Mismatch-Sensitive Hybridization Detection by Peptide Nucleic Acids Immobilized on a Quartz Crystal Microbalance

Wang, Joseph; Nielsen, Peter E.; Jiang, Mian; Cai, Xiaohua; Fernandes, João Roberto; Grant, Douglas H.; Özsöz, Mehmet; Beglieter, and Asher; Mowat, Michael

doi:10.1021/ac9706077

Cited by 150 publications

(96 citation statements)

References 16 publications

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“…16 The nanopores were prepared by electroless Au plating of track etch polycarbonate membranes. 10 In order to obtain regular pore diameters and better control of the plating process, the original recipe was slightly modified in that the membranes were dried in N 2 atmosphere before placing them in the Au plating solution of pH 10 kept at 1 °C.…”

mentioning

confidence: 99%

Hybridization-Modulated Ion Fluxes through Peptide-Nucleic-Acid- Functionalized Gold Nanotubes. A New Approach to Quantitative Label-Free DNA Analysis

et al. 2007

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The inner walls of gold nanotubules, prepared by template synthesis in the nanopores of polycarbonate track etch membranes, have been chemically modified with peptide nucleic acid (PNA) and used for label-free quantification of complementary DNA sequences. Selective binding of DNA to the PNA modified nanotubules are shown to decrease the flux of optically detected anionic markers through the nanotubules in a concentration-dependent manner. The strong dependence of the biorecognition-modulated ion transport through the nanopores on the ionic strength suggests a dominantly electrostatic exclusion mechanism of the ion flux decrease as a result of DNA binding to the PNA-modified nanopores.The extremely low detection limits required for bioanalysis are usually achieved with some chemical or physical amplification mechanism. 1,2 In ion channel-mimetic sensors, the target species functions as a stimulus, actuating (opening or closing) ion channels and, thus, modulating the flux of the marker ions to be detected. 3 Amplification is achieved because the concentration of markers exceeds the concentration of the target species by many orders of magnitude. In one approach, electrodes are modified with artificial receptors having intramolecular channels that can be blocked by the formation of inclusion complexes with the analyte and, thus, control the heterogeneous redox reactions of electroactive species. 4 Another method in these lines makes use of genetically and/or chemically engineered receptors built into cell membranes. 5-7 In a third approach based on gold nanopores, pioneered by the group of Martin, 8-10 limitations due to the fragility of lipid bilayer membranes, in which biological nanopores are suspended, are eliminated. Modulations of the ionic permeability due to polarity changes (hydrophobic to hydrophilic) 11 or steric effects (high molecular weight analytes binding to small molecular weight receptors in the nanopores) have already been explored. 12,13 In a previous study, we have demonstrated the feasibility of the ion channel-mimetic biosensing with gold nanoporous membranes modified by biotin. The selective recognition of avidin modulates the Ca 2+ ion transport, which is detected with ion-selective potentiometry. 13 Later, the protein detection system has been extended by using single conically shaped gold nanopores. 12In this paper, for the first time, gold nanopores are functionalized, with a peptide nucleic acid (PNA) 14 in view of a label-free detection of complementary DNA strands. The PNAs are shown to bind their complementary nucleic acid sequence 15 with higher affinity and specificity NIH-PA Author ManuscriptNIH-PA Author Manuscript NIH-PA Author Manuscript compared with DNA probes. 16 The nanopores were prepared by electroless Au plating of track etch polycarbonate membranes. 10 In order to obtain regular pore diameters and better control of the plating process, the original recipe was slightly modified in that the membranes were dried in N 2 atmosphere before placing them in the Au pla...

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mentioning

confidence: 99%

Hybridization-Modulated Ion Fluxes through Peptide-Nucleic-Acid- Functionalized Gold Nanotubes. A New Approach to Quantitative Label-Free DNA Analysis

et al. 2007

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“…They are easily manufactured and modified and have good hybridization properties compared with DNA oligos. PNA has been used in a handful of SNP genotyping assays (13)(14)(15)(16)(17)(18)(19) and as RNA capture probe coupled to the surface of microspheres (25).…”

Section: Discussionmentioning

confidence: 99%

“…We recently reported that short PNA beacons can successfully replace DNA-based probes in two real-time polymerase chain reaction (PCR) genotyping assays (13). Other groups have reported PNA-based allele discrimination using mass spectroscopy (14 -16), quartz crystal microbalance biosensors (17), surface plasmon resonance (18), or fluorescence polarization (19).…”

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confidence: 99%

SNP genotyping using microsphere‐linked PNA and flow cytometric detection

Rockenbauer

Petersen²,

Vogel

et al. 2005

Cytometry Pt A

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Background: Single nucleotide polymorphisms (SNPs) represent the most frequent form of genetic variations. Some of the most sensitive methods for SNP genotyping employ synthetic oligonucleotides, such as the peptide nucleic acid (PNA). We introduce a new method combining allele-specific hybridization, PNA technology, and flow cytometric detection. We tested the design by genotyping a Danish basal cell carcinoma cohort of 80 individuals for an A/C SNP in exon 6 of the XPD gene. Methods: Genomic DNA was amplified by a two-step polymerase chain reaction (PCR) in the presence of fluorescein-dyed primers and fluorescein-12-dUTP. The allelespecific PNA molecules were covalently coupled to carboxylated microspheres with and without rhodamine. Allele-specific hybridization between PCR products and

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“…PNA was developed [1] as a new oligomer having high affinity hybridization with single-strand DNA. PNA is a nucleic acid analogue of DNA, in which the phosphate backbone of DNA is replaced with a structurally homomorphous pseudopeptide backbone.…”

Section: Introductionmentioning

confidence: 99%

Hybridization energies of double strands composed of DNA, RNA, PNA and LNA

Natsume¹,

Ishikawa²,

Dedachi³

et al. 2007

Chemical Physics Letters

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The electronic properties of double strands composed of trimeric LNA, PNA, DNA and RNA single strands were investigated by density-functional molecular orbital calculations. The computed hybridization energies for the double strands involving PNA or LNA are larger than those for DNA-DNA and RNA-RNA. The larger stability is attributed to the presence of a larger positive charge of the hydrogen atoms contributing to the hydrogen bonds in the PNA-DNA and LNA-DNA doublestrands. These results are comparable to the experimental finding that PNA and LNA single strands display high affinity toward a complementary DNA or RNA single strand.

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Mismatch-Sensitive Hybridization Detection by Peptide Nucleic Acids Immobilized on a Quartz Crystal Microbalance

Cited by 150 publications

References 16 publications

Hybridization-Modulated Ion Fluxes through Peptide-Nucleic-Acid- Functionalized Gold Nanotubes. A New Approach to Quantitative Label-Free DNA Analysis

Hybridization-Modulated Ion Fluxes through Peptide-Nucleic-Acid- Functionalized Gold Nanotubes. A New Approach to Quantitative Label-Free DNA Analysis

SNP genotyping using microsphere‐linked PNA and flow cytometric detection

Hybridization energies of double strands composed of DNA, RNA, PNA and LNA

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