DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides

Parinov, Sergei; Barsky, V. E.; Yershov, Gennady; Kirillov, Eugene; Timofeev, Edward N.; Belgovskiy, Alexander; Mirzabekov, Andrei D.

doi:10.1093/nar/24.15.2998

Cited by 90 publications

(48 citation statements)

References 22 publications

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“…However, it may be possible to improve PCR-based genotyping by replacing the gel electrophoresis analysis of the PCR products with DNA-DNA hybridization. The DNA-DNA hybridization enables unambiguous detection of target sequences regardless of the possible presence of nonspecific DNA products and allows the use of PCR primers with broader specificity, permitting a more sensitive and robust amplification of a wider range of organisms.The hybridization of DNA samples with miniature arrays (microchips) of immobilized gene-specific DNA or oligonucleotide probes has recently become a powerful tool for the quantitative study of gene expression (21,22), DNA resequencing (11,17), phylogenetic classification of bacteria (10), mapping of genes (4), and analysis of single-nucleotide polymorphisms …”

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confidence: 99%

“…The hybridization of DNA samples with miniature arrays (microchips) of immobilized gene-specific DNA or oligonucleotide probes has recently become a powerful tool for the quantitative study of gene expression (21,22), DNA resequencing (11,17), phylogenetic classification of bacteria (10), mapping of genes (4), and analysis of single-nucleotide polymorphisms (12,19). This format permits the simultaneous monitoring and analysis of a large number of genetic features in one easy hybridization experiment (20).…”

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Detection and Genotyping of Human Group A Rotaviruses by Oligonucleotide Microarray Hybridization

et al. 2002

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A rapid and reliable method for the identification of five clinically relevant G genotypes (G1 to G4 and G9) of human rotaviruses based on oligonucleotide microarray hybridization has been developed. The genotypespecific oligonucleotides immobilized on the surface of glass slides were selected to bind to the multiple target regions within the VP7 gene that are highly conserved among individual rotavirus genotypes. Rotavirus cDNA was amplified in a PCR with primers common to all group A rotaviruses. A second round of nested PCR amplification was performed in the presence of indodicarbocyanine-dCTP and another pair of degenerate primers also broadly specific for all genotypes. The use of one primer containing 5-biotin allowed us to prepare fluorescently labeled single-stranded hybridization probe by binding of another strand to magnetic beads. The identification of rotavirus genotype was based on hybridization with several individual genotype-specific oligonucleotides. This approach combines the high sensitivity of PCR with the selectivity of DNA-DNA hybridization. The specificity of oligonucleotide microchip hybridization was evaluated by testing 20 coded rotavirus isolates from different geographic areas for which genotypes were previously determined by conventional methods. Analysis of the coded specimens showed that this microarray-based method is capable of unambiguous identification of all rotavirus strains. Because of the presence of random mutations, each individual virus isolate produced a unique hybridization pattern capable of distinguishing different isolates of the same genotype and, therefore, subgenotype differentiation. This strain information indicates one of several advantages that microarray technology has over conventional PCR techniques.Rotaviruses are the most important etiological agents of severe diarrhea in infants and young children in both developed and developing countries (15). The rotavirus outer capsid proteins VP4 and VP7 represent neutralization antigens that are the basis for the classification of rotaviruses by P and G serotypes, respectively. VP4-and VP7-specific antibodies provide serotype-specific protection against rotavirus diarrhea (14). Accurate and rapid serological identification is important for the diagnosis of rotavirus infections, host range determination, and global epidemiological surveillance. It is also an important part of molecular epidemiology and can be used for tracing lines of viral transmission, monitoring molecular evolution, identifying new strains, and determining genotype distribution in clinical trials of experimental vaccines. The current classification of rotaviruses is based on neutralization assays with polyclonal or monoclonal antibodies (13). At least 14 G serotypes (VP7 protein) and 13 (not including subtypes) P serotypes (VP4 protein) have been identified by this approach (7,15).Nucleotide sequence analysis of the VP7 and VP4 genes allows rotaviruses to be classified into a number of distinct genotypes. The G genotypes have been shown to consi...

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Detection and Genotyping of Human Group A Rotaviruses by Oligonucleotide Microarray Hybridization

et al. 2002

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“…Achieving amplification of and discrimination between very similar DNA targets is difficult to accomplish with a single-platform assay. We took advantage of base-stacking energy transfer techniques to assist in reporter discrimination of SNPs (14,17,23). Amplification primers were designed sur-FIG.…”

Section: Methodsmentioning

confidence: 99%

Antimicrobial Resistance and Bacterial Identification Utilizing a Microelectronic Chip Array

Westin¹,

Miller²,

Vollmer³

et al. 2001

J Clin Microbiol

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Species-specific bacterial identification of clinical specimens is often limited to a few species due to the difficulty of performing multiplex reactions. In addition, discrimination of amplicons is time-consuming and laborious, consisting of gel electrophoresis, probe hybridization, or sequencing technology. In order to simplify the process of bacterial identification, we combined anchored in situ amplification on a microelectronic chip array with discrimination and detection on the same platform. Here, we describe the simultaneous amplification and discrimination of six gene sequences which are representative of different bacterial identification assays: Escherichia coli gyrA, Salmonella gyrA, Campylobacter gyrA, E. coli parC, Staphylococcus mecA, and Chlamydia cryptic plasmid. The assay can detect both plasmid and transposon genes and can also discriminate strains carrying antibiotic resistance single-nucleotide polymorphism mutations. Finally, the assay is similarly capable of discriminating between bacterial species through reporter-specific discrimination and allele-specific amplification. Anchored strand displacement amplification allows multiplex amplification and complex genotype discrimination on the same platform. This assay simplifies the bacterial identification process greatly, allowing molecular biology techniques to be performed with minimal processing of samples and practical experience.

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“…The resulting sandwich complex is stabilized by stacking interactions between adjacent bases of the two oligonucleotides (DNA probe and biotinylated DNA), while forming a contiguous duplex with miRNA [56]. Either avidin-HRP or poly-HRP was added to react with the biotin tag of the signal probe, followed by the addition of H2O2.…”

Section: Electroanalysismentioning

confidence: 99%

Electrochemical Detection of miRNAs

Lautner

Gyurcsányi

2014

Electroanalysis

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The recent progress made in the development of electrochemical methods for microRNA (miRNA) detection is presented. This progress is conceived to be largely due to the invention of novel assay methodologies and the use of various bioreagents and nanostructures. These enable a rigorous control over the sensing interface, provide enormous signal amplifications and single-base mismatch specificity. Femtomolar or even subfemtomolar detection limits were shown to be feasible by electrochemical assays. Thus electrochemical detection methodologies are of perspective for diagnostic miRNA detection.

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DNA sequencing by hybridization to microchip octa-and decanucleotides extended by stacked pentanucleotides

Cited by 90 publications

References 22 publications

Detection and Genotyping of Human Group A Rotaviruses by Oligonucleotide Microarray Hybridization

Detection and Genotyping of Human Group A Rotaviruses by Oligonucleotide Microarray Hybridization

Antimicrobial Resistance and Bacterial Identification Utilizing a Microelectronic Chip Array

Electrochemical Detection of miRNAs

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