• BMB Reports
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• 제29권2호
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• pp.122-126
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• 1996

A series of oligonucleotides were synthesized by automatic DNA synthesizer. The purity of crude products was checked and their molecular weights determined by matrix assisted laser desorption ionization mass spectrometry (MALDI-MS) with an accuracy of better than 0.05% deviation even without using an internal standard. This mass determining technology in combination with partial digestion of oligonucleotides by 5'- and 3'-exonuclease provides a straightforward and simple method to obtain sequence information of oligonucleotides. The extension of this technology to the sequencing of modified oligonucleotides and genomic DNA and RNA might become possible.

• Journal of Microbiology and Biotechnology
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• 제11권5호
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• pp.876-879
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• 2001

${\gamma}$ -Tubulin is an essential component involved in microtubule nucleation. The present work examined whether the fast proliferation of cancer cells can be retarded by the depletion of ${\gamma}$ -tubulin expression. Two different gastric cancer cell lines and one control cell line were treated with antisence oligonucleotides complementary to the messenger RNA of ${\gamma}$ -tubulin. The$[^3H]$ -thymidine incorporation in the two gastric cancer cell lines, SNU-1 and SNU-216, was dramatically reducd by treatment with the ${\gamma}$ -tubulin antisense oligonucleotides in a dosage-dependent manner. In contrast, the control cell line, NIH/3T3, showed no significant effect from the antisense oligonucleotides even at a high concentration. The ablation of ${\gamma}$ -tubulin expression in the tumor cells resulted in an altered DNA synthesis during mitosis and it decreased the cell progression. Accordingly, the use of antisense oligonucleotides may be an effective way of inhibiting the proliferation of human gastric cancers.

• 한국발생생물학회지:발생과생식
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• 제20권4호
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• pp.379-385
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• 2016

Seven oligonucleotides primers were shown to generate the shared loci, specific loci, unique shared loci to each species and shared loci by the three species which could be obviously scored. In the present study, 7 oligonucleotides primers produced 401 total loci in the Styela clava (SC) species, 390 in the Halocynthia roretzi (HR) and 434 in the Styela plicata (SP), respectively. Seven oligonucleotides primers generated 275 specific loci in the SC, 341 in the HR and 364 in the SP species, respectively. The oligonucleotides primer BION-23 generated 28 unique loci to each species in the SP species. Especially, the oligonucleotides primer BION-25 produced 7 unique loci to each species, which were identifying each species in the SP species. BION-17 distinguished 21 shared loci by the three ascidian species, major and/or minor fragments of sizes, which were identical in almost all of the samples. Based on the average bandsharing values of all samples, the similarity matrix ranged from 0.519 to 0.774 in the SC species, from 0.261 to 0.683 in the HR species and from 0.346 to 0.730 in the SP species. As regards average bandsharing value (BS) results, individuals from SC species ($0.661{\pm}0.081$) exhibited higher bandsharing values than did individuals from HR species ($0.555{\pm}0.074$) (P<0.05). The dendrogram obtained by the seven oligonucleotides primers indicates three genetic groups. In three ascidian species, the shortest genetic distance (0.071) exhibiting significant molecular difference was also between individual no. 20 and no. 21 within the SP species.

• Molecules and Cells
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• 제28권4호
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• pp.341-345
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• 2009

MiRNAs are non-coding RNAs that play a role in the regulation of major processes. The inhibition of miRNAs using antisense oligonucleotides (ASOs) is a unique and effective technique for the characterization and subsequent therapeutic targeting of miRNA function. Recent advances in ASO chemistry have been used to increase both the resistance to nucleases and the target affinity and specificity of these ASOs. Peptide nucleic acids (PNAs) are artificial oligonucleotides constructed on a peptide-like backbone. PNAs have a stronger affinity and greater specificity to DNA or RNA than natural nucleic acids and are resistant to nucleases, which is an essential characteristic for a miRNA inhibitor that will be exposed to serum and cellular nucleases. For increasing cell penetration, PNAs were conjugated with cell penetrating peptides (CPPs) at N-terminal. Among the tested CPPs, Tat-modified peptide-conjugated PNAs have most effective function for miRNA inhibition. PNA-based ASO was more effective miRNA inhibitor than other DNA-based ASOs and did not show cytotoxicity at concentration up to 1,000 nM. The effects of PNA-based ASOs were shown to persist for 9 days. Also, PNA-based ASOs showed considerable stability at storage temperature. These results suggest that PNA-based ASOs are more effective ASOs of miRNA than DNA-based ASOs and PNA-based ASO technology, compared with other technologies used to inhibit miRNA activity can be an effective tool for investigating miRNA functions.

• BMB Reports
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• 제39권3호
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• pp.329-334
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• 2006

RNAi (RNA interference) has become a popular means of knocking down a specific gene in vivo. The most common approach involves the use of chemically synthesized short interfering RNAs (siRNAs), which are relatively easy and fast to use, but which are costly and have only transient effects. These limitations can be overcome by using short hairpin RNA (shRNA) expression vectors. However, current methods of generating shRNA expression vectors require either the synthesis of long (50-70 nt) costly oligonucleotides or multi-step processes. To overcome this drawback, we have developed a one-step short-oligonucleotides-based method with preparation costs of only 15% of those of the conventional methods used to obtain essentially the same DNA fragment encoding shRNA. Sequences containing 19 bases homologous to target genes were synthesized as 17- and 31-nt DNA oligonucleotides and used to construct shRNA expression vectors. Using these plasmids, we were able to effectively silence target genes. Because our method relies on the onestep ligation of short oligonucleotides, it is simple, less error-prone, and economical.

• 생태와환경
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• 제33권3호통권91호
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• pp.206-212
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• 2000

남조류 분리균주들은 주어진 배양조건에 따라서 특징적인 세포모양이 결핍되거나 형태가 변형되기 쉽기 때문에, 형태학적으로 종을 정확하게 구분하기 어렵다. 형태학적 지표대신에 단일 혹은 조합된 반복염기를 프라이머로 이용한 repetitive oligonucleotides-primed PCR (ROP-PCR)을 수행하여 담수계 오염을 일으키는 독성 남조류 Anabaena와 Oscillatoria 속의 구성원들의 DNA 밴드양상을 구별하였다. 그람음성 세균에 빈번하게 분포한 것으로 알려진 ERIC및 REP 반복염기, 남조류의 게놈으로부터 파생된 STRRIA와 LTRR 반복염기, 그리고 진핵생물의 반복염기를 이용하여 수행한 ROP-PCR은 남조류 분리균주들의 특이적이고 반복적인 DNA 지문 및 뚜렷한 유전형을 동정하게 하였다. 분리균주의 그룹분석은 ROP-PCR에 이용된 프라이머에 따라서 유의성있는 차이를 나타내었다.

• Archives of Pharmacal Research
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• 제26권3호
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• pp.183-191
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• 2003

Nucleic acid therapies represent a direct genetic approach for cancer treatment. Such an approach takes advantage of mechanisms that activate genes known to confer a growth advantage to neoplastic cells. The ability to block the expression of these genes allows exploration of normal growth regulation. Progress in antisense technology has been rapid, and the traditional antisense inhibition of gene expression is now viewed on a genomic scale. This global view has led to a new vision in antisense technology, the elimination of nonspecific and undesirable side effects, and ultimately, the generation of more effective and less toxic nucleic acid medicines. Several antisense oligonucleotides are in clinical trials, are well tolerated, and are potentially active therapeutically. Antisense oligonucleotides are promising molecular medicines for treating human cancer in the near future.

• Animal Bioscience
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• 제34권10호
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• pp.1579-1589
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• 2021

Objective: This study was conducted to generate single stranded DNA oligonucleotides with selective affinity to bovine spermatozoa, assess its binding potential and explore its potential utility in trapping spermatozoa from suspensions. Methods: A combinatorial library of 94 mer long oligonucleotide was used for systematic evolution of ligands by exponential enrichment (SELEX) with bovine spermatozoa. The amplicons from sixth and seventh rounds of SELEX were sequenced, and the reads were clustered employing cluster database at high identity with tolerance (CD-HIT) and FASTAptamer. The enriched nucleotides were predicted for secondary structures by Mfold, motifs by Multiple Em for Motif Elicitation and 5' labelled with biotin/6-FAM to determine the binding potential and binding pattern. Results: We generated 14.1 and 17.7 million reads from sixth and seventh rounds of SELEX respectively to bovine spermatozoa. The CD-HIT clustered 78,098 and 21,196 reads in the top ten clusters and FASTAptamer identified 2,195 and 4,405 unique sequences in the top three clusters from the sixth and seventh rounds, respectively. The identified oligonucleotides formed secondary structures with delta G values between -1.17 to -26.18 kcal/mol indicating varied stability. Confocal imaging with the oligonucleotides from the seventh round revealed different patterns of binding to bovine spermatozoa (fluorescence of the whole head, spot of fluorescence in head and mid- piece and tail). Use of a 5'-biotin tagged oligonucleotide from the sixth round at 100 pmol with 4×10⁶ spermatozoa could trap almost 80% from the suspension. Conclusion: The binding patterns and ability of the identified oligonucleotides confirms successful optimization of the SELEX process and generation of aptamers to bovine spermatozoa. These oligonucleotides provide a quick approach for selective capture of spermatozoa from complex samples. Future SELEX rounds with X- or Y- enriched sperm suspension will be used to generate oligonucleotides that bind to spermatozoa of a specific sex type.

• 한국발생생물학회지:발생과생식
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• 제20권2호
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• pp.135-140
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• 2016

Genomic DNAs isolated from crucian carp of four rivers, belonging to the family Cyprinidae was amplified by seven oligonucleotides primers. In the present study, we employed hierarchical clustering method in order to reveal genetic distances and variations. Crucian carp was acquired from Hangang river (CAH), Geumgang river (CAG), Nakdonggang river (CAN) and Yeongsangang river (CAY). The primer BION-12 generated the most loci (a total of 50) with an average of 10 in the CAY population. The primer BION-10 generated the least loci (a total of 19), with an average of 3.8 in the CAG population, in comparison to the other primers used. Seven oligonucleotides primers made 16.7 average no. per primer of specific loci in the CAH population, 7.4 in the CAG population, 8.6 in the CAN population and 0.9 in the CAY population, respectively. The specific loci generated by oligonucleotides primers revealed inter-individual-specific characteristics, thus disclosing DNA polymorphisms. The dendrogram obtained by the seven oligonucleotides primers indicates four genetic clusters. The genetic distance that displayed significant molecular differences was between individuals no.06 and no.08 from the CAG population (genetic distance = 0.036), while the genetic distance among the five individuals that displayed significant molecular differences was between individuals no.08 and no.09 from the CAG population (genetic distance = 0.088). With regard to average bandsharing value (BS) results, individuals from CAY population ($0.985{\pm}0.009$) exhibited higher bandsharing values than did individuals from CAH population ($0.779{\pm}0.049$) (P<0.05). Relatively, individuals of CAY population were fairly closely related to that of CAN location (genetic distance between two populations<0.016).

• 한국패류학회지
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• 제32권4호
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• pp.255-261
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• 2016

The selected seven oligonucleotides primers BION-32, BION-33, BION-35, BION-38, BION-40, BION-46 and BION-58 generated the shared loci, specific loci, unique shared loci to each population and shared loci by the three T. granosa populations in Beolgyo, a Chinese site and Wonsan, respectively. The bandsharing value between individuals' no. 03 and no. 04 was 0.816, which was the highest value identified within the Beolgyo population. The primer BION-35 generated the most loci (a total of 70), with an average of 10.0 in the Wonsan population. On average, seven oligonucleotides primers generated 16.1 specific loci in the Beolgyo population, 22.3 in the Chinese population and 39.3 in the Wonsan population. 126 unique shared loci to each population, with an average of 18 per primer, were observed in the Beolgyo population, 63 loci, with an average of 9 per primer, were observed in the Chinese population, and 49 loci, with an average of 7 per primer, and were observed in the Wonsan population. The oligonucleotides primer BION-32 generated 14 unique loci to each population, which were identifying each population in the Beolgyo population. Interestingly, every primer had not distinguished the shared loci by the three populations, major and/or minor fragments of sizes, which were identical in almost all of the samples. As regards average bandsharing value (BS) results, individuals from Beolgyo population ($0.717{\pm}0.057$) exhibited higher BS values than did those from Wonsan population ($0.552{\pm}0.104$) (P < 0.05). The dendrogram resulted from truthful seven oligonucleotides primers, representing three genetic clusters comprising group I (BEOLGYO 01, 02, 03, 04, 05, 06 and 07), group II (CHINESE 08, 09, 10, 11, 12, 13 and 14) and group III (WONSAN 15, 16, 17, 18, 19, 20 and 21). In three T. granosa populations, the longest genetic distance (0.874) displaying significant molecular difference was also between individual no. 02 within the Beolgyo population and individual no. 12 within the Chinese population. Relatively, individuals of the CHINESE population were fairly closely related to those of the WONSAN population.