• 대한화학회지
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• 제42권5호
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• pp.506-511
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• 1998

생체 내에서 양이온을 가지는 폴리아민류인 스퍼민이 DNA에 결합할 경우 안정화도를 증가시킴과 동시에 구조적인 변환(B형태→Z형태 변환)을 유발하는 것으로 알려져 있다. 그러나, 스퍼민의 분광학적 비활성 때문에 DNA에 대한 정확한 결합 위치를 분광학적으로 결정하는 것은 불가능했으므로 그 결합메커니즘에 관한 구체적인 보고는 없다. 본 실험에서는 스퍼민에 대한 탐침 작용을 할 수 있는 물질로 분광 활성이 있으며 결합 자리를 잘 알고 있는 DAPI를 사용하였다. 합성 DNA에서 스퍼민의 결합 자리와 염기 선택성을 연구한 결과, 스퍼민의 농도가 커질수록 아데닌-티민 염기쌍이 교대로 나선을 이루는 $poly[d(A-T)_{2}]$ 에서는 스퍼민이 DNA의 작은 홈 주위의 인산기 뼈대에 걸쳐지면 DAPI의 소수성 환경을 증가시켜 형광스펙트럼의 세기를 급격히 증가시킨다. 구아닌-시토신 염기쌍이 교대로 반복되며 만들어진 $poly[d(G-C)_{2}]$에서는 스퍼민이 DNA의 큰 홈 속에 결합하면서 큰 홈에 걸쳐 있으면서 부분적으로 염기쌍사이에 삽입된 DAPI를 밀어내는 것으로 생각할 수 있다. 이 두 가지의 경우에 스퍼민이 염기쌍에 대해 특별한 선택성을 보이지 않았다.

• Bulletin of the Korean Chemical Society
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• 제34권7호
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• pp.2117-2124
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• 2013

The binding properties and sequence selectivities of ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ (bip = 4,4'-biphenylene (imidazo [4,4-f][1,10]phenanthroline) complexes with $poly[d(A-T)_2]$ and $poly[d(G-C)_2]$ were investigated using conventional spectroscopic methods. When bound to $poly[d(A-T)_2]$, a large positive circular dichroism (CD) spectrum was induced in absorption region of the bridging moiety for both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes, which suggested that the bridging moiety sits in the minor groove of the polynucleotide. As luminescence intensity increased, decay times became longer and complexes were well-protected from the negatively charged iodide quencher compared to that in the absence of $poly[d(A-T)_2]$. These luminescence measurements indicated that Ru(II) enantiomers were in a less polar environment compared to that in water and supported by minor groove binding. An angle of $45^{\circ}$ between the molecular plane of the bridging moiety of the ${\Delta}{\Delta}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex and the local DNA helix axis calculated from reduced linear dichroism ($LD^r$) spectrum further supported the minor groove binding mode. In the case of ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex, this angle was $55^{\circ}$, suggesting a tilt of DNA stem near the binding site and bridging moiety sit in the minor groove of the $poly[d(A-T)_2]$. In contrast, neither ${\Delta}{\Delta}$-nor ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complex produced significant CD or $LD^r$ signal in the absorption region of the bridging moiety. Luminescence measurements revealed that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes were partially accessible to the $I^-$ quencher. Furthermore, decay times became shorter when bis-Ru(II) complexes bound to $poly[d(G-C)_2]$. These observations suggest that both the ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ complexes bind at the surface of $poly[d(G-C)_2]$, probably electrostatically to phosphate group. The results indicate that ${\Delta}{\Delta}$- and ${\Lambda}{\Lambda}-[{\mu}-Ru_2(phen)_4(bip)]^{4+}$ are able to discriminate between AT and GC base pairs.

• Bulletin of the Korean Chemical Society
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• 제30권11호
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• pp.2815-2818
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• 2009

• Bulletin of the Korean Chemical Society
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• 제26권4호
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• pp.537-542
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• 2005

It was proposed that Ru(II)[(1,10-phenanthroline)$_2$dipyrido[3,2-a:2',3'-c]phenazine ([Ru(phen)$_2$DPPZ]$^{2+}$)complexes and 4',6-diamidino-2-phenylindole (DAPI) simultaneously bind to poly[d(A-T)$_2$] (Biophysics. J. 2003, 85, 3865). Förster type resonance energy transfer from excited DAPI to [Ru(phen)2DPPZ]$^{2+}$ complexes was observed. In this study, we synthesized $\Delta$- and $\wedge$-[Ru(phenanthroline)$_2$dipyrido[3,2-a:2’3’c]6-azaphenazine] ([Ru(phen)$_2$DPAPZ]$^{2+}$) at which the DNA intercalating ligand DPPZ was replaced and we studied its binding properties to poly[d(A-T)$_2$] in the presence and absence of DAPI using polarized spectroscopy and fluorescence techniques. All the spectroscopic properties of the [Ru(phen)$_2$DPAPZ]$^{2+}$-poly[d(A-T)$_2$] complex were the same in the presence and absence of DAPI that blocks the minor groove of polynucleotide, suggesting both $\Delta$- and $\wedge$-[Ru(phen)$_2$DPAPZ]$^{2+}$ complexes are located at the major groove of poly[d(A-T)2]. On the other hand, in contrast with [Ru(phen)$_2$DPPZ]$^{2+}$, both $\Delta$- and $\wedge$-[Ru(phen)$_2$DPAPZ]$^{2+}$ exhibited almost twice the efficiency in the fluorescence quenching of DAPI that binds at the minor groove of poly[d(A-T)$_2$]. This observation indicates that the efficiency of the Förster type resonance energy transfer can be controlled by a small change in the chemical structure of the intercalated ligand.

• 한국자기공명학회논문지
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• 제8권2호
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• pp.96-107
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• 2004

We prepared two oligonucleotides containing same base pairing, but different base sequence in the middle region, d(CGAATTCG) and d(CGTATACG). NMR and UV absorbance data represented that such variation in base sequence could cause a significant difference in melting temperature and dynamics between d(CGAATTCG)$_2$ and d(CGTATACG)$_2$ duplexes, which are regarded to be associated with the stacked structure and the width of the minor groove of them. The latter showed poor stability compared to the former, because of poor stacking of bases. And berenil could bind to the minor groove of d(CGAATTCG)$_2$ which is relatively narrow, more strongly than d(CGTATACG)$_2$ and this gave rise to large improvement in thermal stability of the d(CGAATTCG)$_2$ duplex, compared to d(CGTATACG)$_2$.

• 대한화학회지
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• 제42권4호
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• pp.391-397
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• 1998

퓨란 고리를 포함하는 bis-furan lexitropsin에서, DNA minor groove의 염기쌍과 결합하는 중요 부분인 퓨란의 기하학적 구조를 반경험적 방법(MNDO)과 ab initio(Hartree-Fock) 방법으로 최적화 시켰다. 최적화된 구조에 대해 6-31G와 $6-31G^{\ast}$ basis set을 사용하여 전자적 구조와 양성자 친화도를 구하였다. 아울러 퓨란의 양성자 친화도에 미치는 치환기 효과를 알아보기 위해 전자를 주는 기와 전자를 끄는 기를 갖는 여러 치환 퓨란에 대해 양성자 친화도를 조사하였다. 그 결과 전자를 주는 기는 퓨란의 양성자 친화도를 증가시키는 반면 전자를 끄는 기는 양성자 친화도를 감소시켰으며, 이 결과 치환 퓨란의 산소 원자의 atomic charge와 전자밀도로 설명할 수 있었다

• 한국전기전자재료학회논문지
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• 제17권7호
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• pp.729-737
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• 2004

In this paper, a DNA chip with a microelectrode array was fabricated using microfabrication technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5 end were immobilized on the gold electrodes by DNA arrayer. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 concentrated at the electrode surface through association with formed hybrid. It suggested that this DNA chip could recognize the sequence specific genes.

• 대한전기학회:학술대회논문집
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• 대한전기학회 2004년도 하계학술대회 논문집 C
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• pp.2125-2127
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• 2004

In this paper, a DNA chip with a microelectrode array was fabricated using microfabrication technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5 end were immobilized on the gold electrodes by DNA arrayer. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 concentrated at the electrode surface through association with formed hybrid. It suggested that this DNA chip could recognize the sequence specific genes.

• 한국전기전자재료학회논문지
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• 제18권6호
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• pp.560-570
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• 2005

In this paper, a microelectrode away DNA chip was fabricated on glass slide using photolithography technology. Several probe DNAs consisting of mercaptohexyl moiety at their 5' end were immobilized on the gold electrodes by DNA arrayer utilizing the affinity between gold and sulfu. Then target DNAs were hybridized and reacted with Hoechst 33258, which is a DNA minor groove binder and electrochemically active dye. Cyclic voltammetry in 5mA ferricyanide/ferrocyanide solution at 100 mV/s confirmed the immobilization of probe DNA on the gold electrodes. Linear sweep voltammetry or cyclic voltammetry showed a difference between target DNA and control DNA in the anodic peak current values. It was derived from Hoechst 33258 concentrated at the electrode surface through association with formed hybrid. It suggested that this DNA chip could recognize the sequence specific genes. It suggested that multichannel electrochemical DNA microarray is useful to develop a portable device for clinical gene diagnostic system.

• 대한화학회지
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• 제39권7호
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• pp.493-500
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• 1995

옥사졸 고리를 포함하는 lexitropsin에서, DNA minor groove의 염기쌍(G-C sequence)과 결합하는 부분인 옥사졸의 최적화된 기하학적 구조를 MM+ 및 ab initio(Hartree-Fock) 계산을 통해 밝혔다. 최적화딘 구조에 대해 6-31G 및 $6-31G^{\ast}$ basis set를 사용하여 양성자 친화도와 전자적 구조를 계산하였다. 아울러 옥사졸의 양성자 친화도에 미치는 치환기 효과를 알아보기 위해 전자를 주는 기와 전자를 끄는 기를 갖는 여러 치환 옥사졸에 대해 양성자 친화도를 조사하였다. 그 결과 전자를 주는 기는 옥사졸의 양성자 친화도를 증가시키는 반면 전자를 끄는 기는 양성자 친화도를 감소시킴을 알았으며, 이 결과를 치환 옥사졸의 산소의 atomic charge와 전자밀도로 설명할 수 있었다.