolled Keywords: solid-state nanopores; PNA/DNA hybridization; biosensor; polymer membrane; heavy ion irradiation; track-etching
Divisions: 11 Department of Materials and Earth Sciences > Material Science > Material Analytics
11 Department of Materials and Earth Sciences > Material Science
11 Department of Materials and Earth Sciences
Date Deposited: 05 Jan 2011 13:45
Official URL: http://dx.doi.org/10.1021/nn102119q
Funders: The authors gratefully acknowledge financial support by the Beilstein-Institut, Frankfurt/Main, Germany, within the research collaboration NanoBiC.
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