• Proceedings of the Korean Society for Bioinformatics Conference
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• 2005.09a
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• pp.147-150
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• 2005

Proper PCR primer design determines the success or failure of Polymerase Chain Reaction (PCR) reactions. In this project, we develop GENE-PRIMER, a genomes specific PCR primer design program that is amenable to a genome-wide scale. To achieve this, we incorporated various parameters with biological significance into our program, namely, primer length, melting temperature of primers Tm, guanine/cytosine (GC) content of primer, homopolymeric runs in primer and self-hybridization tendency of primer. In addition, BLAST algorithm is utilized for the purpose of primer specificity check. In summary, selected primers adhered to both physico-chemical criteria and also display specificity to intended binding site in the genome.

• Biomedical Science Letters
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• v.24 no.4
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• pp.390-397
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• 2018

For the specific detection of human Parvovirus B19 (HuPaV-B19), we designed ten specific PCR primers from 3,800~4,500 nucleotides of HuPaV-B19 complete genome (NC_000883.2). Seventeen candidate PCR primer sets for specific detecting HuPaV-B19 were constructed. In specific reaction of HuPaV-B19, seventeen PCR primer sets showed specific band, however five PCR primer sets were selected basis of band intensity, amplicon size and location. In non-specific reaction with seven reference viruses, four PCR primer sets showed non-specific band, however one PCR primer set is not. Detection sensitivity of final selective PCR primer set was $100fg/{\mu}L$ for 112 minute, and PCR amplicon is 539 base pairs (bp). In addition, nested PCR primer set was developed, for detection HuPaV-B19 from a low concentration of contaminated samples. Selection of nested PCR primer set was basis of sensitivity and groundwater sample tests. Detection sensitivity of final selective PCR and nested PCR primer sets for the detection of HuPaV-B19 were $100fg/{\mu}L$ and $100ag/{\mu}L$ basis of HuPaV-B19 plasmid, it was able to rapid and highly sensitive detection of HuPaV-B19 than previous reports. We expect developed PCR primer set in this study will used for detection of HuPaV-B19 in various samples.

• KSBB Journal
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• v.22 no.5
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• pp.362-365
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• 2007

Cyanobacteria have been identified as one of the most promising group producing novel biochemically active natural products. Cyanobacteria are a very old group of prokaryotic organisms that produce very diverse secondary metabolites, especially non-ribosomal peptide and polyketide structures. Large multienzyme complexes which are responsible for the non-ribosomal biosynthesis of peptides are modular for the addition of a single amino acid. An activation of amino acid substrates results in an amino adenylate occuring via an adenylation domain (A-domain). A-domains are responsible for the recognition of amino acids as substrates within NP synthesis. The A-domain contains ten conserved motifs, A1 to A10. In this study, ten conserved motifs from A1 to A10 were checked regarding their amino acid sequence of the NRPS-module of Microcystis aeruginosa PCC 7806. The part of the amino acid sequence chosen was that which contained as many conserved motives as possible, and then these amino sequence were compared between other cyanobacteria to design a new degenerate primer. A new degenerate primer (A3/A7 primer) was designed to detect any putative NP synthetase region in unkwon cyanobacteria by a reverse translation of the conserved amino acid sequence and a search for cyanobacterial DNA bank.

• Journal of Food Hygiene and Safety
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• v.18 no.2
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• pp.67-72
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• 2003

Random amplified Polymorphic DNA (RAPD) analysis Is based on the amplification of random DNA segment using a single arbitrary primer. Polymorphic DNA patterns identified by this method can be used for typing Listeria monocytogenes. To select the primers for RAPD typing Listeria spp., the performance of 31 primers were compared by analyzing 13 Listeria spp. reference strains. Reproducible electrophoresis patterns were obtained. Among 31 primers, 6 primers (primer 6, HLWL74, UBC155, UBC127, Lis5, Lis11) showed better differentiation, when discrimination index, band clarity, band number, difficulty of band scoring were considered than the others. These primers will be useful far typing Listeria spp. in the future. Currently, we are under investigation for the RAPD typing of contaminated L. monocytogenes for the risk analysis of pork processing plant using these primers.

• Journal of the Society of Naval Architects of Korea
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• v.47 no.5
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• pp.743-749
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• 2010

Multi-nozzle spray painting procedure of the inorganic zinc shop primer was established in order to obtain uniform film thickness. The shop primer paint prevents the corrosion of steel block during shipbuilding. When the dry film thickness of shop primer is insufficient, rust will be generated on the steel block. Otherwise, thick coating of shop primer may be a problem of weld defect. So, it is important to obtain the uniform film thickness of shop primer. The uniformity of dry film thickness is affected by spray speed, distance from spray gun to target surface and overlapping span of spray path. In order to uniformly maintain coating thickness of shop primer, the coating procedure was established based on the correlation of shop primer spray variables.

• The korean journal of orthodontics
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• v.32 no.4 s.93
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• pp.293-300
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• 2002

The purpose of this study was to evaluate the clinical effectiveness of hydrophilic primer, which claim to retain adequate bond strength on moistened enamel resulting from moisture or saliva contamination, by comparing the shear bond strength and adhesive failure patterns of brackets bonded using hydrophilic primer and conventional hydrophobic primer. Brackets were bonded to human premolars embedded in metal cylinders utilizing light cured adhesive, primed with either a hydrophilic primer(Transbond fm primer) or a conventional hydrophobic primer(Transbond XT primer). Each sample was exposed to varying degrees of artificial saliva contamination during the priming process. The shear bond strength was measured using a universal testing machine, and the adhesive failure patterns after debonding were visually examined by strereomicroscope and assessed using the adhesive remnant index(ARI). The results were as follows 1. In dry conditions, no significant differences in shear bond strength between Transbond W and Transbond XT primers were found. 2. Transbond MIP primer exhibited a significantly higher shear bond strength than Transbond XT primer in saliva-contaminated conditions, regardless of the degree of contamination. 3. When contaminated with one coat of saliva, Transbond MIP primer did not exhibit significant differences in shear bond strength compared to the dry condition. When contaminated with two coats of saliva, Transbond MIP primer exhibited a singnificantly lower shear bond strength compared to the dry condition. 4. The adhesive remnant index of the adhesive failure pattern had a tendency to decrease, as the degree of saliva contamination increased. Bracket-adhesive interface failure was observed in more than half of the saliva contaminated samples utilizing Transbond MIP primer, whereas the bond failure sites of the Transbond XT primer samples occurred almost exclusively at the adhesive-enamel interface in saliva-contaminated conditions. The results of this study suggest that in cases where moisture control is difficult, Transbond MIP primer is an effective alternative to conventional hydrophobic primers.

• The korean journal of orthodontics
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• v.34 no.4 s.105
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• pp.325-332
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• 2004

A self-etching primer that combines the etchant and primer in one chemical compound saves time and should be mote cost-effective to the clinician and patient. The purpose of this study was to evaluate the clinical effectiveness of a self-etching primer by measuring shear bond strengths according to various conditions and observing adhesive failure patterns. For this Investigation, 120 upper and lower premolars extracted for orthodontic purposes were used and randomly divided into six groups of twenty teeth each. Human premolars were embedded in a metal cylinder with orthodontic resin. Metal brackets and ceramic brackets were bonded with XT primer and self-etching primer by means of XT adhesive. Upon curing, plasma arc light and visible light were used. After bonding, the shear bond strength was tested by Instron universal testing machine, and the amount of residual adhesive that remained on the tooth after debonding was measured by stereoscope and assessed with an adhesive remnant index. The results were as fellows: 1. When brackets were bonded, if other conditions remained the same, there was no significant difference in shear bond strength due to the type of primer - either self-etching primer or XT primer. 2. When metal brackets were bonded, there was no significant difference in shear bond strength according to the source of light - plasma arc light or visible light - and type of primer. 3. There was a very significant difference in shear bond strength according to the type of brackets - metal or ceramic brackets. The shear bond strength of ceramic brackets was stronger than metal brackets. 4. When the adhesive failure patterns of metal brackets bonded with self-etching primer were observed by using the adhesive remnant index, the bond failure of the metal bracket occurred more frequently at the bracket-adhesive. The failure of the ceramic bracket, however, occurred more frequently at the enamel-adhesive interface. The adhesive failure patterns of metal brackets bonded with XT primer observed the same patterns. The above results suggest that self-etching primer can be clinically useful for bonding the brackets without fear of a decrease in shear bond strength.

• The korean journal of orthodontics
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• v.37 no.4
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• pp.283-292
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• 2007

The purpose of this study was to evaluate the clinical usefulness of 4 self etching primers by measuring the shear bond strength of orthodontic brackets and examining the failure pattern of bracket-tooth interfaces. Methods: Seventy-five, defect-free, premolars were randomly assigned into five groups: control group (37% phosphoric acid + Transbond XT primer) and self etching primer treated groups (Transbond Plus self etching primer, Unifil bond, Clearfil SE bond, and Adhese). The shear bond strength was measured with a universal testing machine and the amount of residual adhesive remaining on the brackets after debonding was assessed by the adhesive remnant index (ARI). Results: The results showed that the groups conditioned with self etching primer had significantly lower shear bond strength than the control group (p < 0.05), although clinically acceptable. However, there were no significant differences in shear bond strength among the self etching primer groups (p > 0.05). Evaluation of the ARI scores indicated there was less resin remnant on the teeth in the groups conditioned with self etching primers, although not statistically significant. Conclusion: The results of this study suggest that all four of the self etching primers have shown acceptable bond strength for clinical use.

• Korean Journal of Microbiology
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• v.44 no.2
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• pp.164-167
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• 2008

Recently, rolling circle amplification (RCA) technique has been widely focused in the field of gene amplification just like PCR method. We have developed RCA-mer, which is a web-based program searching for primer candidates from a given sequence. It can be applied to find primer lists in DNA amplification experiment based on RCA method. The RCA-mer compares 8-mer primer lists with user's input sequence such as vector, mitochondria, and microbial genome sequence. After calculating 8-mers existences in a given sequence, it displays matched and no-matched primer lists with their GC-contents. In addition to it, RCA-mer can search the existence of 8-mer primer lists in two sequences whether they are co-existed or not. Users can apply candidate primer lists to their researches which use RCA techniques.

• Korean Journal of Oriental Medicine
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• v.13 no.1 s.19
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• pp.147-152
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• 2007

As a result to amplifying 12 samples of 'Sok-dan' through an random amplified polymorphic DNA (RAPD) method using eighteen DEC and URP primers, distinct band forms enabling discrimination of Phlomus umbrosa and Dipsacus asperoides were observable in the UBC 320 primer, UBC 367 primer, UBC 385 primer, UBC 414 primer, UBC 423 primer, URP 3 primer, URP 5 primer and URP 9 primer. The polymorph result amplified with a random primer was evaluated through Gelcompar II, showing a result dividable into two groups. The divided groups were the dried sample group of Dipsacus asperoides and the group of Phlomis umbrosa. In order to recognize the distinction between Dipsaci Radix types, the genetic variation of 'Sok-dan' produced domestically and imported was evaluated through RAPD, and the potential to distinguish these in forms of dried medicine was identified, presenting a method to authentification of Phlomis umbrosa and Dispacus asperoides.