• BMB Reports
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• 제32권6호
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• pp.529-534
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• 1999

Asymmetric PCR and single-strand conformation polymorphism (SSCP) methods were combined to analyze human leukocyte antigen (HLA)-DRB allele polymorphism. Asymmetric PCR amplification was applied to generate single-stranded DNA (ssDNA) using the nonradioactive oligonucleotide primers desinged for the polymorphic exon 2 region. The conformational differences of ssDNAs, depending on the allele type, were analyzed by nondenaturing polyacrylamide gel electrophoresis and visualized by ethidium bromide staining. The ssDNAs were clearly separated from double-stranded DNA without interference and obviously migrated depending on their allele type. This method was applied to the genomic DNA either from homozygous or from heterozygous cell lines containing the DR4 allele as template DNA using DR4-specific primers, and satisfying results were obtained. Compared to the standard PCR-SSCP method, this asymmetric PCR-SSCP method has advantages of increased speed, reproducibility, and convenience. Along with PCR-SSP or sequence-based typing, this method will be useful in routine typing of HLA-DRB allele.

• 한국발생생물학회지:발생과생식
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• 제22권2호
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• pp.193-198
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• 2018

The author undertook PCR-founded genetic platform to investigate the hierarchical dendrogram of Euclidean genetic distances of one razor clam population, particularly for Solen corneus, which was further associated with those of the other clam population, by engaging with the precisely designed oligonucleotide primer sets. Seven oligonucleotides primers were used producing a total of 639 counted bands in population A and 595 in population B, respectively, ranging in size of DNA fragments from larger than approximately 50 bp to less than 1,100 bp. Their primers generated 39 specific fragments (6.10%) in population A and 47 (7.90%) in population B, respectively Comparatively, individuals of one razor clam population were fairly related to that of the other clam population, as shown in the hierarchical dendrogram of Euclidean genetic distances. The analysis of genetic variation between razor clam populations could offer important statistics for fisheries and mariculture. Generally the results showed specific and/or conserved genetic loci between razor clam populations. Specific markers established by the author will be valuable for the genetic analysis, species protection and increase of razor clam individuals in coastal region of the Korean Peninsula.

• Fisheries and Aquatic Sciences
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• 제16권4호
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• pp.273-277
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• 2013

Vibriosis caused by Vibrio anguillarum and edwardsiellosis caused by Edwardsiella tarda are septicemic diseases of many commercially important freshwater and marine fishes, and threaten the aquaculture industry in Korea. Early diagnosis and accurate identification of these two bacterial species could help to prevent these diseases and minimize the damage to cultured marine species. This study designed a duplex polymerase chain reaction (PCR) method for the simultaneous detection of two major fish pathogens: V. anguillarum and E. tarda. Each pair of oligonucleotide primers exclusively amplified the target groEL gene of the specific microorganism. Twenty-two Vibrio and ten non-Vibrio enteric species were used to check the specificity of the primers, which were found to be highly specific for the target species, even among closely related species. The detection limit was 400 pg for V. anguillarum and 4 ng for E. tarda when mixed purified DNA was used as the template. This assay showed high specificity and sensitivity in the simultaneous detection of V. anguillarum and E. tarda from artificially inoculated seawater and fish.

• 한국육종학회지
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• 제43권4호
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• pp.265-272
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• 2011

This study is to generate SCARs markers for identification of Perilla species. A SCAR is a genomic DNA fragment at a single genetically defined locus that is identified by PCR amplification using a pair of specific oligonucleotide primers. We derived SCARs by sequencing and cloning the both ends of the amplified products of RAPD markers. Sixteen sequence-specific primers were synthesized from eight RAPD markers, which were completely sequenced. We developed the species-specific SCAR markers which could be used successfully in detecting genetic variation in four Perilla species. These markers could be used to verify species-origins of various forms of Perilla germplasms.

• Restorative Dentistry and Endodontics
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• 제24권1호
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• pp.13-25
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• 1999

P. endodontalis which was known to be associated with the infected root canals and periapical lesions is very difficult to detect by culture methods or traditional methods. Detection of bacteria using polymerase chain reaction(PCR) for 16S ribosomal DNA(rDNA) is fast, simple, and accurate with relatively small amount of target cells. 16S rDNA consist of conserved regions those are same to all species, and variable regions which represent species specificity. The 16S rDNA sequences of P. endodontalis and P. gingivalis were aligned and two highly variable regions were selected as a pair of species specific oligonucleotide primers for P. endodontalis. And then the pair of primers for PCR amplification was synthesized to identify P. endodontalis. The sequences of the species specific primers for the 16S rDNA of P. endodontalis were as follows ; sense primer[endo1]: 5'-CTATATTCTTCTTTCTCCGCATGGAGGAGG-3' antisense primer[endo2]: 5'-GCATACCTTCGGTCTCCTCTAGCATAT-3' In this study, for the identification of P. endodontalis without culture from the mixed clinical samples, PCR was done with species specific primers for the 16S rDNA sequences of P. endodontalis. The results were as follows : 1. The species specificity of the primers for the 16S rDNA of P. endodntalis was determined by the PCR methods. About 490bp amplicon which was specific only for P. endodntalis was produced with P. endodontalis. No amplicon was produced by PCR with other strains similar to P. endodontalis. 2. The synthesized species specific primers reacted with conventionally identified P. endodontalis which we have in conservative dentistry laboratory. 3. The identification of P. endodontalis using PCR technique with samples collected from infected root canals or periapical lesions was more sensitive than that of culture methods. 4. Seven samples revealed including P. endodontalis by PCR technique. Five of them were related with pains, two of them with sinus tract, three of them with foul odor, and three of them with purulent drainage. P. endodontalis was shown to have great relation with pains.

• Journal of Plant Biology
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• 제38권3호
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• pp.267-274
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• 1995

Based upon the nucleotide sequence of As strain of cucumber mosaic virus (CMV-As0 RNA4, coat protein (CP) gene was selected for the design of oligonucleotide primers of polymerase chain reaction (PCR) for detection and identification of the virus. Reverse transcription and polymerase chain reaction (RT-PCR) was performed with a set of 18-mer CMV CP-specific primers to amplify a 671 bp fragment from crude nucleic acid extracts of virus-infected leaf tissues as well as purified viral RNAs. The minimum concentrations of template viral RNA and crude nucleic acids from infected tobacco tissue required to detect the virus were 1.0 fg and 1:65,536 (w/v), respectively. No PCR product was obtained when potato virus Y-VN RNA or extracts of healthy plants were used as templates in RT-PCR using the same primers. The RT-PCR detected CMV-Y strain as well as CMV-As strain. Restriction analysis of the two individual PCR amplified DNA fragments from CMV-As and CMV-Y strains showed distinct polymorphic patterns. PCR product from CMV-As has a single recognition site for EcoRI and EcoRV, respectively, and the product from CMV-Y has no site for EcoRI or EcoRV but only one site for HindIII. The RT-PCR was able to detect the virus in the tissues of infected pepper, tomato and Chinese cabbage plants.

• 한국약용작물학회지
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• 제9권3호
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• pp.205-210
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• 2001

50여개의 primer를 사용하여 잔대 Adenophora triphylla와 층층잔대 A. radiatifolia Nakai, 그리고 더덕 Codonopsis laceolata Trautv의 지역간, 속간의 차이점과 감별여부를 RAPD법으로 시행한 결과, 잔대와 층층잔대의 차이점은 거의 없었으며, 더덕의 지역차이는 0.889의 유전적거리를 나타내었다. 두 종(種)을 구별할 수 있는 특이 band로는 primer 357, 361, 363, 393 이었으며, 건조약재와 비교하였을 때 재현성이 확인되었고, 또한 잔대와 더덕의 건조약재를 각각 혼합시켰을 때 이를 구별할 수 있는 major band가 뚜렷이 나타나 혼용되어있는 건조약재에서의 감별이 가능함을 알 수 있었다..

• 한국패류학회지
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• 제22권2호
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• pp.97-108
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• 2006

Genomic DNA samples isolated from geographical purple Washington clam (Saxidomus purpuratus) were obtained from two different regions in Korean Peninsula: Gunsan (Gunsan population; GSP), and Haeju (Haeju population; HJP), a collection area in the vicinity of the West Sea. The seven arbitrarily primers, OPA-07, OPA-09, OPA-18, OPA-20, OPC-03, OPC-06 and OPC-09 were shown to generate the total loci, loci observed per primer, shared loci by each population, specific, and polymorphic loci which could be clearly scored. We also generated the unique shared loci to each population and shared loci by the two populations in purple Washington clam. The size of the DNA fragments also varied wildly, from 50 to 2,400 bp. Here, 304 total loci were identified in the GSP purple Washington clam population, and 282 in the HJP: 91 polymorphic loci (29.9%) in the GSP and 47 (16.7) in the HJP. 198 shared loci, with an average of 28.3 per primer, were observed in the GSP population. The decamer primer OPA-07 generated the shared loci by the two populations, approximately 1,000 bp, between the two Saxidomus populations. The oligonucleotide primer OPC-03 also generated the shared loci by the two populations, approximately 500 bp and 1,000 bp, in GSP population from Gunsan and HJP population from Haeju. The other primer, OPC-06 generated the shared loci by two Gomphina populations (approximately 400 bp). The dendrogram, generated by seven reliable primers, indicates three genetic clusters. The dendrogram obtained by the seven primers indicates three genetic clusters: cluster 1 (GUNSAN 01-GUNSAN 02), cluster 2 (GUNSAN 03-GUNSAN 11), and cluster 3 (HAEJU 12-HAEJU 22). The genetic distance between the two geographical populations ranged from 0.043 to 0.506. Especially, the longest genetic distance displaying significant molecular differences, 0.506, was found to exist between individuals GUNSAN no. 11 of Gunsan and HAEJU no. 17 of Haeju.

• 생명과학회지
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• 제21권1호
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• pp.15-21
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• 2011

재배종 토마토(Lycopersicum esculentum)는 중요 작물의 하나이다. 36 재배종에 대해 80개 RAPD (random amplified polymorphic DNA) 마커로 동정과 다형성을 조사하였다. 80개 마커 중 36개(45.0%)는 다형성을 나타내었다. 재배종 토마토에서 다형성의 탐지는 유익한 유전자형의 선택에 의한 분자 지도 발전 가능성을 제공할 수 있다. 분자 마커는 역시 식물 육종 지적 권리(PBRs)의 동정과 보호를 위해 사용될 수 있다. 한 예로써 OPC-13 시발체를 사용한 DNA 다형은 Junk Pink와 Ailsa Craighp 품종은 OPC-13-01 밴드가 결여되어 있다. OPA-12-03와 OPB-15-07는 TK-70 품종에 특이 마커로 다른 품종에는 없다. 본 연구의 재배종 토마토에서 DNA 다형은 일부 예외는 있지만 개화 타입과 관련이 있다. 이런 접근은 바람직한 토마토 품종 육성에 유전적 정보를 높이는데 유익할 것으로 사료된다.

• 한국한의학연구원논문집
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• 제1권1호
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• pp.471-476
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• 1995

Natural products used for oriental medicine often come from various geographical sources, after several different distribution channels. Therefore some form of quality control procedure is required to safeguard naturl products for prescriptions purposes. To achieve this, systematic apprroaches such as morphological examination, microscopic analysis of powdered herbs and chemical analysis can be carried out. However, to ensure absolute criteria for quality assurance of natural products, DNA fingerprinting method such as RAPD(Random amplified polymorphism DNA) analysis can be used for authentication of natural products for authenticatin of natural products. In this study, warious oligonucleotide primers will be synthesized for the detection of RAPD markers and also parameters of affecting PCR(Polymerase Chain Reaction) in the detection of RAPD markers of rare and high-priced natural products will be studied with genomic DNA of chosen samples.