Interaction of methyl green with an oligonucleotide in intramolecular duplex and triplex conformations - Circular dichroism studies

Interaction of methyl green with the oligonucleotide 5'-dGGAAAAGG-[T-4]-GGAAAAGG-[T-4]-CCTTTTCC (where [T-4] is a nucleotide sequence of four thymines) in hairpin duplex and in intramolecular tripler structures has been studied by circular dichroism. We found that methyl green binding to the duplex form shows a complex pattern, exhibiting an exciton contribution when the number of bound molecules increases. Differences between this pattern and previously published results on other DNAs reveals the presence of different types of complexes. In contrast to previous findings with the triple helix poly(dA).2poly(dT) we show that the methyl green is not totally excluded from this tripler structure made of Pur:Pur:Pyr triplets.