DNA Cleavage Activity Research Articles

Biological Performance of Hexadeca-Substituted Metal Phthalocyanine/Reduced Graphene Oxide Nanobioagents.

This study presents a tetra-substituted phthalonitrile derivative, namely, diethyl 2-(3,4-dicyano-2,5-bis(hexyloxy)-6-(4-(trifluoromethoxy)phenoxy)phenyl)malonate (a), cyclotetramerizing in the presence of some metal salts. The resultant hexadeca-substituted metal phthalocyanines [M= Co, Zn, InCl)] (b-d) were used for the modification of reduced graphene oxide for the first time. The effect of the phthalonitrile/metal phthalocyanines on biological features of reduced graphene oxide (rGO) was extensively examined by the investigation of antioxidant, antimicrobial, DNA cleavage, cell viability, and antibiofilm activities of nanobioagents (1-4). The results were compared with those of unmodified rGO (nanobioagent 5), as well. Modification of reduced graphene oxide with the synthesized compounds improved its antioxidant activity. The antioxidant activities of all the tested nanobioagents also enhanced as the concentration increased. The antibacterial activities of all the nanobioagents improved by applying the photodynamic therapeutic (PDT) method. All the phthalonitrile/phthalocyanine-based nanobioagents (especially phthalocyanine-based nanocomposites) exhibited DNA cleavage activities, and complete DNA fragmentation was observed for nanobioagents (1-4) at 200 mg/L. They can be used as potent antimicrobial and antimicrobial photodynamic therapy agents as well as Escherichia coli microbial cell inhibitors. As a result, the prepared nanocomposites can be considered promising candidates for biomedicine.

Design, synthesis, and characterization of M(II)-Schiff base complexes containing 3,5-di-tert-butyl salicylaldehyde: DNA binding/cleavage, DPPH radical scavenging activity, cytotoxic activity, and catalytic activity investigation

Two mononuclear Cu(II) and Zn(II) based complexes were synthesized via microwave-assisted method utilizing Schiff base ligand based on 3,5-di-tertbutylsalicylaldehyde. The compounds were characterized using elemental and spectroscopic analysis methods. The ligand posed as an ON-donor ligand, confirmed by spectrum analysis in the complexes. A geometry optimization analysis was also performed using density functional theory to obtain the geometry, stability, and electronic properties of the synthesized compounds. CuL1 has a distorted square planar geometry, whereas ZnL1 has a distorted tetrahedral geometry. Fluorescence and absorbance spectroscopy were utilized to explore the interaction properties of calf thymus-deoxyribonucleic acid (CT-DNA) with the complexes. The CuL1 and ZnL1 are highly sensitive to DNA binding, with binding constant (Kb) in the range of 105 M−1, representing substantial interaction with CT-DNA, combining intercalation and electrostatic interactions. The Stern-Volmer constant (Ksv) obtained from the fluorescence spectroscopy method varied from 3.31 x 104 to 8.42 x 104 M−1, indicating moderate DNA binding. Circular dichroism spectroscopy confirmed the presence of intercalative binding among the DNA and the complexes. The in-vitro DNA cleavage activity revealed that complexes could efficiently break the supercoiled plasmid DNA without using any external agents. The complex CuL1 induced significant cytotoxicity for Dalton’s lymphoma cancer cell lines, having IC50 values of 18.96 ± 0.021 μM. The antioxidant activity of the compounds was also studied, confirming CuL1 to be the most active antioxidant with IC50 = 399.27 µM. A molecular docking simulation was also conducted to comprehend the compounds' interaction mechanism with CT-DNA (1BNA) and cancer cells (BCL-family proteins). Furthermore, the catalytic activity of the zinc metal complex was assessed for multi-component reactions involving substituted benzaldehydes, malononitrile, and resorcinol.

Protein Engineering with Lightweight Graph Denoising Neural Networks.

Protein engineering faces challenges in finding optimal mutants from a massive pool of candidate mutants. In this study, we introduce a deep-learning-based data-efficient fitness prediction tool to steer protein engineering. Our methodology establishes a lightweight graph neural network scheme for protein structures, which efficiently analyzes the microenvironment of amino acids in wild-type proteins and reconstructs the distribution of the amino acid sequences that are more likely to pass natural selection. This distribution serves as a general guidance for scoring proteins toward arbitrary properties on any order of mutations. Our proposed solution undergoes extensive wet-lab experimental validation spanning diverse physicochemical properties of various proteins, including fluorescence intensity, antigen-antibody affinity, thermostability, and DNA cleavage activity. More than 40% of ProtLGN-designed single-site mutants outperform their wild-type counterparts across all studied proteins and targeted properties. More importantly, our model can bypass the negative epistatic effect to combine single mutation sites and form deep mutants with up to seven mutation sites in a single round, whose physicochemical properties are significantly improved. This observation provides compelling evidence of the structure-based model's potential to guide deep mutations in protein engineering. Overall, our approach emerges as a versatile tool for protein engineering, benefiting both the computational and bioengineering communities.

Development of cancer-targeted nano gold functionalized ruthenium(III)-doxorubicin complex: Synthesis, characterization and evaluation of DNA cleavage, anticancer and bioimaging activity

Metal-based drugs have attracted greater attention for cancer diseases because of biological relevance. However, some drawbacks are present in the metal complexes such as low stability and low bioavailability. Nanomaterials functionalized metal complexes can protect the stability and enhanced the bioavailability. In the present study, Nano gold functionalized ruthenium(III) complex from doxorubicin have been synthesized from ruthenium(III) complex and characterized using various spectrochemical techniques such as IR, UV, and NMR. In the metal complex, Doxorubicin (DOX) acts as a monobasic bidentate ligand and is coordinated through the carbonyl oxygen and phenolate oxygen of the anthracene ring. Based on spectral evidences, the complex [Ru(DOX)(PPh3)2Cl2] has an octahedral geometry. The Nano Au-Ru(III) DOX is analysed for their size, and morphology using XRD, SEM and HRTEM. X-ray diffraction pattern revealed that the complex has nanocrystalline in nature. The Nano Au-Ru(III) DOX is spherical shape and particle size is less than 15 nm. The DNA cleavage activity of [Ru(DOX)(PPh3)2Cl2] and Nano Au-Ru(III) DOX has been evaluated using pUC18 plasmid DNA and the results showed significant cleavage. The [Ru(DOX)(PPh3)2Cl2] and Nano Au-Ru(III) DOX have been tested against human breast cancer (MCF-7) and leukemia cancer cell lines (K-562) in vitro for its antitumor effects. The tumour activity of the Nano Au-Ru(III) DOX showed more promising activity than the [Ru(DOX)(PPh3)2Cl2]. The cell imaging of the Nano Au-Ru(III) DOX was examined against epithelial human breast cancer cell line (MDA-MB-231) using fluorescent microscopy. The fluorescence images showed high scattering light in tumour tissue at 100 µg/mL Hence, Nano Au-Ru(III) DOX can serve as a promising drug for cancer therapy and cellular imaging.

Why Does the E1219V Mutation Expand T-Rich PAM Recognition in Cas9 from Streptococcus pyogenes?

Popular RNA-guided DNA endonuclease Cas9 from Streptococcus pyogenes (SpCas9) recognizes the canonical 5'-NGG-3' protospacer adjacent motif (PAM) and triggers double-stranded DNA cleavage activity. Mutations in SpCas9 were demonstrated to expand the PAM readability and hold promise for therapeutic and genome editing applications. However, the energetics of the PAM recognition and its relation to the atomic structure remain unknown. Using the X-ray structure (precatalytic SpCas9:sgRNA:dsDNA) as a template, we calculated the change in the PAM binding affinity in response to SpCas9 mutations using computer simulations. The E1219V mutation in SpCas9 fine-tunes the water accessibility in the PAM binding pocket and promotes new interactions in the SpCas9:noncanonical T-rich PAM, thus weakening the PAM stringency. The nucleotide-specific interaction of two arginine residues (i.e., R1333 and R1335 of SpCas9) ensured stringent 5'-NGG-3' PAM recognition. R1335A substitution (SpCas9R1335A) completely disrupts the direct interaction between SpCas9 and PAM sequences (canonical or noncanonical), accounting for the loss of editing activity. Interestingly, the double mutant (SpCas9R1335A,E1219V) boosts DNA binding affinity by favoring protein:PAM electrostatic contact in a desolvated pocket. The underlying thermodynamics explain the varied DNA cleavage activity of SpCas9 variants. A direct link between the energetics, structures, and activity is highlighted, which can aid in the rational design of improved SpCas9-based genome editing tools.

Biofouling mitigation of Nb2AlC and Mo3AlC2 MXene-precursors doped polyether sulfone mixed matrix membranes for pathogen microorganisms

This study explores the incorporation of Nb2AlC and Mo3AlC2 MAX phases, known for their nano-layered structure, into polyether sulfone (PES) membranes to enhance their antifouling and permeability properties for pathogen microorganism filtration against bovine serum albumin (BSA) and Escherichia coli (E. coli). The composite membranes were characterized for their structural and morphological properties, and their performance in mitigating biofouling was evaluated. The structural characterizations have been performed for all the prepared MAX phases and corresponding composite membranes. The antioxidant ability of Nb2AlC and Mo3AlC2 MAX phases was defined by the DPPH radical scavenging assay, and the highest antioxidant ability was found to be 59.35 %, while 53.69 % scavenging potential was recorded at 100 mg/L. The percentage scavenging ability was raised with an increase in concentrations. The antimicrobial properties of MAX phases, evaluated as the minimum inhibitory concentration, were stated against several pathogen microorganisms. The tested compounds of Nb2AlC and Mo3AlC2 composites containing MAX phases exhibited excellent chemical nuclease activity, and it was determined that Nb2AlC caused double strand DNA cleavage activity while Mo3AlC2 induced the complete fragmentation of the DNA molecule. Biofilm inhibition of Nb2AlC and Mo3AlC2 MAX phases was studied against Staphylococcus aureus, and Pseudomonas aeruginosa and the maximum biofilm inhibition of Nb2AlC and Mo3AlC2 MAX phases was found to be 77.15 % and 69.07 % against S. aureus and also 69.74 % and 65.01 % against P. aeruginosa. Furthermore, Nb2AlC and Mo3AlC2 MAX phases demonstrated excellent E. coli growth inhibition of 100 % at 125 and 250 mg/L.

DNA binding, potential anticancer, antioxidant and molecular docking simulations of some isonicotinohydrazide metal complexes with the impact of high energy γ-rays irradiation doses: Synthesis and structural characterization

This work focuses on the preparation and characterization of some VO(II), Co(II), Cu(II), Zn(II) and Hg(II) complexes (1–5) of N'-(2-aminobenzoyl)isonicotinohydrazide ligand (HL). The compounds were characterized using various analytical and spectral tools. The resulting powder samples of the as prepared complexes (3,5) were exposed to two gamma ray doses up to 150 and 200 kGy from highly-energetic 60Co γ-irradiation (hereafter referred to as (3F,5F) at dose value of 150 kGy and (3F*,5F*) at dose value of 200 kGy). The impact of γ-irradiation on the possible structural changes of these samples after gamma irradiation was studied. The ligand and as prepared Cu(II) (3), Hg(II) (5) and their γ-irradiated (3F,5F) and (3F*,5F*) samples were tested for free radical scavenging activity using the DPPH assay. The DNA cleavage activity using supercoiled plasmid DNA (calf thymus ct-DNA) was explored. The tested ligand (HL) and complexes (3,5) showed excellent DNA binding. Additionally, the in vitro antitumor activity of (HL) and its Cu(II) (3) and Hg(II) (5) complexes was scrutinized against the human breast carcinoma (MCF-7), human hepatocarcinoma (Hep-G2) cell lines and kidney epithelial normal cells extracted from African green monkey kidney (Vero) to investigate the potential safety towards the normal cells. Also, docking simulation was done on the active site of 4FM9 and 1H7K protein for liver cancer and breast cancer cell line, respectively and showed excellent results.

Discovery and structural mechanism of DNA endonucleases guided by RAGATH-18-derived RNAs

CRISPR-Cas systems and IS200/IS605 transposon-associated TnpBs have been utilized for the development of genome editing technologies. Using bioinformatics analysis and biochemical experiments, here we present a new family of RNA-guided DNA endonucleases. Our bioinformatics analysis initially identifies the stable co-occurrence of conserved RAGATH-18-derived RNAs (reRNAs) and their upstream IS607 TnpBs with an average length of 390 amino acids. IS607 TnpBs form programmable DNases through interaction with reRNAs. We discover the robust dsDNA interference activity of IS607 TnpB systems in bacteria and human cells. Further characterization of the Firmicutes bacteria IS607 TnpB system (ISFba1 TnpB) reveals that its dsDNA cleavage activity is remarkably sensitive to single mismatches between the guide and target sequences in human cells. Our findings demonstrate that a length of 20 nt in the guide sequence of reRNA achieves the highest DNA cleavage activity for ISFba1 TnpB. A cryo-EM structure of the ISFba1 TnpB effector protein bound by its cognate RAGATH-18 motif-containing reRNA and a dsDNA target reveals the mechanisms underlying reRNA recognition by ISFba1 TnpB, reRNA-guided dsDNA targeting, and the sensitivity of the ISFba1 TnpB system to base mismatches between the guide and target DNA. Collectively, this study identifies the IS607 TnpB family of compact and specific RNA-guided DNases with great potential for application in gene editing.

Deciphering the Substrate Specificity Reveals that CRISPR-Cas12a Is a Bifunctional Enzyme with Both Endo- and Exonuclease Activities

The class 2 CRISPR-Cas9 and CRISPR-Cas12a systems, originally described as adaptive immune systems of bacteria and archaea, have emerged as versatile tools for genome-editing, with applications in biotechnology and medicine. However, significantly less is known about their substrate specificity, but such knowledge may provide instructive insights into their off-target cleavage and previously unrecognized mechanism of action. Here, we document that the Acidaminococcus sp. Cas12a (AsCas12a) binds preferentially, and independently of crRNA, to a suite of branched DNA structures, such as the Holliday junction (HJ), replication fork and D-loops, compared with single- or double-stranded DNA, and promotes their degradation. Further, our study revealed that AsCas12a binds to the HJ, specifically at the crossover region, protects it from DNase I cleavage and renders a pair of thymine residues in the HJ homologous core hypersensitive to KMnO4 oxidation, suggesting DNA melting and/or distortion. Notably, these structural changes enabled AsCas12a to resolve HJ into nonligatable intermediates, and subsequently their complete degradation. We further demonstrate that crRNA impedes HJ cleavage by AsCas12a, and that of Lachnospiraceae bacterium Cas12a, without affecting their DNA-binding ability. We identified a separation-of-function variant, which uncouples DNA-binding and DNA cleavage activities of AsCas12a. Importantly, we found robust evidence that AsCas12a endonuclease also has 3′-to-5′ and 5′-to-3′ exonuclease activity, and that these two activities synergistically promote degradation of DNA, yielding di- and mononucleotides. Collectively, this study significantly advances knowledge about the substrate specificity of AsCas12a and provides important insights into the degradation of different types of DNA substrates.

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.

Biochemical characterization of the meiosis-essential yet evolutionarily divergent topoisomerase VIB-like protein MTOPVIB from Arabidopsis thaliana.

Formation of programmed DNA double-strand breaks is essential for initiating meiotic recombination. Genetic studies on Arabidopsis thaliana and Mus musculus have revealed that assembly of a type IIB topoisomerase VI (Topo VI)-like complex, composed of SPO11 and MTOPVIB, is a prerequisite for generating DNA breaks. However, it remains enigmatic if MTOPVIB resembles its Topo VI subunit B (VIB) ortholog in possessing robust ATPase activity, ability to undergo ATP-dependent dimerization, and activation of SPO11-mediated DNA cleavage. Here, we successfully prepared highly pure A. thaliana MTOPVIB and MTOPVIB-SPO11 complex. Contrary to expectations, our findings highlight that MTOPVIB differs from orthologous Topo VIB by lacking ATP-binding activity and independently forming dimers without ATP. Most significantly, our study reveals that while MTOPVIB lacks the capability to stimulate SPO11-mediated DNA cleavage, it functions as a bona fide DNA-binding protein and plays a substantial role in facilitating the dsDNA binding capacity of the MOTOVIB-SPO11 complex. Thus, we illustrate mechanistic divergence between the MTOPVIB-SPO11 complex and classical type IIB topoisomerases.

Novel Bis(2-cyanoacrylamide) Linked to Sulphamethoxazole: Synthesis, DNA Interaction, Anticancer, ADMET, Molecular Docking, and DFT Studies.

In the light of advancement and potential extensive use of medication design and therapy, new bis(cyanoacrylamides) incorporating sulphamethoxazole derivatives (7 a-7 f) were synthesized and confirmed by different spectral tools. In vitro anticancer activity towards different human cancer cells (HCT116, MDA-MB-231 and A549) was assessed using MTT assay. Among all derivatives, 4C- and 6C-spacer derivatives (7 e and 7 f) had the most potent growth inhibitory activities against HCT116 cells with IC50 values of 39.7 and 28.5 μM, respectively. 7 e and 7 f induced apoptosis and suppressed migration of HCT116 cells. These compounds also induced a significant increase in caspase-3 and CDH1 activities, and a downregulation of Bcl2 using ELISA. pBR322 DNA cleavage activities of cyanoacrylamides were determined using agarose gel electrophoresis. Furthermore, 7 e and 7 f showed good DNA and BSA binding affinities using different spectroscopic techniques. Furthermore, molecular docking for 7 e and 7 f was performed to anticipate their binding capabilities toward various proteins (Bcl2, CDH1 and BSA). The docking results were well correlated with those of experimental results. Additionally, density functional theory and ADMET study were performed to evaluate the molecular and pharmacokinetic features of 7 e and 7 f, respectively. Thus, this work reveals promising antitumor lead compounds that merit future research and activity enhancement.

Target-Mediated Fluoroquinolone Resistance in Neisseria gonorrhoeae: Actions of Ciprofloxacin against Gyrase and Topoisomerase IV.

Fluoroquinolones make up a critically important class of antibacterials administered worldwide to treat human infections. However, their clinical utility has been curtailed by target-mediated resistance, which is caused by mutations in the fluoroquinolone targets, gyrase and topoisomerase IV. An important pathogen that has been affected by this resistance is Neisseria gonorrhoeae, the causative agent of gonorrhea. Over 82 million new cases of this sexually transmitted infection were reported globally in 2020. Despite the impact of fluoroquinolone resistance on gonorrhea treatment, little is known about the interactions of this drug class with its targets in this bacterium. Therefore, we investigated the effects of the fluoroquinolone ciprofloxacin on the catalytic and DNA cleavage activities of wild-type gyrase and topoisomerase IV and the corresponding enzymes that harbor mutations associated with cellular and clinical resistance to fluoroquinolones. Results indicate that ciprofloxacin interacts with both gyrase (its primary target) and topoisomerase IV (its secondary target) through a water-metal ion bridge that has been described in other species. Moreover, mutations in amino acid residues that anchor this bridge diminish the susceptibility of the enzymes for the drug, leading to fluoroquinolone resistance. Results further suggest that ciprofloxacin primarily induces its cytotoxic effects by enhancing gyrase-mediated DNA cleavage as opposed to inhibiting the DNA supercoiling activity of the enzyme. In conclusion, this work links the effects of ciprofloxacin on wild-type and resistant gyrase to results reported for cellular and clinical studies and provides a mechanistic explanation for the targeting and resistance of fluoroquinolones in N. gonorrhoeae.

A Comparison of In Vitro Studies between Cobalt(III) and Copper(II) Complexes with Thiosemicarbazone Ligands to Treat Triple Negative Breast Cancer

Metal complexes have gained significant attention as potential anti-cancer agents. The anti-cancer activity of [Co(phen)2(MeATSC)](NO3)3•1.5H2O•C2H5OH 1 (where phen = 1,10-phenanthroline and MeATSC = 9-anthraldehyde-N(4)-methylthiosemicarbazone) and [Cu(acetylethTSC)Cl]Cl•0.25C2H5OH 2 (where acetylethTSC = (E)-N-ethyl-2-[1-(thiazol-2-yl)ethylidene]hydrazinecarbothioamide) was investigated by analyzing DNA cleavage activity. The cytotoxic effect was analyzed using CCK-8 viability assay. The activities of caspase 3/7, 9, and 1, reactive oxygen species (ROS) production, cell cycle arrest, and mitochondrial function were further analyzed to study the cell death mechanisms. Complex 2 induced a significant increase in nicked DNA. The IC50 values of complex 1 were 17.59 μM and 61.26 μM in cancer and non-cancer cells, respectively. The IC50 values of complex 2 were 5.63 and 12.19 μM for cancer and non-cancer cells, respectively. Complex 1 induced an increase in ROS levels, mitochondrial dysfunction, and activated caspases 3/7, 9, and 1, which indicated the induction of intrinsic apoptotic pathway and pyroptosis. Complex 2 induced cell cycle arrest in the S phase, ROS generation, and caspase 3/7 activation. Thus, complex 1 induced cell death in the breast cancer cell line via activation of oxidative stress which induced apoptosis and pyroptosis while complex 2 induced cell cycle arrest through the induction of DNA cleavage.

Low-Toxicity and High-Efficiency Streptomyces Genome Editing Tool Based on the Miniature Type V-F CRISPR/Cas Nuclease AsCas12f1.

Genome editing tools based on SpCas9 and FnCpf1 have facilitated strain improvements for natural product production and novel drug discovery in Streptomyces. However, due to high toxicity, their editing requires high DNA transformation efficiency, which is unavailable in most streptomycetes. The transformation efficiency of an all-in-one editing tool based on miniature Cas nuclease AsCas12f1 was significantly higher than those of SpCas9 and FnCpf1 in tested streptomycetes, which is due to its small size and weak DNA cleavage activity. Using this tool, in Streptomyces coelicolor, we achieved 100% efficiency for single gene or gene cluster deletion and 46.7 and 40% efficiency for simultaneous deletion of two genes and two gene clusters, respectively. AsCas12f1 was successfully extended to Streptomyces hygroscopicus SIPI-054 for efficient genome editing, in which SpCas9/FnCpf1 does not work well. Collectively, this work offers a low-toxicity, high-efficiency genome editing tool for streptomycetes, particularly those with low DNA transformation efficiency.

Environmental Energy Production and Wastewater Treatment Using Synthesized Pd Nanoparticles with Biological and Photocatalytic Activity

AbstractMetallic nanoparticles have attracted great attention in catalytic, medical diagnosis, and treatment research in recent years. The formation of palladium nanoparticles using rosemary (Rosmarinus officinalis L.) extract was carried out using the green synthesis method. The plant was extracted using 70% ethanol by microwave techniques. The novelty of this study is the investigation of the biological activities of green synthesis of Pd nanoparticles, such as DNA cleavage activity, antimicrobial activity, DPPH scavenging activity, and its electro-catalytic performance in alcohol oxidation. Additionally, photocatalytic activities were also evaluated. The characterization of synthesized palladium nanoparticles (Pd NPs) was performed by UV-spectrometry, XRD, FTIR, and TEM. According to TEM results, Pd nanoparticles were observed to have a spherical shape and an average particle size of 4.91 nm. The Pd NPs showed the photodegradation of MB solution by up to 79.9% at 120 min. The newly synthesized plant-mediated green synthesized Pd NPs showed the max and the min antimicrobial activity at 16 µg/mL and 256 µg/mL against L. pneumophila and C. albicans, respectively. The current density ratio of 48.22 mA/cm2 obtained in the study indicates that the obtained materials may be of interest in different applications. According to the results obtained, a direct relationship of extract use is observed in the synthesis of Pd nanoparticles and is a good way to reduce and stabilize metal salts. It has been determined that green Pd NPs have potential for use in energy production from alcohol oxidation and in medical applications.

Pyrococcus furiosus argonaute based Alicyclobacillus acidoterrestrsis detection in fruit juice

Alicyclobacillus acidoterrestris is the major threat to fruit juice for its off-odor producing characteristic. In this study, Pyrococcus furiosus Argonaute (PfAgo), a novel endonuclease with precise DNA cleavage activity, was used for A. acidoterrestrisdetection, termed as PAD. The partially amplified 16 S rRNA gene of A. acidoterrestris can be cleaved by PfAgo activated by a short 5′-phosphorylated single strand DNA, producing a new guide DNA (gDNA). Then, PfAgo was activated by the new gDNA to cut a molecular beacon (MB) with fluorophore-quencher reporter, resulting in the recovery of fluorescence. The fluorescent intensity is positively related with the concentration of A. acidoterrestris. The PAD assay showed excellent specificity and sensitivity as low as 101 CFU/mL, which can be a powerful tool for on-site detection of A. acidoterrestris in fruit juice industry in the future, reducing the economic loss.

DNA Sequence Control of Enzyme Filamentation and Activation of the SgrAI Endonuclease.

Enzyme polymerization (also known as filamentation) has emerged as a new layer of enzyme regulation. SgrAI is a sequence-dependent DNA endonuclease that forms polymeric filaments with enhanced DNA cleavage activity as well as altered DNA sequence specificity. To better understand this unusual regulatory mechanism, full global kinetic modeling of the reaction pathway, including the enzyme filamentation steps, has been undertaken. Prior work with the primary DNA recognition sequence cleaved by SgrAI has shown how the kinetic rate constants of each reaction step are tuned to maximize activation and DNA cleavage while minimizing the extent of DNA cleavage to the host genome. In the current work, we expand on our prior study by now including DNA cleavage of a secondary recognition sequence, to understand how the sequence of the bound DNA modulates filamentation and activation of SgrAI. The work shows that an allosteric equilibrium between low and high activity states is modulated by the sequence of bound DNA, with primary sequences more prone to activation and filament formation, while SgrAI bound to secondary recognition sequences favor the low (and nonfilamenting) state by up to 40-fold. In addition, the degree of methylation of secondary sequences in the host organism, Streptomyces griseus, is now reported for the first time and shows that as predicted, these sequences are left unprotected from the SgrAI endonuclease making sequence specificity critical in this unusual filament-forming enzyme.

Biological Applications of The Newly Designed Phthalocyanine‐Modified Gold Nanorods

AbstractIn this study, a new di‐substituted phthalonitrile derivative namely 2‐[2‐{(3,5‐bis (trifluoromethyl) phenyl) ethynyl}‐4,5 dicyanophenyl] malonate was synthesized. The cycloteramerization of the resultant compound in the presence of the related metal salts resulted in a number of metal {M=Co, Mn, and Lu} phthalocyanines. The newly synthesized macromolecules were used for the functionalization of gold nanorods. To study the effect of modification and metal ion on the biological properties of the gold nanorods, the biological features of the phthalocyanines, phthalocyanine‐gold nanorod conjugates, and gold nanorods were examined by performing different biological approaches. In this study, the anti‐diabetic activities of fluorinated phthalocyanines and their gold nanorod conjugates were examined for the first time using pancreatic alpha‐amylase. The antioxidant activities of the studied nano/structures were analyzed using 2,2‐diphenyl‐1‐picrylhydrazil (DPPH) radical scavenging assay. Their antimicrobial and antimicrobial photodynamic therapy activities (APDT) were investigated, as well. They exhibited good DNA cleavage activities. The highest biofilm inhibition activities were obtained 97.49 and 91.53 % for 200 mg/L of nanoconjugate (7) against S. aureus and P. aeruginosa, respectively. All the studied biological candidates also displayed effective microbial cell viability inhibition activities against E. coli.

Repurposing the antihistamine drug bilastine as an anti-cancer metallic drug entity: synthesis and single-crystal X-ray structure analysis of metal-based bilastine and phen [Co(II), Cu(II) and Zn(II)] tailored anticancer chemotherapeutic agents against resistant cancer cells.

Bilastine (BLA), 2-(4-(2-(4-(1-(2-ethoxyethyl)-1H-benzo[d]imidazole-2-yl)-piperidin-1-yl)-ethyl)-phenyl)-2-methylpropanoic acid, is an active antihistamine drug. With the idea of repurposing drugs from the existing pool of 'active' pharmaceutical ingredients, the therapeutic potency of bilastine as an anticancer agent was investigated via the tailored synthesis of a metal-based anticancer drug formulation of the type [BLA(phen)2M(II)]+·X-, where M = Co, Cu, and Zn and X- = NO3 and ClO4. The synthesized metal-based chemotherapeutics derived from the bilastine drug that acts as a ligand were thoroughly characterized using spectroscopic techniques, namely, UV-vis, FT-IR, and EPR (in the case of 1 and 2); 1H-NMR and 13C-NMR (in the case of 3); ESI-MS and single-crystal X-ray diffraction studies. Comprehensive biological studies (DNA binding, cleavage, and cytotoxic activity) using various biophysical and gel electrophoretic methods were carried out to validate their potential as anticancer agents. The cytotoxic activity of 'therapeutically promising' copper(II)-based drug candidate 2 was evaluated against MCF-7, MBA-MD-231, HeLa, HepG2, and Mia-PaCa-2 cancer cells via an SRB assay, and the results demonstrated 2 as a potent anticancer agent at low nanomolar concentrations against all tested cancer cells, preferably with a much superior anticancer efficacy against human pancreatic cancer cells.