Single-nucleotide polymorphism analysis by hybridization protection assay on solid support.

Susumu Goto; Aki Takahashi; Keiichi Kamisango; Koichi Matsubara

doi:10.1016/s0003-2697(02)00019-2

Home/Archive/PubMed

PubMed · 12137775

Single-nucleotide polymorphism analysis by hybridization protection assay on solid support.

Susumu Goto·Aki Takahashi·Keiichi Kamisango·Koichi Matsubara

View original source ↗Export metadata ↓

Abstract

The clinical need for high-throughput typing methods of single-nucleotide polymorphisms (SNPs) has been increasing. Conventional methods do not perform well enough in terms of speed and accuracy to process a large number of samples, as in clinical testing. We report a new DNA microarray method that uses hybridization protection assay (HPA) by acridinium-ester-labeled DNA probes. Probes were immobilized on the bottom of streptavidin-coated microtiter plates by streptavidin-biotin binding. We studied aldehyde dehydrogenase 2 (ALDH2) genotyping using two probes, discriminating A/G polymorphism. We also designed four probes to type the Alzheimer's disease-related gene ApoE, which has three genotypes (ApoE2, 3, and 4) determined by two SNP loci (C/T polymorphism). SNP analysis of the ALDH2 gene or the ApoE gene from human genome samples by solid-phase HPA was successful. Unlike other methods, the microarray by HPA does not require a washing step and can be completed within 30min. It also has advantages in discriminating one-base mismatch in targets. These characteristics make it a good candidate for practical SNP analysis of disease-related genes or drug-metabolizing enzymes in large numbers of samples.

Explore related subjects

Acridines Aldehyde Dehydrogenase Aldehyde Dehydrogenase, Mitochondrial Apolipoproteins E Biotinylation DNA DNA Primers DNA Probes Genome, Human Genotype Humans Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Polymerase Chain Reaction Polymorphism, Single Nucleotide Reproducibility of Results Journal Article

Keep this discovery

Explore connections, maps & timelines

BibTeX RIS

Susumu Goto, Aki Takahashi, Keiichi Kamisango, Koichi Matsubara. 2002-08-01. Single-nucleotide polymorphism analysis by hybridization protection assay on solid support.. https://doi.org/10.1016/s0003-2697(02)00019-2

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related citations

PubMed2003

Improved potency of the hypoxic cytotoxin tirapazamine by DNA-targeting.

To improve the potency of the hypoxic cytotoxin tirapazamine (TPZ), we have constructed an analog, SN26955, with the TPZ moiety attached to an acridine chromophore to target the drug to DNA. The underlying reason for this is our previous finding that the hypoxic cytotoxicity of TPZ is a result of its ability to produce DNA double-strand breaks, whereas many of the toxicities of the drug in clinical use are likely the result of its metabolism in the cytoplasm and effects on mitochondria. We found that the DNA-targeted TPZ analog was more potent than TPZ in killing hypoxic cells by 1-2 orders of magnitude, yet it retained the hypoxic selectivity for cell killing of TPZ. We show that SN26955 is only active in producing DNA damage when it is enzymatically reduced while bound to, or in close association with, the DNA. We also show that it has a different cofactor dependence than TPZ for reduction leading to DNA double-strand breaks, suggesting the involvement of a different reductase for production of the lethal lesion than for TPZ. These results show the promise of DNA-targeting of TPZ to produce a DNA compound with greater clinical efficacy than TPZ itself.

Acridines↗

PubMed2003

Evaluation of the probes 2',7'-dichlorofluorescin diacetate, luminol, and lucigenin as indicators of reactive species formation.

This study attempts to provide a critical assessment of three different common approaches to identifying teactive species formed in biological systems: the 2',7'-dichlorofluorescin diacetate (DCFH-DA) assay, and the luminol- and lucigenin-amplified chemiluminescence assays. There have been several contradictory reports about the specificity of these methods. Our results show that DCFH is oxidized to the fluorescent compound 2',7'-dichlorofluorescin (DCF) in human neutrophils exposed to the following compounds: Aroclor (A)1242, hydrogen peroxide (H(2)O(2)), nitric oxide (NO), and FeSO(4). Use of a cell-free DCFH system showed increased formation of DCF by peroxynitrite (ONOO(-)), horseradish peroxidase (HRP) alone, and HRP in combination with H(2)O(2), FeSO(4) alone, and a mixture of FeSO(4) and H(2)O(2). The hydroxyl radical (z.rad;OH) scavenger formate and the iron ion chelator deferoxamine reduced the DCF formation induced by FeSO(4) in combination with H(2)O(2). DCFH was insensitive to NO and H(2)O(2) in the cell-free system. In the presence of neutrophils, the A1242-induced luminol chemiluminescence was decreased by the superoxide dismutase inhibitor diethyldithiocarbamic acid (DDC) and the myeloperoxidase inhibitor salicylhydroxamic acid (SHA). Exposure of the neutrophils to NO, FeSO(4), or H(2)O(2) alone did not have any effect. A1242-induced lucigenin chemiluminescence in the neutrophils was increased slightly by DDC, but was not affected by SHA, NO, FeSO(4), or H(2)O(2). In conclusion, we suggest that the DCF assay is only suitable for measurements of ONOO(-), H(2)O(2) in combination with cellular peroxidases, and z.rad;OH. Luminol is sensitive towards HOCl, while lucigenin is oxidized by O(2)z.rad;(-).

Acridines↗

PubMed2003

Pyridoacridine alkaloids inducing neuronal differentiation in a neuroblastoma cell line, from marine sponge Biemna fortis.

A new and three known pyridoacridine alkaloids were isolated from the Indonesian marine sponge Biemna fortis as neuronal differentiation inducers against a murine neuroblastoma cell line, Neuro 2A. The chemical structure of the new compound, labuanine A (1), was determined by spectroscopic study and chemical conversion. These pyridoacridine alkaloids induced multipolar neuritogenesis in more than 50% of cells at 0.03-3 micro M concentration. Compound 3, which showed the strongest neuritogenic activity among them, also induced increase of acetylcholinesterase, a neuronal marker in Neuro 2A and arrested cell cycle at the G2/M phase.

Acridines↗