Insight into externally bound 5,10,15,20-tetrakis(2-N-methylpyridyl) porphyrinatopalladium(II), PdP(2), with B-form DNA duplexes poly(G-c)2, poly(A-t)2, and CT DNA by using combined MCD, CD, and optical data.

The Soret (B0) region of free and externally DNA-bound 5,10,15,20-tetrakis(2-N-methylpyridyl) porphyrinatopalladium(II), PdP(2), was investigated by electronic magnetic circular dichroism (MCD), natural circular dichroism (CD), and optical (UV-visible) absorption spectroscopies. We conclude that four-coordinate, "thick" PdP(2) binds to the exterior of each of poly(A-T)2 and calf thymus DNA (CT DNA) by two distinctly different AT-specific minor and major groove modes, with site 5'TA3' being favored for both modes. The minor groove mode involves an edge-on orientation of PdP(2), for which porphyrin electric dipole transition moments (edtms) mu x (most perturbed direction of the bound porphyrin) and mu y (least perturbed direction) have approximate orientation angles of alpha/beta/beta' = approximately 90 degrees/0 degree/0 degree and approximately 45 degrees/0 degree/90 degrees, respectively. Major groove binding is by a face-on mode, which results in the porphyrin plane being approximately parallel to the helix axis, such that mu x (most perturbed direction) and mu y (least perturbed direction) have approximate orientation angles of alpha/beta/beta' = approximately 45 degrees/180 degrees/90 degrees and approximately 45 degrees/180 degrees/270 degrees, respectively. The Soret MCD and optical band alterations upon binding (i.e., sign retention of the tetragonal, genuine MCD (+) A-term on becoming the (+) pseudo-A-term of similar amplitude and small DNA-induced optical red (delta lambda) and hypochromic (H) shifts) are all consistent with exterior binding perturbations of the porphyrin's p pi MOs (1a1u 3a2u 4eg) by the A and T bases of each polymer being weaker than caused by intercalation. Furthermore, that the (+) A-term of PdP(2) retains the (+) sign upon binding informs that the 4eg splitting, or delta LUMO, is less than the energy separation magnitude of 1a1u-3a2u, or delta HOMO. For the third system, PdP(2)/poly (G-C)2, the B0 CD spectrum has two extremely weak (+) and (-) CD bands at higher and lower energy, respectively, indicating that weak outside binding (wob) interactions are taking place between the cationic porphyrin and the electron-rich phosphate backbone of this rigid polymer. The composite of our CD, MCD, and optical data are suggestive of a face-on mode at the GC major groove. Band parameter extraction is performed on the Soret CD and MCD bands of each of the three bound systems, and it is determined that (1) very little spatial rotation of molecular charge is induced during CD excitation and (2) the excited state angular momentum, 'Lj', changes very little upon binding of PdP(2) to each duplex. These findings are also consistent with each PdP(2)/B-DNA interaction not being very strong.