STUDIES OF THE BASE-DEPENDENT BINDING OF CU(T4) TO DNA HAIRPINS (H(2)T4 = MESO-TETRAKIS(4-(N-METHYLPYRIDIUMYL))PORPHYRIN)

Water-soluble, cationic metalloporphyrins that bind to DNA show promis e as artificial nucleases and as sensitizers for photodynamic therapy, but fundamental questions remain about the binding motifs and sequenc e specificities. To address these issues, we have studied the interact ions of Cu(T4) with a series of oligonucleotides that form hairpin str uctures (H(2)T4 = meso-tetrrkis(4-(N-methylpyridiniumyl))porphyrin). E ach oligonucleotide is a 16-mer with a central run of four thymine (T) bases and complementary ends that can combine to form a specific sequ ence of six adenine-thymine (A=T) and guanine-cytosine (G=C) base pair s. The techniques employed include thermal melting as well as circular dichroism (CD), absorbance, and emission spectroscopies. The number o f G=C base pairs in the stem is the most important factor that determi nes the melting temperature of the hairpin, and in every case investig ated, the uptake of Cu(T4) stabilizes the hairpin. Depending on the na ture of the adduct that forms, Delta epsilon varies from -22 to +17 M- 1 cm(-1) in the Soret region of the CD spectrum, and the emission inte nsity from Cu(T4) changes by an order of magnitude. The results yield several useful insights regarding the binding interactions. One is tha t robust hydrogen bonding within a B-form duplex promotes intercalativ e binding of Cu(T4). Thus, if the composition is at least 50% G=C base pairs, intercalation will occur even in the absense of a G=C step. On the other hand, a run of four A=T base pairs defines a groove-binding site with an affinity comparable to that for intercalation at a G=C s tep. Finally, at least in solutions containing excess oligonucleotide, there is no sign that either loop binding or hemiintercalation is a p revalent mode of interaction between Cu(T4) and hairpin hosts.