Structure/nuclease activity relationships of DNA cleavers based on cationic metalloporphyrin-oligonucleotide conjugates

Designed Metal-ATCUN Derivatives: Redox- and Non-redox-Based Applications Relevant for Chemistry, Biology, and Medicine

The designed “ATCUN” motif (amino-terminal copper and nickel binding site) is a replica of naturally occurring ATCUN site found in many proteins/peptides, and an attractive platform for multiple applications, which include nucleases, proteases, spectroscopic probes, imaging, and small molecule activation. ATCUN motifs are engineered at periphery by conjugation to recombinant proteins, peptides, fluorophores, or recognition domains through chemically or genetically, fulfilling the needs of various biological relevance and a wide range of practical usages. This chemistry has witnessed significant growth over the last few decades and several interesting ATCUN derivatives have been described. The redox role of the ATCUN moieties is also an important aspect to be considered. The redox potential of designed M-ATCUN derivatives is modulated by judicious choice of amino acid (including stereochemistry, charge, and position) that ultimately leads to the catalytic efficiency. In this context, a wide range of M-ATCUN derivatives have been designed purposefully for various redox- and non-redox-based applications, including spectroscopic probes, target-based catalytic metallodrugs, inhibition of amyloid-β toxicity, and telomere shortening, enzyme inactivation, biomolecules stitching or modification, next-generation antibiotic, and small molecule activation.

Assembling multiporphyrin stacks inside the DNA double helix

Double stranded DNA hybrids containing up to four consecutive, face-to-face stacked porphyrins are described. Non-nucleosidic, 5,15-bisphenyl-substituted porphyrin building blocks were incorporated into complementary oligonucleotide strands. Upon hybridization multiple porphyrins are well accommodated inside the DNA scaffold without disturbing the overall B-DNA structure. The formation of double strands containing up to four free base porphyrins is enabled without compromising duplex stability. UV/vis, fluorescence, and CD spectroscopy demonstrate the formation of porphyrins H-aggregates inside the DNA double helix and provide evidence for the existence of strong excitonic coupling between interstrand stacked porphyrins. H-aggregation results in considerable fluorescence quenching. Most intense CD effects are observed in stacks containing four porphyrins. The findings demonstrate the value of DNA for the controlled formation of molecularly defined porphyrin aggregates.

Synthesis of DNA conjugates with metalated tetracationic porphyrins by postsynthetic cycloadditions

Tetracationic porphyrins of the TMPP (meso-tetra-(4-N-methylpyridyl)porphyrin) type, metalated with Cu(II) or with Au(III), were conjugated covalently to oligonucleotides. The Cu(I)-catalyzed cycloaddition (between an azide and an ethynyl group) and the Diels-Alder cycloaddition (between a furan and a maleimide functionality) were successfully applied as two alternative postsynthetic methods to modify the 2'-position of an internal uridine. Melting temperatures and UV/vis absorption properties were compared. CD measurements indicated that the type of conjugation chemistry determines the grade of intercalation of the attached and positively charged porphyrins.

DNA-Interaction and nuclease activity of porphyrin-hydroxamic acid derivatives in the presence of lanthanides

The DNA-binding modes and nuclease activity of methylpyridiniumyl/phenyl-hydroxamic acid porphyrin adducts (PHAs) have been studied. These compounds are derived from the tetracationic meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (H2TMPyP-4) by replacing one or two pyridinium rings by a phenyl group. A hydroxamic acid function was connected by a polymethylenic chain of 3 to 5 carbon atoms to the meta or para position of the phenyl group. Different DNA-interaction modes were observed depending on the number of charges and hydroxamic acid functions. The nuclease activity in the presence of lanthanides was shown to be depending on the 1/r0 ratio and the nature of the lanthanide ion, and the optimum conditions are depicted after a systematic study.

Aggregation and DNA binding characteristics of tetrakis(N,N',N″,N‴-tetramethyltetra-3,4-pridino)porphyrazine cobalt(II)

The association behavior of tetrakis( N , N ', N ″, N ‴-tetramethyltetra-3,4-pridino)porphyrazine cobalt(II) ([ Co (II)3,4- TMTPPA ]4+) was investigated in aqueous solution at 25°C and various ionic strengths using optical absorption and resonance light scattering spectroscopies. The results show that [ Co (II)3,4- TMTPPA ]4+ does not have any affinity for aggregation due to increasing salt concentration and exists as the monomer form even in homogeneous aqueous solutions at high ionic strengths (more than 1 M concentration of NaCl ). The interaction of [ Co (II)3,4- TMTPPA ]4+ with calf thymus DNA in aqueous solution has also been studied in 5 mM phosphate buffer pH 7.2, by optical absorption and resonance light scattering spectroscopies, and thermal denaturation experiments. The appearance of hypochromicity of less than 10% and a bathochromic shift of Δλ ≤ 8 nm in the UV-vis spectra of [ Co (II)3,4- TMTPPA ]4+, an increase in the thermal melting point of DNA, and no enhancement in resonance light scattering spectra of porphyrazine due to interaction with DNA, indicates the minor outside-groove binding mode without any stack aggregate formation. The thermodynamics of the binding of [ Co (II)3,4- TMTPPA ]4+-DNA has also been studied. The binding constant (K) was obtained by analysis of optical absorption spectra of the above-mentioned complex at various DNA concentrations using SQUAD software. The value of K was estimated as 1.31 × 106 ± 1.174 M-1 at 25°C. The thermodynamic parameters were calculated by van't Hoff equation. The enthalpy and entropy changes were 48.77 ± 2.50 kJ . mol -1 and 280.77 ± 9.62 J . mol -1. K -1 at 25°C, respectively. The results indicate that the process is entropy driven suggesting that hydrophobic interactions are the main driving forces for complex formation. The increase of ionic strength due to the addition of NaCl , destabilized porphyrazine-DNA complexes, which indicates the competition of Na + ions with porphyrazine complexes for occupation of minor groove binding sites.

Oxidative DNA damage mediated by transition metal ions and their complexes

DNA damage by redox-active metal complexes depends on the interaction of the metal complex with DNA together with the mechanism of oxygen activation. Weak interaction, tight binding, and direct involvement of DNA in the coordination sphere of the metal are described. Metal complexes acting through the production of diffusing radicals and metal complexes oxidizing DNA by metal-centered active species are compared. Metal complexes able to form high-valent metal-oxo species in close contact with DNA and perform DNA oxidation in a way reminiscent of enzymatic chemistry are the most elegant systems.

Functionalized nanostructures: redox-active porphyrin anchors for supramolecular DNA assemblies

We have synthesized and studied a supramolecular system comprising a 39-mer DNA with porphyrin-modified thymidine nucleosides anchored to the surface of large unilamellar vesicles (liposomes). Liposome porphyrin binding characteristics, such as orientation, strength, homogeneity, and binding site size, was determined, suggesting that the porphyrin is well suited as a photophysical and redox-active lipid anchor, in comparison to the inert cholesterol anchor commonly used today. Furthermore, the binding characteristics and hybridization capabilities were studied as a function of anchor size and number of anchoring points, properties that are of importance for our future plans to use the addressability of these redox-active nodes in larger DNA-based nanoconstructs. Electron transfer from photoexcited porphyrin to a lipophilic benzoquinone residing in the lipid membrane was characterized by steady-state and time-resolved fluorescence and verified by femtosecond transient absorption.

Aggregation behavior of tetrakis(N, N′, N″, N‴-tetramethyl tetra-2,3-pyridino)porphyrazine copper(II) and its interaction with ct-DNA: a thermodynamic approach

The association behavior of tetrakis( N , N ′, N ″, N ‴-tetramethyl tetra-2,3-pyridino)porphyrazine copper(II) ([ Cu(II) 2,3- tmtppa ]4+) was investigated in aqueous solutions at 25 °C and various ionic strengths using optical absorption and resonance light scattering (RLS) spectroscopies. The results show that ([ Cu(II) 2,3- tmtppa ]4+) does not have any affinity for aggregation due to increasing of salt concentration and exists as monomers even in homogeneous aqueous solutions of high ionic strengths (more than 1 M NaCl ). Interaction of ([ Cu(II) 2,3- tmtppa ]4+) with calf thymus DNA has also been studied in 1 mM aqueous phosphate buffer of pH 7.0, by optical absorption and RLS spectroscopies, and thermal denaturation experiments. The appearance of hypochromicity of less than 10% and bathochromicity shift of Δλ ≤ 2 nm in UV-vis spectra of ([ Cu(II) 2,3- tmtppa ]4+), increasing of thermal melting point of DNA, and no change in RLS spectra of porphyrazine due to interaction with DNA, represent the minor outside groove binding mode without any stack aggregate formation. The thermodynamic of the binding of ([ Cu(II) 2,3- tmtppa ]4+)-DNA also has been studied. The binding constant (K) was obtained by analysis of the optical absorption spectra of the complex at various DNA concentrations using SQUAD software. The value of K was estimated to be 2.34 × 105 ± 0.06 M -1 at 25 °C. The thermodynamic parameters were calculated by van't Hoff equation. The enthalpy and entropy changes were 41.83 ± 3.28 kJ/mol and 242.08 ± 9.88 J/mol.K at 25 °C, respectively. The results indicate that the process is entropy-driven and suggest that hydrophobic interactions are the main driving forces for the complex formation. Increasing of the ionic strength due to addition of NaCl destabilized porphyrazine-DNA complexes, indicating the competition of Na + ions with porphyrazine complexes for occupation of minor groove binding sites.

Long-range charge transport through double-stranded DNA mediated by manganese or iron porphyrins

Guanine oxidation by electron transfer results in the formation of a guanine radical cation, which is at the origin of long-range charge transport through double-stranded DNA. It is possible to observe guanine lesions at a long distance from the oxidative reagent covalently bound to DNA owing to the migration of the positive hole in the DNA pi-stacks. This phenomenon of long-range hole transport is classically studied in the literature with photosensitizers used as one-electron oxidants. It is shown in the present work that the process of long-range charge transport and the concomitant formation of guanine lesions at a long distance can be observed also in the case of two-electron oxidants. This is the signature of the formation of a transient guanine radical cation in the course of the two-electron abstraction process and consequently evidence of the separated one plus one electron abstraction steps. Long-range charge transport is likely to be a universal mechanism for any two-electron oxidant acting by electron abstraction provided that the second electron abstraction is slower than hole transfer.

Microcalorimetric investigation of DNA, poly(dA)poly(dT) and poly[d(A-C)]poly[d(G-T)] melting in the presence of water soluble (meso tetra (4 N oxyethylpyridyl) porphyrin) and its Zn complex

Thermodynamic parameters of melting process (DeltaHm, Tm, DeltaTm) of calf thymus DNA, poly(dA)poly(dT) and poly(d(A-C)).poly(d(G-T)) were determined in the presence of various concentrations of TOEPyP(4) and its Zn complex. The investigated porphyrins caused serious stabilization of calf thymus DNA and poly poly(dA)poly(dT), but not poly(d(A-C))poly(d(G-T)). It was shown that TOEpyp(4) revealed GC specificity, it increased Tm of satellite fraction by 24 degrees C, but ZnTOEpyp(4), on the contrary, predominantly bound with AT-rich sites and increased DNA main stage Tm by 18 degrees C, and Tm of poly(dA)poly(dT) increased by 40 degrees C, in comparison with the same polymers without porphyrin. ZnTOEpyp(4) binds with DNA and poly(dA)poly(dT) in two modes--strong and weak ones. In the range of r from 0.005 to 0.08 both modes were fulfilled, and in the range of r from 0.165 to 0.25 only one mode--strong binding--took place. The weak binding is characterized with shifting of Tm by some grades, and for the strong binding Tm shifts by approximately 30-40 degrees C. Invariability of DeltaHm of DNA and poly(dA)poly(dT), and sharp increase of Tm in the range of r from 0.08 to 0.25 for thymus DNA and 0.01-0.2 for poly(dA)poly(dT) we interpret as entropic character of these complexes melting. It was suggested that this entropic character of melting is connected with forcing out of H2O molecules from AT sites by ZnTOEpyp(4) and with formation of outside stacking at the sites of binding. Four-fold decrease of calf thymus DNA melting range width DeltaTm caused by increase of added ZnTOEpyp(4) concentration is explained by rapprochement of AT and GC pairs thermal stability, and it is in agreement with a well-known dependence, according to which DeltaT approximately TGC-TAT for DNA obtained from higher organisms (L. V. Berestetskaya, M. D. Frank-Kamenetskii, and Yu. S. Lazurkin. Biopolymers 13, 193-205 (1974)). Poly (d(A-C))poly(d(G-T)) in the presence of ZnTOEpyp(4) gives only one mode of weak binding. The conclusion is that binding of ZnTOEpyp(4) with DNA depends on its nucleotide sequence.

Diastereochemically controlled porphyrin dimer formation on a DNA duplex scaffold

DNA-porphyrin conjugates were designed and synthesized for the preparation of the conformationally controlled porphyrin dimer structures constructed on a d(GCGTATACGC)2. Porphyrin derivatives were introduced to the central TATpA sequence where p represents the phosphoramidate for the attachment of the free-base porphyrin (FbP) and zinc-coordinated porphyrin (ZnP), which allows contact of the two porphyrins in the minor groove. The porphyrin dimers were characterized using CD, UV-vis, steady-state, and time-resolved fluorescence spectroscopies, indicating that the porphyrins form face-to-face conformations. Also the co-facial conformation was confirmed by comparison with spectra of the non-self-complementary duplex containing one porphyrin moiety. Introduction of zinc into porphyrin moiety destabilized the duplex formation. Two diastereomers showed different thermal stabilities and affected the conformations of porphyrin dimers. The temperature-dependent assembly and the conformational change of the porphyrin dimer on the duplex DNA were observed in the UV-vis spectra, indicating that the dynamic movement of the porphyrin dimer occurs on the duplex. The results indicate that the porphyrin dimers of DNA-FbP conjugates are overlapped clockwise and are located in the minor groove of the usual B-form DNA backbone. The interaction and conformation of two porphyrin moieties are controlled by the following three factors: (1) temperature change during and after formation of the duplex porphyrins at lower temperature; (2) diastereochemistry of the phosphoramidates where porphyrins are connected via a linker; and (3) zinc ion coordination that destabilizes the interaction of porphyrins as well duplex formation.

Binding, electrochemical activation, and cleavage of DNA by cobalt(II) tetrakis-N-methylpyridyl porphyrin and its beta-pyrrole brominated derivative

The binding of nucleic acids by water-soluble cobalt(II) tetrakis-N-methylpyridyl porphyrin, (TMPyP)Co, and its highly electron-deficient derivative cobalt(II) tetrakis-N-methyl pyridyl-beta-octabromoporphyrin, (Br(8)TMPyP)Co, was investigated by UV-visible absorption, circular dichroism (CD), and electrochemical and gel electrophoresis methods. The changes of the absorption spectra during the titration of these complexes with polynucleotides revealed a shift in the absorption maxima and a hypochromicity of the porphyrin Soret bands. The intrinsic binding constants were found to be in the range of 10(5)-10(6) M(-1). These values were higher for the more electron-deficient (Br(8)TMPyP)Co. Induced CD bands were noticed in the Soret region of the complexes due to the interaction of these complexes with different polynucleotides, and an analysis of the CD spectra supported a mainly external mode of binding. Electrochemical studies revealed the cleavage of polynucleotides by (TMPyP)Co and (Br(8)TMPyP)Co in the presence of oxygen preferentially at the A-T base pair region. Gel electrophoresis experiments further supported the cleavage of nucleic acids. The results indicate that the beta-pyrrole brominated porphyrin, (Br(8)TMPyP)Co, binds strongly and cleaves nucleic acids efficiently as compared with (TMPyP)Co. This electrolytic procedure offers a unique tool in biotechnology for cleaving double-stranded DNA with specificity at the A-T regions.

Porphyrins as spectroscopic sensors for conformational studies of DNA

Molecular systems containing two or more interacting porphyrins show remarkable spectroscopic features that allow for a very sensitive detection of conformational changes on the microscale level by different methods, such as fluorescence and electronic circular dichroism (ECD). Covalent porphyrin-DNA assemblies can provide a CD profile (exciton couplet) within the porphyrin Soret band region which is very diagnostic for DNA conformational changes. Additionally, covalently linked porphyrins have been shown to function as DNA molecular caps and to stabilize the non-self-complementary non-Watson-Crick guanine-adenine DNA sequence via their strong π-π stacking.

Synthesis and cellular studies of PEG-functionalized meso-tetraphenylporphyrins

The total syntheses of four PEG-functionalized porphyrins, containing one to four low molecular weight PEG chains linked via amide bonds to the para-phenyl positions of meso-tetraphenylporphyrin, are reported. The hydrophobic character of the PEG-porphyrins decreases with the number of PEG chains linked to the porphyrin ring, while their tendency for aggregation in buffered aqueous solution increases. The porphyrins containing one or two PEG chains accumulated within human HEp2 cells to a much higher extent than those having three or four PEGs at the macrocycle periphery. All PEG-porphyrins were found to be non-toxic in the dark, and only those containing one or two PEG chains were phototoxic (IC(50)=2 microM at 1J/cm(2) light dose). The preferential sites of subcellular localization of the porphyrins containing one or two PEG chains were found to be the mitochondria and endoplasmic reticulum (ER), while those containing three or four PEG chains localize preferentially in the lysosomes.

Use of short duplexes for the analysis of the sequence-dependent cleavage of DNA by a chemical nuclease, a manganese porphyrin

A manganese porphyrin, manganese(III)-bis(aqua)-meso-tetrakis(4-N-methylpyridiniumyl)porphyrin, in the presence of KHSO5 is able to perform deoxyribose or guanine oxidation depending on its mode of interaction with DNA. These two reactions involve an oxygen-atom transfer or an electron transfer, respectively. The oxidative reactivity of the manganese-oxo porphyrin was compared on short oligonucleotide duplexes of different sequences. The major mechanism of DNA damage is due to deoxyribose hydroxylation at a site of strong interaction, an (A.T)3 sequence. Guanine oxidation by electron transfer was found not to be competitive with this major mechanism. It was found that a single intrastrand guanine was three orders of magnitude less reactive than an (A.T)3 sequence. The reactivity of a 5'-GG sequence was found to be intermediate and was estimated to be two orders of magnitude less than that of an (A.T)3 site. Short oligonucleotide duplexes, as double-stranded-DNA models, proved to be convenient tools for the study of the comparative reactivity of this reagent toward different sequences of DNA. However, they showed a particular reactivity at their terminal base pairs (the "end effect") that biased their modeling capacity for double-helix-DNA models.

5'-Porphyrin-oligonucleotide conjugates: neutral porphyrin-DNA interactions

[chemical reaction: see text]. Incorporation of hydrophilic tetraarylporphyrin phosphoramidites into the 5'-termimus of the DNA as well as noncharged porphyrin-DNA interactions have been studied. Porphyrin-modified oligonucleotides show lower melting temperatures than their unmodified analogues. Single-stranded DNA interacts more strongly with porphyrin and causes more intense chiral disturbance in the porphyrin environment than the corresponding double strand.

Peptide-mediated cell transport of water soluble porphyrin conjugates

Five new porphyrin-peptide conjugates bearing a nuclear localizing sequence SV40 or a fusogenic peptide (HIV-1Tat 40-60 or octa-arginine) linked by low molecular weight poly(ethylene glycol) have been synthesized. In vitro studies using human HEp2 cells show that the cellular uptake of the conjugates depends significantly on the nature and sequence of amino acids in the peptide and on the nature of the substituents on the porphyrin macrocycle. The fusogenic peptide sequences HIV-1Tat 40-60 and octa-arginine were the most effective in delivering the conjugates to the cells. The subcellular distribution of the conjugates was found to be dependent on the nature of substituents on the porphyrin macrocycle. The conjugates bearing a hydrophobic porphyrin localized preferentially in the endoplasmic reticulum and were significantly more phototoxic to HEp2 cells than the carboxylic acid functionalized porphyrin conjugates, which localized mainly in the lysosomes.

Porphyrin substituted phosphoramidites: new building blocks for porphyrin-oligonucleotide syntheses

Thymidine phosphoramidites containing trispyridylphenyl and tetraphenylporphyrin chromophores attached via a short amide linker in the 3'-position have been synthesized and used as building blocks in solid-phase synthesis of self-complementary 8-mer oligonucleotides 3'-T-5'-GCGCGCA-3' and 5'-ACGCGCGT-3'. To our knowledge, these are the first porphyrin-oligonucleotide conjugates carrying the porphyrin chromophores in the 3'-position. Chain assembly was achieved by automated solid-phase synthesis and by inexpensive straightforward 'in flask' modification of commercially available solid supported oligonucleotides. This approach allows the synthesis of modified oligonucleotides without using costly instrumentation for automated DNA synthesis. Porphyrin-containing self-complementary oligonucleotides are expected to be a valuable model for drug binding studies and determination of conformational changes in DNA sequences using circular dichroism.

Synthesis and circular dichroism of tetraarylporphyrin-oligonucleotide conjugates

The preparation and circular dichroic (CD) studies of self-complimentary 8-mer DNA sequences with a porphyrin at the 3' end are presented. Electronic interaction between the two porphyrins (the interchromophoric distance is in the range of 28-40 A), attached to both ends of the double-stranded helix, gives rise to a long-range exciton-coupled CD in the visible region (400-450 nm). The porphyrin chromophores act as sensitive probes of geometrical changes in the DNA backbone and sensitively reflect the double-strand to single-strand transition. This study demonstrates the possibility of using exciton-coupled porphyrin CDs for conformational studies of DNA.

Comparison of the cleavage profiles of oligonucleotide duplexes with or without phosphorothioate linkages by using a chemical nuclease probe

A manganese porphyrin complex, Mn-TMPyP, associated with KHSO(5) is a chemical nuclease able to selectively recognize the minor groove of three consecutive AT base pairs of DNA and to mediate very precise cleavage chemistry at that particular site. This specific recognition and cleavage were used to probe the accessibility of the minor groove of DNA duplexes composed of one phosphodiester strand and one phosphorothioate strand. The cleavage of 5'-GCAAAAGC/5'-GCTTTTGC duplexes by Mn-TMPyP/KHSO(5) was monitored by HPLC coupled to electrospray mass analysis. Each single strand was synthesized with all-phosphate, all- Rp-phosphorothioate and all- Sp-phosphorothioate internucleotide bonds. We found that the manganese porphyrin was able to recognize its favorite (AT)(3)-box binding site within the heteroduplexes, as in the case of natural DNA. Molecular modeling studies on the interactions of the reactive porphyrin manganese-oxo species with both types of duplexes confirmed the experimental data.

Interaction of monosulfonate tetraphenyl porphyrin, a competitive inhibitor, with acetylcholinesterase

Monosulfonate tetraphenyl porphyrin (TPPS(1)) forms a 1:1 complex with electric eel acetylcholinesterase (AChE) inducing a loss in TPPS(1) absorbance at 402 nm and the appearance of a new absorbance centered at 442 nm. In the presence of AChE, the fluorescence of TPPS(1) at 652 nm is slightly narrowed, with the maximal 652 nm fluorescence shifted from 407 to 412 nm excitation wavelength. The fluorescence peak of TPPS(1) at 712 nm shifts to 716 nm in the presence of AChE. TPPS(1) is a competitive inhibitor of AChE. The addition of acetylcholine iodide (AChI) or the competitive inhibitor tetracaine to the preformed AChE-TPPS(1) complex results in a loss of the 442 nm absorbance band as the porphyrin is displaced from AChE. The absorbance peak does not decrease in the presence of procaine, a non-competitive inhibitor.

High-performance liquid chromatography with spectrophotometric and electrochemical detection of a series of manganese(III) cationic porphyrins

Recent studies have revealed potent pharmacological activities of manganese-containing cationic porphyrins. An analytical method employing high-performance liquid chromatography with spectrophotometric and electrochemical detection (HPLC-UV/EC) suitable for in vivo applications is described for a series of manganese(III) cationic porphyrins with good separation and resolution. In particular, this method resolved the four atropisomers of manganese(III) meso-tetrakis(N-ethylpyridinium-2-yl)porphyrin (MnTE-2-PyP5+ or AEOL-10113), verified by mass spectrometry. Electrochemical and spectrophotometric methods of detection were compared using manganese(III) meso-tetrakis(1,3-diethylimidazolium-2-yl)porphyrin (MnTDE-2-ImP5+ or AEOL-10150), the lead catalytic antioxidant of this series. Both methods of detection were quantitative, but electrochemical detection, although less specific for in vivo applications, appears to be considerably more sensitive than spectrophotometric detection.

A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling

The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 A. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.

Super-Charged Porphyrazines: Synthesis and Physical Properties of Octacationic Tetraazaporphyrins

We report the synthesis of octacationic macrocycles based on the porphyrazine (tetraazaporphyrin) core. The first stage is the synthesis of Mg(II) 2,3,7,8,12,13,17,18-octakis(4-pyridyl)porphyrazine, [Mgpz(pyr)(8)], and the parent [H(2)pz(pyr)(8)]. Both compounds are freely soluble in aqueous acid due to protonation of the pyridyl groups but with concomitant loss of Mg(2+) by the latter. Methylation of [H(2)pz(pyr)(8)] gives the octacation, 2,3,7,8,12,13,17,18-octakis(N-methyl-4-pyridiniumyl)porphyrazine, [H(2)pz(Me-pyr)(8)](8+), which is freely soluble in water as the chloride salt. The peripheral charges greatly lower the pK(a) values of the pyrrole protons of [H(2)pz(Me-pyr)(8)](8+) in aqueous solution. Global fitting of optical pH titration curves gives pK(a) values for the first and second deprotonations of 6.3 and 8.8 in 2.0 M NaCl and 4.1 and 5.6 at 0.1 M NaCl. The analysis further gives the UV-visible spectra of the [H(2)pz(Me-pyr)(8)](8+), [Hpz(Me-pyr)(8)](7+), and [pz(Me-pyr)(8)](6+) species. The free-base compound [H(2)pz(Me-pyr)(8)](8+) rapidly incorporates a variety of metal ions (Ba(II), Cd(II), Co(II), Cu(II), Mn(III), Ni(II), Pd(II), and Zn(II)) to form [Mpz(Me-pyr)(8)](8+). We present the complete synthesis and characterization of the [Nipz(Me-pyr)(8)](8+) and [Cupz(Me-pyr)(8)](8+) derivatives.

Capillary electrophoretic separation of cationic porphyrins

Cationic porphyrins have a wide variety of uses including those as nucleic acid binding and cleaving agents, as potential pharmacological agents, as electron donor/acceptors in intramolecular electron transfer processes and as analytical reagents. Herein, we report the separation of cationic porphyrins by capillary electrophoresis on fused silica in phosphate buffer at pH 2-5. The porphyrins studied in this work were synthesized from alkylation of the parent tetrapyridylporphyrin (TPyP) to give various pyridinium porphyrins. For example, methylation of TPyP gives a mixture of the mono-, cis-di-, trans-di-, tri- and tetramethylated porphyrins [e.g., 5,10,15,20-tetrakis(N-methyl-4-pyridiniumyl)-21H,23H-p orphyrin, TMPyP(4)]. Capillary electrophoresis on a synthetic mixture showed separation of four of these compounds. Mixtures after alkylation with iodopropionic acid and bromopropylamine were also separated. The cis-di- and trimethylated TMPyP derivatives were separated on a small preparative scale by centrifugal partition chromatography. Capillary electrophoresis was also used to separate metallo TMPyP(4) complexes including those of cobalt, copper, iron, manganese, palladium, tin, vanadium and zinc. The conformational isomers (atropisomers) of 5,10,15,20-tetrakis(N-methyl-2-pyridiniumyl)-21H,23H-p orphyrin, TMPyP(2), were also separated. Net charge, molecular mass and molecular shape all contribute to the differential retention of cationic porphyrins under capillary electrophoresis conditions. Additional factors affecting the separations, including aggregation and protonation of the porphyrins, were probed by evaluating the separation of TMPyP(4) and its butyl and octyl analogs as a function of solution conditions. Cationic porphyrins are difficult to separate using traditional chromatographic methods; capillary electrophoresis and centrifugal partition chromatography provide excellent new techniques for separation of this class of compounds.