@article{barnes_stroud_robinson_horton_schreiner_1999, title={5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrinato-palladium(II) as a differentiation probe for sensing binding modes with B-DNA duplexes: Electronic MCD and CD spectra}, volume={5}, ISSN={["1075-4261"]}, DOI={10.1002/(SICI)1520-6343(1999)5:3<179::AID-BSPY7>3.0.CO;2-U}, abstractNote={We report our detailed electronic MCD, CD, and optical spectroscopic measurements and analysis of the porphyrin Soret (B(o)) region of four-coordinate 5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrinatopalladium( II), PdP(4), and its bound states with B-DNA duplexes poly(A-T)2, poly(G-C)2, and calf thymus DNA (CT DNA). For system PdP(4)/poly(A-T)2 it was possible to conclude that the porphyrin is bound edge-on in the major groove, specifically at the 5'AT3' site. For this orientation the porphyrin's electric dipole transition moments (edtm), mu(x) (most perturbed direction) and mu(y) (least perturbed direction), have tilt angles alpha approximately 90 degrees and approximately 45 degrees , respectively, relative to the helix axis. It was further concluded from the small shifts of B(o) optical and MCD band intensities and wavelengths and from the net MCD (+) A-term sign retention upon binding that the porphyrin's frontier ppi MOs (1a(1u) 3a(2u) 4eg) are only weakly perturbed by the heterocyclic bases of poly(A-T)2, and therefore that the LUMO (4eg) splitting is less than the |1a(1u)-3a(2u| energy separation, deltaHOMO, that is, deltaLUMO < deltaHOMO for the bound state in PdP(4)/poly(A-T)2. For intercalation systems PdP(4)/ poly(G-C)2 and /CT DNA, with PdP(4) centered in the intercalation "pocket" and having two of its 4-N-methylpyridyls extending into each of the major and minor grooves, the edtms mu(x) and mu(y) were determined to be oriented perpendicular (gamma approximately 0 degrees) and parallel (gamma approximately 90 degrees) to the hydrogen bonds of the base pairs, respectively. Intercalation is characterized by a much stronger binding interaction, viz., the B(o) optical band and net MCD extrema wavelength shifts are relatively large, and the net MCD (+) A-term of PdP(4) is substantially quenched as it becomes the (-) pseudo-A-term of intercalated PdP(4)/poly(G-C)2. This A-term sign reversal informs that the porphyrin MOs are so strongly perturbed by the GC base pairs that deltaLUMO > deltaHOMO, which gives rise to a (-) pseudo-A-term. Also, the findings demonstrate (1) the potential of PdP(4) as a sensitive, discriminating analytical probe of DNA sequences and (2) the diagnostic capability of the composite of five spectra [net MCD, CD, and optical of free and bound PdP(4)] in differentiating the site and sequence selectivity and preferred binding mode of this porphyrin.}, number={3}, journal={BIOSPECTROSCOPY}, author={Barnes, NR and Stroud, PD and Robinson, KE and Horton, C and Schreiner, AF}, year={1999}, pages={179–188} }
 @article{barnes_schreiner_1998, title={B-DNA binding with cobalt(III) and vanadyl(2+) derivatives of tetracationic 5,10,15,20-tetrakis(4-N-methylpyridyl)porphine: Combined CD, optical, and electronic MCD spectra}, volume={37}, ISSN={["0020-1669"]}, DOI={10.1021/ic980349b}, abstractNote={Electronic MCD is used for the first time to obtain electronic and geometric structural insight into the free and DNA-bound states of the six-coordinate CoIII and VO2+ derivatives of 5,10,15,20-tetrakis(4-N-methylpyridyl)porphine. Correlations between MCD, CD, and optical spectra measured in the porphyrin Soret band (or B0) region, and FLDr literature data, are consistent with each metalloporphyrin having a face-on orientation in the major groove of CT DNA, sites 5‘AT3‘ and 5‘CG3‘ being preferred, and with porphyrin electric dipole transition moments (edtms) μexD (most perturbed direction in the bound porphyrin) and μexD (least perturbed) having orientation angles of α/β/β‘ = ∼45°/180°/90° and ∼45°/180°/270°, respectively.}, number={26}, journal={INORGANIC CHEMISTRY}, author={Barnes, NR and Schreiner, AF}, year={1998}, month={Dec}, pages={6935–6938} }
 @article{barnes_schreiner_finnegan_johnson_1998, title={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}, volume={4}, ISSN={["1075-4261"]}, DOI={10.1002/(SICI)1520-6343(1998)4:5<341::AID-BSPY5>3.0.CO;2-E}, abstractNote={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.}, number={5}, journal={BIOSPECTROSCOPY}, author={Barnes, NR and Schreiner, AF and Finnegan, MG and Johnson, MK}, year={1998}, pages={341–352} }
 @article{barnes_schreiner_dolan_1998, title={Measurement and interpretation of Q(0) and Q(1) band property changes of two cationic metalloporphyrins upon binding with B-DNA: electronic MCD, CD, and optical absorption}, volume={72}, DOI={10.1016/s0162-0134(98)10050-8}, abstractNote={Room-temperature Q-band electronic MCD, CD, and optical spectra are reported for the first time for two free and nucleic acid-bound cationic metalloporphyrins. Metalloporphyrins are the high-symmetry (C4vorD4h), four-coordinate tetragonal type MP(X) [M=CuII and PtII; P(X)=meso-tetrakis(X-N-methylpyridyl)porphine; X=2 or 4], and the nucleic acid is native, B-form calf thymus DNA (CT DNA). For intercalation system PtP(4)/CT DNA, large optical (λ0,ϵmax) and MCD (λpeak,λtrough,Aaj,Aaj/Daj, and Δ[θ]Mp–t/ϵmax) band parameter shifts, as well as a single negative (−) induced CD peak for each of Q0 and Q1, were observed upon binding of the porphyrin to chiral DNA. The directions and magnitudes of these changes are comparable to those observed for the Soret (B0) band of this system. Decreases of MCD/optical ratio Δ[θ]Mp–t/ϵmax(∝Aaj/Daj) of 30% (Q0) and 50% (Q1) upon intercalation indicate substantial reductions of the Q0[1Eu(a)(0,0),∼1a1u14eg1] and Q1[1Eu(a)(0,1),∼1a1u14eg1] excited state angular momenta, 〈Lj〉. It is of additional interest that intercalation leads to intensity cancellation of one of the four A-term lobes, the (+) lobe of the Q0 MCD (+) pseudo-A-term, which was also observed previously for intercalation systems PdP(4)/poly(G–C)2 and /CT DNA. Application of the CD sector method to the constituent x- and y-polarized porphyrin edtms, √Daj, of the Q0 (edtms μ0x and μ0y) and Q1 (edtms μ1x and μ1y) CD bands leads to the conclusion that PtP(4) is symmetrically intercalated between adjacent GC base pairs, specifically at 5′GC3′ sites, with each of two adjacent 4-N-methylpyridyl groups extending into each of the major and minor grooves. For outside binder CuP(2), small optical and MCD band parameter shifts and smaller, single positive (+) induced CD peaks are observed for Q0 and Q1 upon interaction with CT DNA, similar to what is found for B0. Little or no change in the MCD/optical ratio, Δ[θ]Mp–t/ϵmax, informs that external binding has only small effects on the excited state angular momenta, 〈Lj〉, of these bands. The composite of MCD, CD, and optical spectra are consistent with CuP(2) binding to CT DNA by one or both of two competing external modes, i.e., by an AT-specific, edge-on minor groove mode at 5′TA3′ sites and/or a face-on major groove mode with high selectivity for 5′AT3′ or 5′CG3′ sites. For Q0 and Q1 of each of the CuP(2)/CT DNA and PtP(4)/CT DNA systems, we observe that the genuine MCD (+) A-terms of these free MP(X)s retain their (+) sign on becoming pseudo-A-terms upon binding to the low-symmetry, asymmetric DNA sites, and this indicates that the external and intercalative modes result in the 4eg splitting, or ΔLUMO, being less than the |1a1u–3a2u| energy separation, or ΔHOMO.}, number={1-2}, journal={Journal of Inorganic Biochemistry}, author={Barnes, N. R. and Schreiner, A. F. and Dolan, M. A.}, year={1998}, pages={1–12} }