High-affinity DNA Binding Research Articles

Near-Infrared Laser-Switching DNA Phase Separation Nanoinducer for Glioma Therapy.

DNA phase separation participates in chromatin packing for the modulation of gene transcription, but the induction of DNA phase separation in living cells for disease treatment faces huge challenges. Herein, we construct a Ru(II)-polypyridyl-loaded upconversion nanoplatform (denoted as UCSNs-R) to achieve the manipulation of DNA phase separation and production of abundant singlet oxygen (1O2) for efficient treatment of gliomas. The utilization of the UCSN not only facilitates high loading of Ru(II)-polypyridyl complexes (RuC) but also promotes the conversion of near-infrared (NIR) laser to ultraviolet light for efficient 1O2 generation. The released RuC exhibit DNA "light-switch" behavior and high DNA binding affinity that induce phase separation of DNA in living cells, thus resulting in DNA damage and suppressing tumor-cell growth. In vivo investigation demonstrates the high capability of UCSNs-R in inhibiting tumor proliferation under NIR laser illumination. This work represents a paradigm for designing a DNA phase separation nanoinducer through integration of the UCSN with Ru(II)-polypyridyl-based complexes for efficient therapy of gliomas.

Apoptosis-inducing, anti-angiogenic and anti-migratory effects of a dinuclear Pd(II) complex on breast cancer: A promising novel compound

Because of the high mortality and morbidity rate of breast cancer, successful management of the disease requires synthesis of novel compounds. To this end, ongoing attempts to create new candidates include synthesis of multinuclear metal complexes. The high DNA binding affinity and cytotoxic activity of these complexes makes them promising as breast cancer treatments. This study investigated anti-growth/cytotoxic effect of the dinuclear Pd(II) complex on breast cancer cell lines (MCF-7, MDA-MB-231) using various methods of staining, flow cytometry, and immunoblotting. The study conducted colony formation, invasion, and migration assays were to assess the effect of the complex on metastasis. Increased caspase-3/7 levels and positive annexin V staining were observed in both cell lines, proving apoptosis. Altered TNFR1 and TRADD expression with caspase-8 cleavage followed by BCL-2 inactivation with loss of mitochondrial membrane potential confirmed the presence of apoptosis in MCF-7 and MDA-MB-231, regardless of p53 expression status. The results implied anti-migration properties. Finally, the study used the CAM assay to assess antiangiogenic properties and showed that the complex inhibited angiogenesis. The study concluded the dinuclear Pd(II) complex warrants further in vivo experiments to show its potential in the treatment of breast cancer.

DNA Binding and Cleavage, Stopped-Flow Kinetic, Mechanistic, and Molecular Docking Studies of Cationic Ruthenium(II) Nitrosyl Complexes Containing "NS4" Core.

This work aimed to evaluate in vitro DNA binding mechanistically of cationic nitrosyl ruthenium complex [RuNOTSP]+ and its ligand (TSPH2) in detail, correlate the findings with cleavage activity, and draw conclusions about the impact of the metal center. Theoretical studies were performed for [RuNOTSP]+, TSPH2, and its anion TSP-2 using DFT/B3LYP theory to calculate optimized energy, binding energy, and chemical reactivity. Since nearly all medications function by attaching to a particular protein or DNA, the in vitro calf thymus DNA (ctDNA) binding studies of [RuNOTSP]+ and TSPH2 with ctDNA were examined mechanistically using a variety of biophysical techniques. Fluorescence experiments showed that both compounds effectively bind to ctDNA through intercalative/electrostatic interactions via the DNA helix's phosphate backbone. The intrinsic binding constants (Kb), (2.4 ± 0.2) × 105 M-1 ([RuNOTSP]+) and (1.9 ± 0.3) × 105 M-1 (TSPH2), as well as the enhancement dynamic constants (KD), (3.3 ± 0.3) × 104 M-1 ([RuNOTSP]+) and (2.6 ± 0.2) × 104 M-1 (TSPH2), reveal that [RuNOTSP]+ has a greater binding propensity for DNA compared to TSPH2. Stopped-flow investigations showed that both [RuNOTSP]+ and TSPH2 bind through two reversible steps: a fast second-order binding, followed by a slow first-order isomerization reaction via a static quenching mechanism. For the first and second steps of [RuNOTSP]+ and TSPH2, the detailed binding parameters were established. The total binding constants for [RuNOTSP]+ (Ka = 43.7 M-1, Kd = 2.3 × 10-2 M-1, ΔG0 = -36.6 kJ mol-1) and TSPH2 (Ka = 15.1 M-1, Kd = 66 × 10-2 M, ΔG0 = -19 kJ mol-1) revealed that the relative reactivity is approximately ([RuNOTSP]+)/(TSPH2) = 3/1. The significantly negative ΔG0 values are consistent with a spontaneous binding reaction to both [RuNOTSP]+ and TSPH2, with the former being very favorable. The findings showed that the Ru(II) center had an effect on the reaction rate but not on the mechanism and that the cationic [RuNOTSP]+ was a more highly effective DNA binder than the ligand TSPH2 via strong electrostatic interaction with the phosphate end of DNA. Because of its higher DNA binding affinity, cationic [RuNOTSP]+ demonstrated higher cleavage efficiency towards the minor groove of pBR322 DNA via the hydrolytic pathway than TSPH2, revealing the synergy effect of TSPH2 in the form of the complex. Furthermore, the mode of interaction of both compounds with ctDNA has also been supported by molecular docking.

Cooperative action of separate interaction domains promotes high-affinity DNA binding of Arabidopsis thaliana ARF transcription factors

The signaling molecule auxin coordinates many growth and development processes in plants, mainly through modulating gene expression. Transcriptional response is mediated by the family of auxin response factors (ARF). Monomers of this family recognize a DNA motif and can homodimerize through their DNA-binding domain (DBD), enabling cooperative binding to an inverted binding site. Most ARFs further contain a C-terminal PB1 domain that is capable of homotypic interactions and mediating interactions with Aux/IAA repressors. Given the dual role of the PB1 domain, and the ability of both DBD and PB1 domain to mediate dimerization, a key question is how these domains contribute to DNA-binding specificity and affinity. So far, ARF-ARF and ARF-DNA interactions have mostly been approached using qualitative methods that do not provide a quantitative and dynamic view on the binding equilibria. Here, we utilize a DNA binding assay based on single-molecule Förster resonance energy transfer (smFRET) to study the affinity and kinetics of the interaction of several Arabidopsis thaliana ARFs with an IR7 auxin-responsive element (AuxRE). We show that both DBD and PB1 domains of AtARF2 contribute toward DNA binding, and we identify ARF dimer stability as a key parameter in defining binding affinity and kinetics across AtARFs. Lastly, we derived an analytical solution for a four-state cyclic model that explains both the kinetics and the affinity of the interaction between AtARF2 and IR7. Our work demonstrates that the affinity of ARFs toward composite DNA response elements is defined by dimerization equilibrium, identifying this as a key element in ARF-mediated transcriptional activity.

The Dengue virus protease NS2B3 cleaves cyclic GMP-AMP synthase to suppress cGAS activation

Dengue virus (DENV) is one of the most prevalent mosquito-transmitted human viruses that causes significant morbidity and mortality worldwide. To persist in the cell and consequently cause disease, DENV is evolved with mechanisms to suppress the induction of type I interferons by antagonizing cGAS-STING signaling. Using recombinant proteins and invitro cleavage assays, we have shown that the DENV protease NS2B3 is capable of cleaving cGAS in the N-terminal region without disrupting the C-terminal catalytic center. This generates two major cleavage products: cleavage product N-terminal (CP-N) and cleavage product C-terminal (CP-C). We observed reduction in DNA-binding affinity of CP-C as compared to full-length cGAS. Reduction in DNA-binding affinity is also correlated with the decrease in enzymatic activity of CP-C. CP-N, on the other hand, has almost comparable DNA-binding ability as that of the full-length cGAS. In fact, CP-N competitively inhibits cyclic GMP-AMP production by both full-length cGAS and CP-C. We hypothesize that high DNA-binding affinity of CP-N enables it to sequester the DNA from CP-C and noncleaved full-length cGAS and thus reduces the rate of enzyme activation and cyclic GMP-AMP synthesis. Furthermore, we found that NS2B3 physically interacts with full-length cGAS and CP-C, laying the basis for their shuttling to and eventual degradation in the autophagosome. Overall, our study highlights a multifaceted and effective strategy by which an RNA virus antagonizes cGAS-STING signaling which may be useful for the design of antivirals targeting viral proteases.

Biosynthesis of silver nanoparticles of Tribulus terrestris food supplement and evaluated antioxidant activity and collagenase, elastase and tyrosinase enzyme inhibition: In vitro and in silico approaches

Food supplements from plants are source of many antioxidant substances. Tribulus terrestris food supplement (TtFS) is highlighted as one of these supplements that has presented potential to prevent damages and diseases caused by oxidative stress. In addition, new formulations that enhance the benefits of food supplement have been developed and metallic nanoparticles, the so-called green synthesis, has been of great interest. UV–visible spectroscopy, energy dispersive spectroscopy (EDS), Zeta potential (ZP), scanning transmission electron microscopy (STEM), scanning electron microscope (SEM) were used to characterize the synthesized silver nanoparticles (AgNPs). Antioxidant activity was determined by DPPH radical scavenging, ferric ion reducing power (FRAP); ABTS radical scavenging, and oxygen radical absorption capacity (ORAC-FL). Molecular docking analyses were performed to evaluate molecular interactions. Antioxidant evaluation of TtFS demonstrated 83.6% antioxidant activity (DPPH), 714.82 μM Trolox Equivalent (TE)/g sample (FRAP), 91.24 μM TE/g sample (ABTS), and antioxidant activity in ORAC assay. It presented inhibition activity on collagenase (75.33%), elastase (54.04%) and tyrosinase (59.07%). In addition, in silico assays showed an interaction between T. terrestris steroidal saponins and DNA, and the highest DNA binding affinity was observed with protodioscin. Steroidal saponins also presented interaction with all enzymes evaluated. The characterization of AgNPs demonstrated that they were formed as a spherical shape. These AgNPs showed greater protective properties against oxidative stress (85.41% antioxidant activity (DPPH) and 957.55 μM TE/g sample (FRAP)). The results represent an important indicator for the development and discovery of new nanoestructured pharmaceutical and cosmetic formulation using plants and natural products.

Unexpected moves: a conformational change in MutSα enables high-affinity DNA mismatch binding.

The DNA mismatch repair protein MutSα recognizes wrongly incorporated DNA bases and initiates their correction during DNA replication. Dysfunctions in mismatch repair lead to a predisposition to cancer. Here, we study the homozygous mutation V63E in MSH2that was found in the germline of a patient with suspected constitutional mismatch repair deficiency syndrome who developed colorectal cancer before the age of 30. Characterization of the mutant in mouse models, as well as slippage and repair assays, shows a mildly pathogenic phenotype. Using cryogenic electron microscopy and surface plasmon resonance, we explored the mechanistic effect of this mutation on MutSα function. We discovered that V63E disrupts a previously unappreciated interface between the mismatch binding domains (MBDs) of MSH2 and MSH6 and leads to reduced DNA binding. Our research identifies this interface as a 'safety lock' that ensures high-affinity DNA binding to increase replication fidelity. Our mechanistic model explains the hypomorphic phenotype of the V63E patient mutation and other variants in the MBD interface.

Complementary Roles of Two DNA Protection Proteins from Deinococcus geothermalis.

The roles of two interrelated DNA protection protein in starved cells (Dps)-putative Dps Dgeo_0257 and Dgeo_0281-as orthologous proteins to DrDps1 for DNA binding, protection, and metal ion sensing were characterised in a Deinococcus geothermalis strain. Dgeo_0257 exhibited high DNA-binding affinity and formed a multimeric structure but lacked the conserved amino acid sequence for ferroxidase activity. In contrast, the Dgeo_0281 (DgDps1) protein was abundant in the early exponential phase, had a lower DNA-binding activity than Dgeo_0257, and was mainly observed in its monomeric or dimeric forms. Electrophoretic mobility shift assays demonstrated that both purified proteins bound nonspecifically to DNA, and their binding ability was affected by certain metal ions. For example, in the presence of ferrous and ferric ions, neither Dgeo_0257 nor Dgeo_0281 could readily bind to DNA. In contrast, both proteins exhibited more stable DNA binding in the presence of zinc and manganese ions. Mutants in which the dps gene was disrupted exhibited higher sensitivity to oxidative stress than the wild-type strain. Furthermore, the expression levels of each gene showed an opposite correlation under H2O2 treatment conditions. Collectively, these findings indicate that the putative Dps Dgeo_0257 and DgDps1 from D. geothermalis are involved in DNA binding and protection in complementary interplay ways compared to known Dps.

Mechanistic insights into the nickel-dependent allosteric response of the Helicobacter pylori NikR transcription factor

In Helicobacter pylori, the nickel-responsive NikR transcription factor plays a key role in regulating intracellular nickel concentrations, which is an essential process for survival of this pathogen in the acidic human stomach. Nickel binding to H.pylori NikR (HpNikR) allosterically activates DNA binding to target promoters encoding genes involved in nickel homeostasis and acid adaptation, to either activate or repress their transcription. We previously showed that HpNikR adopts an equilibrium between an open conformation and DNA-binding competent cis and trans states. Nickel binding slows down conformational exchange between these states and shifts the equilibrium toward the binding-competent states. The protein then becomes stabilized in a cis conformation upon binding the ureA promoter. Here, we investigate how nickel binding creates this response and how it is transmitted to the DNA-binding domains. Through mutagenesis, DNA-binding studies, and computational methods, the allosteric response to nickel was found to be propagated from the nickel-binding sites to the DNA-binding domains via the β-sheets of the metal-binding domain and a network of residues at the inter-domain interface. Our computational results suggest that nickel binding increases protein rigidity to slow down the conformational exchange. A thymine base in the ureA promoter sequence, known to be critical for high affinity DNA binding by HpNikR, was also found to be important for the allosteric response, while a modified version of this promoter further highlighted the importance of the DNA sequence in modulating the response. Collectively, our results provide insights into regulation of a key protein for H.pylori survival.

Biological Activity of Two Anticancer Pt Complexes with a Cyclohexylglycine Ligand against a Colon Cancer Cell Line: Theoretical and Experimental Study.

Because of their extraordinary ability to disrupt the natural structure of nucleic acids, metal complexes could be used in cancer therapy. In this study, cyclohexylglycine (HL) as a ligand and two new Pt complexes, [Pt(NH3)2(L)]NO3 (1) and [Pt(bipy)(L)]NO3 (2), were synthesized and characterized by elemental analysis, LC-MS, UV-vis spectrometry, FT-IR, 1H NMR spectroscopy, 13C NMR spectroscopy, 195Pt NMR spectroscopy, HPLC analysis, and single-crystal X-ray diffraction. Complex 2 crystallized in the orthorhombic Pbca space group, and density functional theory (DFT) was used to describe its structural parameters were described in detail. These complexes can be classified as oral medications and drug-like molecules based on a comparison of their absorption, distribution, metabolism, and excretion assessment. Quantum chemical descriptors (QCDs) were determined using DFT calculations to predict the tendency of DNA to approach these complexes. During the determination of the function of the metallodrug in DNA binding, the fluorescence data indicated that static quenching took place for all ligands and complexes with higher DNA binding affinity. CD and isothermal absorption studies indicate the presence of electrostatic and groove binding for the amine derivative and that DNA binds with the bipy moiety via groove binding. Furthermore, the interaction modes were determined using molecular docking to investigate the binding of these compounds with the target DNA molecule. According to docking investigations, binding energies of -5.7, -11.56, and -10.00 kcal/mol for HL and complexes 1 and 2, respectively, indicate partially electrostatic and groove binding. The anticancer activities of the Pt(II) complexes were tested against the HCT116 human colon cancer cell line, with IC50 values of 35.51 and 51.33 μM for 1 and 2, respectively, after 72 h. These values show that the inhibitory effect of complex 1 was better than those of 2 and carboplatin (IC50 = 51.94 μM).

Surface chemistry of spiky silica nanoparticles tailors polyethyleneimine binding and intracellular DNA delivery

Cellular delivery of DNA using silica nanoparticles has attracted great attention. Typically, polyethyleneimine (PEI) is used to form a silica/PEI composite vector. Understanding the interactions at the silica and PEI interface is important for successful DNA delivery and transfection, especially for silica with different surface functionality. Herein, we report that a higher content of hydrogen boning formed between PEI molecules and phosphonate modified silica nanoparticles could slow down the PEI dissolution from the freeze-dried solid composites into aqueous solution than the bare silica counterpart. The pronounced PEI retention ability through phosphonation of silica nanoparticles effectively improves the transfection efficiency due to the high DNA binding affinity extracellularly, effective lysosome escape and high nuclear entry of both PEI and DNA intracellularly. Our study provides a fundamental understanding on designing effective silica-PEI-based nano-vectors for DNA delivery applications.

A Biophysical Investigation of DNA-Binding Interactions of Push-Pull Dibenzodioxins and Implications for in Vitro anti-Cancer Activity

Dibenzodioxin-DNA interactions were studied using biophysical techniques. UV-visible spectral titrations were performed against calf thymus (CT)-DNA to determine the binding constants. Spectrofluorimetric dye-displacement assay and DNA viscometric assay were used to understand the nature of binding interactions. Molecules with intercalative binding preference increased DNA viscosity, similar to a standard intercalator. Dibenzodioxin cytotoxicity was evaluated against HeLa cells. The most active molecules also had the highest binding constants with CT-DNA. Select dibenzodioxins were docked against DNA in silico. The binding behavior was compared using a known DNA binding small molecule. Dibenzodioxins with good cytotoxicity also had high DNA-binding affinity, implying that DNA could be a likely target for these dibenzodioxins. One fluorescent dibenzodioxin was used to study intra-cellular localization in HeLa cells using fluorescence microscopy. This derivative with weaker cytotoxicity was located mainly in the cytoplasm than in the nuclei, again hinting toward dibenzodioxin-DNA-binding interaction as the main mechanism of cytotoxicity.

EP183: Functional assessment of a novel POU4F3 missense variant

The POU-domain family of transcription factors have a wide variety of functions and are critical regulators of many developmental processes. They are characterized by a common bipartite DNA-binding structure with POU-specific and POU-homeodomain subdomains, joined by an unstructured linkage region. Both subdomains are required for high affinity DNA binding of POU transcription factors. The POU4F3 gene has been found to be essential for inner-ear hair cell maintenance and is associated with autosomal-dominant nonsyndromic hearing loss with variable age of onset. Here we describe an individual with a novel heterozygous missense variant in POU4F3 exhibiting bilateral childhood onset sensorineural hearing loss. The proband’s mother also exhibited hearing loss. Functional assessment of this variant was performed to determine the impact on protein localization, and familial segregation studies were performed to better understand the pathogenicity of this variant. The proband underwent exome sequencing (ES) which revealed a maternally inherited missense variant in POU4F3 (NM_002700.2, c.856A>G, p.(Lys286Glu)). Family members were subsequently given audiograms and tested for this variant. To functionally assess the variant HA-tagged wild-type and mutant POU4F3 were expressed by using the mammalian expression vector pcDNA3.1 and transfected in Hek293 cells. To determine the subcellular localization of the HA-tagged wild-type and mutant POU4F3, transiently transfected cells were fixed with 4% paraformaldehyde, incubated with primary anti-HA and secondary goat-anti-mouse Alexa488-labelled antibodies. Images were taken with a fluorescence microscope and processed using ImageJ. To determine the number of cells expressing POU4F3 outside the nucleus, slides were blinded and 100 cells of each transfected mutant were scored; each construct was transfected in duplicate. Audiograms revealed that one of the proband’s brothers had mild hearing loss, while the other was unaffected. Familial variant testing then showed that the affected brother is heterozygous for the POU4F3 variant while the unaffected brother does not harbor the variant. The mother was previously shown to have hearing loss, and the variant was maternally inherited. Functional assessment of the variant demonstrated that it results in significant mis-localization from the nucleus to the cytoplasm compared to wild type controls (p value: 0.009). This affect was more significant than positive controls included in the analysis. The proband’s variant is not reported in population databases and is predicted to be deleterious by REVEL (0.89) and CADD (27.7). This variant was clinically classified as a VUS, with the following criteria applied: PM2+PP3. This variant falls within the homeodomain of the protein, which is required for DNA binding of POU transcription factors. Pathogenic missense variants in POU4F3 have previously been shown to disrupt the nuclear localization of the protein, so this was assessed in cells expressing the p.(Lys286Glu) variant. The proband’s variant was found to result in significant mis-localization of POU4F3 to the cytoplasm, suggesting an impact on the protein function. Finally, the variant was found to segregate with hearing loss in the proband’s mother and affected brother, allowing us to apply PP1 criteria based on the ClinGen hearing loss evaluation guidelines. Taken together these data are suggestive that this variant is causative for the proband, however this remains a VUS.

Bridging the macroscopic and microscopic: a volumetric approach to DNA recognition

Living cells adapt to osmotically variable conditions in their environment. To understand the molecular basis of these adaptations, it is necessary to study the hydration properties of the biomolecular interactions that mediate the osmotic stress response. Gene expression studies have shown that the transcription factor PU.1 regulates target genes in response to cellular hyperosmotic stress, and osmotic pressure studies in vitro have shown that the high-affinity and low-affinity DNA binding modes of PU.1 are differentially hydrated.

Bichromophoric ruthenium(II) bis-terpyridine-BODIPY based photosensitizers for cellular imaging and photodynamic therapy.

Two multichromophoric homoleptic ruthenium(II) complexes [Ru(tpy-BODIPY)2]Cl2 (complexes 1 and 2, tpy = 4-phenyl-2,2:6,2-terpyridine, BODIPY = boron-dipyrromethene) were prepared, characterized and their phototherapeutic activity and bioimaging properties were studied. The complexes having structural similarity differ only by a phenylethynyl linker, and its overall influence on their physicochemical and photobiological behavior was evaluated. The terpyridine-BODIPY ligand L1 was structurally characterized by X-ray crystallography. The complexes showed intense absorption near 500 nm (ε: ∼1.5 × 105 M-1 cm-1 in DMSO), have a high singlet oxygen quantum yield (ΦΔ: ∼0.6 in DMSO), and displayed low photobleaching thus making them suitable for PDT applications. The complexes showed high DNA binding affinity and induced DNA damage on light activation via multiple types of ROS production. Confocal laser scanning microscopy experiments revealed their incorporation in the cancer cells and complex 1 predominantly accumulated in lysosomes. The complexes displayed a significant PDT effect in cancerous cells with visible light activation with a high photocytotoxicity index (PI) value in HeLa cells. Both type-I and type-II photosensitization processes were involved in the PDT effect. The photodynamic action of complex 2 initiated cellular apoptosis. Finally, their diagnostic potential was evaluated against clinically relevant 3D multicellular tumor spheroids (MCTs).

P53-mediated G1 arrest requires the induction of both p21 and Killin in human colon cancer cells

ABSTRACT The main biological function of the tumor suppressor p53 is to control cell cycle arrest and apoptosis. Among the p53 target genes, p21 has been identified as a key player in p53-mediated G1 arrest, while Killin, via its high DNA binding affinity, has been implicated in S and G2/M arrest. However, whether Killin is involved in G1 arrest remains unclear. This research aimed to explore the role of Killin in p53-mediated G1 arrest. Knockout of killin in human colorectal cells led to a dramatic decrease in p53-mediated G1 arrest upon DNA damage. Moreover, double knockout of killin and p21 completely abolished G1 arrest, similar to that of p53 knockout cells. We further showed that Killin could upregulate p21 protein expression independent of p53 via ubiquitination pathways. Immunoprecipitation studies indicated that Killin may directly bind to proteasome subunits, thereby disrupting proteasomal degradation of p21. Together, these results demonstrate that Killin is involved in multiple cell cycle checkpoint controls, including p53-mediated G1 arrest.

Mixed ligand copper(II) complexes of diimine co-ligands: Synthesis, characterization, DNA binding and DNA cleavage activity

Four mixed ligand copper(II) complexes having general formula [Cu(acox)(diimine)]2+1–4, (acox is acenaphthylene-1,2-dione dioxime) have been synthesised and characterized by suitable analytical techniques. The diimine ligands used for the isolation of complexes are bipyridine (bpyn 1), phenanthroline (phne, 2), phenanthroline-5,6-dione (5,6-dione, 3) and dipyridoquinoxaline (dpqn, 4). The degree of binding affinity of complexes with DNA has been assessed using UV–Visible absorption spectroscopic technique, which reveals that the complex that possesses dpqn ligand binds with DNA more strongly than its analogue complexes. The planar geometry of dpqn ligand assists the intercalation of complex partially in between the nucleobases of DNA. On the other hand, the higher hydrophobicity of 5,6-dione in 3 is accountable for its higher DNA-binding affinity than that of bpyn and phne complexes. The trend of DNA binding affinity of complexes observed by ethidium bromide displacement assay and viscosity studies attest the results observed in absorption spectral titration of complexes with DNA. All the four Cu(II) complexes cleave supercoiled plasmid DNA in ACN/Tris(HCl)-NaCl buffer in the absence of an activating agent. Also, these complexes display prominent DNA cleavage activity in presence of hydrogen peroxide and the results indicated that the DNA-cleaving ability of complexes varies in the order 4 > 3 > 2 > 1, and the highest ability of 4 in H2O2 to cleave DNA indicates that it could be developed as efficient chemical nuclease.

Targeting multiple mediators of sepsis using multifunctional tannic acid-Zn2+-gentamicin nanoparticles

Targeting multiple mediators of sepsis using multifunctional tannic acid-Zn2+-gentamicin nanoparticles

Induction and Monitoring of DNA Phase Separation in Living Cells by a Light-Switching Ruthenium Complex.

Phase separation of DNA is involved in chromatin packing for the regulation of gene transcription. Visualization and manipulation of DNA phase separation in living cells present great challenges. Herein, we present a Ru(II) complex (Ru1) with high DNA binding affinity and DNA "light-switch" behavior that can induce and monitor DNA phase separation both in vitro and in living cells. Molecular dynamics simulations indicate that the two phen-PPh3 ligands with positively charged lipophilic triphenylphosphine substituents and flexible long alkyl chains in Ru1 play essential roles in the formation of multivalent binding forces between DNA molecules to induce DNA phase separation. Importantly, the unique environmental sensitive emission property of Ru1 enables direct visualization of the dynamic process of DNA phase separation in living cells by two-photon phosphorescent lifetime imaging. Moreover, Ru1 can change the gene expression pattern by modulating chromatin accessibility as demonstrated by integrating RNA-sequencing and transposase-accessible chromatin with high-throughput sequencing. In all, we present here the first small-molecule-based tracer and modulator of DNA phase separation in living cells and elucidate its impact on the chromatin state and transcriptome.

Unraveling the interaction between doxorubicin and DNA origami nanostructures for customizable chemotherapeutic drug release.

Doxorubicin (DOX) is a common drug in cancer chemotherapy, and its high DNA-binding affinity can be harnessed in preparing DOX-loaded DNA nanostructures for targeted delivery and therapeutics. Although DOX has been widely studied, the existing literature of DOX-loaded DNA-carriers remains limited and incoherent. Here, based on an in-depth spectroscopic analysis, we characterize and optimize the DOX loading into different 2D and 3D scaffolded DNA origami nanostructures (DONs). In our experimental conditions, all DONs show similar DOX binding capacities (one DOX molecule per two to three base pairs), and the binding equilibrium is reached within seconds, remarkably faster than previously acknowledged. To characterize drug release profiles, DON degradation and DOX release from the complexes upon DNase I digestion was studied. For the employed DONs, the relative doses (DOX molecules released per unit time) may vary by two orders of magnitude depending on the DON superstructure. In addition, we identify DOX aggregation mechanisms and spectral changes linked to pH, magnesium, and DOX concentration. These features have been largely ignored in experimenting with DNA nanostructures, but are probably the major sources of the incoherence of the experimental results so far. Therefore, we believe this work can act as a guide to tailoring the release profiles and developing better drug delivery systems based on DNA-carriers.