Minor groove binding of Co(III)meso-tetrakis(N-methylpyridinium-4-yl)porphyrin to various duplex and triplex polynucleotides.
The binding site and the geometry of Co(III)meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (CoTMPyP) complexed with double helical poly(dA).poly(dT) and poly(dG).poly(dC), and with triple helical poly(dA).[poly(dT)](2) and poly(dC).poly(dG).poly(dC)(+) were investigated by circular and linear dichroism (CD and LD). The appearance of monomeric positive CD at a low [porphyrin]/[DNA] ratio and bisignate CD at a high ratio of the CoTMPyP-poly(dA).poly(dT) complex is almost identical with its triplex counterpart. Similarity in the CD spectra was also observed for the CoTMPyP-poly(dG).poly(dC) and -poly(dC).poly(dG).poly(dC)(+) complex. This observation indicates that both monomeric binding and stacking of CoTMPyP to these polynucleotides occur at the minor groove. However, different binding geometry of CoTMPyP, when bind to AT- and GC-rich polynucleotide, was observed by LD spectrum. The difference in the binding geometry may be attributed to the difference in the interaction between polynucleotides and CoTMPyP: in the GC polynucleotide case, amine group protrude into the minor groove while it is not present in the AT polynucleotide.
Jin
Biao
B
Department of Chemistry, Yeungnam University, Daedong, Gyeongsan City, Gyeong-buk 712-749, Republic of Korea.
Sub Shin
Jong
J
Hwan Bae
Chang
C
Kim
Jong-Moon
JM
Kim
Seog K
SK
D001665:Binding Sites; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry; D006863:Hydrogen-Ion Concentration; D008665:Metalloporphyrins / Q000737:chemistry*; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009711:Nucleotides / Q000737:chemistry*; D011166:Porphyrins / Q000737:chemistry / Q000494:pharmacology*; D011485:Protein Binding
D008665:Metalloporphyrins; D009711:Nucleotides; D011166:Porphyrins; C512795:cobalt(III)meso-tetrakis(N-methylpyridinium-4-yl)porphyrin; C051802:triplex DNA; D004247:DNA