A comparison of existing global DNA methylation assays to low-coverage whole-genome bisulfite sequencing for epidemiological studies

DNA methylation is an epigenetic mark at the interface of genetic and environmental factors relevant to human disease. Quantitative assessments of global DNA methylation levels have therefore become important tools in epidemiology research, particularly for understanding effects of environmental exposures in complex diseases. Among the available methods of quantitative DNA methylation measurements, bisulfite sequencing is considered the gold standard, but whole-genome bisulfite sequencing (WGBS) has previously been considered too costly for epidemiology studies with high sample numbers. Pyrosequencing of repetitive sequences within bisulfite-treated DNA has been routinely used as a surrogate for global DNA methylation, but a comparison of pyrosequencing to WGBS for accuracy and reproducibility of methylation levels has not been performed. This study compared the global methylation levels measured from uniquely mappable (non-repetitive) WGBS sequences to pyrosequencing assays of several repeat sequences and repeat assay-matched WGBS data and determined uniquely mappable WGBS data to be the most reproducible and accurate measurement of global DNA methylation levels. We determined sources of variation in repetitive pyrosequencing assays to be PCR amplification bias, PCR primer selection bias in methylation levels of targeted sequences, and inherent variability in methylation levels of repeat sequences. Low-coverage, uniquely mappable WGBS showed the strongest correlation between replicates of all assays. By using multiplexing by indexed bar codes, the cost of WGBS can be lowered significantly to improve the accuracy of global DNA methylation assessments for human studies.     

Systematic assessment of reduced representation bisulfite sequencing to human blood samples: A promising method for large-sample-scale epigenomic studies

Complementary to the time- and cost-intensive direct bisulfite sequencing, we applied reduced representation bisulfite sequencing (RRBS) to the human peripheral blood mononuclear cells (PBMC) from YH, the Asian individual whose genome and epigenome has been deciphered in the YH project and systematically assessed the genomic coverage, coverage depth and reproducibility of this technology as well as the concordance of DNA methylation levels measured by RRBS and direct bisulfite sequencing for the detected CpG sites. Our result suggests that RRBS can cover more than half of CpG islands and promoter regions with a good coverage depth and the proportion of the CpG sites covered by the biological replicates reaches 80-90%, indicating good reproducibility. Given a smaller data quantity, RRBS enjoys much better coverage depth than direct bisulfite sequencing and the concordance of DNA methylation levels between the two methods is high. It can be concluded that RRBS is a time and cost-effective sequencing method for unbiased DNA methylation profiling of CpG islands and promoter regions in a genome-wide scale and it is the method of choice to assay certain genomic regions for multiple samples in a rapid way.     

A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data

DNA methylation plays an important role in disease etiology. The Illumina Infinium HumanMethylation450 (450K) BeadChip is a widely used platform in large-scale epidemiologic studies. This platform can efficiently and simultaneously measure methylation levels at ∼480,000 CpG sites in the human genome in multiple study samples. Due to the intrinsic chip design of 2 types of chemistry probes, data normalization or preprocessing is a critical step to consider before data analysis. To date, numerous methods and pipelines have been developed for this purpose, and some studies have been conducted to evaluate different methods. However, validation studies have often been limited to a small number of CpG sites to reduce the variability in technical replicates. In this study, we measured methylation on a set of samples using both whole-genome bisulfite sequencing (WGBS) and 450K chips. We used WGBS data as a gold standard of true methylation states in cells to compare the performances of 8 normalization methods for 450K data on a genome-wide scale. Analyses on our dataset indicate that the most effective methods are peak-based correction (PBC) and quantile normalization plus β-mixture quantile normalization (QN.BMIQ). To our knowledge, this is the first study to systematically compare existing normalization methods for Illumina 450K data using novel WGBS data. Our results provide a benchmark reference for the analysis of DNA methylation chip data, particularly in white blood cells.     

Synthesis, DNA binding, photo-induced DNA cleavage, cytotoxicity and apoptosis studies of copper(II) complexes

Two new Cu(II) complexes, [Cu(acac)(dpq)Cl] () and [Cu(acac)(dppz)Cl] () (acac = acetylacetonate, dpq = dipyrido[3,2-d:20,30-f]quinoxaline, dppz = dipyrido[3,2-a:20,30-c] phenazine), have been synthesized and their DNA binding, photo-induced DNA cleavage activity and cell cytotoxicity are studied. The complexes show good binding propensity to calf thymus DNA in the order: 2(dppz) > 1(dpq). Furthermore, two complexes exhibit efficient DNA cleavage activity on natural light or UV-A (365 nm) irradiation via a mechanistic pathway involving formation of singlet oxygen as the reactive species. The photo-induced DNA cleavage activity of the dppz complex 2 is found to be more efficient than its dpq analogue. In vitro study of the photocytotoxicity of two complexes on HeLa cells indicate that both of them have the potential to act as effective anticancer drugs, with IC₅₀ values of 5.25 ± 0.83 μM (1) and 4.40 ± 0.52 μM (2) in the natural light, and 2.57 ± 0.92 μM (1) and 2.18 ± 0.52 μM (2) in UV-A light. In addition, to detect an apoptotic HeLa body, cells were stained with Hoechst 33342 dye.     

A complex composed of at least two HeLa nuclear proteins protects preferentially one DNA strand of the simple (gt)n(ga)m containing region of intron 2 in HLA-DRB-genes

Electrophoretic mobility shift assays reveal that HeLa neuclear proteins bind fast and with measurable affinity to target DNAs containing mixed simple repetitive (gt)_n(ga)_m stretches. Preincubation of the proteins at elevated temperature prevents the formation of the major DNA/protein complex in favour of several distinct assemblies. A similar pattern of retarded bands was observed employing higher salt concentrations in binding reaction. Thus conformational changes of different proteins appear to influence the complex rather than alternating DNA structures. Separation of the total nuclear extract into a water soluble and an insoluble protein fraction leads to a complete loss of target DNA bindinlg capability of the fractions. The binding capacity is restored by combining the two fractions suggesting that at least two protein components are necessary to form a complex with the target sequence. The proteins can be differentiated into head sensitive, water soluble and temporary stable, water insoluble, respectively. Furthermore, specifically binding polypeptides are not detectable by Southwestern analyses, probably because the essential components are separated during electrophoresis. DNase 1 footpoint analyses yield four different protein binding regions only on the (gt)_n(ga)_m harbouring strand. The footprints cover larger portions of the mixed simple repeat in addition to a portion 5′ of the (gt)_n part. Hence at lealst two nuclear protein components of unknown biological function have to be present simultaneously to protect preferentially the (gt)_n(ga)_m-containing strand intron 2 in HLA-DRB genes     

Murine DNA cytosine C(5)-methyltransferase: in vitro studies of de novo methylation spreading

The preference of murine DNA (cytosine-5)-methyltransferase (Dnmt1) for single stranded DNA substrates is increased up to 50-fold by the presence of a proximal 5-methyl cytosine (5(me)C). This modulation is distance-dependent and is due to an enhanced binding affinity and minor changes in catalytic efficiency. No modulation was observed with double stranded DNA. Modulation requires that the 5(me)C moiety be attached to the DNA strand containing the CpG methylation target. Our results support a model in which 5(me)C binding by the enzyme occurs to at least one site outside the region involved in CpG recognition. No modulation in response to 5(me)C is observed with the bacterial enzyme M.SssI, which lacks the large N-terminal regulatory domain found in Dnmt1. We suggest that this allosteric modulation involves the N-terminal domain of Dnmt1.     

High Throughput BAC DNA Isolation for Physical Map Construction of Sorghum (Sorghum bicolor)

With the aim of constructing a physical map of sorghum, we developed a rapid, high throughput approach for isolating BAC DNA suitable for restriction endonuclease digestion fingerprinting, PCR- based STS-content mapping, and BAC-end sequencing. The system utilizes a programmable 96 channel liquid handling system and associated accessories that permit bacterial cultivation and DNA isolation in 96-well plate format. This protocol details culture conditions that optimize bacterial growth in deep-well plates and criteria for BAC DNA isolation to obtain high yields of quality BAC DNA. The system is robust, accurate, and relatively cost-effective. The BAC DNA isolation system has been tested during efforts to construct a physical map of sorghum.     

Synthesis, structural characteristics, DNA binding properties and cytotoxicity studies of a series of Ru(III) complexes

Four related ruthenium(III) complexes, with the formula mer-[RuCl₃(dmso)(N−N)] (dmso = dimethyl sulfoxide; N−N = 2,2′-bipyridine (1), 1,10-phenantroline (2), dipyrido[3,2-f:2′,3′-h]quinoxaline (3) and dipyrido[3,2-a:2′,3′-c]phenazine (4)), have been reported. Complexes 3 and 4 are newly synthesized and characterized by X-ray diffraction. The hydrolysis process of 1-4 has been studied by UV-vis measurement, and it has been found that the extension of the N−N ligands can increase the stability of the complexes. The binding of these complexes with DNA has been investigated by plasmid cleavage assay, competitive binding with ethidium bromide (EB), DNA melting experiments and viscosity measurements. The DNA binding affinity is increased with the extension of the planar area of the N−N ligands, and complex 4 shows an intercalative mode of interaction with DNA. The in vitro anticancer activities of these compounds are moderate on the five human cancer cell lines screened.     

The conformation and orientation of copper(II)-bleomycin intercalated with DNA

EPR data are used to describe the conformation and identity of the atoms coordinated to Cu(II) in Cu(II)-bleomycin bound to oriented DNA fibers. The fibers were slowly drawn from viscous solutions of Cu(II)-bleomycin-DNA containing one Cu(II)-bleomycin to 200 basepairs. EPR measurements were made at room temperature and 90 K for different orientations of the external magnetic field with respect to the helical axes of the fibers. The g-values ($\text{g}{}_{\mathrm{}}\text{=2.21}$, g_⊥ =2.04) and the hyperfine constant ($\text{A}{}_{\mathrm{}}\text{=175}\text{G}$) are consistent with values expected for Cu(II) chelated to a square planar array of ligands. In the oriented fibers, the square planar arrays do not all have the same orientations with respect to the fiber axes. At room temperature the chelated ions have rotational freedom in which the normal to the planar array has almost complete freedom of rotation about axes perpendicular to the DNA fiber axes. The normal maintains an angle of 75° with respect to the axis, in the plane of the basepair, about which it rotates. Nine superhyperfine peaks on the high field side of the EPR spectrum were partially resolved. The number and splitting (12 G) of these superhyperfine peaks indicate that four nitrogen atoms are chelated to Cu(II) in a square planar array. These data on Cu(II)-bleomycin bound to DNA give information on the orientation of the metal-containing portion of bleomycin which lies outside the double helix.     

A new Schiff base copper (II) complex derived from estrone and d-glucosamine: Synthesis,characterization and its interaction with DNA

A novel copper (II) complex of Schiff base prepared through condensation between 2-formyl-17-deoxyestrone and d-glucosamine was synthesized and characterized. Fluorescence spectroscopy was conducted to assess their binding ability with CT-DNA. The results showed that the copper (II) complex could bind to DNA with a weak intercalative mode. The interaction between the copper (II) complex and DNA was also investigated by gel electrophoresis. Interestingly, we found that the complex could cleave plasmid DNA (pUC19) to nicked and linear forms through an oxidative mechanism without the use of exogenous agents.     

A new blue luminescent dichlorido-bridged dinuclear copper(II) complex with DNA binding and cytotoxic activities: Synthesis, structure and DFT studies

A blue luminescent dichlorido-bridged dinuclear copper(II) (S = 1/2) complex, [Cu^II₂(HL)₂(μ-Cl)₂]·2H₂O, 1a was synthesized with the 1:1 reaction of the acyclic tridentate salicylaldehyde 2-pyridyl hydrazone ligand, HL, 1. The complex 1a displays multiple bands in the visible region (400-470 nm). The association constant (K_ass, UV-Vis) was found to be 1.186 × 10⁴ for 1a at 298 K. The copper(II)-copper(III) oxidation potential lies near 0.32 V versus Ag/AgCl electrode. On excitation at 390 nm, the ligand 1 strongly emits at 444 nm due to an intraligand ¹(π-π^∗) transition. Upon complexation with copper(II) the emission peak is slightly red shifted (λ_ex 390 nm, λ_em 450 nm, F/F₀ 0.81) with little quenching. Molecular structure of 1a (Cu···Cu 3.523 Å) has been determined by single crystal X-ray diffraction studies. DFT and TDDFT calculations strongly support the spectral behavior of the ligand and the complex. The complex 1a exhibits a strong interaction towards DNA as revealed from the K_b (intrinsic binding constant) 2.05 × 10⁴ M⁻¹ and K_sv (Stern-Volmer quenching constant) 2.47 values. The complex exhibits cytotoxic effect and the LD₅₀ value for HeLa cells was calculated as 5.44 μM at which the cell cycle was arrested at G₂/M phase.     

Structure-activity relationship on DNA binding and anticancer activities of a family of mixed-ligand oxidovanadium(V) hydrazone complexes

The title family of mixed-ligand oxidovanadium(V) hydrazone complexes are [V^VO(HL¹)(hq)] (1) and [V^VO(HL²)(hq)] (2), where (HL¹)^2? and (HL²)^2? are the dinegative form of 2-hydroxybenzoylhydrazone of acetylacetone (H₃L¹) and benzoylacetone (H₃L²), respectively, and hq^? is the mononegative form of 8-hydroxyquinoline (Hhq). Complexes were used to determine their binding constant with CT DNA using various spectroscopic techniques namely, electronic absorption, fluorescence and circular dichroism spectroscopy. The binding constant values suggest the intercalative mode of binding with the CT DNA and follow the order: 2 > 1. The bulky size as well as electron withdrawing property of the phenyl group (which is present in the β-diketone part of the hydrazone moiety in complex 2 in place of a CH₃ group in complex 1) is responsible for the higher activity of 2 than 1. Complexes were screened for cytotoxic activity on cervical cancer cells and were found to be potentially active (IC₅₀ value for 1 and 2 is 33 and 29 μM, respectively), even better than the widely used cis-platin (IC₅₀ = 63.5 μM) and carboplatin (IC₅₀ = > 200 μM) which is evident from the respective IC₅₀ value. Nuclear staining experiment suggests that these complexes kill the SiHa cancer cells through apoptotic mode. The molecular docking study also suggested the intercalative mode of binding of these complexes with CT DNA and HPV 18 DNA.     

Synthesis,spectral studies,DNA binding,photocleavage, antimicrobial and anticancer activities of isoindol Ru(II) polypyridyl complexes

Abstract

Three new Ru(II) polypyridyl complexes [Ru(phen)₂CIIP]²⁺ (1) {CIIP = 2-(5-Chloro-3a H-Isoindol-3-yl)-1H-Imidazo[4,5-f][1, 10]phenantholine} (phen = 1, 10 phenanthroline), [Ru(bpy)₂CIIP]²⁺ (2) (bpy = 2, 2′ bipyridine) and [Ru(dmb)₂CIIP]²⁺ (3) (dmb = 4, 4′-dimethyl 2, 2′ bipyridine) were synthesized and characterized by different spectral methods. The DNA-binding behavior of these complexes was investigated by absorption, emission spectroscopic titration and viscosity measurements, indicating that these three complexes bind to CT-DNA in an intercalative mode, but binding affinities of these complexes were different. The DNA-binding constants K_b of complexes 1, 2 and 3 were calculated in the order of 10⁶. All three complexes cleave pBR322 DNA in photoactivated cleavage studies and exhibit good antimicrobial activity. Anticancer activity of these Ru(II) complexes was evaluated in MCF7 cells. Cytotoxicity by MTT assay showed growth inhibition in a dose dependent manner. Cell cycle analysis by flow cytometry data showed an increase in Sub G1 population. Annexin V FITC/PI staining confirms that these complexes cause cell death by the induction of apoptosis.     

Cobalt (II) complex with novel unsymmetrical tetradentate Schiff base (ON) ligand: in vitro cytotoxicity studies of complex,interaction with DNA/protein,molecular docking studies,and antibacterial activity

[C₂₀H₁₇N₃O₂] and cobalt (II) complex [Co(L²)(MeOH)₂].ClO₄, (L² = 4-((E)-1-((2-(((E)-pyridin-2-ylmethylene) amino) phenyl) imino) ethyl) benzene-1, 3-diol) novel Schiff base has been synthesiszed and chracterized by Fourier transform infrared, UV–vis, ¹H-NMR spectroscopy, and elemental analysis techniques. The interaction of Co(II) complex with DNA and BSA was investigated by electronic absorption spectroscopy, fluorescence spectroscopy, circular dichroism, and thermal denaturation studies. Our experiments indicate that this complex could strongly bind to CT-DNA via minor groove mechanism. In addition, fluorescence spectrometry of BSA with the complex showed that the fluorescence quenching mechanism of BSA was of static type. The complex exhibited significant in vitro cytotoxicity against three human cancer cell lines (JURKAT, SKOV3, and U87). The molecular docking experiment effectively proved the binding of complex to DNA and BSA. Finally, antibacterial assay over gram-positive and gram-negative pathogenic bacterial strains was studied.     

HPV-2E2蛋白(A338V)突变体对E2蛋白DNA结合能力增强的研究

HPV-2是引起皮肤寻常疣的常见HPV型别,病毒E2蛋白可抑制病毒早期启动子的活性。我们曾经报道来自一例巨大寻常疣患者的HPV-2突变E2蛋白对病毒早期启动子活性的抑制作用明显减弱,该E2蛋白在其C末端的DNA结合区域带有A338V的点突变。本研究利用原核表达系统表达纯化了突变E2(A338V)和HPV-2原毒株的羧基端和全长蛋白。电泳迁移率实验结果显示,E2蛋白可与带有E2蛋白特异性结合位点的寡核苷酸探针形成复合物,突变E2蛋白比原毒株E2蛋白的DNA结合能力强。这提示DNA结合能力的增强可能为E2蛋白对病毒启动子活性影响的分子基础,与患者出现罕见巨大寻常疣这一临床表型关联。     

A potential rhodium cancer therapy: Studies of a cytotoxic organorhodium(I) complex that binds DNA

Described is a novel organorhodium(I) complex that is cytotoxic to the colon cancer cell line HCT116 and alters cell migration, DNA replication, and DNA condensation. Most importantly, the mechanism observed is not seen for the parent organorhodium dimer complex [{RhCl(COD)}₂], RhCl₃, or the free ligand/proligands (COD and 1-ⁿbutyl-3-methylimidazolium chloride). Thus, the activity of this organorhodium complex is attributable to its unique structure.     

Arene-Ru(II)-chloroquine complexes interact with DNA, induce apoptosis on human lymphoid cell lines and display low toxicity to normal mammalian cells

The complexes [Ru(η⁶-p-cymene)(CQ)Cl₂] (1), [Ru(η⁶-benzene)(CQ)Cl₂] (2), [Ru(η⁶-p-cymene)(CQ)(H₂O)₂][BF₄]₂ (3), [Ru(η⁶-p-cymene)(en)(CQ)][PF₆]₂ (4), [Ru(η⁶-p-cymene)(η⁶-CQDP)][BF₄]₂ (5) (CQ = chloroquine base; CQDP = chloroquine diphosphate; en = ethylenediamine) interact with DNA to a comparable extent to that of CQ and in analogous intercalative manner with no evidence for any direct contribution of the metal, as shown by spectrophotometric and fluorimetric titrations, thermal denaturation measurements, circular dichroism spectroscopy and electrophoresis mobility shift assays. Complexes 1-5 induced cytotoxicity in Jurkat and SUP-T1 cancer cells primarily via apoptosis. Despite the similarities in the DNA binding behavior of complexes 1-5 with those of CQ the antitumor properties of the metal drugs do not correlate with those of CQ, indicating that DNA is not the principal target in the mechanism of cytotoxicity of these compounds. Importantly, the Ru-CQ complexes are generally less toxic toward normal mouse splenocytes and human foreskin fibroblast cells than the standard antimalarial drug CQDP and therefore this type of compound shows promise for drug development.     

A novel approach for uniform (13)C and (15)N labeling of DNA for NMR studies.

A novel method is proposed for large-scale synthesis of (13)C- and (15)N-labeled DNA for NMR studies. In this methodology, endonuclease-sensitive repeat amplification (ESRA), a modified PCR strategy, has been used to amplify tandem repeats of the target DNA sequence. The design of the template is such that restriction enzyme (RE) sites separate repeats of the target sequence. The ESRA product is then cloned into a suitable vector. The Escherichia coli cells harboring the plasmid are grown in minimal medium containing [(13)C]glucose and (15)NH(4)Cl as the sole source of carbon and nitrogen, respectively. The target sequence is released by RE digestion of the plasmid, followed by purification using PAGE. Under optimized conditions, the yield ( approximately 5 mg/liter of culture) of (13)C/(15)N-labeled DNA prepared using this approach is found to be several times higher compared to other known enzymatic methods. Successful incorporation of the isotopes has been confirmed using 2D NMR techniques.