ArticleApplied and environmental microbiology2003
Optimization of single-base-pair mismatch discrimination in oligonucleotide microarrays.
Article in Applied and environmental microbiology, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed, 143 citations in OpenAlex.
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- Toward a Rational Approach to Design Split G-Quadruplex Probes.ACS chemical biology · 2019Article
- Endonuclease IV recognizes single base mismatch on the eighth base 3' to the abasic site in DNA strands for ultra-selective and sensitive mutant-type DNA detection.RSC advances · 2018Article
- Haplotype-Contained PCR Products Analysis by Sequencing with Selective Restriction of Primer Extension.BioMed research international · 2017Article
- Impact of Heat Stress on Cellular and Transcriptional Adaptation of Mammary Epithelial Cells in Riverine Buffalo (Bubalus Bubalis).PloS one · 2016Article
- Microarray experiments and factors which affect their reliability.Biology direct · 2015Review
- Influence of the length of target DNA overhang proximal to the array surface on discrimination of single-base mismatches on a 25-mer oligonucleotide array.BMC research notes · 2014Article
- Molecular techniques for pathogen identification and fungus detection in the environment.IMA fungus · 2011Article
- Sequence-specific single-molecule analysis of 8-oxo-7,8-dihydroguanine lesions in DNA based on unzipping kinetics of complementary probes in ion channel recordings.Journal of the American Chemical Society · 2011Article
- Isothermal discrimination of single-nucleotide polymorphisms via real-time kinetic desorption and label-free detection of DNA using silicon photonic microring resonator arrays.Analytical chemistry · 2011Article
- Hybridization kinetics between immobilized double-stranded DNA probes and targets containing embedded recognition segments.Nucleic acids research · 2011Article
- Sizing up the future of microRNA analysis.Analytical and bioanalytical chemistry · 2010Review
- Salt concentration effects on equilibrium melting curves from DNA microarrays.Biophysical journal · 2010Article
- Oligonucleotide-based microarray for detection of plant viruses employing sequence-independent amplification of targets.Journal of virological methods · 2010Article
- Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip arrays and 16S rRNA gene clone library sequencing.Applied and environmental microbiology · 2009Article
- Mismatch oligonucleotides in human and yeast: guidelines for probe design on tiling microarrays.BMC genomics · 2008Article
- A short-oligonucleotide microarray that allows improved detection of gastrointestinal tract microbial communities.BMC microbiology · 2008Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in parallel by using an imposed temperature step gradient. We derived an optimum wash temperature for each probe and target by using a simple formula to calculate a discrimination index for each temperature of the step gradient. This optimum corresponded to the output of an independent analysis using a customized neural network program. These results together provide an experimental and analytical framework for optimizing mismatch discrimination among all probes on a DNA microarray.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.