• Bulletin of the Korean Chemical Society
• /
• 제28권12호
• /
• pp.2203-2208
• /
• 2007

Three possible binding modes of cationic meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) to d[(GCATATATGC)2] duplex were investigated by the molecular dynamics (MD) simulation. Among the three binding modes namely, “along the groove”, “across the groove” and “face on the groove”, the “across the groove” model exhibited the largest negative binding free energy and the DNA backbone remained as the B form. In this model, the molecular plain of the TMPyP tilts 45o with respect to the DNA helix axis and is largely exposed to the solvent. TMPyP was stabilized mainly by the interaction between the positively charged neighboring pyridinium moieties of TMPyP and negatively charged phosphate groups of DNA. The result obtained in this work by MD and the report (Jin, B. et al., J. Am. Chem. Soc. 2005, 127, 2417.) that the spectral properties of poly[d(A-T)2] bound TMPyP in the presence and absence of the minor groove binding drug 4',6- diamidino-2-phenylindole are similar, we propose that TMPyP bind across the minor groove of the AT rich- DNA.

• Bulletin of the Korean Chemical Society
• /
• 제34권10호
• /
• pp.2895-2899
• /
• 2013

Direction of intercalation to DNA of the planar dipyrido[3,2-a:2',3'-c]phenazine ligands (dppz) of a bis-Ru(II) complex namely, $[Ru(1,10-phenanthroline)_2dipyrido[3,2-a:2^{\prime},3^{\prime}-c]phenazine]^{2+}$ linkered by a 1,3-bis(4-pyridyl)propane, was investigated by probing the behavior of 4',6-diamidino-2-phenylindole (DAPI) that bound deep in the minor groove. Bis-intercalation of DPPZ resulted in a little blue shift and hyperchromism in DAPI absorption band, and a large decrease in DAPI fluorescence intensity which accompined by an increase in the dppz emission intensity. Diminishing the intenisty of the positive induced circular dichroism (CD) and linear dichroism (LD) were also observed. These spectral changes indicated that insertion of dppz ligand caused the change of the binding mode of DAPI, which probably moved to the exterior of DNA from the minor groove and interacted with the phospghate groups of DNA by electrostatic interaction. At the surface of DNA, DAPI binds at the phosphate groups of DNA by electrostatic attraction. Consequently, this observation indicated that the dppz ligand intercalated from the minor groove.

• 대한화학회지
• /
• 제42권1호
• /
• pp.1-8
• /
• 1998

티아졸 고리를 포함하는 lexitroposin에서, DNA minor groove의 염기쌍과 결합하는 부분인 티아졸의 분자정전기전위를 ab initio계산을 통해 구하였으며 protonate된 티아졸의 두 가지 가능한 형태에 대해 MNDO 및 ab initio방법으로 기하학적 구조를 최적화 하였다. 최적화된 구조에 대해 6-31G및 6-31G* basis set을 사용하여 양성자 친화도를 구하였으며 아울러 티아졸의 양성자 친화도에 미치는 치환기 효과를 알아보기 위해 전자를 주는 기와 전자를 끄는 기를 치환시킨 여러 치환 치아졸에 대해 양성자 친화도를 조사하였다. 그 결과 티아졸의 질소 원자가 DNA minor groove 쪽으로 배향되고 전자를 주는 기가 치환될 때 양성자 친화도가 증가됨을 알 수 있었다.

• 대한화학회지
• /
• 제51권1호
• /
• pp.7-13
• /
• 2007

옥사졸 고리를 포함하는 lexitropsin에서, DNA minor groove의 구아닌-시토신 염기쌍의 구아닌과 수소결합을 형성하는데 중요 역할을 하는 옥사졸에 대해, 양성자화 될 때 가능한 두 가지 형태에 대해 DFT 계산을 통해 구조를 최적화시켰다. 최적화된 구조에 대해 B3LYP/6-31G* 수준에서 양성자 친화도를 계산하였다. 그 결과 옥사졸의 가능한 두 가지 형태 가운데 옥사졸의 질소 원자가 DNA minor groove 쪽으로 배향된 구조가 산소 원자가 minor groove 쪽으로 배향된 구조보다 양성자 친화도가 더 큼을 알 수 있었으며, 분자정전기 전위로 확인할 수 있었다. 아울러 양성자 친화도에 미치는 치환기 효과를 알아보기 위하여 여러 전자 주는 기와 전자 받는 기를 치환시켜 치환기 성질에 따른 양성자 친화도를 조사하였으며, 전자를 받는 기 보다 전자를 주는 기가 치환 되었을 때 양성자 친화도가 증가함을 알았다.

• Biomolecules & Therapeutics
• /
• 제29권5호
• /
• pp.562-570
• /
• 2021

Topoisomerase IIα has been a representative anti-cancer target for decades thanks to its functional necessity in highly proliferative cancer cells. As type of topoisomerase IIα targeting drugs, topoisomerase II poisons are frequently in clinical usage. However, topoisomerase II poisons result in crucial consequences resulted from mechanistically induced DNA toxicity. For this reason, it is needed to develop catalytic inhibitors of topoisomerase IIα through the alternative mechanism of enzymatic regulation. As a catalytic inhibitor of topoisomerase IIα, AK-I-191 was previously reported for its enzyme inhibitory activity. In this study, we clarified the mechanism of AK-I-191 and conducted various types of spectroscopic and biological evaluations for deeper understanding of its mechanism of action. Conclusively, AK-I-191 represented potent topoisomerase IIα inhibitory activity through binding to minor groove of DNA double helix and showed synergistic effects with tamoxifen in antiproliferative activity.

• KIEE International Transactions on Electrophysics and Applications
• /
• 제4C권4호
• /
• pp.145-148
• /
• 2004

In this study, 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 a 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 and concentrated at the electrode surface through association with the formed hybrid. This suggested that this DNA chip could recognize the sequence specific genes.

• 약학회지
• /
• 제54권1호
• /
• pp.62-66
• /
• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• 약학회지
• /
• 제54권1호
• /
• pp.67-74
• /
• 2010

Some of the benzopyrene (BP)-DNA adduct are known to build intercalated motif between flanking base pairs in damaged DNA depending on the structural condition. The size of benzopyrene itself is definitely not comparable with any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular dynamics simulation based on the theory of molecular mechanics. The specific consequences about the structural properties of the intercalated structures and benzopyrene motif in minor groove of the double helix are deduced after 5 ns simulation time.

• 한국자기공명학회논문지
• /
• 제8권2호
• /
• pp.96-107
• /
• 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)$_2$.

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