High DNA Cleavage Research Articles

Green synthesis, characterization and biological activity of silver nanoparticles of Hypnum cupressiforme Hedw extract

Mosses are one of the oldest land plants that constitute the second largest group of the plant kingdom, are found in almost every region, have known therapeutic effects, are rich in secondary metabolites, can withstand harsh climatic conditions and thirst for a long time. Volatile extracts of Hypnum cupressiforme Hedw. were analyzed by gas chromatography-mass spectrometry in this study, and the presence of 18 different phytocompounds was determined as secondary metabolites. Using these extracts, silver nanoparticles (AgNPs) were synthesized using a green synthesis method. The AgNPs that were created were characterized. The extracts and AgNPs were tested for antibacterial, antibiofilm, antioxidant, mutagenic, and DNA-cleavage activity. The tests revealed no evidence of mutagenicity. Antibiofilm and antibacterial activity of AgNPs against P. vulgaris, P. aeruginosa, and E. faecalis were demonstrated. Both oxidatively and hydrolytically, H. cupressiforme the extract was found to have higher antioxidant properties and high DNA cleavage activity.

Engineered lentivirus-derived nanoparticles (LVNPs) for delivery of CRISPR/Cas ribonucleoprotein complexes supporting base editing, prime editing and in vivo gene modification.

Implementation of therapeutic in vivo gene editing using CRISPR/Cas relies on potent delivery of gene editing tools. Administration of ribonucleoprotein (RNP) complexes consisting of Cas protein and single guide RNA (sgRNA) offers short-lived editing activity and safety advantages over conventional viral and non-viral gene and RNA delivery approaches. By engineering lentivirus-derived nanoparticles (LVNPs) to facilitate RNP delivery, we demonstrate effective administration of SpCas9 as well as SpCas9-derived base and prime editors (BE/PE) leading to gene editing in recipient cells. Unique Gag/GagPol protein fusion strategies facilitate RNP packaging in LVNPs, and refinement of LVNP stoichiometry supports optimized LVNP yield and incorporation of therapeutic payload. We demonstrate near instantaneous target DNA cleavage and complete RNP turnover within 4 days. As a result, LVNPs provide high on-target DNA cleavage and lower levels of off-target cleavage activity compared to standard RNP nucleofection in cultured cells. LVNPs accommodate BE/sgRNA and PE/epegRNA RNPs leading to base editing with reduced bystander editing and prime editing without detectable indel formation. Notably, in the mouse eye, we provide the first proof-of-concept for LVNP-directed in vivo gene disruption. Our findings establish LVNPs as promising vehicles for delivery of RNPs facilitating donor-free base and prime editing without formation of double-stranded DNA breaks.

Comparative DNA-/BSA-binding, DNA cleavage, and cytotoxic properties of copper(II) amino/salicyl-phenolate Schiff bases (phen) complexes that induce generation of phenoxyl radicals

A series of mixed-ligand Cu(II) complexes of the type [Cu(L1-5)(diimine)(H2O)](ClO4) (1–5) and [Cu(L6)(diimine)](ClO4) (6), where HL1-HL4 are aminophenolate Schiff base ligands viz., 2-(benzylideneamino)phenol (HL1, 1), 2-(4-fluorobenzylideneamino)phenol (HL2, 2), 2-(4-chlorobenzylideneamino)phenol (HL3, 3), and 2-(4-nitrobenzylideneamino)phenol (HL4, 4) whereas HL4 and HL5 are salicyl-phenolate Schiff base ligands viz.,2-((phenylimino)methyl)phenol (HL5, 5) and (E)-2-(((2-(dimethylamino)ethyl)imino)methyl)phenol (HL6, 6) as primary ligands and the diimine 1,10-phenanthroline (phen) as co-ligand have been isolated. TheSchiffbaseligandsand their mixedligandchelates were characterizedby spectral techniques (UV–Visible, IR, mass, 1H, and 13C NMR), elemental analysis, cyclic voltammetry (CV), and differential pulse voltammetric (DPV) techniques. The molecular structure of 6, which alone formed appreciable crystals, was determined by single-crystal X-ray studies, and two crystallographically independent molecules (a and b) existed in square pyramidal distorted trigonal bipyramidal (SPDTBP) geometry. The complexes 1–4 showed a reversible (ΔEp for 3; 64), quasi-reversible (2; 105 and 4; 115), and irreversible (1; 181 mV) oxidation waves discernible at E1/2 ranging from + 0.035 V to −0.120 V (DPV) which are attributed to the formation of copper(II)-phenoxyl radical species. Among them, 2 and 3 showed a well-defined reversible phenoxyl radical formation in CV and DPV. Also, these two complexes exhibited more stable phenoxyl radical in the presence of CAN (cerium ammonium nitrate). The DNA binding studies revealed that the fluoro- and chloro-substituted complexes 2 and 3 exhibited higher DNA binding propensity than the other complexes. All the complexes displayed moderate to high oxidative DNA cleavage property in the presence of H2O2, wherein complexes 2 and 3 exhibited higher DNA cleavage than the others. Interestingly, complex 3 exhibited less AC50 value (18.26 µM) than complex 2 (43.3 µM). The mechanistic study led to the inference that the DNA cleavage is possibly mediated via copper(II)-bound phenoxyl-radical. The cytotoxicity of complexes 1–6 was investigated in A549 non-small cell lung carcinoma cell. The amino-phenolate complexes 2 (IC50 = 3.52 µM) and 3 (IC50 = 3.4 µM) brought about higher cytotoxicity and ≈ 3.8-times more potency than cisplatin. The complex 3 showed to be 47-times less toxic to non-cancerous peripheral blood mononuclear cells (PBMC). Fluorescent staining assay revealed that the complexes 1–6 induced apoptotic cell death with some degree of necrosis. JC-1 staining assay revealed that complex 3 efficiently depolarized the mitochondrial membrane potential. Put together, the results substantiate that amino-phenolate-containing copper(II) mixed ligand complexes are more cytotoxic than salicyl-phenolate-containing copper(II) complexes.

Predicting the relationship between pesticide genotoxicity and breast cancer risk in South Indian women in in vitro and in vivo experiments

Breast cancer is the third most common cancer in women after skin and lung cancer. Pesticides are of interest in etiologic studies of breast cancer because many pesticides mimic estrogen, a known breast cancer risk factor. In this study, we discerned the toxic role of the pesticides atrazine, dichlorvos, and endosulfan in inducing breast cancer. Various experimental studies, such as biochemical profiling of pesticide-exposed blood samples, comet assays, karyotyping analysis, pesticide and DNA interaction analysis by molecular docking, DNA cleavage, and cell viability assays, have been carried out. Biochemical profiling showed an increased level of blood sugar, WBC, hemoglobin, and blood urea in the patient exposed to pesticides for more than 15 years. The comet assay for DNA damage performed on patients exposed to pesticides and pesticide-treated blood samples revealed more DNA damage at the 50 ng concentration of all three pesticides. Karyotyping analysis showed enlargements in the heterochromatin region and 14pstk+, and 15pstk+in the exposed groups. In molecular docking analysis, atrazine had the highest glide score (− 5.936) and glide energy (− 28.690), which reveals relatively high binding capability with the DNA duplex. The DNA cleavage activity results showed that atrazine caused higher DNA cleavage than the other two pesticides. Cell viability was the lowest at 50 ng/ml (72 h). Statistical analysis performed using SPSS software unveiled a positive correlation (< 0.05) between pesticide exposure and breast cancer. Our findings support attempts to minimize pesticide exposure.

Characterization of a new IN-I-PpoI fusion protein and a homology-arm containing transgene cassette that improve transgene expression persistence and 28S rRNA gene-targeted insertion of lentiviral vectors.

Targeting transgene integration into a safe genomic locus would be very important for gene therapy. We have generated lentivirus vectors containing the ribosomal RNA-recognising I-PpoI endonuclease fused to viral integrase, and transgene cassettes with target site homology arms to enhance insertion targeting. These new vectors were characterised with respect to the persistence of transgene expression, insertion targeting efficiency and chromosomal integrity of the transduced cells. The aim was to find an optimally safe and effective vector for human gene therapy. Fusion protein vectors with high endonuclease activity were the most effective in the accurate targeting of transgene insertion. The homology construct increased the insertion targeting efficiency to 28% in MRC-5 cells. However, karyotyping analysis showed that the high endonuclease activity induced the formation of derivative chromosomes in as many as 24% of the analysed primary T lymphocytes. The persistence of transgene expression was excellent in homology arm-containing fusion protein vectors with reduced endonuclease activity, and these fusion proteins did not cause any detectable chromosomal rearrangements attributable to the endonuclease activity. We thus conclude that instead of the fusion protein vectors that carry a highly active endonuclease, our vectors with the ability to tether the lentivirus preintegration complex to benign loci in the genome without high ribosomal DNA cleavage activity are better suited for lentivirus-based gene therapy applications.

Loosely-packed dynamical structures with partially-melted surface being the key for thermophilic argonaute proteins achieving high DNA-cleavage activity.

Prokaryotic Argonaute proteins (pAgos) widely participate in hosts to defend against the invasion of nucleic acids. Compared with the CRISPR-Cas system, which requires a specific motif on the target and can only use RNA as guide, pAgos exhibit precise endonuclease activity on any arbitrary target sequence and can use both RNA and DNA as guide, thus rendering great potential for genome editing applications. Hitherto, most in-depth studies on the structure-function relationship of pAgos were conducted on thermophilic ones, functioning at ∼60 to 100°C, whose structures were, however, determined experimentally at much lower temperatures (20–33°C). It remains unclear whether these low-temperature structures can represent the true conformations of the thermophilic pAgos under their physiological conditions. The present work studied three pAgos, PfAgo, TtAgo and CbAgo, whose physiological temperatures differ significantly (95, 75 and 37°C). By conducting thorough experimental and simulation studies, we found that thermophilic pAgos (PfAgo and TtAgo) adopt a loosely-packed structure with a partially-melted surface at the physiological temperatures, largely different from the compact crystalline structures determined at moderate temperatures. In contrast, the mesophilic pAgo (CbAgo) assumes a compact crystalline structure at its optimal function temperature. Such a partially-disrupted structure endows thermophilic pAgos with great flexibility both globally and locally at the catalytic sites, which is crucial for them to achieve high DNA-cleavage activity. To further prove this, we incubated thermophilic pAgos with urea to purposely disrupt their structures, and the resulting cleavage activity was significantly enhanced below the physiological temperature, even at human body temperature. Further testing of many thermophilic Agos present in various thermophilic prokaryotes demonstrated that their structures are generally disrupted under physiological conditions. Therefore, our findings suggest that the highly dynamical structure with a partially-melted surface, distinct from the low-temperature crystalline structure, could be a general strategy assumed by thermophilic pAgos to achieve the high DNA-cleavage activity.

Biological properties of hexadeca-substituted metal phthalocyanines bearing different functional groups

In this study, a new tetra-substituted phthalonitrile (diethyl 2-(2-chloro-4,5-dicyano-3,6-bis(hexyloxy)phenyl)malonate) bearing three different substituents was synthesized and characterized. Due to the basic medium, transesterification occurred during the synthesis of the target phthalocyanines [M = Zn (II), Cu (II), Co (II), In (III), Lu (III)] in n-pentanol and the ethyl groups were replaced with pentyl groups. The biological features of the resultant compounds were studied for the first time in this study. All the compounds exhibited high antioxidant, antimicrobial, and DNA cleavage activities. The highest antioxidant activity was obtained 90.39% for lutetium phthalocyanine at 100 mg/L. The most effective MIC value was obtained 8 mg/L against Candida parapisilosis. The most effective microbial cell viability inhibition was obtained 100% for cobalt and lutetium phthalocyanines. They exhibited excellent biofilm inhibiton activities. Higher biofilm inhibition was achieved using light irradiation. The compounds exhibited higher biofilm inhibition activities with photodynamic against Staphylococcus aureus compared with Pseudo aureginosa.

Synthesis and biological properties of maleimide-based macrocyclic lactone enediynes.

Natural enediyne antibiotics are powerful DNA-cleavage agents due to the presence of the highly reactive hex-3-ene-1,5-diyne units. However, the complicated chemical structure and thermal instability make their synthesis, derivatization, and storage challenging. Heterocycle-fused enediynes, which exhibit strong antineoplastic activity, are promising analogues of natural enediynes for medicinal applications. To this end, a series of maleimide-based enediynes with macrocyclic lactone moieties were synthesized through the Sonagashira coupling reaction. Differential scanning calorimetry and electron paramagnetic resonance results showed that these macrocyclic enediynes exhibited a rather low onset temperature and the ability to generate radicals at physiological temperature. In addition, the structure-activity relationship of enediynes was analyzed by changing the ring size and the substituents on the propargyl group. Cellular experiments indicated that the diradicals produced by these enediynes efficiently cleaved DNA and disrupted the cell cycle distribution, and consequently induced tumor cell death via an apoptosis pathway at low half inhibitory concentrations. Computational studies suggested that the maleimide moiety promoted the propargyl-allenyl rearrangement of the cyclic enediyne, enabling the generation of diradical species through the Myers-Saito cyclization, and then abstracted hydrogen atoms from the H-donors.

Erratum: CRISPR/Cas9-mediated Targeted Integration In Vivo Using a Homology-mediated End Joining-based Strategy.

An erratum was issued for: Studying TGF-β Signaling and TGF-β-induced Epithelial-to-mesenchymal Transition in Breast Cancer and Normal Cells. The phrases"surveyor assay"and"SurveyorNuclease" havebeen updated to "T7E1 assay" to " T7endonuclease I" respectively. Step 1.2 inthe Protocol has been updated from: Surveyor nucleaseassay of sgRNA NOTE: The targeting efficiency of the sgRNA used for the knock-in experiment is evaluated by surveyor nuclease assay (also known as T7 endonuclease I (T7EI) assay)17. Select the sgRNA with high DNA cleavage efficiency and a low distance between the sgRNA cutting site and the stop codon. to: T7 endonuclease assay of sgRNA NOTE: The targeting efficiency of the sgRNA used for the knock-in experiment is evaluated by T7 endonuclease (T7EI)assay17. Select the sgRNA with high DNA cleavage efficiency and a low distance between the sgRNA cutting site and the stop codon. Figure 1 in the Representative Results has been updatedfrom: Figure 1: HMEJ-mediated targeted integration in vitro. (A) Experimental scheme for selection of sgRNAs: Six different sgRNAs (Cdx2-sgRNA1~Cdx2-sgRNA6) around the stop codon of the Cdx2 locus with a higher rank and off-target potential were chosen based on online CRISPR design tool. The protospacer adjacent motif (PAM) sequence is in red. (B) Experimental design: The Cas9-CMV-GFP expression plasmids expressing sgRNA, Cas9, and GFP were introduced into N2acells. GFP+ cells were sorted at day 3 for surveyor assay. (C) Surveyor assay for Cdx2 targeting: 6 different sgRNAs were designed for surveyor assay. Normal N2a cell genomic DNA serves as control. *, the sgRNA used for Cdx2-2A-mCherry knock-in experiment. (D) Schematic overview of construction of HMEJ donors using Gibson assembly. (E) Schematic overview of HMEJ-mediated gene targeting strategy at Cdx2 locus. HAL/HAR, left/right homology arm; triangles, sgRNA target sites; OF/OR, outer forward/reverse primer; IF/IR, inner forward/reverse primer. Figure modified from previous report10.Please click here to view a larger version of this figure. to: Figure 1: HMEJ-mediated targeted integration in vitro. (A) Experimental scheme for selection of sgRNAs: Six different sgRNAs (Cdx2-sgRNA1~Cdx2-sgRNA6) around the stop codon of the Cdx2 locus with a higher rank and off-target potential were chosen based on online CRISPR design tool. The protospacer adjacent motif (PAM) sequence is in red. (B) Experimental design: The Cas9-CMV-GFP expression plasmids expressing sgRNA, Cas9, and GFP were introduced into N2acells. GFP+ cells were sorted at day 3 for T7EIassay. (C) T7EI assay for Cdx2 targeting: 6 different sgRNAs were designed for T7EI assay. Normal N2a cell genomic DNA serves as control. *, the sgRNA used for Cdx2-2A-mCherry knock-in experiment. (D) Schematic overview of construction of HMEJ donors using Gibson assembly. (E) Schematic overview of HMEJ-mediated gene targeting strategy at Cdx2 locus. HAL/HAR, left/right homology arm; triangles, sgRNA target sites; OF/OR, outer forward/reverse primer; IF/IR, inner forward/reverse primer. Figure modified from previous report10.Please click here to view a larger version of this figure.

In vitro and in vivo antitumoral activity of a ternary copper (II) complex

Recently, a high number of copper derivatives has been evaluated as DNA-targeting metallodrugs, due to the lower toxicity and its potential to cleave DNA. Several strategies have been testing to develop metal compounds effective against tumour cells. In this work, the ternary copper (doxycycline)-(1,10-phenanthroline) complex [Cu(dox)(phen)]2+ was especially designed as an antitumoral drug, previously showing high cytotoxicity and DNA cleavage activity. We aimed to further investigate the in vitro cytotoxic activity in both tumoral and non-tumoral cells, in vitro genotoxic potential, and in vivo antitumor activity using BALB/C mouse injected with sarcoma S180 and Ehrlich cell lines. Our results indicated that this compound exhibits a moderate genotoxic potential, with selective growth inhibition of tumor cells, especially the murine melanoma B16F10. Its main mechanism of action seems to be through ROS generation. We have further shown a significant reduction of the implanted tumor size in the animal model, suggesting that this compound has great antitumoral potential against many tumor types. [Cu(dox)(phen)]2+ is selectively cytotoxic for melanoma B16F10 and showed high chemotherapeutic potential in vivo against implanted sarcoma S180 and Ehrlich ascites tumours.

A novel thermal Cas12b from a hot spring bacterium with high target mismatch tolerance and robust DNA cleavage efficiency

Clustered regularly interspaced short palindromic repeats (CRISPR)-associated proteins (Cas), such as Cas9 and Cpf1, are RNA-guided endonucleases that target and degrade nucleic acids, providing powerful genomic editing and molecular diagnostic tools. Cas12b enzymes are distinct effectors; however, their features and catalytic boundaries require further characterization. We identified BrCas12b from the thermophile bacterium Brevibacillus sp. SYSU G02855 as a novel ortholog of cas12b. Biochemical analyses revealed that BrCas12b is a dual-RNA-guided endonuclease with higher optimum reaction temperature than that of other reported members of Cas12b. The seed sequence of BrCas12b is only 4 nt in length, indicating that it has greater target mismatch tolerance than that of previously reported Cas effectors; however, it contains a compensatory effect at the position of the cleavage site. Using fluorescence-based detection method to evaluate target cleavage efficiency, we showed that BrCas12b has robust enzymatic cleavage activity (Kcat/Km (s−1 M−1) = 8.80 × 1011), which is significantly higher than that of AacCas12b (Kcat/Km (s−1 M−1) = 7.56 × 108) from Alicyclobacillus acidoterrestris. The results increase our understanding of the catalytic mechanism of Cas12b family members and suggest that BrCas12b might be useful in the application of genomic editing and molecular diagnosis.

Synthesis and characterization of binary and ternary oxovanadium complexes of N,N′‐(2‐pyridyl)thiourea and curcumin: Catalytic oxidation potential, antibacterial, antimicrobial, antioxidant and DNA interaction studies

Two binary and two ternary mono‐oxovanadium (IV) complexes of acetylacetonate, curcumin and N,N′‐bis(2‐pyridyl)thiourea were synthesized. They were characterized using elemental analysis, infrared and UV–visible spectroscopies and magnetic and conductivity measurements. The formation constants Kf were determined from spectrophotometric measurements. The catalytic potential of the VO complexes was investigated for the oxidation of 1‐octene by aqueous H2O2 in acetonitrile. They display high catalytic potential for the conversion of 1‐octene with low chemoselectivity to the epoxy product. The VO complexes exhibit good antibacterial and antimicrobial activities. The antioxidant activity of the VO complexes and their ligands was investigated. The VO complexes show high DNA affinity and DNA cleavage ability.

Construction and characterization of adenoviral vectors for the delivery of TALENs into human cells

Transcription activator-like effector nucleases (TALENs) are designed to cut the genomic DNA at specific chromosomal positions. The resulting DNA double strand break activates cellular repair pathways that can be harnessed for targeted genome modifications. TALENs thus constitute a powerful tool to interrogate the function of DNA sequences within complex genomes. Moreover, their high DNA cleavage activity combined with a low cytotoxicity make them excellent candidates for applications in human gene therapy. Full exploitation of these large and repeat-bearing nucleases in human cell types will benefit largely from using the adenoviral vector (AdV) technology. The genetic stability and the episomal nature of AdV genomes in conjunction with the availability of a large number of AdV serotypes able to transduce various human cell types make it possible to achieve high-level and transient expression of TALENs in numerous target cells, regardless of their mitotic state. Here, we describe a set of protocols detailing the rescue, propagation and purification of TALEN-encoding AdVs. Moreover, we describe procedures for the characterization and quantification of recombinant viral DNA present in the resulting AdV preparations. The protocols are preceded by information about their underlying principles and applied in the context of second-generation capsid-modified AdVs expressing TALENs targeted to the AAVS1 “safe harbor” locus on human chromosome 19.

Synthesis and Biological Activity of Some New Pyrazole Copper(II) Complexes

As a part of systematic investigation of synthesis and biologically active compounds of pyrazole derivatives containing transition metal, several new pyrazole copper(II) complexes 3a−f were synthesized from pyrazole sodium salts 2a−f, which were produced from spiro‐pyrazoles 1a−f and sodium hydride by a ring‐opening reaction. All the synthesized compounds were characterized by spectroscopic analysis. Pyrazole copper(II) complexes 3a−d and 3f exhibited high DNA cleavage activity in vitro. Furthermore, compounds 3a−f were tested for their growth inhibitory activity in A549 lung cancer, B16F10 murine melanoma, and HeLa human uterine carcinoma cells. Compounds 3c,d displayed moderate B16F10 and HeLa inhibitory activity levels (3c: IC50 = 45 μM in B16F10 cells and 34 μM in HeLa cells, 3d: IC50 = 50 μM in B16F10 cells and 32 μM in HeLa cells).

Phosphodiester Cleavage Properties of Copper(II) Complexes of 1,4,7-Triazacyclononane Ligands Bearing Single Alkyl Guanidine Pendants

Three new metal-coordinating ligands, L(1)·4HCl [1-(2-guanidinoethyl)-1,4,7-triazacyclononane tetrahydrochloride], L(2)·4HCl [1-(3-guanidinopropyl)-1,4,7-triazacyclononane tetrahydrochloride], and L(3)·4HCl [1-(4-guanidinobutyl)-1,4,7-triazacyclononane tetrahydrochloride], have been prepared via the selective N-functionalization of 1,4,7-triazacyclononane (tacn) with ethylguanidine, propylguanidine, and butylguanidine pendants, respectively. Reaction of L(1)·4HCl with Cu(ClO(4))(2)·6H(2)O in basic aqueous solution led to the crystallization of a monohydroxo-bridged binuclear copper(II) complex, [Cu(2)L(1)(2)(μ-OH)](ClO(4))(3)·H(2)O (C1), while for L(2) and L(3), mononuclear complexes of composition [Cu(L(2)H)Cl(2)]Cl·(MeOH)(0.5)·(H(2)O)(0.5) (C2) and [Cu(L(3)H)Cl(2)]Cl·(DMF)(0.5)·(H(2)O)(0.5) (C3) were crystallized from methanol and DMF solutions, respectively. X-ray crystallography revealed that in addition to a tacn ring from L(1) ligand, each copper(II) center in C1 is coordinated to a neutral guanidine pendant. In contrast, the guanidinium pendants in C2 and C3 are protonated and extend away from the Cu(II)-tacn units. Complex C1 features a single μ-hydroxo bridge between the two copper(II) centers, which mediates strong antiferromagnetic coupling between the metal centers. Complexes C2 and C3 cleave two model phosphodiesters, bis(p-nitrophenyl)phosphate (BNPP) and 2-hydroxypropyl-p-nitrophenylphosphate (HPNPP), more rapidly than C1, which displays similar reactivity to [Cu(tacn)(OH(2))(2)](2+). All three complexes cleave supercoiled plasmid DNA (pBR 322) at significantly faster rates than the corresponding bis(alkylguanidine) complexes and [Cu(tacn)(OH(2))(2)](2+). The high DNA cleavage rate for C1 {k(obs) = 1.30 (±0.01) × 10(-4) s(-1) vs 1.23 (±0.37) × 10(-5) s(-1) for [Cu(tacn)(OH(2))(2)](2+) and 1.58 (±0.05) × 10(-5) s(-1) for the corresponding bis(ethylguanidine) analogue} indicates that the coordinated guanidine group in C1 may be displaced to allow for substrate binding/activation. Comparison of the phosphate ester cleavage properties of complexes C1-C3 with those of related complexes suggests some degree of cooperativity between the Cu(II) centers and the guanidinium groups.

A novel TALE nuclease scaffold enables high genome editing activity in combination with low toxicity

Sequence-specific nucleases represent valuable tools for precision genome engineering. Traditionally, zinc-finger nucleases (ZFNs) and meganucleases have been used to specifically edit complex genomes. Recently, the DNA binding domains of transcription activator-like effectors (TALEs) from the bacterial pathogen Xanthomonas have been harnessed to direct nuclease domains to desired genomic loci. In this study, we tested a panel of truncation variants based on the TALE protein AvrBs4 to identify TALE nucleases (TALENs) with high DNA cleavage activity. The most favorable parameters for efficient DNA cleavage were determined in vitro and in cellular reporter assays. TALENs were designed to disrupt an EGFP marker gene and the human loci CCR5 and IL2RG. Gene editing was achieved in up to 45% of transfected cells. A side-by-side comparison with ZFNs showed similar gene disruption activities by TALENs but significantly reduced nuclease-associated cytotoxicities. Moreover, the CCR5-specific TALEN revealed only minimal off-target activity at the CCR2 locus as compared to the corresponding ZFN, suggesting that the TALEN platform enables the design of nucleases with single-nucleotide specificity. The combination of high nuclease activity with reduced cytotoxicity and the simple design process marks TALENs as a key technology platform for targeted modifications of complex genomes.

A trigonal-prismatic Ag(I) complex and an octahedral Cu(II) complex incorporating with oxamide Ni(II) complex ligand: Syntheses, crystal structures and oxidative nuclease activities

A mononuclear macrocyclic complex NiIIL3a (L3a=dianion of 2,3-dioxo-5,6:13,14-dibenzo-9,10-cyclohexyl-7,12-bis(methoxycarbonyl)-1,4,8,11-tetraazacyclotetradeca-7,11-diene), which shows high DNA cleavage activity in the presence of H2O2, was reported in our previous work. Considering that many systems for natural enzyme-mediated DNA cleavage contain two or more metal active sites, two new trinuclear complexes [Cu(NiL3a)2(dca)2]·2CH3OH (abbreviated as Cu(NiL3a)2) and [Ag(NiL3a)2(NO3)]·2CH3OH·0.5H2O (abbreviated as Ag(NiL3a)2) were synthesized in this work, where dca is the dicyanamide. The complexes were structurally characterized by single crystal X-ray analysis. The central Cu(II) or Ag(I) atom is linked to two [NiL3a] ligands by oxamido bridges forming a trinuclear structure. In Cu(NiL3a)2, the central Cu(II) ion is in an octahedral coordination geometry. Whereas in Ag(NiL3a)2, the central Ag(I) ion is in a rarely reported trigonal-prismatic coordination geometry. The DNA cleavage behavior of the complexes in the presence of H2O2 was studied in detail. Comparing with the NiL3a, the trinuclear complex Ag(NiL3a)2 nearly has no ability to cleave DNA, whereas Cu(NiL3a)2 is a much better DNA cleavage agent. Cu(NiL3a)2 can efficiently convert supercoiled DNA to nicked DNA with a rate constant of 0.074±0.002min−1 when 40μM Cu(NiL3a)2 and 0.6mM H2O2 are used. The cleavage mechanism between the complex Cu(NiL3a)2 and plasmid DNA is likely to involve singlet oxygen as reactive oxygen species. Circular dichroism (CD) and fluorescence spectroscopy indicate that both Cu(NiL3a)2 and NiL3a bind to DNA by a groove binding mode, and the binding between Cu(NiL3a)2 and DNA is much stronger than that between NiL3a and DNA. The present results may provide some information for the design of efficient multinuclear artificial nucleases.

High nuclease activity of a copper(II)-bipyridyl complex containing cytosine pendants

A new copper(II) complex bearing 2,2′-bipyridine (bpy) derivatives with cytosine nucleobases [Cu(L)Cl2] · 2H2O has been synthesized and characterized, where L = 5,5′-di[(4-amino-2-oxo-1(2H)-pyrimidinyl)methyl]-2,2′-bipyridine. Circular dichroism spectra reveal interactions between ligand and pBR322 DNA and showed that the local DNA structure was perturbed by the ligand. Cleavage of pBR322 DNA by the title complex was carried out in 20 mmol L−1 HEPES (pH 7.5) at 37°C. The calculated pseudo-Michaelis–Menten kinetic parameter (k cat) of the complex was 8.80 h−1. The cleavage efficiency was 17-fold higher than that of its simple analog [Cu(bpy)Cl2] (k cat = 0.50 h−1). Hydrolytic mechanisms involved in DNA cleavage were explored using radical scavengers and T4 ligase. Competitive experiments with special binding agents showed that the complex could preferentially bind to the minor groove of double-stranded DNA, suggesting specific DNA binding characteristics. High DNA cleavage reactivity and selectivity of the complex could be attributed to the synergic effects of the metal center and the cytosine pendants.

ChemInform Abstract: Bifunctional 2-Naphthyl Propargylic Sulfones Exhibiting High DNA Intercalating and Alkylating Activity.

A number of novel 2-naphthyl propargylic sulfones were synthesized as nucleic base alkylating agents. Extremely high DNA cleavage activity was observed for the sulfones with a free ω-hydroxyl group in the carbon chain in contrast to the ester conjugates possessing an additional intercalating unit.

An effective approach to artificial nucleases using copper(ii) complexes bearing nucleobases

Novel copper(ii) complexes bearing 2,2'-bipyridine (bpy) derivatives with adenine, thymine and uracil nucleobases [Cu(L(1))Cl(2)].2H(2)O (1), [Cu(L(2))Cl(2)] (2) and [Cu(L(3))Cl(2)].H(2)O (3) (L(1) = 5,5'-Di[N9-adenylmethyl]-2,2'-bipyridine, L(2) = 5,5'-Di[N1-thyminylmethyl]-2,2'-bipyridine and L(3) = 5,5'-Di[N1-uracilmethyl]-2,2'-bipyridine) were synthesized and characterized. Structure simulation was performed for these complexes. Circular dichroism (CD) spectra revealed the interactions between these ligands and pBR322 DNA and showed that the local DNA structure was perturbed by these ligands. Cleavage of pBR322 DNA by these complexes was carried out in 20 mM HEPES (pH 7.5) at 37 degrees C. The calculated pseudo-Michaelis-Menten kinetic parameters (k(cat)) were 14.7 +/- 0.6 and 40.4 +/- 1.3 h(-1) for and . The cleavage efficiency of was 80-fold higher than that of its simple analogue [Cu(bpy)Cl(2)] (k(cat) = 0.50 h(-1)) and very close to the catalytic rate constant of natural EcoRI endonuclease (k(cat) = 43.2 h(-1)) at similar conditions. Thus, complex might be one of the most effective artificial nucleases that could catalyze double-stranded DNA hydrolytic cleavage so far. Hydrolytic mechanisms involved in DNA cleavage were explored using radical scavengers and T4 ligase. Competitive experiments with special binding agents showed that complexes could preferentially bind to the minor groove of double-stranded DNA, suggesting specific DNA binding characteristics. Molecular docking calculations also indicated that complexes could bind to the minor groove of targeted DNA much more strongly than their simple analogues and preferentially bind at the AT region of the dodecamer. Such high DNA cleavage ability and selectivity of these copper(ii) complexes could be attributed to the synergic effects of the metal center and the pendant nucleobases.