• Bulletin of the Korean Chemical Society
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• v.21 no.10
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• pp.1052-1054
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• 2000

Binding geometries of $[Ru(II)(110-phenanthroline)_2L]^2+$, complexes (where L = dipyrido [3,2-a:2',3'-c]phena-zine (DPPZ) or benzodipyrido[3,2-a:2',3'-c] phenazine (BDPPZ)) to poly(dG)${\cdot}$poly(dC)${\cdot}$poly(dC) + triplex DNA (CGC + triplex) has been investigated by linear dichroism and normal absorption spectroscopy. Analysis of the linear dichroism for the CGC+ triplex and $[Ru(II)(phen)_2BDPPZ]^2+$ complex indicates that the extended ligand of the metal complex lie perpendicular to the polynucleotide helix axis. Together with strong hypochromism and red shift in the interligand absorption region, we concluded that the extended BDPPZ or DPPZ ligand in-tercalated between the bases of polynucleotide. The spectral properties of the metal complexes bound to CGC+ triplex are similar to those bound to $poly(dA)[poly(dT)]^2$ triplex (Choi et al., Biochemistry 1997, 36, 214), sug-gesting that the metal complex is located in the minor groove of the CGC+ triplex.

• Journal of Microbiology and Biotechnology
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• v.25 no.5
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• pp.745-752
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• 2015

Tuberculosis (TB) is the most common mycobacterial infection in developing countries, requiring a rapid, accurate, and well-differentiated detection/diagnosis. For the rapid detection and discrimination of Mycobacterium tuberculosis complex (MTC) from non-tuberculous mycobacteria (NTM), a novel, simple, and primer-combined single-step multiplex PCR using three primer pairs (6110F-6110R, 1081F-1081R, and 23SF-23SR; annealing on each of IS6110, IS1081, and 23S rDNA targets), hereafter referred to as a triplex PCR, has been developed and evaluated. The expected product for IS6110 is 416 bp, for IS1081 is 300 bp, and for 23S rDNA is 206 bp by single PCR, which was used to verify the specificity of primers and the identity of MTC using DNA extracted from the M. tuberculosis H37Rv reference strain (ATCC, USA) and other mycobacteria other than tuberculosis (MOTT) templates. The triplex PCR assay showed 100% specificity and 96% sensitivity; the limit of detection for mycobacteria was ~100 fg; and it failed to amplify any target from DNA of MOTT (50 samples tested). Of 307 blinded clinical samples, overall 205 positive M. tuberculosis samples were detected by single PCR, 142 by conventional culture, and 90 by AFB smear methods. Remarkably, the triplex PCR could subsequently detect 55 positive M. tuberculosis from 165 culture-negative and 115 from 217 AFB smear-negative samples. The triplex PCR, targeting three regions in the M. tuberculosis genome, has proved to be an efficient tool for increasing positive detection/discrimination of this bacterium from clinical samples.

• BMB Reports
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• v.30 no.6
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• pp.426-430
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• 1997

The helical periodicity of the triple-stranded $(dT)_n{\cdot}(dA)_n{\cdot}(dT)_n$ sequence was determined by measuring gel-mobilities of bent DNA fragments containing the sequence. In the bent DNA fragments, a $GA_{22}G$ $CT_{22}C$ sequence was located between two bent DNA loci composed of six $A_{6}{\cdot}T_{6}$ repeats. and the DNA length between the bent DNA loci was varied by 1 base pair over a full helical turn. The gel mobility of each bent DNA fragment reflected the overall extent of DNA bending and varied with the DNA length between the two bent loci. Mobilities of the bent DNA fragments in 5% polyacrylamide gel were measured after preincubating the DNA fragments both in the presence and absence of $CT_{22}C$ oligonucleotide. By comparing the bent DNA fragments containing an intermolecular triplex structure with those of a genuine duplex structure in the gel mobilities, the helical periodicity of the $T_n{\cdot}A_n{\cdot}T_n$ triplex DNA was determined to be $11.5({\pm}0.3)bp/turn$.

• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2691-2696
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• 2009

Effects of representative group II and transition metal ions on the stability of the $poly(dA){\cdot}[poly(dT)]_2$ triplex were investigated by the van’t Hoff plot constructed from a thermal melting curve. The transition, $poly(dA){\cdot}[poly(dT)]_2\;{\rightarrow}\;poly(dA){\cdot}poly(dT)\;+\;poly(dT)$, was non-spontaneous with a positive Gibb’s free energy, endothermic (${\Delta}H^{\circ}$ > 0), and had a favorable entropy change (${\Delta}S^{\circ}$ > 0), as seen from the negative slope and positive y-intercept in the van’t Hoff plot. Therefore, the transition is driven by entropy change. The $Mg^{2+}$ ion was the most effective at stabilization of the triplex, with the effect decreasing in the order of $Mg^{2+}\;>\;Ca^{2+}\;>\;Sr^{2+}\;>\;Ba^{2+}$. A similar stabilization effect was found for the duplex to single strand transition: $poly(dA){\cdot}poly(dT)\;+\;poly(dT)\;→\;poly(dA)\;+\;2poly(dT)$, with a larger positive free energy. The transition metal ions, namely $Ni_{2+},\;Cu_{2+},\;and\;Zn_{2+}$, did not exhibit any effect on triplex stabilization, while showing little effect on duplex stabilization. The different effects on triplex stabilization between group II metal ions and the transition metal ions may be attributed to their difference in binding to DNA; transition metals are known to coordinate with DNA components, including phosphate groups, while group II metal ions conceivably bind DNA via electrostatic interactions. The $Cd_{2+}$ ion was an exception, effectively stabilizing the triplex and melting temperature of the third strand dissociation was higher than that observed in the presence of $Mg_{2+}$, even though it is in the same group with $Zn_{2+}$. The detailed behavior of the $Cd_{2+}$ ion is currently under investigation.

• Bulletin of the Korean Chemical Society
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• v.18 no.5
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• pp.528-534
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• 1997

The conformation and stabilization effects of acridine derivatives 9-aminoacridine, an acridine with an aminoalkyl side chain, bis acridine (two acridines linked by an aminoalkyl side chain), and proflavin in the triplex helical poly(dA)·[poly(dT)]2 were investigated by optical spectroscopies. Based on the negative LD and weak positive CD in the acridine absorption wavelength region, we concluded that the acridine moiety of all derivatives are intercalated. We also examined the melting temperatures. Of all the compounds examined, the acridine with an amino alkyl side chain had the strongest effect on the stabilization of the third strand of a poly (dA)·[poly(dT)]2 triplex. The role of the side chain, based on this observation, is discussed.

• Korean Journal of Microbiology
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• v.34 no.4
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• pp.231-235
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• 1998

We have introduced a genetic assay to study the existence of intramolecular triplexes in Escherichia coli. A plasmid containing the gene that encodes a temperature-sensitive EcoRI methylase was cotransformed with different plasmids containing inserts, $(G)_9AATTC(G)_9$ and $(GAA)_9TTC(GAA)_8$, that are able to form intramolecular triplexes in vitro. Inhibition of methylation in vivo was found for $(G)_9AATTC(G)_9$ and $(GAA)_9TTC(GAA)_8$, suggesting that the pur pyr sequences adopt unusual strucures in E. coli. In addition, experiments using two dimensional gel electrophoresis confirmed that intramolecular triplexes are formed for the pur pyr sequences under negative supercoiling. These results demonstrate the existence of intramolecular triplexes in E. coli.

• Journal of the Korean Magnetic Resonance Society
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• v.10 no.2
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• pp.175-187
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• 2006

Binding interactions between a positively charged porphyrin derivative TMAP(meso-tetra(p-trimethylanilinium-4-yl)porphyrin) and triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, as well as double helical $(dA)_{12}{\cdot}(dT)_{12}$ have been studied with NMR, UV and CD spectroscopy to obtain the detailed information about the binding mode and binding site. UV melting studies showed both DNA duplex and triple helix represented very similar UV absorption patterns upon binding TMAP, but the presence of third strand of triple helical $(dT)_{12}{\cdot}(dA)_{12}{\cdot}(dT)_{12}$, inhibited improvement in thermal stability in terms of melting temperature, $T_m$. In addition, the TMAP molecule is thought to bind to the major groove, according to CD and NMR data. But absence of the clear isosbestic point in UV absorption spectra represented that binding of TMAP to DNA duplex as well as DNA triplex did not show a single binding mode, rather complex binding modes.

• Journal of Oral Medicine and Pain
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• v.24 no.3
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• pp.335-345
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• 1999

법의학적 개인식별 및 친생자 감정시 여러 개의 single tandem repeats(STR) 유전좌위 검색이 필요하다. 그 이유는 STR 유전좌위는 대립유전자 수가 적고 이형접합도가 낮아 서로 다른 개체간에도 동일한 유전좌위를 가질 확률이 높기 때문에 개인식별에 대한 기여도가 떨어지게 된다. 따라서 여러 개의 다양한 STR 유전좌위들을 동시에 분석함으로써 우연적으로 개체간에 유전자형이 일치할 가능성을 낮추어야 감정의 신뢰성을 높일 수 있으며 이에는 각 STR 유전좌위에 대한 유전좌위의 분포가 인종별, 지역별로 달라 이에 대한 유전자분포를 구하는 것이 선행조건이다. 이에 본 연구에서는 법의학적 개인식별 및 친자감정시 기초자료로 활용하기 위하여 서로 혈연관계가 없는 201명의 한국인 혈액에서 DNA를 추출하여 STR 유전좌위증 human coagulation factor XIII A subunit gene(F13A0l Locus), human c-fes/fps proto-oncogene(FESFPS Locus), human von Willebrand factor gene (vWA Locus)등 FFv Triplex 유전자를 중합효소반응에 의하여 동시에 증폭하고, 폴리아크릴아마이드겔을 이용한 전기영동 및 질산은 염색을 시행한 후 FFv Triplex유전자의 유전자형 및 대립유전자 빈도 등을 분석하여 다음과 같은 결과를 얻었다. (1) F13A01유전자는 5개의 대립유전자, 12개의 유전자형을 검출하였으며, 이형접합도는 60.7%로 나타났고 대립유전자 및 유전자빈도는 3.2, 4, 5, 6, 16 대립유전자에서 각각 0.34 3, 0.114, 0.062, 0.475, 0.005로 나타났으며, 대립유전자 7, 8, 9, 10, 11, 12, 13, 14, 15는 검출되지 않았다. (2) F13A01 대립유전자다양성 (allelic diversity value)은 0.641, 개인식별력(PD)은 0.814를 보였으며 대립유전자다양성 및 이형접합도가 다른 민족과 비교할 때 다소 낮았다. (3) FESFPS유전자는 8개 대립유전자 모두 나타났으며, 15개의 유전자형을 검출하였으며, 이형접합도는 66.7%로 나타났고 대립유전자 및 유전자빈도는 7, 8, 9, 10, 11, 11, 12, 13, 14 대립유전자에서 각각 0.002, 0.002, 0.005, 0.032, 0.507, 0.264, 0.197, 0.007로 나나났다. (4) FESFPS 대립유전자다양성(allelic diversity value)은 0.641, 개인식별력(PD)은 0.804를 보였다. (5) vWA유전자는 9개의 대립유전자, 23개의 유전자형을 검출하였으며, 이형접합도는 80.1%로 나타났고 대립유전자 및 유전자 빈도는 11, 12, 14, 15, 16, 17, 18, 19, 20 대립유전자 에서 각각 0.002, 0.002, 0.219, 0.032, 0.187, 0.279, 0.189, 0.072, 0.017로 나타났으며, 대립 유전자 13, 21는 검출되지 않았다. (6) vWA 대립유전자다양성(allelic diversity value)은 0.799, 개인식별력(PD)은 0.924로 매우 높게 나타냈다.

• Journal of Microbiology and Biotechnology
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• v.10 no.6
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• pp.873-876
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• 2000

Short tendem repeat (STR) loci have been used in the field of forensic science. There are literally hundreds of STR systems which have been mapped throughout the human genome. These STR loci are found in almost every chromosome in the genome. They may be amplified using a variety of PCR primers. In this study, a DNA genotyping system based on the multiplex amplification of highly polymorphic STR loci was developed. Three STR loci with nonoverlapping allele size ranges have been utilized in the multiplex amplification including the Neurotensin receptor gene, D21S11, and Human tyrosine hydroxylase gene. The optimal condition for triplex PCr was obtained in a solution with a total volume of $25{\mu}l$ containing 2.0 U of Taq polymerase, 3 mM of $MgCl_2$, $300{\mu}M$ of dNTP, 10 pmole of each primer set, an annealing temperature of $62^{\circ}C$, and 35 cycles. The optimized condition was successfully employed in a family paternity test.

• Journal of Oral Medicine and Pain
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• v.24 no.2
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• pp.219-234
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• 1999

치석에는 박리상피세포, 백혈구 등이 포함되어 있어 이들의 핵 내에 있는 DNA의 유전자형을 찾아내 개인식별을 할 수 있을 것으로 추정된다. 본 연구에서는 치석만으로 개인식별이 가능한지를 알아보고자 40명으로부터 채취한 치석을 증류수에 세척한 군과 세척하지 않은 군으로 나누어 DNA를 추출하고 중합효소연쇄반응법을 이용하여 증폭절편다형(AMP-FLPs)을 실시한 후 성별검사를 위한 X-Y homologous amelogenin gene과 유전자지문검사를 위한 STR유전좌위 LPL, F13B, Triplex(F13A01, FESFPS, vWA) 등 6개의 유전자를 검색하여 - X-Y homologous amelogenin gene과 LPL, F13B는 각각 증폭하였으며 F13A01, FESFPS, vWA 세 유전자는 동시에 증폭하였음 - 다음과 같은 결과를 얻었다. 1) X-Y homologous amelogenin gene 검색으로 세척군에서 27개의 검체 중 8개, 비세척군에서 13개 중 11개에서 성별검사가 가능하였다. 2) LPL유전자는 세척군, 비세척군에서 각각 27개 검체중 2개, 13개 검체 중 5개가 검색되었으며 3개의 대립유전자(10, 11, 12)와 4개의 유전자형 (10-10, 10-11, 10-12, 11-12)이 나타났다. 3) F13B유전자는 세척군, 비세척군에서 각각 27개 검체 중 1개, 13개 검체 중 4개가 검색되었으며 2개의 대립유전자(9, 10)와 2개의 유전자형(9-10, 10-10)을 관찰하였다. 4) F13A01유전자는 비세척군에서만 13개 검체 중 3개가 검색되었고 3개의 대립유전자(3.2, 4, 6)와 3개의 유전자형(3.2-3.2, 4-5, 4-6)을 관찰하였고, 세척군에서는 나타나지 않았다. 5) FESFPS유전자는 비세척군에서만 13개 검체 중 1개가 검색되었고 유전자 형은 11-12로 나타났다. 6) vWA유전자는 세척군, 비세척군에서 각각 1개씩 검색되었으며, 3개의 대립유전자형(14, 16, 17)와 2개의 유전자형(14-16, 14-17)을 관찰하였다. 이상의 결과를 종합해 볼 때, 치석은 X-Y homologous amelogenin gene증폭을 통한 성별검사와 단일 STR유전좌위 증폭을 통한 유전자지문형 검사에는 유용하나 복합 STR유전좌위의 검색에는 부적합한 것으로 나타났으며 법의학적시료로 응용이 가능한 것으로 사료된다.