DNA Photocleavage Research Articles

Near-IR/Visible-Emitting Thiophenyl-Based Ru(II) Complexes: Efficient Photodynamic Therapy, Cellular Uptake, and DNA Binding.

Near-IR-emitting and/or efficiently photodynamic water-soluble Ru(II) complexes that hold great application potentials as photodynamic therapy and/or photodetection agents for cancers have been poorly explored. In this paper, the solvatochromism, calf thymus DNA binding, and singlet oxygen generation properties of a known ruthenium(II) complex of visible-emitting [Ru(bpy)2(dtdpq)](ClO4)2 (Ru1) and a new homoleptic complex of near-IR-emitting [Ru(dtdpq)3](ClO4)2 (Ru2) (bpy = 2,2'-bipyridine, dtdpq = 2,3-bis(thiophen-2-yl)pyrazino[2,3-f][1,10]phenanothroline) in water are reported. Moreover, DNA photocleavage, singlet oxygen generation in HeLa cells, cellular uptake/localization, and in vitro photodynamic therapy for cancer cells of water-soluble Ru1 are described in detail. The results show that Ru1 acted as potent photodynamic cancer therapy and mitochondrial imaging agents. Ru2 exhibited very strong solvatochromism from a visible emission maximum at 588 nm in CH2Cl2 to the near-IR region at 700 nm in water and singlet oxygen generation yield in water (23%) and DNA binding properties (intercalative DNA binding constant on the order of 106 M-1) comparable to those of Ru1, which should make Ru2 attractive for the aforementioned applications of Ru1 if the water solubility of Ru2 can be improved enough for the studies above.

Topoisomerase I inhibitory and photocleavage activity by ruthenium complexes containing a new polyaza ligand

Two new ruthenium complexes containing a new polyaza ligand were found to inhibit the DNA supercoiled relaxation mediated by topoisomerase I (topo I), cleave DNA under irradiation and interact with CT-DNA by intercalation. Both complexes exhibited fast singlet oxygen generation rate, and DNA photocleavage reaction should be initiated by 1O2. Furthermore, complex 2 showed higher photocleavage activity, topo I inhibition activity, and DNA affinity than complex 1. This work shows that two complexes can act as DNA binders with high affinity and good DNA photocleavers. Furthermore, complex 2 can act as a good topo I inhibitor.

Photocytotoxic Activity of Copper(II) and Zinc(II) Complexes of Curcumin and (Acridinyl)dipyridophenazine

AbstractCopper(II) and zinc(II) β‐diketonates of N,N‐donor ligands, viz. [Cu(dppz)(cur)](NO3) (1), [Cu(acdppz)(cur)](NO3) (2), [Cu(acdppz)(acac)](NO3) (3), [Zn(dppz)(cur)](NO3) (4) and [Zn(acdppz)(cur)](NO3) (5), where dppz is dipyrido[3,2‐a:2’,3’‐c]phenazine, acdppz is 11‐(9‐acridinyl)dipyrido[3,2‐a:2’,3’‐c]phenazine, cur and acac are mono‐deprotonated curcumin (Hcur) and acetyl acetone (Hacac), were synthesized, characterized and their photocytotoxicity studied. An analogue of complex 3, viz. [Cu(acdppz)(acac)(H2O)]Cl1/2(NO3)1/2 (3 a), structurally characterized by X‐ray crystallography, has a cationic complex in square‐pyramidal geometry with CuN2O3 core with an axial aqua ligand. Complexes 1, 2, 4 and 5 displayed emission at ∼520 nm (λexc: 430 nm) in dimethyl sulfoxide (DMSO) giving a fluorescence quantum yield value within 0.01‐0.06. The complexes, in contrast to free curcumin, were fairly stable in cellular media up to 36 h, with no apparent degradation of the bound curcumin. The complexes were photocytotoxic (IC50: 0.3 ‐ 4.5 μM) in human cervical cancer (HeLa), breast cancer (MCF‐7) and liver cancer (HepG2) cells. The apoptotic cell death is due to reactive oxygen species formation. Complexes 2 and 5 showed significant uptake in HeLa cells, localizing predominantly in the cytoplasm. Mechanistic data from the pUC19 DNA photocleavage study suggest involvement of acridine and curcumin in photo‐generation of singlet oxygen and hydroxyl radicals as the ROS in light of 400–700 nm.

Synthesis and Spectral Investigations of Polymeric Hydrazone Schiff Base and its Transition Metal Complexes with Promising Antimicrobial, Anti-Angeogenic and DNA Photo-Cleavage Activities

This report describes the synthesis and exploration of novel Schiff base ligand in the form of a polymer (heptamer) which was prepared by reaction between 3,4-diacetyl-2,5-hexanedione and hydrazine hydrate in ethanol. On further reaction of Schiff base with transition metals ions (Co and Cu) leads to formation of its transition metal complexes. The structural identification of Schiff base ligand and its transition metal complexes were characterized by classical structural techniques like FT-IR, NMR and mass spectra. The free ligand and its transition metal complexes have been screened for in vitro biological activities against various strains of bacteria and fungi. The prepared Schiff base and its metal complexes were also screened for antiangiogenic activity. The results have shown the remarkable antimicrobial and antiangiogenic activities of the Schiff base and its metal complexes.

Molecular docking, QSAR properties and DNA/BSA binding, anti-proliferative studies of 6-methoxy benzothiozole imine base and its metal complexes

The molecular and QSAR (Quantitative Structure–Activity Relationship) properties of title compound 2-((6-Methoxybenzo[d]thiazol-2-ylimino)methyl)-6-ethoxyphenol (HL) were evaluated employing HyperChem 7.5 tools. The interaction of the 1a–1e complexes of HL with calf thymus DNA (CT-DNA) was investigated by absorption titrations, Fluorescence quenching and viscosity measurements. The experimental data suggest that these complexes bind to CT-DNA through an intercalative mode, wherein DNA-binding affinity of 1e is found to be greater compared to other complexes. The tryptophan emission-quenching with bovine serum albumin (BSA) experiment revealed stronger binding of 1e than other complexes in the hydrophobic region of protein. The photocleavage of plasmid pBR322 DNA investigated in the presence of the title complexes inferred conversion of supercoiled form of DNA plasmid to circular nicked form. Free-radical scavenging activity studies of HL and its metal complexes determined by their interaction with the stable free-radical DPPH have shown promising antioxidant property. Further cytotoxicity studies with HeLa and MCF-7 cell lines indicated that the compounds can efficiently inhibit the cell proliferation in a dose dependent manner. The DAPI staining assay studies revealed the higher potency of 1e to induce apoptosis. Abbreviations BSA Bovine serum albumin protein CT-DNA Calf thymus DNA DMSO Dimethyl sulfoxide DAPI 4′,-6-Diamidino-2-phenylindole dihydrochloride ESI–MS Electrospray ionization mass spectrometry IC50 Half-maximal inhibitory concentration MBTYE 2-((6-methoxybenzo[d]thiazol-2-ylimino) methyl)-6-ethoxyphenol MTT 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide PBS Phosphate-buffered saline Tris Tris(hydroxymethyl)aminomethane Communicated by Ramaswamy H. Sarma

Correction to Anaerobic Photocleavage of DNA in Red Light by Dicopper(II) Complexes of 3,3'-Dithiodipropionic Acid.

Correction to Anaerobic Photocleavage of DNA in Red Light by Dicopper(II) Complexes of 3,3'-Dithiodipropionic Acid.

A ruthenium(II) complex with a methylated polypyridine ligand: synthesis, DNA binding, and antiproliferation activity

A ruthenium polypyridine complex, [Ru(mptpy)(Mmptpy)Cl][PF6]2 (Ru1, mptpy = 4-(4-methylphenyl)-2,2′,6′,2″-mptpyridine, Mmptpy = 2-[4-(4-methylphenyl)-2,2′-bipyridin-6-yl]-1-methylpyridinum), was synthesised and characterised. The structure of the complex was determined by single-crystal X-ray crystallography. The ruthenium(II) core has an octahedral coordination environment. The interactions of the complex with DNA were analysed by UV–Vis and fluorescence spectroscopy, revealing a high binding affinity for double-stranded DNA. DNA photocleavage studies monitored by agarose gel electrophoresis showed that the complex cleaved DNA efficiently, whilst mechanistic studies showed that the complex produced reactive oxygen species including singlet oxygen, superoxide anions, and carbon-based radicals that cleave DNA. The complex also showed notable antiproliferation activity towards cancer cells in methyl thiazolyl tetrazolium assays.

Correction to "Ternary Iron(III) Complex Showing Photocleavage of DNA in the Photodynamic Therapy Window".

Correction to "Ternary Iron(III) Complex Showing Photocleavage of DNA in the Photodynamic Therapy Window".

Synthesis, singlet oxygen generation and DNA photocleavage of β,β′-conjugated polycationic porphyrins

In this paper, three [Formula: see text],[Formula: see text]-conjugated cationic porphyrin compounds were designed and synthesized. The structure of the intermediates and desired porphyrins were confirmed by UV, IR, 1H NMR, MS and elemental analysis. The interaction modes between these porphyrins and ct-DNA were studied by UV-vis spectroscopy and fluorescence emission spectroscopy. The results showed that PCP 1 had an external binding mode with DNA at low DNA concentration and could intercalate DNA with the increase of concentration. PCP 2 interacted with DNA through an external binding mode, and PCP 3 could insert into DNA. The binding constants ([Formula: see text] between PCP1[Formula: see text]PCP3 and ct-DNA were calculated to be 8.41 × 104, 7.33 × 104 and 4.14 × 104 M[Formula: see text], respectively. The singlet oxygen (1O[Formula: see text] generation of PCP1[Formula: see text]PCP3 was determined by the 1,3-diphenylisobenzofuran (DPBF) method using tetrapyridylporphyrin (H2TMPyP) as a reference. The 1O2 generation rate of PCP1[Formula: see text]PCP3 followed the order of PCP2 >PCP1>H2TMPyP >PCP3. Subsequently, the photocleavage effect of porphyrins on pBR322 plasmid DNA was studied by gel electrophoresis. At 10.0 [Formula: see text]M, PCP1 and PCP2 could cleave DNA completely. At 2.0 [Formula: see text]M, the cleavage rate of DNA by PCP3 was 57.5%, which was significantly higher than that of H2TMPyP (38.8%). These results verified that the amount of cationic ions in the porphyrin structure could affect the binding modes of porphyrins with DNA and their cleavage ability of DNA.

N-Methylmesoporphyrin IX Exhibits G-Quadruplex-Specific Photocleavage Activity.

N-Methylmesoporphyrin IX (NMM) has long been known as a G-quadruplex DNA (G4) ligand. However, there has been little investigation into its G-quadruplex photocleavage activity. Herein, we demonstrate that NMM is a highly selective photocleavage agent for G4 structures but not duplex DNA. Analysis of the cleavage products by PAGE demonstrates that G4 photocleavage by NMM occurs at sites similar to those cleaved by TMPyP4, a nonselective DNA photocleavage agent. Although NMM is shown here to generate singlet oxygen in the presence of both duplex and G4, the lack of increased photocleavage in D2 O indicated that singlet oxygen is not involved in the photocleavage of G4 by NMM.

Design, synthesis and photoinduced DNA cleavage studies of [1,2,4]-triazolo[4,3-a]quinoxalin-4(5H)-ones

An expedient and eco-friendly synthesis of 1-aryl/heteroaryl-[1,2,4]-triazolo[4,3-a]quinoxalin-4(5H)-ones (4) has been accomplished via iodobenzene diacetate mediated oxidative intramolecular cyclization of 3-(2-(aryl/heteroarylidene)hydrazinyl)-quinoxalin-2(1H)-ones (3). Ten synthesized compounds 3 and 4 (10–40 μg) on irradiation with UV light at λmax 312 nm could lead to cleavage of supercoiled pMaxGFP DNA (Form I) into the relaxed DNA (Form II) without any additive. Further, DNA cleaving ability of triazoles was quantitatively evaluated and was found to be dependent on its structure, concentration, and strictly on photoirradiation time. Mechanistic investigations using several additives as potential inhibitors/activator revealed that the DNA photocleavage reaction involves Type-I pathway leading to formation of superoxide anion radicals (O2−) as the major reactive oxygen species responsible for photocleavage process.

Specific Photocleavage Activity of N‐Methylmesoporphyrin IX on G‐Quadruplex DNA Structures

G‐rich regions, at which G‐quadruplexes (G4) are proposed to form, are associated with promoter regions within proto‐oncogenes and may play a role in cell proliferation and carcinogenesis. The ability to identify the formation of G4 structures in these regions, including the temporal aspects of G‐quadruplex formation, is essential to establish the role of these structures in transcriptional regulation. We have focused on identifying highly selective G4 photocleavage agents as molecular probes for establishing the location and timing of G4 formation. N‐methylmesoporphyrin IX (NMM) has long been known as a G4 ligand; however, there has been little investigation into its DNA photocleavage activity. Here we report the ability of NMM to act as a highly selective photocleavage agent for specific G4 structures. We first studied the interaction of NMM with the G4 structures formed by DNA oligonucleotides containing the c‐MYC promoter or human telomeric (hTel) sequences formed in the presence of either Na+ or K+‐containing buffers using a FRET‐based Tm assay and CD spectroscopy. We employed a fluorescence‐based solution assay for G4 cleavage to establish that NMM effects photocleavage (420 nm) of c‐MYC more efficiently than the hTel G4 under both Na+ and K+ conditions, and effects photocleavage of c‐MYC G4 even under white light irradiation. Using denaturing polyacrylamide gel electrophoresis (PAGE), we confirmed this selective photocleavage and demonstrate that cleavage occurs at specific guanine residues of the c‐MYC G4. In order to determine if the photocleavage proceeds through the generation of reactive oxygen species like singlet oxygen, we carried out photocleavage reactions in the presence of H2O and D2O, and employed a turn‐on fluorescent singlet oxygen sensor to detect 1O2 generation. We find that NMM acts to destabilize specific G4 topologies, but oligonucleotides annealed in the presence of NMM form alternative topologies that are thermally stabilized. NMM photocleavage is highly selective for G4 DNA versus duplex DNA, and the K+‐stabilized c‐MYC G4 is preferentially cleaved compared to the Na+‐stabilized structure and the hTel G4 in either Na+ or K+. PAGE analysis indicates that NMM photocleavage of c‐MYC G4 occurs preferentially at the 3′ G‐tetrad residues. This photocleavage does not appear to be due to 1O2. These results indicate that NMM may be a useful tool for elucidating the role of promoter G‐quadruplex structures.Support or Funding InformationSupport for this work by the Cancer Prevention and Research Institute of Texas (RP160852) and Texas State University is gratefully acknowledged.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Mechanism of coralyne-mediated DNA photo-nicking process

Previously, we reported that coralyne and UVA combination sensitized a wide range of human carcinoma cells regardless of their p53 status. The coralyne induced photosensitization of cancer cells may be clinically attractive, as mutation in the p53 gene is prevalent in many types of tumors. Coralyne mediated photosensitization of cancer cells is attributable to its ability to cause extensive DNA single strand breaks (SSB). However, the precise mechanism of coralyne induced DNA photo-damage is not yet known. The present study was aimed to understand the hitherto unknown mechanism of the coralyne-induced DNA photo-cleavage process. To this end, we compared the DNA photo-nicking properties of berberine, jatrorrhizine and coralyne, and deciphered involvement of the photochemical processes in the photo-nuclease action of coralyne using absorption and electron spin resonance spectroscopy, high performance liquid chromatography and mass spectroscopy (MS) techniques in conjunction with relevant in vitro studies with plasmid DNA. In association with UVA, coralyne, but not berberine and jatrorrhizine induced significant nicking of plasmid DNA via an O2-independent photo-chemical process. The Job's plot of our spectrophotometric data suggested that one coralyne molecule remains intercalated with two DNA base pairs (i. e., 1:2) and starts forming aggregates beyond this molar ratio. The DNA photo-nicking by the combination of coralyne and UVA (designated as CUVA) was primarily caused by the coralyne aggregates without any significant contribution from the DNA-intercalated coralyne monomer.

DNA binding, photocleavage, antimicrobial and cytotoxic properties of Ru(II) polypyridyl complexes containing BOPIP ligand, (BOPIP = {2-(4-(benzyloxy) phenyl)-1H-imidazo [4,5-f] [1,2]phenanthroline})

A novel ligand BOPIP (BOPIP = {2-(4-(benzyloxy)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline}) and its mononuclear Ru(II) polypyridyl complexes [Ru(phen)2 BOPIP]2+(1) (phen = 1,10-Phenanthrolene), [Ru(bpy)2 BOPIP]2+(2) (bpy = 2,2′ bipyridyl), [Ru(dmb)2 BOPIP]2+(3) (dmb = 4, 4′ -dimethyl 2, 2′ -bipyridine), [Ru(Hdpa)2 BOPIP]2+(4) (Hdpa = 2,2′dipyridylamine) have been synthesized successfully and characterized by elemental analysis, UV-vis, IR, 1H, 13C-NMR, and ESI-MS Spectroscopy. The interaction of these complexes with CT-DNA was studied using absorption, emission techniques, viscosity measurements and molecular docking studies. The docking study also supports the binding ability of complexes obtained through the absorption and emission techniques. These studies reveal that the Four Ru(II) polypyridyl complexes bind to DNA predominantly by intercalation. The Antimicrobial activity and cytotoxicity of these complexes are also reported.

Synthesis, Characterization and Biological Studies of Novel Schiff Base viz. Bis-1,1'-(pyridine-2,6-diyldieth-1-yl-1-ylidene) biguanidine and Their Transition Metal Complexes

Novel Schiff base and its two transition metal complexes derived from the condensation reaction of 2,6-diacetylpyridine with biguanide, characterized by 1H NMR, IR and elemental analysis. The ligand and its cobalt(II) and nickel(II) complexes showed potent DNA photo-cleavage activity. Antimicrobial activity of this Schiff base and its cobalt(II) and nickel(II) complexes against bacteria and fungi viz. S. aureus, K. pneumoniaae and A. niger, Trichophyton rubrum, respectively was evaluated in terms of zone of inhibition.

Study of the interaction of Co(III) polypyridyl complexes with DNA: an experimental and computational approach

Three new cobalt(III) polypyridyl complexes, [Co(L - L)2IIP]3+ where IIP = 2-(2H-isoindol-1-yl)-2H-imidazo[4,5-f][1, 10]phenanthroline, L = 1) phen (1,10-phenanthroline), 2) bpy (2,2’bipyridyl), 3) dmb (4, 4-dimethyl 2, 2’-bipyridine) have been synthesized, characterized (UV –VIS, IR, 1HNMR and 13C NMR spectroscopy) and screened for their in vitro antibacterial activity against E.coli, Staphylococcus aureus and Bacillus subtilis. The binding of these complexes with calf-thymus DNA (CT-DNA) has been investigated by absorption and fluorescence spectroscopy, viscosity measurements. The experimental studies indicate that complexes bind to CT-DNA by means of intercalation, but with different binding affinities due to differences in the planarity of the ancillary ligand. The complexes promote photocleavage of plasmid DNA from super coiled form I to the open circular form II. The antibacterial activities suggest that the metal complexes are more active as compared to the prepared un-complexed IIP ligand.In addition, a conformational search was carried out by Molecular Dynamics Simulations, and docking revealed that complexes intercalate between base pairs of DNA. The experimental and computational approaches reveal that the length of the intercalator and the nature of ancillary ligand are highly important factors for DNA binding.

Study on Five Porphyrin‐Based Photosensitizers for Singlet Oxygen Generation

AbstractFive porphyrin derivatives were synthesized and characterized in order to be utilized as photosensitizers for singlet oxygen generation. UV‐Vis absorption properties of porphyrins were experimentally and theoretically discussed. The results indicated that the increase in π‐conjugation of porphyrin core can lower the S1‐T1 energy gap and is favorable for efficient energy transfer. The singlet oxygen generation ability of porphyrins was measured and compared under both simulated sunlight and yellow light. As for the results using simulated sunlight, EBHPP and CEBHPP exhibited best and similar performance because they bear strong near‐IR absorption and S1‐T1 interactions. However, under yellow light conditions CEBHPP has better ability for singlet oxygen generation because of its strong absorbance from 650–750 nm. The DNA photocleavage measurements were performed to evaluate the biological activity of the porphyrin derivatives. The photocleavage activities were in the order of TPP < TPP‐NO2 < BHPP < EBHPP < CEBHPP, and the possible reasons were discussed. This work is useful for the design of more efficient photosensitizers.

Depicting the DNA binding and photo-nuclease ability of anti-mycobacterial drug rifampicin: A biophysical and molecular docking perspective

Rifampicin, an important member of ansamycin family, exhibits various biological activities. It is frequently used for the treatment of tuberculosis and leprosy. Recently, its interaction with protein is evidenced. But, its interaction with DNA is still unknown. Whether, exhibition of anti-cancer activity of rifampicin is associated with DNA-cleavage activity is also unknown. In this study, an attempt has been taken to understand these two unknown aspects. Spectroscopic studies indicated that rifampicin binds to CT-DNA with a binding constant of ~5.22 × 105 M−1. Several independent experiments like CD analysis, competitive displacement experiments and viscosity measurements revealed that rifampicin intercalates into the CT-DNA. Molecular docking studies corroborate this fact and depicted that this drug binds to the GC-rich region of DNA through multiple hydrogen bonding having the relative binding energy of −9.21 kcal mol−1. Besides, DNA binding ability, rifampicin causes the photo-cleavage of pUC19 DNA via singlet oxygen pathway. To the best of our knowledge, we report for the first time the DNA binding and DNA cleavage ability of rifampicin. This study provides a clue behind the execution of the anti-cancer activity of rifampicin. Overall, all these information can be used for further understanding the pharmacological effects of rifampicin.

Single photon DNA photocleavage at 830 nm by quinoline dicarbocyanine dyes.

We have synthesized symmetrical carbocyanine dyes in which two 4-quinolinium rings are joined by a pentamethine bridge that is meso-substituted with H or Cl. Irradiation of the halogenated dye at 830 nm produces hydroxyl radicals that generate DNA direct strand breaks. This represents the first reported example of DNA photocleavage upon single photon excitation of a chromophore at wavelengths above 800 nm.

Comparative Studies on DNA Binding, Photocleavage, and Photophysical Properties of Ru(II) Complexes Containing TIP {TIP = 2-(Thiophen-2-yl)-1H-imidazo[4,5-f][1,10]-phenanthroline} Ligand

A thiophene contained imidazo phenanthroline ligand TIP {TIP = 2-(thiophen-2-yl)-1H-imidazo-[4,5-f][1,10]phenanthroline{ and its mononuclear Ru(II) polypyridyl complexes [Ru(phen)2TIP]2+ (1) (phen = 1,10-phenanthrolene) and [Ru(bpy)2TIP]2+ (2) (bpy = 2,2'-bipyridyl), are synthesized and characterized by UVVis, IR, 1H and 13C NMR, and ESI-MS spectra. Interaction of these complexes with CT-DNA is studied using UV-Vis and florescence spectra, viscosity measurements and molecular docking studies. The latter supports binding ability of complexes with stability constants deduced from UV-Vis and florescence spectra. The studies reveal that both Ru(II) polypyridyl complexes bind to DNA predominantly by intercalation, and the binding constant of complex 1 is greater than that of complex 2. Complexes 1 and 2 cleave the pBR 322 DNA under UV light.