Structure of DNA-porphyrin complex

Interaction of MnTOEtPyP4 porphyrin with DNA

The binding of water-soluble meso-tetra-(4N-oxyethylpyridyl) porphyrin (H2TOEtPyP4) and its manganese (III) derivative (MnTOEtPyP4) with calf thymus DNA have been quantitatively studied using UV/Vis spectrophotometry, Circular Dichroism (CD), thermal melting curves and viscometry. The results show, that porphyrins interact with DNA via one binding mode at low relative concentrations (r) and two binding modes at high values of r. The binding constant (Kb) and stoichiometry (n) were determined from binding isotherms for both porphyrin-DNA complexes. The thermal melting analysis indicates that the double-helical structure of DNA molecules is stabilizing in presence of studied porphyrins. At certain concentrations of porphyrin, two-stage melting curves were observed, which indicates the existence of two different binding modes. Obtained results show that MnTOEtPyP4 associates with DNA duplex via outside binding mode.Communicated by Ramaswamy H. Sarma.

Excited-State Dynamics Leading Either to Triplet Formation or Coordinative Expansion following Photolysis of Cu(II)-Porphyrins: A DFT, TD-DFT, Luminescence and Femtosecond Time-Resolved Absorbance Study

The photophysical properties of Cu(II) complexes with 5,10,15,20-meso-tetrakis(phenyl)porphyrin and 5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin are examined via the luminescence and femtosecond time-resolved absorbance methods, respectively. These studies are supported by DFT and TD-DFT calculations, which highlight the important role played by ligand-to-metal charge-transfer states in directing the system toward either intersystem crossing to the triplet hypersurface or coordinative expansion to a five-coordinate quasi-stable intermediate. The latter processes occur when the porphyrin is photolyzed in the presence of suitably located Lewis bases. Femtosecond time-resolved absorbance measurements of Cu(II)-5,10,15,20-meso-tetrakis(N-methylpyridium-4-yl)porphyrin confirm that the coordinative expansion in water occurs in approximately 700 fs, while crossing to the triplet hypersurface takes approximately 140 fs in the same solvent. These processes are mutually exclusive, although both can occur simultaneously depending on the environment of the porphyrin. The ratio of the two processes depends on the relative orientation of the Lewis base with respect to the copper atom at the time of excitation. As a consequence, copper porphyrins such as these are excellent probes in the environment of the porphyrin and can be used to identify the location of the porphyrin when interacting with DNA fragments.

The structural features of poly(dG-dC).poly(dG-dC) at complexation with some porphyrins

The binding peculiarities of the water-soluble meso-tetra-(4N-hydroxyethylpyridyl) porphyrin (H₂TOEtPyP4) and its Cu- and Co-derivatives (CuTOEtPyP4 and CoTOEtPyP4) with synthetic double-stranded alternating polynucleotide poly(dG-dC).poly(dG-dC) were investigated by UV/Vis absorption and circular dichroism (CD) methods. It was shown that the porphyrins with planar structure such as H₂TOEtPyP4 and CuTOEtPyP4 interact with poly(dG-dC).poly(dG-dC) via intercalation at low relative concentrations (r = [porphyrin]/[polynucleotide]), while at high r - via intercalation and external binding modes. In the case of no planar porphyrin CoTOEtPyP4 complexation occurs only by external binding mode. The binding constant K_b and the exclusion parameter n calculated for H₂TOEtPyP4, CuTOEtPyP4 and CoTOEtPyP4 porphyrins with poly(dG-dC).poly(dG-dC) complexes was 1.50 x10⁷, M^-1 (n = 1.76); 9.29 x10⁷, M^-1 (n = 1.18); and 0.28 x10⁷, M^-1 (n = 2.65) correspondingly. The values of binding parameters for each porphyrin-poly(dG-dC).poly(dG-dC) complexes demonstrated good agreement with the proposed binding models. Communicated by Ramaswamy H. Sarma.

Time-resolved infra-red studies of photo-excited porphyrins in the presence of nucleic acids and in HeLa tumour cells: insights into binding site and electron transfer dynamics

Cationic porphyrins based on the 5,10,15,20-meso-(tetrakis-4-N-methylpyridyl) core (TMPyP4) have been studied extensively over many years due to their strong interactions with a variety of nucleic acid structures, and their potential use as photodynamic therapeutic agents and telomerase inhibitors. In this paper, the interactions of metal-free TMPyP4 and Pt(II)TMPyP4 with guanine-containing nucleic acids are studied for the first time using time-resolved infrared spectroscopy (TRIR). In D2O solution (where the metal-free form exists as D2TMPyP4) both compounds yielded similar TRIR spectra (between 1450-1750 cm-1) following pulsed laser excitation in their Soret B-absorption bands. Density functional theory calculations reveal that vibrations centred on the methylpyridinium groups are responsible for the dominant feature at ca. 1640 cm-1. TRIR spectra of D2TMPyP4 or PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP), double-stranded {d(GC)5}2 or {d(CGCAAATTTGCG)}2 contain negative-going signals, 'bleaches', indicative of binding close to guanine. TRIR signals for D2TMPyP4 or PtTMPyP bound to the quadruplex-forming cMYC sequence {d(TAGGGAGGG)}2T indicate that binding occurs on the stacked guanines. For D2TMPyP4 bound to guanine-containing systems, the TRIR signal at ca. 1640 cm-1 decays on the picosecond timescale, consistent with electron transfer from guanine to the singlet excited state of D2TMPyP4, although IR marker bands for the reduced porphyrin/oxidised guanine were not observed. When PtTMPyP is incorporated into HeLa tumour cells, TRIR studies show protein binding with time-dependent ps/ns changes in the amide absorptions demonstrating TRIR's potential for studying light-activated molecular processes not only with nucleic acids in solution but also in biological cells.

Porphyrin induced structural destabilization of a parallel DNA G-quadruplex in human MRP1 gene promoter

Porphyrins are among the first ligands that have been tested for their quadruplex binding and stabilization potential. We report the differential interaction of the positional cationic porphyrin isomers TMPyP3 and TMPyP4 with a parallel G-quadruplex (GQ) formed by 33-mer (TP) regulatory sequence present in the promoter region of the human multidrug resistance protein 1 (MRP1) transporter gene. This GQ element encompasses the three evolutionary conserved SP1 transcription factor binding sites. Taking into account that SP1 binds to a non-canonical GQ motif with higher affinity than to a canonical duplex DNA consensus motif, it is suggestive that GQ distortion by cationic porphyrin will have important implications in the regulation of MRP1 expression. Herein, we employed biophysical analysis using circular dichroism, visible absorption, UV-thermal melting and steady-state fluorescence spectroscopy, reporting destabilization of MRP1 GQ by cationic porphyrins. Results suggest that TMPyP4 and TMPyP3 interact with GQ with a binding affinity of 10⁶ to 10⁷  M^-1 . Thermodynamic analysis indicated a significant decrease in melting temperature of GQ (ΔTm of 15.5°C-23.5°C), in the presence of 2 times excess of porphyrins. This study provides the biophysical evidence indicating the destabilisation of a parallel DNA G-quadruplex by cationic porphyrins.

meso-Tetra-(4-pyridyl)porphyrin/palladium(II) complexes as anticancer agents

This study reports the synthesis, structural characterization and cytotoxic activity of four new palladium/pyridylporphyrin complexes, with the general formula {TPyP[PdCl(P-P)]₄}(PF₆)₄, where P-P is 1,2-bis(diphenylphosphino)ethane (dppe), 1,3-bis(diphenylphosphino)propane (dppp), 1,2-bis(diphenylphosphino)butane (dppb) or 1,1'-bis(diphenylphosphino)ferrocene (dppf). The complexes were characterized by elemental analysis, and by FT-IR, UV/Vis, ¹H and ³¹P{¹H} NMR (1D/2D) spectroscopy. The slow evaporation of a methanolic solution of {TPyP[PdCl(dppb)]₄}(PF₆)₄ (in an excess of NaBF₄ salt) resulted in single crystals suitable for X ray diffraction, allowing the determination of the tridimensional structure of this complex, which crystallized in the P2₁/a space group. The cytotoxicity of the complexes against MDA-MB-231 (breast cancer cells) and MCF-10A (non-tumor breast cancer cells), was determined by the colorimetric MTT method, which revealed that all four complexes show selective indexes close to 1.2, lower than that of cisplatin for the same cells (12.12). The interaction of the complexes with CT-DNA was evaluated by UV-visible and viscosity measurements and it was determined that the complexes interact moderately with CT-DNA, probably by H-bonding/π-π stacking and electrostatic interactions.

Porphyrins as Colorimetric and Photometric Biosensors in Modern Bioanalytical Systems

Advances in porphyrin chemistry have provided novel materials and exciting technologies for bioanalysis such as colorimetric sensor array (CSA), photo-electrochemical (PEC) biosensing, and nanocomposites as peroxidase mimetics for glucose detection. This review highlights selected recent advances in the construction of supramolecular assemblies based on the porphyrin macrocycle that provide recognition of various biologically important entities through the unique porphyrin properties associated with colorimetry, spectrophotometry, and photo-electrochemistry.

Recent advances in porphyrin-based nanocomposites for effective targeted imaging and therapy

Porphyrins are organic compounds that continue to attract much theoretical interest, and have been called the "pigments of life". They have a wide role in photodynamic and sonodynamic therapy, along with uses in magnetic resonance, fluorescence and photoacoustic imaging. There is a vast range of porphyrins that have been isolated or designed, but few of them have real clinical applications. Due to the hydrophobic properties of porphyrins, and their tendency to aggregate by stacking of the planar molecules they are difficult to work with in aqueous media. Therefore encapsulating them in nanoparticles (NPs) or attachment to various delivery vehicles have been used to improve delivery characteristics. Porphyrins can be used in a composite designed material with properties that allow specific targeting, immune tolerance, extended tissue lifetime and improved hydrophilicity. Drug delivery, healing and repairing of damaged organs, and cancer theranostics are some of the medical uses of porphyrin-based nanocomposites covered in this review.

Functional DNA-based hydrogel intelligent materials for biomedical applications

Multifunctional intelligent DNA hydrogels have been reviewed for many biomedical applications.

Development of viscometric methods for studying the interaction of various porphyrins with DNA. Part IV: Meso-tetra-(4N-allylpyridyl) porphyrin and its Cu-, Co- and Zn-containing derivatives

The influence of water soluble cationic meso-tetra-(4N-allylpyridyl) porphyrin (H2TAlPyP4) and its metal complexes with Cu, Co and Zn on hydrodynamic and spectral behavior of DNA solutions has been studied by viscometry, CD and UV-vis spectroscopy methods. The results were compared with the results of previously conducted similar studies on meso-tetra-(3N-allylpyridyl) porphyrin (H2TAllPyP3). It has been shown that the change in position of peripheral radicals on the pyridylic ring has absolutely no effect on the rules of interaction of investigated porphyrins with DNA in the case of outside binders CoTAllPyP4 and ZnTAllPyP4. Planar porphyrin H2TAllPyP4 interacts with DNA predominantly by the intercalation mode at low relative concentrations of [Formula: see text] ([Formula: see text] [Porphyrin]/[DNA]) and by external binding mode at high values of [Formula: see text]. CuTAllPyP4 shows unusual behavior by interacting with DNA via a non-classical (partial) intercalation binding mode. It was shown that H[Formula: see text]TAllPyP3 and its metal complexes bind to DNA much more intensely than H2TAllPyP4 and its metal complexes.

Sequence selective photoinduced electron transfer of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to various DNAs (calf thymus DNA (Ct-DNA), poly[d(G-C)2], and poly[d(A-T)2]) have been investigated using circular dichroism and linear dichroism measurements. Based on the polarization spectroscopic results, it can be shown that the pyrenyl and porphryin planes are skewed to a large extent for PyTMPyP in an aqueous environment and in the binding site of poly[d(G-C)2]. In this complex, a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties occurs. On the other hand, PET was not observed in the PyTMPyP-poly[d(A-T)2] complex, whereas the fluorescence intensity of TMPyP was enhanced. The molecular planes of the pyrene and porphyrin moieties are almost parallel in the poly[d(A-T)2] and Ct-DNA adducts. Moreover, the generation of 1O2 species occurs only for the PyTMPyP-Ct-DNA and PyTMPyP-poly[d(A-T)2] complexes. We discuss the photophysical properties of PyTMPyP which are attributed to the binding patterns and the sequence of DNA bases.

Relationship between the photoinduced electron transfer and binding modes of a pyrene-porphyrin dyad to DNA

The binding modes of a pyrene-porphyrin dyad, (1-pyrenyl)-tris(N-methyl-p-pyridino)porphyrin (PyTMpyP), to DNA and its photophysical properties have been investigated using various spectroscopic techniques. The circular dichroism (CD) spectrum of PyTMpyP bound to DNA (PyTMpyP-DNA) showed one negative and two positive bands in the Soret region. The CD signal in the pyrene absorption region was positive. The shape of the CD spectrum does not support an intercalative binding mode of TMpyP, which would typically afford a negative CD band in the absence of the pyrene moiety. Linear dichroism (LD) experiments revealed a very small signal in the Soret region, which also challenges the intercalation of TMpyP into DNA. Upon excitation of the pyrene moiety, the emission intensity of porphyrin in aqueous solution was quenched due to a photoinduced electron transfer (PET) process between the pyrenyl and porphyrin moieties. On the other hand, the emission of porphyrin was markedly enhanced upon binding to DNA, as the PET process from the excited pyrene moiety to TMpyP was suppressed when bound to DNA. The PET process occurs in the timescale of 65 ps, and could be detected by femtosecond transient absorption spectroscopic methods. Two fluorescence decay times were observed for PyTMpyP in aqueous solution (0.78 and 4.8 ns). Both decay times increased upon binding to DNA owing to environment and/or conformational changes in PyTMpyP. The driving force (ΔG) of the PET process was evaluated under conditions of minor and major groove binding. The PET process and photophysical properties of the PyTMpyP dyad were concluded to be influenced by the binding mode.

Comparison of the Binding Geometry of Free-Base and Hexacoordinated Cationic Porphyrins to A- and B-Form DNA

Although the transition from B-DNA to the A-form is essential for many biological concerns, the properties of this transition have not been resolved. The B to A equilibrium can be analyzed conveniently because of the significant changes in circular dichroism (CD) and absorption spectrum. CD and linear dichroism (LD) methods were used to examine the binding of water-soluble meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) and its derivatives, Co-TMPyP, with B- and A-calf thymus DNA. B- to A-transitions occurred when the physiological buffer was replaced with a water-ethanol mixture (∼80 v/v %), and the fluorescence emission spectra of TMPyP bound to DNA showed a different pattern under ethanol-water conditions and water alone. The featureless broad emission bands of TMPyP were split into two peaks near at 658 and 715 nm in the presence of DNA under an aqueous solution. In the case of an ethanol-water system, however, the emission bands are split in two peaks near at 648 and 708 nm and 656 and 715 nm with and without DNA, respectively. This may be due to a change in the solution polarity. On the basis of the CD and LD data, TMPyP interacts with B-DNA via intercalation at a low ratio under a low ionic strength, 1 mM sodium phosphate. On the other hand, the interaction with A-DNA (80 v/v % ethanol-water system) occurs in a nonintercalating manner. This difference might be because the structural conformations, such as the groove of A-DNA, are not as deep as in B-DNA and the bases are much more tilted. In the case of Co-TMPyP, porphyrin binds preferably via an outside self-stacking mode with B- and A-DNA.

Thermodynamics of interaction of meso-tetra-(4N-oxyethylpyridyl) porphyrin and its Cu(II)- and Co(II)- containing derivatives with A and B forms of DNA

The interaction of water soluble meso-tetra-(4N-oxyethylpyridyl) porphyrin (TOEPyP4) and its Cu(II)- and Co(II)-containing derivatives (CuTOEPyP4 and CoTOEPyP4) with A and B forms of DNA at low ionic strength was studied via UV-vis spectrophotometry and Circular Dichroism. It is shown that the binding constant of TOEPyP4 and CuTOEPyP4 with A–DNA is two times larger than with B–DNA, and the binding constant of CoTOEPyP4 does not depend on the form of DNA. The thermodynamical analysis based on spectral data indicates the preferable entropic character of porphyrins binding with both forms of DNA. This result shows that at low ionic strength the external groove binding mode is a preferred binding mechanism of these porphyrins with both forms of DNA.

DNA binding of sunitinib: Spectroscopic evidence via circular dichroism and nuclear magnetic resonance

Sunitinib is a non-selective tyrosine kinase inhibitor, but in its chemical structure there can be discovered certain features, which suggest the ability to bind to DNA. These elements are the planar aromatic system and the tertiary amine function, which is protonated at the pH of the organism. In this study, the binding of the drug sunitinib to DNA was investigated using circular dichroism (CD), ¹H NMR and UV spectroscopies, along with CD melting. For these studies DNA was isolated from calf thymus (CT), salmon fish sperm (SS), and chicken erythrocyte (CE), however for our purposes an artificially constructed and highly purified plasmid DNA (pUC18) preparation proved to be the most suitable. DNA binding of the drug was confirmed by shifts in the characteristic CD bands of the DNA, the appearance of an induced CD (ICD) signal in the upper absorption region of sunitinib (300 nm-500 nm), and the evidence from CD melting studies and the NMR. Based on the CD and NMR measurements, it can be assumed that sunitinib has a multiple-step binding mechanism.

Photoactive meso-tetra(4-pyridyl)porphyrin-tetrakis-[chloro(2,2′bipyridine)platinum(ii) derivatives recognize and cleave DNA upon irradiation

Photoactive platinum porphyrins may be interesting as photosensitizers in photodynamic therapy and photochemotherapy, and we demonstrate their activity towards DNA cleavage under exposure to light.

DNA binding of Pd(TC3), a conformable cationic porphyrin with a long-lived triplet state

The goal of this work has been to synthesize and investigate Pd(TC3), an intercalating porphyrin that has conformable substituents capable of groove binding to B-form DNA. (TC3 denotes the doubly deprotonated form of 5,10,15,20-tetra[3-(3'-methylimidazolium-1'-yl)prop-1-yl]porphyrin.) Palladium(ii) is an apt choice for the central metal ion because it remains strictly four-coordinate and provides for a luminescent triplet excited state with a long lifetime. The DNA hosts are hairpin-forming sequences programmed to differ in base composition. Luminescence, absorbance, and circular dichroism results are consistent with the idea that congruent structural reorganization takes place at the host and ligand during uptake. Photoexcitation of DNA-bound Pd(TC3) generates a comparatively modest steady state concentration of singlet oxygen, due to a relatively slow reaction with molecular oxygen in solution. The sheer size of the substituent groups disfavors quenching, but groove-binding interactions compound the problem by inhibiting mobility. The results show how ligand design affects adduct structure as well as function.

Synthesis, Characterization, and Biological Activities of Pendant Arm-Pyridyltetrazole Copper(II) Complexes: DNA Binding/Cleavage Activity and Cytotoxic Studies

2-(1H-Tetrazol-5-yl)pyridine (L) has been reacted separately with Me2NCH2CH2Cl⋅HCl and ClCH2CH2OH to yield two regioisomers in each case, N,N-dimethyl-2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanamine (L1)/N,N-dimethyl-2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanamine (L2) and 2-[5-(pyridin-2-yl)-1H-tetrazol-1-yl]ethanol (L3)/2-[5-(pyridin-2-yl)-2H-tetrazol-2-yl]ethanol (L4), respectively. These ligands, L1-L4, have been coordinated with CuCl2 ⋅H2O in 1 : 1 composition to furnish the corresponding complexes 1-4. EPR Spectra of Cu complexes 1 and 3 were characteristic of square planar geometry, with nuclear hyperfine spin 3/2. Single X-ray crystallographic studies of 3 revealed that the Cu center has a square planar structure. DNA binding studies were carried out by UV/VIS absorption; viscosity and thermal denaturation studies revealed that each of these complexes are avid binders of calf thymus DNA. Investigation of nucleolytic cleavage activities of the complexes was carried out on double-stranded pBR322 circular plasmid DNA by using a gel electrophoresis experiment under various conditions, where cleavage of DNA takes place by oxidative free-radical mechanism (OH(⋅)). In vitro anticancer activities of the complexes against MCF-7 (human breast adenocarcinoma) cells revealed that the complexes inhibit the growth of cancer cells. The IC50 values of the complexes showed that Cu complexes exhibit comparable cytotoxic activities compared to the standard drug cisplatin.

Ground and excited state interactions of metalloporphyrin PtTMPyP4 with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2

The ground- and excited-state interactions of Pt(ii) meso-tetrakis(4-N-methylpyridyl)porphyrin (PtTMPyP4) with polynucleotides [poly(dG-dC)]2 and [poly(dA-dT)]2 have been investigated using UV/visible, circular dichroism, and steady-state and time-resolved emission spectroscopy. PtTMPyP4 intercalates into [poly(dG-dC)]2 with K∼ 10(6) M(-1). When bound to [poly(dG-dC)]2 in aerated solution there is a six-fold emission enhancement with 18 nm red-shift in emission maximum. Emission lifetimes are biexponential. In the presence of [poly(dA-dT)]2 at least two distinct groove-binding modes are observed, depending on the binding ratio. In [poly(dA-dT)]2 the emission intensity increases by a maximum factor of 17 with no shift in the emission spectrum. Three exponentials were required for lifetime fitting. The lower extent of emission enhancement in the presence of [poly(dG-dC)]2 suggests that a slow electron transfer may take place to guanine, which is significantly less efficient than that previously observed for PtTMPyP4 in the presence of guanosine 5'-monophosphate (GMP). The results are compared to those previously recorded with free base H2TMPyP4.

Synthesis, characterization and biomolecule-binding properties of novel tetra-platinum(ii)-thiopyridylporphyrins

New tetra-platinum(ii)-thiopyridylporphyrin complexes and their DNA binding studies.

E, Cruces M. MP, Sánchez M. JC. Genetic damage induced by CrO3 can be reduced by low doses of Protoporphyrin-IX in somatic cells of Drosophila melanogaster

Several epidemiological studies have reported the relation between chromium exposure (used in different industrial processes) and cancer risk. Evidence indicates that the hexavalent form is mutagenic and carcinogenic. Chemoprevention has emerged as a good strategy for reducing the risk from exposure to heavy metals. There is evidence that some tetrapyrrols such as protoporphyrin IX (PP-IX), a porphyrin without a metal center and which is a precursor of hemoglobin and cytochrome, acts as an antioxidant modulating the induction of antioxidant enzymes. The present study was performed to evaluate their antimutagenic potential of PP-IX against genetic damage induced by chromium trioxide (CrO3). The wing spot test was used. Groups of 48 h-old larvae were pretreated for 24 h with 0, 0.69, 6.9, or 69 mM of PP-IX, after which groups of larvae were fed 0.025-2.5 mM CrO3 solution in Drosophila instant medium. The results indicated that the lower PP-IX concentration (0.69 mM) significantly reduced the genetic damage induced by all CrO3 concentrations tested. In contrast, 6.9 and 69 mM only inhibited the damage induced by CrO3 2.5 mM. Absence of an inhibitor effect of PP-IX against 20 Gy gamma rays suggested that this porphyrin acted primarily by forming complexes with chromium at low doses, inactivating its genotoxic action rather than capturing or inactivating the reactive oxygen species generated by the chromium.

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.

Non-covalent assembly of meso-tetra-4-pyridyl porphine with single-stranded DNA to form nano-sized complexes with hydrophobicity-dependent DNA release and anti-tumor activity

DNA and porphyrin based therapeutics are important for anti-cancer treatment. The present studies demonstrate single-stranded DNA (ssDNA) assembles with meso-tetra-4-pyridyl porphine (MTP) forming porphyrin:DNA nano-complexes (PDN) that are stable in aqueous solution under physiologically relevant conditions and undergo dissociation with DNA release in hydrophobic environments, including cell membranes. PDN formation is DNA-dependent with the ratio of porphyrin:DNA being approximately two DNA nucleobases per porphyrin. PDN produce reactive oxygen species (ROS) in a light-dependent manner under conditions that favor nano-complex dissociation in the presence of hydrophobic solvents. PDN induce light-dependent cytotoxicity in vitro and anti-tumor activity towards bladder cancer xenografts in vivo. Light-dependent, PDN-mediated cell death results from ROS-mediated localized membrane damage due to lipid peroxidation with mass spectrometry indicating the generation of the lipid peroxidation products 9- and 13-hydroxy octadecanoic acid. Our results demonstrate that PDN have properties useful for therapeutic applications, including cancer treatment.

FROM THE CLINICAL EDITOR

In this study, porphyrin-DNA nanocomplexes were investigated as anti-cancer therapeutics inducing ROS production in a light-dependent manner. Efficacy is demonstrated in vitro as well as a in a bladder cancer xenograft model.

Structure-based model for light-harvesting properties of nucleic acid nanostructures

Programmed self-assembly of DNA enables the rational design of megadalton-scale macromolecular assemblies with sub-nanometer scale precision. These assemblies can be programmed to serve as structural scaffolds for secondary chromophore molecules with light-harvesting properties. Like in natural systems, the local and global spatial organization of these synthetic scaffolded chromophore systems plays a crucial role in their emergent excitonic and optical properties. Previously, we introduced a computational model to predict the large-scale 3D solution structure and flexibility of nucleic acid nanostructures programmed using the principle of scaffolded DNA origami. Here, we use Förster resonance energy transfer theory to simulate the temporal dynamics of dye excitation and energy transfer accounting both for overall DNA nanostructure architecture as well as atomic-level DNA and dye chemical structure and composition. Results are used to calculate emergent optical properties including effective absorption cross-section, absorption and emission spectra and total power transferred to a biomimetic reaction center in an existing seven-helix double stranded DNA-based antenna. This structure-based computational framework enables the efficient in silico evaluation of nucleic acid nanostructures for diverse light-harvesting and photonic applications.

A method for sensitive staining of DNA in polyacrylamide gels using basic fuchsin

BACKGROUND

PAGE is a widely used analytical method to resolve components of a DNA mixture based on their size. Various DNA visualization methods including fluorescence, visible dye and silver have been used for the detection of gel-separated DNA, with each having different advantages and disadvantages in terms of sensitivity, safety and simplicity.

RESULTS

A fast and sensitive visible dye-based staining method for DNA in polyacrylamide gels using basic fuchsin (BF) is described. As low as 10-20 pg of DNA can be visualized within 10 min; the sensitivity is fourfold more sensitive than that of SYBR® Gold stain, the most sensitive commercial fluorescent probe, but similar to silver staining kit from GE Healthcare. In addition, the mechanism studies suggest that the interaction of BF with DNA is mainly contributed by non-intercalative binding mode.

CONCLUSION

By comprehensive studies of this visible dye-based protocol, we concluded that BF stain is a fast and sensitive method currently available for detecting DNA in polyacrylamide gels.

In vitro assays predictive of telomerase inhibitory effect of G-quadruplex ligands in cell nuclei

G-quadruplex-binding and telomerase-inhibiting capacities of G-quadruplex ligands were examined under a cell nuclei-mimicking condition including excess double-stranded DNA (λ DNA) and molecular crowding cosolute (PEG 200). Under the cell nuclei-mimicking condition, a cationic porphyrin (TMPyP4) did not bind to the G-quadruplex despite the high affinity (Ka = 3.6 × 10(6) M(-1)) under a diluted condition without λ DNA and PEG 200. Correspondingly, TMPyP4 inhibited telomerase activity under the diluted condition (IC50 = 1.6 μM) but not under the cell nuclei-mimicking condition. In contrast, the Ka and IC50 values of an anionic copper phthalocyanine (Cu-APC) under the diluted (2.8 × 10(4) M(-1) and 0.86 μM) and the cell nuclei-mimicking (2.8 × 10(4) M(-1) and 2.1 μM) conditions were similar. In accordance with these results, 10 μM TMPyP4 did not affect the proliferation of HeLa cells, while Cu-APC efficiently inhibited the proliferation (IC50 = 1.4 μM). These results show that the cell nuclei-mimicking condition is effective to predict capacities of G-quadruplex ligands in the cell. In addition, the antiproliferative effect of Cu-APC on normal cells was smaller than that on HeLa cells, indicating that the cell nuclei-mimicking condition is also useful to predict side effects of ligands.

Disturbance of DNA conformation by the binding of testosterone-based platinum drugs via groove-face and intercalative interactions: a molecular dynamics simulation study

BACKGROUND

To explore novel platinum-based anticancer agents that are distinct from the structure and interaction mode of the traditional cisplatin by forming the bifunctional intrastrand 1,2 GpG adduct, the monofunctional platinum+DNA adducts with extensive non-covalent interactions had been studied. It was reported that the monofunctional testosterone-based platinum(II) agents present the high anticancer activity. Moreover, it was also found that the testosterone-based platinum agents could cause the DNA helix to undergo significant unwinding and bending over the non-testosterone-based platinum agents. However, the interaction mechanisms of these platinum agents with DNA at the atomic level are not yet clear so far.

RESULTS

In the present work, we used molecular dynamics (MD) simulations and DNA conformational dynamics calculations to study the DNA distortion properties of the testosterone-based platinum+DNA, the improved testosterone-based platinum+DNA and the non-testosterone-based platinum+DNA adducts. The results show that the intercalative interaction of the improved flexible testosterone-based platinum agent with DNA molecule could cause larger DNA conformational distortion than the groove-face interaction of the rigid testosterone-based platinum agent with DNA molecule. Further investigations for the non-testosterone-based platinum agent reveal the occurrence of insignificant change of DNA conformation due to the absence of testosterone ligand in such agent. Based on the DNA dynamics analysis, the DNA base motions relating to DNA groove parameter changes and hydrogen bond destruction of DNA base pairs were also discussed in this work.

CONCLUSIONS

The flexible linker in the improved testosterone-based platinum agent causes an intercalative interaction with DNA in the improved testosterone-based platinum+DNA adduct, which is different from the groove-face interaction caused by a rigid linker in the testosterone-based platinum agent. The present investigations provide useful information of DNA conformation affected by a testosterone-based platinum complex at the atomic level.

Thermodynamic investigation of manganese(III) 5-(1-(4-carboxybutyl)pyridinium-4-yl) 10,15,20-tris-(1-methylpyridinium-4-yl)porphyrin with calf thymus DNA

Binding properties of two water-soluble porphyrins, manganese(III) 5-(1-(4-carboxybutyl)pyridinium-4-yl) 10,15,20-tris(1-methylpyridinium-4-yl)porphyrin ( Mn(III)5-CBPyP ) and manganese(III) 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin ( Mn(III)TMPyP ), in the presence of various concentration of calf thymus DNA (ct-DNA), has been studied in 7.5 mM phosphate buffer, pH = 7.2 and at various temperatures by UV-vis absorption, resonance light scattering (RLS) and fluorescence spectroscopy and viscosity measurement. Optical absorption and RLS measurements have demonstrated three different species of both porphyrins form in DNA solution. The thermodynamic parameters were calculated by van't Hoff equation at various temperatures. The values of -4.89 kJ.mol-1 and +65.98 J.mol-1.K-1 for Mn(III)5-CBPyP and -14.92 kJ.mol-1 and +15.46 J mol-1.K-1 for TMPyP were estimated for enthalpy and entropy changes of interaction, respectively. The data indicate that the process is exothermic and enthalpy- and entropy-driven, suggesting that electrostatic forces play a considerable role in the interaction process. The binding of both porphyins to DNA quenches fluorescence emission of ethidium bromide (EB) and the quenching process obeys linear Stern-Volmer relationship, indicating the quenching of electron transfer of EB from its binding sites by these porphyrins. The results of using these techniques indicate the external mode of binding for both porphyrins and a higher binding affinity of Mn(III)5-CBPyP with respect to Mn(III)TMPyP .

Electrospray mass spectrometry for the study of the non-covalent interactions of porphyrins and duplex desoxyribonucleotides

An overview of the use of electrospray mass spectrometry for the study of non-covalent interactions of cationic porphyrins and small DNA duplexes, highlighting the work developed in the Mass Spectrometry Laboratory of the University of Aveiro, is presented here.

Interaction of TMPyP4, TMPyP3, and TMPyP2 with Intramolecular G-Quadruplex Formed by Promoter Region of Bcl2 and KRAS NHPPE

Oncogenes are rich in guanine and capable of forming quadruplex structure. Promoter regions oncogenes such as Bcl2 and KRAS NHPPE are rich in guanine content and they can form quadruplex structures. Alterations in the mode and nature of molecular binding to DNA, certainly has effect on the posttranscriptional activities. Recent experiments indicate that structure of quadruplex complex and ligand has predominant role on ligand-quadruplex DNA interaction. In order to understand the nature of each ligand interaction with quadruplex DNA, Bcl2, KRAS NHPPE quadruplex DNA interaction with three porphyrin was studied using spectroscopy, microcalorimetry and mass spectrometry. Our studies, indicate that mode of ligand interaction varies with structure, environment and concentration of ligand. Fluorescence quenching experiments show that TMPyP4 interaction is ligand concentration dependent. Job plots and ITC experiments demonstrate that four molecules of TMPyP4 and two molecules of TMPyP3, TMPyP2 interact with each quadruplex complex. Through ITC titrations, ligand binding constant are higher for TMPyP4 (≈107 M−1) compared to TMPyP3, TMPyP2 (≈105 M−1). ESI-MS experiments confirm the stoichiometry of TMPyP4 : 39Bcl2 is 4 : 1 at saturation and it is 2 : 1 in case of KRAS NHPPE quadruplex.