Comparison of the efficiency and the specificity of DNA-bound and free cationic porphyrin in photodynamic virus inactivation

The risk of transmitting infections by blood transfusion has been substantially reduced. However, alternative methods for inactivation of pathogens in blood and its components are needed. Application of photoactivated cationic porphyrins can offer an approach to remove non-enveloped viruses from aqueous media. Here we tested the virus inactivation capability of meso-Tetrakis(4-N-methylpyridyl)porphyrin (TMPyP) and meso-Tri-(4-N-methylpyridyl)monophenylporphyrin (TMPyMPP) in the dark and upon irradiation. T7 bacteriophage, as a surrogate on non-enveloped viruses was selected as a test system. TMPyP and TMPyMPP reduce the viability of T7 phage already in the dark, which can be explained by their selective binding to nucleic acid. Both compounds proved to be efficient photosensitizers of virus inactivation. The binding of porphyrin to phage DNA was not a prerequisite of phage photosensitization, moreover, photoinactivation was more efficiently induced by free than by DNA bound porphyrin. As optical melting studies and agarose gel electrophoresis of T7 nucleoprotein revealed, photoreactions of TMPyP and TMPyMPP affect the structural integrity of DNA and also of viral proteins, despite their selective DNA binding.     

Photoinduced inactivation of T7 phage sensitized by symmetrically and asymmetrically substituted tetraphenyl porphyrin: comparison of efficiency and mechanism of action

We investigated the efficiency and the mechanism of action of two--one symmetrically and one asymmetrically substituted--glycoconjugated tetraphenyl porphyrins in their photoreaction with T7 phage as a model of nucleoprotein (NP) complexes. A correlation was found between the dark inactivation of T7 and the binding of porphyrins determined by fluorescence spectroscopy. Both types of porphyrin sensitized the photoinactivation of T7, but the slopes of inactivation kinetics were markedly different. There was no correlation between the dark binding and the photosensitizing efficacy of the two derivatives. Inactivation was moderated by 1,3-diphenylisobenzofuran and 1,3-dimethyl-2-thiourea; however, neither of them inhibited T7 inactivation completely. This result suggests that both Type-I and Type-II reactions play a role in the virus inactivation. Optical melting studies revealed structural changes in the protein part but not in the DNA of the photochemically treated NP complex. Polymerase chain reaction analysis of a 555 bp segment of gene 1 and a 3826 bp segment of genes 3 and 4 failed to demonstrate any DNA damage.     

AFM‐Correlated CSM‐Coupled Raman/Fluorescence Studies on Selective Interactions of Water Soluble Porphyrins with DNA

The Raman and fluorescence spectroscopic properties of water‐soluble oxo‐titanium(IV) mesotetrakis (1‐methyl pyridium‐4‐yl) porphyrin (O=Ti(TMPyP)⁴⁺) bound with calf thymus DNA and artificial DNAs such as double stranded poly[d(A‐T)₂] and poly[d(G‐C)₂] have been investigated on the single DNA molecule basis by AFM‐correlated confocal scanning microscope (CSM)‐coupled Raman and fluorescence spectroscopic techniques as well as the ensemble‐averaged spectroscopy. The ensemble‐averaged spectroscopic studies imply that the porphyrin interacts with DNA in different groove binding patterns depending on the base pairs. AFM‐images of the different DNAs bound with O=Ti(TMPyP)⁴⁺ were measured, and their morphologies are found to depend on kind of base pairs interacting with O=Ti(TMPyP)⁴⁺. Being correlated with the AFM images, the CSM‐coupled Raman and fluorescence spectral properties of the three different single O=Ti(TMPyP)⁴⁺‐DNA complexes were observed to be highly resolved and sensitive to base pair‐dependent axial ligation of Ti‐O bond as compared to the corresponding ensemble‐averaged spectral properties, which affect the groove binding and its strength of the O=Ti(TMPyP)⁴⁺ with DNA. The axial ligation was found to be accompanied by vibration structural change of the porphyrin ring, leading to keep the shape of double stranded poly[d(A‐T)₂] rigid while poly‐[d(G‐C)₂] and calf thymus DNA flexible after binding with the oxo‐titanyl porphyrin. The base pair dependence of the fluorescence decay times of the DNA‐bound porphyrins was also observed, implying that an excited‐state charge transfer takes place in the G‐C rich major groove in calf thymus DNA. These results suggest that binding of O=Ti(TMPyP)⁴⁺ is more preferential with the G‐C rich major groove than with the A‐T rich minor groove in calf thymus DNA so that the morphology of DNA is changed.     

Fluorescent recognition of deoxyribonucleic acids by a quantum dot/meso-tetrakis(N-methylpyridinium-4-yl)porphyrin complex based on a photo induced electron-transfer mechanism

We have developed a new fluorescent probe of thioglycolic acid (TGA)-capped CdTe quantum dots (QDs) complexed with a model drug, meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) for detecting deoxyribonucleic acids (DNAs). This probe operates with an “Off–On” mode: TMPyP quenches the photoluminescence (PL) of QDs via a photo induced electron-transfer (PIET) process; the presence of DNA can break the QD/TMPyP complexation, interrupting the PIET process, and switch on the PL of QDs. Sensitive detection of DNA with the detection limit of 0.16 nM and a linear detection range of 0.25–6.0 nM are achieved. Importantly, this probe can be used to distinguish the binding modes of DNA–TMPyP interactions, exhibiting the DNA sequence-dependent PL recovery behaviors. The obtained binding constant for poly(dA)·poly(dT) is ∼3.30 × 10⁷ L mol⁻¹, which is approximately one order of magnitude larger than those for native DNAs and poly(dG)·poly(dC). Furthermore, the thymine bases preferential of the TMPyP–DNA interaction is proved by this probe.     

Experimental and DFT studies on DNA binding and photocleavage of two cationic porphyrins. Effects of the introduction of a carboxyphenyl into pyridinium porphyrin

The DNA-binding affinities and DNA photocleavage abilities of cationic porphyrin, 5-(4-carboxyphenyl)-10,15,20-tris(4-methylpyridiniumyl)porphyrin (CTMPyP), and its reference compound meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (H2TMPyP) have been investigated. The DNA-binding behaviors of the two compounds in NaH2PO4 buffer were compared systematically by using absorption, fluorescence and circular dichroism (CD) spectra, thermal denaturation as well as viscosity measurements. The experimental results show that CTMPyP binds to DNA in an outside binding mode, while H2TMPyP in an intercalative mode. Photocleavage experiments reveal that both two compounds employ 1O2-mediated mechanism in cleaving DNA and H2TMPyP can cleave DNA more efficiently than CTMPyP. Theoretical calculations were carried out with the density functional theory (DFT), and the calculated results indicate that the character and energies of some frontier orbitals of CTMPyP are quite different from those of H2TMPyP. These theoretical results can be used to explain their different DNA-binding modes and affinities to a certain extent.     

Model of cooperative interaction of TMPyP4 porphyrine with DNA quadruplex

Intrinsic binding constants of the TMPyP4 porphyrin with G-quadruplex of DNA (ckit2) have been calculated; they can be applied as reference for quantitative evaluation of the possibility of such structures participation in biochemical processes. The conclusion about existence of two different sites of the TMPyP4 binding to ckit2 binding made earlier on the basis of the stepwise complex formation model has been revised using the model of mutual influence (cooperativity) of the ligands bound to the oligonucleotide. The model has been verified using principal component analysis and factor analysis methods. The ckit2 biomolecule can be considered as an oligonucleotide with equivalent mutually affecting binding sites.     

Interaction of water-soluble bridged porphyrin with DNA

A water-soluble porphyrin dimer (Por Dimer) containing eight positive charges, bridged by 4,4′-dicarboxy-2,2′-bipyridine, has been synthesized. With Meso-tetrakis(N-methyl-pyridium-4-yl)porphyrin (H₂TMPyP) as the reference compound, the water-soluble porphyrin dimer was investigated for its interaction with DNA by absorption, fluorescence, and circular dichroism (CD) spectroscopy. The apparent affinity binding constant (K _app = 1.2 × 10⁶) of Por Dimer binding to CT DNA was measured by a competition method with ethidium bromide (EB) (that of H₂TMPyP was 6.9 × 10⁶). The cleavage ability of Por Dimer to pBR322 plasmid DNA was studied by gel electrophoresis. The results suggest that the binding modes of Por Dimer were complex and involve both intercalation and outside binding. __________ Translated from Acta Chimica Sinica, 2007, 65(22): 2597–2603     

Interactions between meso-tetrakis(4-(<Emphasis Type="Italic">N</Emphasis>-methylpyridiumyl))porphyrin TMPyP4 and DNA G-quadruplex of telomeric repeated sequence TTAGGG

The binding properties between meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the parallel DNA G-quadruplex (G4) of telomeric repeated sequence 5′-TTAGGG-3′ have been characterized by means of circular dichroism, steady-state absorption, steady-state fluorescence and picosecond time-resolved fluorescence spectroscopies. The binding constant and the saturated binding number were determined as 1.29×10⁶ (mol/L)⁻¹ and 3, respectively, according to steady-state absorption spectroscopy. Based on the findings by the use of time-resolved fluorescence spectroscopic technique, it is deduced that TMPyP4 binds to a DNA G-quadruplex with both the thread-intercalating and end-stacking modes and at the saturated binding state, one TMPyP4 molecule intercalates into the intervals of G-tetrads while the other two stack to the ends of the DNA G-quadruplex. Supported by the National Natural Science Foundation of China (Grant Nos. 20442004, 10576002 and 20703067)     

Supramolecular design of a porphyrin-[60]fullerene photocurrent generation system on a DNA scaffold fabricated by a conjugate polymer film

DNA which binds monocationic [60]fullerene (1) and tetracationic porphyrin (TMPyP) was readily fabricated by electrochemical oxidative polymerization of 3.4-ethylenedioxythiophene (EDOT) and the resultant poly(EDOT) composite was deposited on an ITO electrode as a stable thin film. Spectral and CV analyses established that one 1 and one TMPyP are bound per 57 nucleobase units, that is, every three pitches of DNA. Photoirradiation of this 1/TMPyP/DNA-poly(EDOT) film generated a photocurrent in 3.8% quantum yield, which was much higher than those obtained from 1/DNA and TMPyP/DNA systems. One can conclude, therefore that the photoexcited energy of TMPyP is transferred to 1, which is collected by the electron-conducting poly(EDOT) film. The present paper shows that DNA is useful as a scaffold to arrange redox-active couples in a one-dimensional matrix.     

DNA-bound lipids: computer modeling of DNA interaction with stearic acid and unsaturated fatty acids

It was shown for the first time by computer experiments that fatty acids are strongly bound to DNA. This is consistent with the presence of free fatty acids in the specimens of DNA-bound lipids isolated from various cells. Binding of all fatty acids to the DNA minor groove is stronger than to the major groove, which is correlated with the presence of two pools of free fatty acids isolated from DNA specimens by biochemical methods. Since DNA polymerase is also bound to the DNA minor groove, fatty acids can play an important role in the regulation mechanism of DNA replication and signal transmission. The energy of interaction of fatty acids with DNA depends on both the number of double bonds and the geometric configuration of the fatty acid and the nucleotide composition of DNA. Dependence on the bond energy in the DNA—fatty acid complex on the nucleotide composition attests to the possibility of site-specific binding of lipids to DNA. On passing from a saturated fatty acid to unsaturated acids containing one, two, or three double trans-bonds, the bond energy of DNA with the fatty acid gradually decreases. The presence of one or three double cis-bonds results in weakening of the strength of the DNA—fatty acid complexes compared to those with the saturated acid. The strongest binding between DNA and fatty acid was found for the unsaturated acid with two double cis-bonds (linoleic). This can be explained by the fact that the bent (boomerang) shape of the molecule of this acid follows the curve of the DNA helix. The pattern of variation of the energy of DNA complexes with stearic, linoleic, oleic, and linolenic acids correlates with experimental data on the melting points of these complexes: the more stable the DNA—fatty acid complex, the lower the melting point of DNA.     

Study on spectroscopic characterization of Cu porphyrin/Co porphyrin and their interactions with ctDNA

The luminescence behaviors of Cu(II) meso-tetrakis (4-N-methyl-pyridiniumyl) porphyrin (Cu(II)TMPyP) and Co(II) meso-tetrakis (4-N-methyl-pyridiniumyl) porphyrin (Co(II)TMPyP) are investigated, and their interactions with calf thymus DNA (ctDNA) are studied by UV-vis, fluorescence and resonance light scattering (RLS) and based on the changes of UV-vis spectra, fluorescence and RLS spectra, the intrinsic binding constants of Cu(II)TMPyP/Co(II)TMPyP with ctDNA are obtained in the case of phosphate buffer solution (pH 7.2), respectively. According to the experimental results, it can be inferred that the interaction model of Cu(II)TMPyP with ctDNA is intercalative binding, while Co(II)TMPyP is the long-range assembly on the molecular surface of ctDNA.     

Photophysical properties and photoinduced electron transfer within host-guest complexes of 5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrin with water-soluble calixarenes and cyclodextrins.

We report the formation of host-guest complexes between water-soluble calix[n]arene-p-tetrasulfonates (n = 4, 6, 8) or 2-hydroxypropyl-cyclodextrins (alpha-, beta-, gamma-) and the tetratosylate salt of 5,10,15,20-tetrakis(4-N-methylpyridyl)porphyrin (TMPyP). The binding constants ranging between 10(2) and 10(5) M-1 were calculated from the absorption and fluorescence changes. Calix[4]arene-p-tetrasulfonate has a high binding affinity and forms with TMPyP a 1:1 complex, whereas other calixarenes bind two molecules of TMPyP. Electrostatic attraction is the dominating binding mode. Binding to calixarenes leads to a considerable decrease of the quantum yields of the triplet and excited singlet states and to shortening of the singlet and triplet lifetimes of TMPyP. The quenching mechanism is attributed to electron transfer between calixarene phenolates and excited TMPyP. Photoinduced electron transfer within a novel supramolecular complex calixarene/TMPyP (electron donor)/methyl viologen (electron acceptor) has been proven by absorption and fluorescence measurements. Electrostatic attraction between the cationic donor and cationic acceptor, on the one hand, and the anionic host, on the other, overcomes the electrostatic repulsion forces. In contrast, the interaction of cyclodextrin with TMPyP is hydrophobic in nature and only slightly influences the photophysical properties of TMPyP. The different behavior of TMPyP bound to either of the hosts has been assigned to the specific effects of the dominant binding modes, viz. the electrostatic attraction for calixarenes and the hydrophobic interactions for inclusion complexes with cyclodextrins.     

Aggregation and solution behavior of 5-(1-(4-carboxybutyl) pyridinum-4-yl) 10,15,20-tris (1-methylpyridinium-4-yl) porphyrin: A resonance light scattering, fluorescence and absorption spectroscopic study

Aggregation behavior of water soluble porphyrins, 5-(1-(4-carboxybutyl) pyridinum-4-yl) 10,15,20-tris (1-methylpyridinium-4-yl) porphyrin (5-CBPyP) in the presence of various concentrations of calf thymus DNA (ct-DNA) and sodium chloride were studied in comparison with meso-tetrakis (4-N-methyl pyridinum) porphyrin (TMPyP), by optical absorption, fluorescence and resonance light scattering (RLS) spectroscopies. Both porphyrins obey Beer’s law in extended range of concentration. Optical absorption and RLS measurements demonstrated nonaggregation for both porphyrins under increasing concentration of ct-DNA and NaCl. However, in comparison, 5-CBPyP had less tendency for aggregation that may be taken as an advantage for its probable application in photodynamic therapy of cancer. The trend of changes in absorption spectra of both porphyrins in the presence of ct-DNA indicates the homogeneous intercalation binding mode. The values of (2.81 ± 0.28) × 10⁶ M^?1 and (0.95 ± 0.09) × 10⁶ M^?1 were obtained for apparent binding constant of TMPyP and 5-CBPyP from analysis of optical absorption data, respectively. This indicates the less affinity of 5-CBPyP to ct-DNA in comparison with TMPyP. The binding of both porphyrins to ct-DNA quenches fluorescence emission of Ethidium bromide (EB) that is bound to ct-DNA. The quenching process obeys linear Stern-Volmer relationship indicating the displacement of EB from its binding sites by these porphyrins. The results of this technique also represent the intercalation mode of binding for both porphyrins and higher binding affinity of TMPyP compared with 5-CBPyP.     

水溶性桥联双卟啉与DNA相互作用的研究

以4,4'-二羧酸-2,2'-联吡啶为桥联试剂, 合成了一种含8个阳离子的水溶性桥联双卟啉(PD). 以5,10,15,20-四(4-N-甲基吡啶盐)卟啉(H₂TMPyP)为参照物, 使用紫外-可见光谱、荧光光谱、圆二色谱研究了水溶性双卟啉与小牛胸腺DNA (CT DNA)的相互作用, 以溴化乙啶(EB)竞争法测定了PD与CT DNA的表观键合常数(K_app)为1.2×10⁶ L•mol^－1 (H₂TMPyP为6.9×10⁶ L•mol^－1), 并使用凝胶电泳研究了PD对pBR322质粒DNA的切割能力. 实验结果表明PD与CT DNA的作用方式是插入和外部结合的混合模式.     

Simultaneous binding of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin and 4',6-diamidino-2-phenylindole at the minor grooves of poly(dA).poly(dT) and poly[d(A-T)(2)]: fluorescence resonance energy transfer between DNA bound drugs

The spectral properties of meso-tetrakis(N-methylpyridinium-4-yl)porphyrin (TMPyP) bound to poly(dA).poly(dT) and poly[d(A-T)(2)] in the presence and in the absence of 4',6-diamidino-2-phenylindole (DAPI) have been studied. DAPI fits deeply into the minor groove of both poly(dA).poly(dT) and poly[d(A-T)(2)], and TMPyP is also situated at the minor groove. The nature of the absorption, circular dichroism (CD), and flow linear dichroism (LD) spectra of the TMPyP-poly(dA).poly(dT) and -poly[d(A-T)(2)] complexes in the Soret band is essentially unaffected whether the minor groove is blocked by DAPI or not, although small variations been noticed in the presence of DAPI. Furthermore, a close analysis of the reduced LD spectrum in the Soret band results in angles of approximately 80 degrees and 55 degrees between transition moments of the TMPyP and DNA helix axes in the absence of DAPI. All these observations indicate that the side of TMPyP whose structure resembles that of classical minor groove binding drugs does not fit deeply into the minor groove. This suggests that TMPyP binds across the minor groove: two positively charged pyridiniumyl rings interact electrostatically with negatively charged phosphate groups of DNA. When DAPI and TMPyP are simultaneously bound to poly(dA).poly(dT) or poly[d(A-T)(2)], the fluorescence intensity of DAPI decreases as TMPyP concentration increases, indicating that the excited energy of DAPI is transferred to TMPyP.     

Validation of phage T7 biological dosimeter by quantitative polymerase chain reaction using short and long segments of phage T7 DNA

Phage T7 can be used as a biological dosimeter; its reading, the biologically effective dose (BED), is proportional to the inactivation rate |ln (n/n0)|. For the measurement of DNA damage in phage T7 dosimeter, a quantitative polymerase chain reaction (QPCR) methodology has been developed using 555 and 3826 bp fragments of phage T7 DNA. Both optimized reactions are so robust that an equally good amplification was obtained when intact phage T7 was used in the reaction mixture. In the biologically relevant dose range a good correlation was obtained between the BED of the phage T7 dosimeter and the amount of ultraviolet (UV) photoproducts determined by QPCR with both fragments under the effect of five various UV sources. A significant decrease in the yield of photoproducts was detected by QPCR in isolated T7 DNA and in heated phage compared with intraphage DNA with all irradiation sources. Because the yield of photoproducts was the same in B, C and A conformational states of T7 DNA, a possible explanation for modulation of photoproduct frequency in intraphage T7 DNA is that the presence of bound phage proteins induces an alteration in DNA structure that can result in increased induction of photoproducts.     

Influence of Phage Proteins on Formation of Specific UV DMA Photoproducts in Phage T7

Phage T7 can be used as a biological UV dosimeter. Its reading is proportional to the inactivation rate expressed in HT7 units. To understand the influence of phage proteins on the formation of DNA UV photoproducts, cyclobutane pyrimidine dimers (CPD) and (6-4)photoproducts ((6-4)PD) were determined in T7 DNA exposed to UV radiation under different conditions: intraphage T7 DNA, isolated T7 DNA and heated phage. To investigate the effects of various wavelengths, seven different UV sources have been used. The CPD and (6-4)PD were determined by lesion-specific antibodies in an immunodot-blot assay. Both photoproducts were HT7 dose-dependently produced in all three objects by every irradiation source in the biologically relevant UV dose range (1-10 HT7). The CPD to (6-4)PD ratios increased with the increasing effective wavelength of the irradiation source and were similar in intraphage T7 DNA, isolated DNA and heated phage with all irradiation sources. However, a significant decrease in the yield of both photoproducts was detected in isolated T7 DNA and in heated phage compared to intraphage DNA, the decrease was dependent on the irradiation source. Both photoproducts were affected the same way in isolated T7 DNA and heated phage, respectively. The yield of CPD and (6-4)PD was similar in B, C-like and A conformational states of isolated T7 DNA, indicating that the conformational switch in the DNA is not the decisive factor in photoproduct formation. The most likely explanation for modulation of photoproduct frequency in intraphage T7 DNA is that the presence of bound phage proteins induces an alteration in DNA structure that can result in an increased rate of dimerization and (6-4)PD production of adjacent based in intraphage T7 DNA.     

Conformational conversion of DNA G-quadruplex induced by a cationic porphyrin

The interactions between cationic meso-tetrakis(4-(N-methylpyridiumyl))porphyrin (TMPyP4) and the G-quadruplex (G4) of human telomeric single-strand oligonucleotide d(TTAGGG)₂ (S12) have been investigated by means of circular dichroism (CD), UV–visible absorption and fluorescence spectroscopies. It is found that TMPyP4 can preferentially induce the conformational conversion of the G4 structure from the parallel type to the parallel/antiparallel mixture in the presence of K⁺, and that it can directly induce the formation of antiparallel G4 structure from the single-strand oligonucleotide S12 in the absence of K⁺. Furthermore, the comparable experiments of TMPyP4 with two single-strand oligonucleotides S6 d(TTAGGG) and S24 d(TAGGG(TTAGGG)₃T) in the absence of K⁺ show that TMPyP4 can also induce the formation of antiparallel G4 from S24 but not from S6, indicating that the end-loops of the G4 structure are the key factors for the formation of G4 induced by TMPyP4.