Liquid-based hybridization assay with real-time detection in miniaturized array platforms

Guerasimova, Anna; Nyársik, Lajos; Liu, Jianping; Schwartz, Regine; Lange, Matthias; Lehrach, Hans; Janitz, Michael

doi:10.1016/j.bioeng.2005.09.005

Cited by 5 publications

(5 citation statements)

References 16 publications

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“…A multitude of bioapplications of LNA materials has recently been reported . These include usage of LNA assemblies as PCR primers and agents affecting RNase H activity , as well as applications as LNAzymes, and in antisense and antigene therapeutics. , Also, LNA has been proposed to be used in diagnostics via microarrays targeting RNA …”

Section: Introductionmentioning

confidence: 99%

The Structure of LNA:DNA Hybrids from Molecular Dynamics Simulations: The Effect of Locked Nucleotides

Ivanova

Rösch

2007

J. Phys. Chem. A

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Locked nucleic acids (LNAs) exhibit a modified sugar fragment that is restrained to the C3'-endo conformation. LNA-containing duplexes are rather stable and have a more rigid structure than DNA duplexes, with a propensity for A-conformation of the double helix. To gain detailed insight into the local structure of LNA-modified DNA oligomers (as a foundation for subsequent exploration of the electron-transfer capabilities of such modified duplexes), we carried out molecular dynamics simulations on a set of LNA:DNA 9-mer duplexes and analyzed the resulting structures in terms of base step parameters and the conformations of the sugar residues. The perturbation introduced by a single locked nucleotide was found to be fairly localized, extending mostly to the first neighboring base pairs; such duplexes featured a B-type helix. With increasing degree of LNA modification the structure gradually changed; the duplex with one complete LNA strand assumed a typical A-DNA structure. The relative populations of the sugar conformations agreed very well with NMR data, lending credibility to the validity of the computational protocol.

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Section: Introductionmentioning

confidence: 99%

The Structure of LNA:DNA Hybrids from Molecular Dynamics Simulations: The Effect of Locked Nucleotides

Ivanova

Rösch

2007

J. Phys. Chem. A

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“…were filtered out from the analysis. The mean background-corrected spot intensity of each sample was used in subsequent data analysis, as described previously [25].…”

Section: Microarray Image Acquisition and Quantificationmentioning

confidence: 99%

Oligonucleotide Fingerprinting of Arrayed Genomic DNA Sequences Using LNA-Modified Hybridization Probes

Liu

Drungowski

Nyársik

et al. 2007

CCHTS

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Recently, we established a robust method for the detection of hybridization events using a DNA microarray deposited on a nanoporous membrane. Here, in a follow-up study, we demonstrate the performance of this approach on a larger set of LNA-modified oligoprobes and genomic DNA sequences. Twenty-six different LNA-modified 7-mer oligoprobes were hybridized to a set of 66 randomly selected human genomic DNA clones spotted on a nanoporous membrane slide. Subsequently, assay sensitivity analysis was performed using receiver operating characteristic (ROC) curves. Comparison of LNA-modified heptamers and DNA heptamers revealed that the LNA modification clearly improved sensitivity and specificity of hybridization experiment. Clustering analysis was applied in order to test practical performance of hybridization experiments with LNA-modified oligoprobes in recognizing similarity of genomic DNA sequences. Comparing the results with the theoretical sequence clusters, we conclude that the application of LNA-modified oligoprobes allows for reliable clustering of DNA sequences which reflects the underlying sequence homology. Our results show that LNA-modified oligoprobes can be used effectively to unravel sequence similarity of DNA sequences and thus, to characterize the content of unknown DNA libraries.

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“…A number of novel liquid phase systems or micro-droplet systems for chemical, biological, environmental researches have been developed. [19][20][21][22][23][24][25][26][27][28][29] Intrinsically the ambient ionization techniques coupled with MS can be a powerful tool for monitoring liquid phase reaction systems, especially the micro-droplet liquid system, due to its quantification and qualification ability. However, the various properties of the liquid phase could affect the thermal desorption procedure of the APCI-related ambient ionization techniques, such as heat capacity, volatility, polarity and viscosity.…”

Section: Introductionmentioning

confidence: 99%

Quantification of low-polar small molecules using room temperature ionic liquids matrix-assisted desorption corona beam ionization

Wang

Guo

et al. 2012

Analyst

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A room temperature ionic liquids (RTILs) matrix-assisted desorption corona beam ionization (DCBI) technique was proposed. The quantification of the DCBI method for low-polar small molecules was improved greatly in terms of accuracy and precision. The thermal desorption processes of analytes in different liquid matrices under DCBI interrogation was investigated with thermal imaging and mass spectrometry simultaneously. When in a volatile liquid matrix, the analyte was not only desorbed thermally from the solid residue phase, but also desorbed along with evaporation of the matrix. The varying matrix evaporation speed and unstable sample introduction path clearly influence the quantitative result. With non-volatile RTILs utilized as the matrix in the sample introduction, a micro slow release system (MSRS) is formed to relieve the fluctuation of analyte evaporation. With the RTILs matrix-assisted DCBI-MS technique, dramatic improvement of the quantification precision (RSD from about 20% to less than 3%) for model analytes was achieved. Seventeen small pharmaceutical and four pesticide molecules were detected successfully. With a shared mechanism, other thermal desorption and/or APCI-related ambient ionization techniques may also benefit from the RTILs matrix.

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Liquid-based hybridization assay with real-time detection in miniaturized array platforms

Cited by 5 publications

References 16 publications

The Structure of LNA:DNA Hybrids from Molecular Dynamics Simulations: The Effect of Locked Nucleotides

The Structure of LNA:DNA Hybrids from Molecular Dynamics Simulations: The Effect of Locked Nucleotides

Oligonucleotide Fingerprinting of Arrayed Genomic DNA Sequences Using LNA-Modified Hybridization Probes

Quantification of low-polar small molecules using room temperature ionic liquids matrix-assisted desorption corona beam ionization

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