Detection of CpG Methylation in G-Quadruplex Forming Sequences Using G-Quadruplex Ligands

Genomic DNA methylation is involved in many diseases and is expected to be a specific biomarker for even the pre-symptomatic diagnosis of many diseases. Thus, a rapid and inexpensive detection method is required for disease diagnosis. We have previously reported that cytosine methylation in G-quadruplex (G4)-forming oligonucleotides develops different G4 topologies. In this study, we developed a method for detecting CpG methylation in G4-forming oligonucleotides based on the structural differences between methylated and unmethylated G4 DNAs. The differences in G4 topologies due to CpG methylation can be discriminated by G4 ligands. We performed a binding assay between methylated or unmethylated G4 DNAs and G4 ligands. The binding abilities of fluorescent G4 ligands to BCL-2, HRAS1, HRAS2, VEGF G4-forming sequences were examined by fluorescence-based microtiter plate assay. The differences in fluorescence intensities between methylated and unmethylated G4 DNAs were statistically significant. In addition to fluorescence detection, the binding of G4 ligand to DNA was detected by chemiluminescence. A significant difference was also detected in chemiluminescence intensity between methylated and unmethylated DNA. This is the first study on the detection of CpG methylation in G4 structures, focusing on structural changes using G4 ligands.     

Promoted electron transport and sustained phonon transport by DNA down to 10 K

This work reports on a pioneering study of the electron transport in nanometer-thick Ir film supported by a DNA fiber, and the phonon transport sustained by the DNA itself. By evaluating the electrical resistivity (ρ_e)∼temperature relation based on the Block-Grüneisen theory, we find the Ir film has weak phonon softening indicated by 7–15% Debye temperature reduction. The Ir film's intrinsic ρ_e is promoted by DNA electron thermal hopping and quantum tunneling, and is identical to that of bulk Ir. Although the nanocrystalline structure in ultrathin metallic films intends to give a higher Lorenz number since it reduces the electrical conductivity more than thermal conductivity, the DNA-promoted electron transport in the Ir film preserves a Lorenz number close to that of bulk crystalline Ir. By defining a new physical parameter entitled “thermal reffusivity”, the residual phonon thermal resistivity of DNA is identified and evaluated for the first time. The thermal reffusivity concept can be widely used to predict the phonon thermal transport potential of defect-free materials. We predict that the thermal diffusivity of defect-free DNA fiber could be 36–61% higher than the samples studied herein. The structure domain size for phonon diffusion/scattering is determined as 0.8 nm in DNA.     

Breast Cancer Predisposition Genes and Synthetic Lethality

BRCA1 and BRCA2 are tumor suppressor genes with pivotal roles in the development of breast and ovarian cancers. These genes are essential for DNA double-strand break repair via homologous recombination (HR), which is a virtually error-free DNA repair mechanism. Following BRCA1 or BRCA2 mutations, HR is compromised, forcing cells to adopt alternative error-prone repair pathways that often result in tumorigenesis. Synthetic lethality refers to cell death caused by simultaneous perturbations of two genes while change of any one of them alone is nonlethal. Therefore, synthetic lethality can be instrumental in identifying new therapeutic targets for BRCA1/2 mutations. PARP is an established synthetic lethal partner of the BRCA genes. Its role is imperative in the single-strand break DNA repair system. Recently, Olaparib (a PARP inhibitor) was approved for treatment of BRCA1/2 breast and ovarian cancer as the first successful synthetic lethality-based therapy, showing considerable success in the development of effective targeted cancer therapeutics. Nevertheless, the possibility of drug resistance to targeted cancer therapy based on synthetic lethality necessitates the development of additional therapeutic options. This literature review addresses cancer predisposition genes, including BRCA1, BRCA2, and PALB2, synthetic lethality in the context of DNA repair machinery, as well as available treatment options.     

A label-free DNA sensor based on impedance spectroscopy

This paper describes a label-free detection system for DNA strands based on gold electrodes and impedance measurements. A single-stranded 18 mer oligonucleotide (ssDNA) was immobilised via a thiol linker on gold film electrodes and served as probe DNA. Residual binding places were filled with mercaptobutanol. The sensor surface clearly distinguished between complementary and non-complementary target ssDNA. Additionally, detection of single base pair mismatches was possible. The electrode was impedimetrically characterised in the presence of the redox system ferri/ferrocyanide before and after DNA hybridisation. Impedance analysis showed that the charge transfer resistance, R_ct, was increasing after DNA duplex formation, whereas the capacitive properties remain rather unaltered. The relative change of R_ct was used as sensor parameter. Concentrations in the nanomolar range have been detected by the system. The sensor was reusable because a denaturation protocol allowed effective double strand dissociation without changing the surface properties of the electrode substantially. The time for DNA detection have been reduced to about 15 min including regeneration. The sensor signal was amplified by about 20% after binding of a negatively charged molecule to the formed DNA duplex. The sensor was also capable of sensing longer target ssDNA strands as shown with 25 mer and 37 mer oligonucleotides.     

A facile method for the detection of DNA by using gold nanoparticle probes coupled with dynamic light scattering

In this paper, we present a simple and rapid method for deoxyribonucleic acid (DNA) detection using gold nanoparticle probes coupled with dynamic light scattering (DLS) analysis. The redox agent 1,4-dithio-dl-threitol cross-links the gold nanoparticles (AuNPs) to form clusters, while the monothiol DNA could terminate the formation and stabilize the assembled clusters by their negatively charge-based repulsions. By varying the concentration of DNA, the different sizes of DNA-AuNP clusters can be obtained. The sizes of the DNA-AuNP clusters were determined by DLS. A linear correlation was obtained between the sizes and the logarithm of DNA concentration from 2 nM to 5 μM with a detection limit of 1 nM (S/N = 3).     

Outer Membrane Vesicles Derived from Klebsiella pneumoniae Are a Driving Force for Horizontal Gene Transfer

Gram-negative bacteria release Outer Membrane Vesicles (OMVs) into the extracellular environment. Recent studies recognized these vesicles as vectors to horizontal gene transfer; however, the parameters that mediate OMVs transfer within bacterial communities remain unclear. The present study highlights for the first time the transfer of plasmids containing resistance genes via OMVs derived from Klebsiella pneumoniae (K. pneumoniae). This mechanism confers DNA protection, it is plasmid copy number dependent with a ratio of 3.6 times among high copy number plasmid (pGR) versus low copy number plasmid (PRM), and the transformation efficiency was 3.6 times greater. Therefore, the DNA amount in the vesicular lumen and the efficacy of horizontal gene transfer was strictly dependent on the identity of the plasmid. Moreover, the role of K. pneumoniae-OMVs in interspecies transfer was described. The transfer ability was not related to the phylogenetic characteristics between the donor and the recipient species. K. pneumoniae-OMVs transferred plasmid to Escherichia coli, Salmonella enterica, Pseudomonas aeruginosa and Burkholderia cepacia. These findings address the pivotal role of K. pneumoniae-OMVs as vectors for antimicrobial resistance genes spread, contributing to the development of antibiotic resistance in the microbial communities.     

New copolymers of N,N-dimethylacrylamide with blocked isocyanates for oligonucleotide immobilization in DNA microarray technology

A family of copolymers of N,N-dimethylacrylamide containing blocked isocyanate functionalities is presented. The copolymers were characterized by DSC, GPC and ¹H NMR. Calorimetric analysis showed for any composition broad endothermal phenomena followed by a stronger exothermal peak, which can be attributed, respectively, to the deblocking and subsequent reaction of generated NCO groups.Characterization of glass slides coated with these polymers was done by contact angle measurements and atomic force microscopy. While the former method revealed minimal differences with formation of moderately hydrophilic surfaces, microscopic images showed a more homogeneous coating formation for the copolymer structure with 50% molar of blocked isocyanate. The efficiency of the coated substrates in the immobilization of amino functionalized oligonucleotides was successfully assessed through binding tests and analysis by confocal fluorescence microscopy.Finally, some model microarrays were fabricated by spotting and hybridization with complementary, fluorescently labelled targets was carried out. It resulted in surfaces coated with copolymers which show well defined circular spots with a fluorescence intensity higher than that obtained by slides treated by silanization, and based on the same immobilization chemistry.     

The bioelectrocatalytic properties of cytochrome C by direct electrochemistry on DNA film modified electrode

The direct electrochemistry of cytochrome C can be performed in weak acidic and basic aqueous solutions. Cytochrome C can be deposited as a stable and electrochemically active film on a deoxyribonucleic acid (DNA) modified glassy carbon electrode. These films can also be produced on gold, platinum, and transparent semiconducting tin oxide electrodes. Two-layer modified electrodes containing cytochrome C and a DNA film were prepared by the deposition of cytochrome C on a DNA film modified electrode. The cytochrome C/DNA film was electrocatalytically oxidation active for l-cysteine in a pH 8.3 tris(hydroxymethyl)aminomethane (TRIS)-buffered aqueous solution through both Fe^III and Fe^IV species. The electrocatalytic oxidation current developed from the anodic peak of the redox couple. The electrocatalytic oxidation properties of ascorbic acid, NH₂OH, N₂H₄, and SO₃²⁻ by a cytochrome C/DNA film were also determined, and shown to be electrocatalytically active. An electrochemical quartz crystal microbalance, cyclic voltammetry, and direct spectroelectrochemistry were used to study in situ DNA deposition on a gold disc electrode and cytochrome C deposition on DNA/Au and DNA/GC films. The direct electrochemistry of cytochrome C can also be performed, and it can be deposited as a stable and electrochemically active film on polyvinyl sulfonate, polystyrene sulfonate, TiO₂, and polyethylene glycol modified glassy carbon electrodes. The results show that cytochrome C interacts with, and deposits on, a DNA film modified electrode, and that the cytochrome C (Fe^III) oxidized form is more easily deposited on a DNA film than the cytochrome C (Fe^II) reduced form.     

The Infection Efficiency and Replication Ability of Circularized HBV DNA Optimized the Linear HBV DNA in Vitro and in Vivo

Studies on molecular mechanisms of the persist infection of hepatitis B virus have been hampered by a lack of a robust animal model. We successfully established a simple, versatile, and reproducible HBV persist infection model in vitro and in vivo with the circularized HBV DNA. The cells and mice were transfected or injected with circularized HBV DNA and pAAV/HBV1.2, respectively. At the indicated time, the cells, supernatants, serum samples, and liver tissues were collected for virological and serological detection. Both in vitro and in vivo, the circularized HBV DNA and pAAV/HBV1.2 could replicate and transcribe efficiently, but the infection effect of the former was superior to the latter (p < 0.05). The injection of circularized HBV genome DNA into the mice robustly supported HBV infection and approximately 80% of HBV infected mice established persistent infection for at least 10 weeks. This study demonstrated that the infection efficiency and replication ability of the circularized structure of HBV DNA overmatched that of the expression plasmid containing the linear structure of HBV DNA in vitro and in vivo. Meanwhile, this research results could provide useful tools and methodology for further study of pathogenic mechanisms and potential antiviral treatments of human chronic HBV infection in vitro and in vivo.     

Exploration of the Effect on Genome-Wide DNA Methylation by miR-143 Knock-Out in Mice Liver

MiR-143 play an important role in hepatocellular carcinoma and liver fibrosis via inhibiting hepatoma cell proliferation. DNA methyltransferase 3 alpha (DNMT3a), as a target of miR-143, regulates the development of primary organic solid tumors through DNA methylation mechanisms. However, the effect of miR-143 on DNA methylation profiles in liver is unclear. In this study, we used Whole-Genome Bisulfite Sequencing (WGBS) to detect the differentially methylated regions (DMRs), and investigated DMR-related genes and their enriched pathways by miR-143. We found that methylated cytosines increased 0.19% in the miR-143 knock-out (KO) liver fed with high-fat diet (HFD), compared with the wild type (WT). Furthermore, compared with the WT group, the CG methylation patterns of the KO group showed lower CG methylation levels in CG islands (CGIs), promoters and hypermethylation in CGI shores, 5′UTRs, exons, introns, 3′UTRs, and repeat regions. A total of 984 DMRs were identified between the WT and KO groups consisting of 559 hypermethylation and 425 hypomethylation DMRs. Furthermore, DMR-related genes were enriched in metabolism pathways such as carbon metabolism (serine hydroxymethyltransferase 2 (Shmt2), acyl-Coenzyme A dehydrogenase medium chain (Acadm)), arginine and proline metabolism (spermine synthase (Sms), proline dehydrogenase (Prodh2)) and purine metabolism (phosphoribosyl pyrophosphate synthetase 2 (Prps2)). In summary, we are the first to report the change in whole-genome methylation levels by miR-143-null through WGBS in mice liver, and provide an experimental basis for clinical diagnosis and treatment in liver diseases, indicating that miR-143 may be a potential therapeutic target and biomarker for liver damage-associated diseases and hepatocellular carcinoma.     

OsMre11 Is Required for Mitosis during Rice Growth and Development

Meiotic recombination 11 (Mre11) is a relatively conserved nuclease in various species. Mre11 plays important roles in meiosis and DNA damage repair in yeast, humans and Arabidopsis, but little research has been done on mitotic DNA replication and repair in rice. Here, it was found that Mre11 was an extensively expressed gene among the various tissues and organs of rice, and loss-of-function of Mre11 resulted in severe defects of vegetative and reproductive growth, including dwarf plants, abnormally developed male and female gametes, and completely abortive seeds. The decreased number of cells in the apical meristem and the appearance of chromosomal fragments and bridges during the mitotic cell cycle in rice mre11 mutant roots revealed an essential role of OsMre11. Further research showed that DNA replication was suppressed, and a large number of DNA strand breaks occurred during the mitotic cell cycle of rice mre11 mutants. The expression of OsMre11 was up-regulated with the treatment of hydroxyurea and methyl methanesulfonate. Moreover, OsMre11 could form a complex with OsRad50 and OsNbs1, and they might function together in non-homologous end joining and homologous recombination repair pathways. These results indicated that OsMre11 plays vital roles in DNA replication and damage repair of the mitotic cell cycle, which ensure the development and fertility of rice by maintaining genome stability.     

Virus-Mediated Targeted DNA Methylation Illuminates the Dynamics of Methylation in an Endogenous Plant Gene

DNA methylation maintains genome stability and regulates gene expression in plants. RNA-directed DNA methylation (RdDM) is critical for appropriate methylation. However, no efficient tools are available for the investigation of the functions of specific DNA methylation. In this study, the cucumber mosaic virus vector was used for targeted DNA methylation. Methylation was rapidly induced but gradually decreased from the 3′ end of the target endogenous sequence in Nicotiana benthamiana, suggesting a mechanism to protect against the ectopic introduction of DNA methylation. Increasing 24-nt siRNAs blocked this reduction in methylation by down-regulating DCL2 and DCL4. RdDM relies on the sequence identity between RNA and genomic DNA; however, this identity does not appear to be the sole determinant for efficient DNA methylation. The current findings provide new insight into the regulation of DNA methylation and promote additional effort to develop efficient targeted DNA methylation in plants.     

Nucleic acid biosensor for DNA hybridization detection using rutin-Cu as an electrochemical indicator

The complex of rutin-Cu (C₈₁H₈₆Cu₂O₄₈, abbreviated by Cu₂R₃, R = rutin) was synthesized and characterized by elemental analysis and IR spectra. Cyclic voltammetry (CV) and fluorescence spectroscopy were used to investigate the interaction of Cu₂R₃ with salmon sperm DNA. It was revealed that Cu₂R₃ could interact with double-stranded DNA (dsDNA) by a major intercalation role. Using Cu₂R₃ as a novel electroactive indicator, an electrochemical DNA biosensor for the detection of specific DNA fragment was developed and its selectivity for the recognition with different target DNA was assessed by differential pulse voltammetry (DPV). The target DNA related to coliform virus gene could be quantified ranged from 1.62 × 10⁻⁸ mol L⁻¹ to 8.10 × 10⁻⁷ mol L⁻¹ with a good linearity (r = 0.9989) and a detection limit of 2.3 × 10⁻⁹ mol L⁻¹ (3σ, n = 7) was achieved by the constructed electrochemical DNA biosensor.     

Non-spherical Janus microgels driven by thiolated DNA interactions

Janus poly (N-isopropylacrylamide)-co-acrylic acid/Au microgels that resemble a “snowman”, “dumbbell”, and an “abalone” were prepared by thermally evaporating a layer of Au on half of the microgel surface, followed by exposure to thiolated single-stranded DNA with complementary sequences. We hypothesize that when the complementary single-stranded DNA attached to the Au forms the more stable double strand, the Au reorganizes on the microgel surface, yielding the observed unique Janus particle structures.     

A Mutation in DNA Polymerase α Rescues WEE1KO Sensitivity to HU

During DNA replication, the WEE1 kinase is responsible for safeguarding genomic integrity by phosphorylating and thus inhibiting cyclin-dependent kinases (CDKs), which are the driving force of the cell cycle. Consequentially, wee1 mutant plants fail to respond properly to problems arising during DNA replication and are hypersensitive to replication stress. Here, we report the identification of the polα-2 mutant, mutated in the catalytic subunit of DNA polymerase α, as a suppressor mutant of wee1. The mutated protein appears to be less stable, causing a loss of interaction with its subunits and resulting in a prolonged S-phase.     

Relationship between Mutagenicity of Heterocyclic Aromatic Amines and Stability of Their DNA Adducts: A Study by Semi-empirical Molecular Orbital Method

Quantitative structure-mutagenicity correlations were investigated for heterocyclic aromatic amines (HCAs) by use of a DNA model with three-base pairs. DNA adducts of thirteen HCAs were optimized by the PM3 method and energy decrease, ΔE, of each HCA due to formation of a DNA adduct was obtained as the stability of the adduct. The calculations for the HCA-DNA adducts revealed the interaction between HCA's methyl group and DNA's phosphate, which plays an important role in the stabilization of the adducts. The ΔE values plotted against the logarithm of HCA's mutagenicity, M, provided an almost straight line with the regression coefficient (R) of ?0.89 (R ²= 0.79). This good correlation suggests that binding reaction between HCA's nitrenium ion and DNA is an important rate-determining step in the metabolic transformation of HCAs.     

Toxic Effects of the Major Components of Diesel Exhaust in Human Alveolar Basal Epithelial Cells (A549)

We investigated the toxicity of benzo[a]pyrene (B[a]P), 1-nitropyrene (1-NP) and 3-nitrobenzanthrone (3-NBA) in A549 cells. Cells were treated for 4 h and 24 h with: B[a]P (0.1 and 1 μM), 1-NP (1 and 10 μM) and 3-NBA (0.5 and 5 μM). Bulky DNA adducts, lipid peroxidation, DNA and protein oxidation and mRNA expression of CYP1A1, CYP1B1, NQO1, POR, AKR1C2 and COX2 were analyzed. Bulky DNA adducts were induced after both treatment periods; the effect of 1-NP was weak. 3-NBA induced high levels of bulky DNA adducts even after 4-h treatment, suggesting rapid metabolic activation. Oxidative DNA damage was not affected. 1-NP caused protein oxidation and weak induction of lipid peroxidation after 4-h incubation. 3-NBA induced lipid peroxidation after 24-h treatment. Unlike B[a]P, induction of the aryl hydrocarbon receptor, measured as mRNA expression levels of CYP1A1 and CYP1B1, was low after treatment with polycyclic aromatic hydrocarbon (PAH) nitro-derivatives. All test compounds induced mRNA expression of NQO1, POR, and AKR1C2 after 24-h treatment. AKR1C2 expression indicates involvement of processes associated with reactive oxygen species generation. This was supported further by COX2 expression induced by 24-h treatment with 1-NP. In summary, 3-NBA was the most potent genotoxicant, whereas 1-NP exhibited the strongest oxidative properties.