Study on the interaction between 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile and DNA by molecular spectra.
The binding geometry of a heterocyclic compound, 4-(2-diethylamino-ethylamino)-8-oxo-8H-acenaphtho[1,2-b]pyrrole-9-carbonitrile (A1) to CT DNA was studied by molecular spectroscopy. Deduced from SYBR Green-DNA melt curve, UV-vis spectroscopy, and fluorescence studies, there were two different interaction mechanisms involved in the whole interaction process depending on the R-value (R, the molar ratio of A1 to CT DNA base pairs). The value R = 0.20 was the turning point. The induced circular dichroism (ICD) spectra of A1 complexed with CT DNA, poly[(G-C)2] and poly[(A-T)2] showed when R < or = 0.20, A1 intercalated into CT DNA and the intercalation orientation of A1 to the dyad axis of DNA double-helix was heterogeneous. When R > 0.20, stacking of A1 on surface helix of DNA occurred driven by the protonation of amidogen group in the N,N-diethyldiamine substitution of A1, which was illustrated by the changes of A1-DNA geometry in different pH solutions. The intrinsic circular dichroism (CD) spectra showed the conformation of DNA converted from the B-form to A-like conformation due to the A1 intercalation.
Zhang
Zhichao
Z
State Key Laboratory of Fine Chemicals, Dalian University of Technology, Dalian 116012, China.
Yang
Yuanyuan
Y
Liu
Fengyu
F
Qian
Xuhong
X
Xu
Qin
Q
D000818:Animals; D001665:Binding Sites; D002417:Cattle; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D018736:DNA Adducts / Q000737:chemistry; D006571:Heterocyclic Compounds / Q000737:chemistry* / Q000378:metabolism*; D066298:In Vitro Techniques; D007364:Intercalating Agents / Q000737:chemistry* / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D013050:Spectrometry, Fluorescence; D013053:Spectrophotometry
D018736:DNA Adducts; D006571:Heterocyclic Compounds; D007364:Intercalating Agents; D004247:DNA