Can energy transfer be an indicator for DNA intercalation?
Contact energy transfer from DNA bases to various ligands, which can be represented by the ratio of the fluorescence intensity Q(lambda)/Q310nm, is measured by conventional fluorometer. 4',6-Diamidino-2-phenylindole and 2'-(4-hydroxyphenyl)-5-(4-methyl-1-piperazinyl)-2,5'-bi-1H-benzimidazole can accept energy from DNA bases and exhibit the ratio Q(lambda)/Q310nm, similar to that of intercalators, although these molecules are known to bind preferentially to the minor groove of the adenine-thymine rich region of DNA. When porphyrin is intercalated in DNA or poly[d(G-C)2], the shape of the ratio Q(lambda)/Q310nm is distinct from that of the ethidium-DNA complex with two maxima at 250 nm and 280 nm. The ratio Q(lambda)/Q310nm of the porphyrin-poly[d(A-T)2] complex, in which porphyrin is known to bind 'outside' of the DNA stem, is similar to that of intercalators. Therefore, energy from excited DNA bases can be transferred not only to an intercalated ligand through direct contact but also to that bound in the minor groove. It follows from this observation that using energy transfer as a criterion for DNA intercalation requires extreme caution.
Hyun
K M
KM
Department of Chemistry, College of Sciences, Yeungnam University, Kyoungsan City, South Korea.
Choi
S D
SD
Lee
S
S
Kim
S K
SK
D004247:DNA / Q000737:chemistry*; D004735:Energy Transfer; D007364:Intercalating Agents / Q000737:chemistry*; D008024:Ligands; D013050:Spectrometry, Fluorescence
D007364:Intercalating Agents; D008024:Ligands; D004247:DNA