• Journal of Microbiology and Biotechnology
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• v.19 no.3
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• pp.265-270
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• 2009

An oligonucleotide array was developed to detect and genotype mollicutes based on the internal transcribed spacer (ITS) sequence. The results of the assay were compared with those of a PCR-RFLP assay. The proposed oligonucleotide array containing 5 genus- and 23 species-specific probes was able to detect Mycoplasma species, including M. penetrans and M. spermatophilum, that were not detected by the PCR-RFLP assay. Therefore, the results demonstrated that the proposed oligonucleotide array was effective for the detection and discrimination of 23 species, including an acholeplasma, 21 mycoplasmas, and a ureaplasma, and showed promise as a countermeasure to ensure that biological products are safe and of good quality.

• Journal of Microbiology and Biotechnology
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• v.19 no.7
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• pp.658-665
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• 2009

Quality control QC for spot-uniformity is a critical point in fabricating an oligonucleotide array, and quantification of targets is very important in array analysis. We developed two new types of QC probes as a means of confirming the quality of the uniformity of attached probes and the quantification of targets. We compared the signal intensities and fluorescent images of the QC and target-specific probes of arrays containing only target-specific probes and those containing both QC and target-specific probes. In a comparison of quality control methods, it was found that the arrays containing QC probes could check spot-uniformity or spot defects during all processes of array fabrication, including after spotting, after washing, and after hybridization. In a comparison of quantification results, the array fabricated by the method using QC probes showed linear and regular results because it was possible to normalize variations in spot size and morphology and amount of attached probe. This method could avoid errors originating in probe concentration and spot morphology because it could be normalized by QC probes. There were significant differences in the signal intensities of all mixtures (P<0.05). This result indicates that the method using QC probes is more useful than the ordinary method for quantification of mixed target. In the quantification of mixed targets, this method could determine a range for mixed targets of various amounts. Our results suggest that methods using QC probes for array fabrication are very useful to the quality control of spots in the fabrication processes of quantitative oligonucleotide arrays.

• Bulletin of the Korean Chemical Society
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• v.25 no.11
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• pp.1667-1670
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• 2004

In DNA microarray produced by DNA-deposition technology, DNA-immobilization and -hybridization yields on a solid support are most important factors for its accuracy and sensitivity. We have developed a dendrimeric support using silylated aldehyde slides and polyamidoamine (PAMAM) dendrimers. An oligonucleotide array was prepared through a crosslinking between the dendrimeric support and an oligonucleotide. Both DNAimmobilization and -hybridization yields on the solid support increased by the modification with the dendrimers. The increase of the immobilization and hybridization efficiency seems to result from a threedimensional arrangement of the attached oligonucleotide. Therefore, our dendrimeric support may provide a simple and efficient solution to the preparation of DNA microarrays with high-density DNA-deposition and high hybridization efficiency.

• Proceedings of the Microbiological Society of Korea Conference
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• 2009.05a
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• pp.147-147
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• 2009

• Molecular & Cellular Toxicology
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• v.4 no.3
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• pp.246-252
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• 2008

Tumor tissue is usually contaminated by normal tissue components, which reduces the sensitivity of analysis for exploring genetic alterations. Although microdissection has been adopted to minimize the contamination of tumor DNA with normal cell components, there is a concern over the amount of microdissected DNA not enough to be applied to array-CGH reaction. To amplify the extracted DNA, several whole genome amplification (WGA) methods have been developed, but objective comparison of the array-CGH outputs using different types of WGA methods is still scarce. In this study, we compared the performance of non-amplified microdissected DNA and DNA amplified in 2 WGA methods such as degenerative oligonucleotide primed (DOP)-PCR, and multiple strand displacement amplification (MDA) using Phi 29 DNA polymerase. Genomic DNA was also used to make a comparison. We applied those 4 DNAs to whole genome BAC array to compare the false positive detection rate (FPDR) and sensitivity in detecting copy number alterations under the same hybridization condition. As a result microdissected DNA method showed the lowest FPDR and the highest sensitivity. Among WGA methods, DOP-PCR amplified DNA showed better sensitivity but similar FPDR to MDA-amplified method. These results demonstrate the advantage and applicability of microdissection for array-CGH analysis, and provide useful information for choosing amplification methods to study copy number alterations, especially based on precancerous and microscopically invaded lesions.

• BMB Reports
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• v.38 no.4
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• pp.399-406
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• 2005

A sensitive method for detection of Hepatitis A virus (HAV) by utilizing gold-DNA probe on an array was developed. Amino- modified oligodeoxynucleotides at the 5' position were arrayed on an activated glass surface to function as capture probes. Sandwich hybridization occurred among capture probes, the HAV amplicon, and gold nanoparticle-supported oligonucleotide probes. After a silver enhancement step, signals were detected by a standard flatbed scanner or just by naked eyes. As little as 100 fM of HAV amplicon could be detected on the array. Therefore, the array technology is an alternative to be applied in detection of HAV due to its low-cost and high-sensitivity.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2006.02a
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• pp.125-126
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• 2006

NimbleGen has developed strategies to use its high-density oligonucleotide microarray platform (385,000 probes per array) to map both promoter binding sites and copy number variation at very high-resolution in the human genome. Here we describe a genome-wide map of active promoters determined by experimentally locating the sites of transcription imitation complex binding throughout the human genome using microarrays combined with chromatin immunoprecipitation. This map defines 10,567 active promoters corresponding to 6,763 known genes and at least 1,196 un-annotated transcriptional units. Microarray-based comparative genomic hybridisation (CGH) is animportant research tool for investigating chromosomal aberrations frequently associated with complex diseases such as cancer, neuropsychiatric disorders, and congenital developmental disorders. NimbleGen array CGH is an ultra-high resolution (0.5-50 Kb) oligo array platform that can be used to detect amplifications and deletions and map the associated breakpoints on the whole-genome level or with custom fine-tiling arrays. For whole-genome array CGH, probes are tiled through genic and intergenic regions with a median probe spacing of 6 Kb, which provides a comprehensive, unbiased analysis of the genome.

• BMB Reports
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• v.39 no.3
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• pp.247-252
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• 2006

A rapid method for the detection of Hepatitis E Virus (HEV) was developed by utilizing nano-gold labeled oligonucleotide probes, silver stain enhancement and the microarray technique. The 5'-end -$NH_2$ modified oligonucleotide probes were immobilized on the surface of the chip base as the capture probe. The detection probe was made of the 3'-end -SH modified oligonucleotide probe and nano-gold colloid. The optimal concentrations of these two probes were determined. To test the detection sensitivity and specificity of this technique, a conservative fragment of the virus RNA was amplified by the RT-PCR/PCR one step amplification. The cDNA was hybridized with the capture probes and the detection probes on microarray. The detection signal was amplified by silver stain enhancement and could be identified by naked eyes. 100 fM of amplicon could be detected out on the microarray. As the results, preparation of nano-gold was improved and faster. Development time also was shortened to 2 min. Thus, considering high efficiency, low cost, good specificity and high sensitivity, this technique is alternative for the detection of HEV.

• 한국생물공학회:학술대회논문집
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• 2001.11a
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• pp.235-236
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• 2001

We developed a DNA probe analytical system with a patterned array of oligonucleotide molecules immobilized on glass surfaces. The detection capability of the system depended mainly on the way the capture probes were attached to the support as wen as the sequence. We optimized major variables to graft DNA molecules onto a glass support and the DNA probe assay was eventually accomplished without purification of the PCR product.

• Journal of Life Science
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• v.19 no.4
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• pp.449-456
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• 2009

Murine Neuro-2a (N2a) cells have been widely used for the investigation of neuronal differentiation, trophic interaction and neurotoxic effects of various compounds and their associated mechanisms. N2a cells have many genomic variations such as gains or losses in DNA copy number, similar to other neuroblastoma cells, and no systematic or high-resolution studies of their genome-wide chromosomal aberrations have been reported. Presently, we conducted a systematic genome-wide determination of chromosomal aberrations in N2a cells using a high-throughput, oligonucleotide array-based comparative genomic hybridization (oaCGH) technique. A hidden Markov Model was employed to assign each genomic oligonucleotide to a DNA copy number state: double loss, single loss, normal, gain, double gain and amplification. Unlike most neuroblastoma cells, Mycn amplification was not observed in N2a cells. In addition, these cells showed gain only in the neuron-derived neurotrophic factor (NF), while other neurotrophic factors such as glial line-derived NF and brain-derived NF presented normal copy numbers. Chromosomes 4, 8, 10, 11 and 15 displayed more than 1000 aberrational oligonucleotides, while chromosomes 3, 17, 18 and 19 displayed less than 20. The largest region of gain was located on chromosome 8 and its size was no less than 26.7 Mb (Chr8:8427841-35162415), while chromosome 4 had the longest region of single deletion, with a size of 15.1 Mb (Chr4:73265785-88374165).