Genotyping single-nucleotide polymorphisms of human genes involved in organophosphate detoxification by high-resolution melting

Paraoxonase-1 (PON1) and butyrylcholinesterase (BCHE) are natural bioscavengers of organophosphate acetylcholinesterase inhibitors in the human body, which can determine individual sensitivity to organophosphate toxicity. Interindividual differences in activity of PON1 (catalytic bioscavenger) and substrate specificity are strongly associated with the substitution of two amino acids: Leu/Met (L/M) at position 55 (rs854560) and Gln/Arg (Q/R) at position 192 (rs662). In the case of BCHE (stoichiometric bioscavenger) substitution, Ala/Thr (A/T) at position 539 produces the so-called “K-variant” of the enzyme (rs1803274). Threonine allele is often co-inherited with an atypical BCHE allele (rs1799807). The atypical variant of BCHE displays a lower affinity for cholinesterase inhibitors. Genotyping rs662 and rs1803274 single-nucleotide polymorphisms (SNP) by high-resolution melting (HRM) is facilitated by the nucleotide substitution A>G (G>A), which resulted in a changed number of hydrogen bonds in the PCR product and, consequently, shifted T _m. In the case of rs854560, genotyping is complicated by the nucleotide substitution T>A, which has no significant effect on the T _m of the PCR product. An addition of a small quantity of LL homozygote DNA into the reaction mixture before PCR discriminates the three genotypes by the melt curves due to different amounts of heteroduplexes formed in the LM and MM samples. HRM analysis can be applied for genotyping human rs854560, rs662, and rs1803274 SNPs.

Label-free genotyping of single-nucleotide polymorphisms for DNA and RNA targets using a cationic polythiophene derivate

By using the specific primer extension reaction, a new assay for genotyping of single-nucleotide polymorphisms (SNPs) has been demonstrated. The assay relies on the conformational and colorimetric change of water-soluble polythiophene derivative, poly[3-(3′-N,N,N-triethylamino-1′-propyloxy)-4-methyl-2,5-thiophene hydrochloride] (PMNT), upon forming interpolyelectrolyte complex with extended double strand DNA and non-extended single strand DNA. All three kinds of SNP genotypes can be colorimetrically identified with one primer extension reaction in homogeneous solution. Moreover, combining with the specific digestion of RNA strands in the RNA/DNA hybrids, the proposed assay can also be applied to SNP genotyping for RNA templates. The SNP genotyping assay does not require chemical modification of oligonucleotide probes and nucleic acid targets and any separation step. It would be useful for routinely SNP detection in ordinary laboratories.     

Genotyping of single nucleotide polymorphism in MDM2 genes by universal fluorescence primer PCR and capillary electrophoresis

Single nucleotide polymorphism (SNP) 309 in the promoter region of the murine double minute 2 (MDM2) gene plays an important role in human tumorigenesis. We established a simple and effective CE method for SNP detection in the MDM2 gene. We designed one universal fluorescence-based nonhuman-sequence primer and one fragment-oriented primer, which were combined in one tube, and proceeded with the polymerase chain reaction (PCR). The amplicons were analyzed by capillary electrophoresis using single-strand conformation polymorphism method. PCR fragments generated from this two-in-one PCR displayed either T/T or G/G homozygosity or T/G heterozygosity. A total of 304 samples were blindly genotyped using this developed method, which included the DNA from 138 healthy volunteers, 43 chronic myeloid leukemia (CML) patients, and 123 colorectal cancer (CRC) patients. The results were confirmed by DNA sequencing and showed good agreement. The SSCP-CE method was feasible for SNP screening of MDM2 in large populations.     

Energy deposition mechanisms and biochemical aspects of DNA strand breaks by ionizing radiation

A theoretical model based on physical, chemical, and biochemical mechanisms has been presented to evaluate the yields of DNA strand breaks (single and double) as a function of linear energy transfer (LET ) or ?dE/dx. Energetic heavy charged particles are considered explicitly to provide a general theory for low- as well as for high-LET radiation. There are three main features of the calculation: (a) track structure considerations for the energy deposition pattern, (b) three-dimensional structure of DNA molecules to provide information on the exact location of damage, and (c) a Monte-Carlo scheme to simulate the diffusion processes of water radicals. To avoid the complexities of a cellular medium, an aqueous solution of DNA is considered in the calculation. When the results of the calculations are compared with experimental measurements of the yields of strand breaks in mammalian DNA (exposed in a cellular complex), reasonable agreement is obtained. However, only those experimental data have been compared where there were no enzyme repair processes. The method of calculation has also been extended to study breaks in higher-order structures of DNA molecules such as chromatin. Specific limitations of the present model have been pointed out for making further improvements.     

Resonant Formation of Strand Breaks in Sensitized Oligonucleotides Induced by Low‐Energy Electrons (0.5–9 eV)

Halogenated nucleobases are used as radiosensitizers in cancer radiation therapy, enhancing the reactivity of DNA to secondary low‐energy electrons (LEEs). LEEs induce DNA strand breaks at specific energies (resonances) by dissociative electron attachment (DEA). Although halogenated nucleobases show intense DEA resonances at various electron energies in the gas phase, it is inherently difficult to investigate the influence of halogenated nucleobases on the actual DNA strand breakage over the broad range of electron energies at which DEA can take place (<12 eV). By using DNA origami nanostructures, we determined the energy dependence of the strand break cross‐section for oligonucleotides modified with 8‐bromoadenine (^8BrA). These results were evaluated against DEA measurements with isolated ^8BrA in the gas phase. Contrary to expectations, the major contribution to strand breaks is from resonances at around 7 eV while resonances at very low energy (<2 eV) have little influence on strand breaks.     

Shape and core‐excited resonances of thionucleobases

Thionucleobases can be used in chemoradiation therapy of cancer. Shape resonances (SRs) and core‐excited resonances (CERs) can lead to fragmentation and eventually result in strand breaks of DNA. In particular, the more energetic CERs are believed to cause double‐strand breaks that can hardly be repaired. In this work, both the SRs and CERs of exemplary 2‐thiouracil, 4‐thiouracil, 2‐thiothymine, 4‐thiothymine, and 6‐aza‐2‐thiothymine are investigated using stabilization method in conjunction with long range corrected time‐dependent density functional theory. Results indicate that the energies of (1) π*₁ and π*₂ SRs, (2) n‐π* CERs, and (3) mixed resonances of π‐π* CERs with π* SRs can be significantly stabilized due to thionation of uracil or thymine. It is noteworthy that the resonant cases of (2) and (3) can be accessed by electrons even at energies below 4 eV. Consequently, the increased decay of temporary anions can enhance strand breaks of DNA.     

Vacuum UV laser induced scission of simian virus 40 DNA

Abstract— The effect of vacuum UV-laser irradiation on Simian virus 40 (SV40) DNA I was studied in vitro. Following exposure of SV40 DNA I to an argon fluoride (ArF) laser (LD = 193 nm), single-strand breaks occur in either strand of the double-stranded superhelical molecule (DNA I) and convert it to the DNA II conformation. Upon increased irradiation times, additional breaks occur in already scissioned strands resulting in the production of smaller fragments as analyzed by alkaline sucrose centrifugation. These results suggest that short periods of irradiation lead to conformational alterations of SV40 DNA I.     

Vacuum-UV and Low-Energy Electron-Induced DNA Strand Breaks – Influence of the DNA Sequence and Substrate

DNA is effectively damaged by radiation, which can on the one hand lead to cancer and is on the other hand directly exploited in the treatment of tumor tissue. DNA strand breaks are already induced by photons having an energy below the ionization energy of DNA. At high photon energies, most of the DNA strand breaks are induced by low-energy secondary electrons. In the present study we quantified photon and electron induced DNA strand breaks in four different 12mer oligonucleotides. They are irradiated directly with 8.44 eV vacuum ultraviolet (VUV) photons and 8.8 eV low energy electrons (LEE). By using Si instead of VUV transparent CaF₂ as a substrate the VUV exposure leads to an additional release of LEEs, which have a maximum energy of 3.6 eV and can significantly enhance strand break cross sections. Atomic force microscopy is used to visualize strand breaks on DNA origami platforms and to determine absolute values for the strand break cross sections. Upon irradiation with 8.44 eV photons all the investigated sequences show very similar strand break cross sections in the range of 1.7–2.3×10⁻¹⁶ cm². The strand break cross sections for LEE irradiation at 8.8 eV are one to two orders of magnitude larger than the ones for VUV photons, and a slight sequence dependence is observed. The sequence dependence is even more pronounced for LEEs with energies <3.6 eV. The present results help to assess DNA damage by photons and electrons close to the ionization threshold.     

Genome-wide association studies combined with k-fold cross-validation identify rs17822931 as an ancestry-informative marker in Han Chinese population

DNA-based ancestry inference has long been a research hot spot in forensic science. The differentiation of Han Chinese population, such as the northern-to-southern substructure, would benefit forensic practice. In the present study, we enrolled participants from northern and southern China, each participant was genotyped at ∼400 K single-nucleotide polymorphisms (SNPs) and data of CHB and CHS from 1000 Genomes Project were used to perform genome-wide association analyses. Meanwhile, a new method combining genome-wide association study (GWAS) analyses with k-fold cross-validation in a small sample size was introduced. As a result, one SNP rs17822931 emerged with a p-value of 7.51E − 6. We also simulated a huge dataset to verify whether k-fold cross-validation could reduce the false-negative rate of GWAS. The identified ABCC11 rs17822931 has been reported to have allele frequencies varied with the geographical gradient distribution in humans. We also found a great difference in the allele frequency distributions of rs17822931 among five different cohorts of the Chinese population. In conclusion, our study demonstrated that even small-scale GWAS can also have potential to identify effective loci with implemented k-fold cross-validation method and shed light on the potential maker of rs17822931 in differentiating the north-to-south substructure of the Han Chinese population.     

Synthesis and In Vitro Biological Evaluation of Psoralen‐Linked Fullerenes

Photodynamic therapy (PDT) is a widely used medicinal treatment for the cancer therapy that utilizes the combination of a photosensitizer (PS) and light irradiation. In this study, we synthesized two novel C₆₀ fullerene derivatives, compounds 1 and 2 , with a psoralen moiety that can covalently bind to DNA molecules via cross‐linking to pyrimidine under photoirradiation. Along with several fullerene derivatives, the biological properties of several novel compounds have been evaluated. Compounds 1 and 2 , which have been shown to induce the production of hydroxyl radicals using several ROS detecting reagents, induced DNA strand breaks with relatively weak activities in the in vitro detection system using a supercoiled plasmid. However, the psoralen‐bound fullerene with carboxyl groups ( 2 ) only showed genotoxicity in the genotoxicity assay system of the umu test. Compound 2 was also seen to have cytotoxic activities in several cancer cell lines at higher doses compared to water‐soluble fullerenes.     

Confirmation that SNPs in the high mobility group‐A2 gene (HMGA2) are associated with adult height in the Japanese population; wide‐ranging population survey of height‐related SNPs in HMGA2

Adult height is a highly heritable trait in that multiple genes are involved. Recent genome‐wide association studies have identified a novel single‐nucleotide polymorphism (SNP) rs1042725 in the high mobility group‐A2 gene (HMGA2) and shown it to be associated with human height in Caucasian populations. We performed a replication study to examine the associations between SNPs in HMGA2 and adult height in the Japanese population based on autopsy cases. Although we could not confirm a significant association between rs1042725 in HMGA2 and adult height, another SNP, rs7968902, in the gene achieved significance for its association in the same populations, and the effect was the same as that documented previously. These findings permit us to conclude that the SNPs in HMGA2 are common variants influencing human height across different populations. Moreover, a worldwide population study of these SNPs using 14 different populations including Asians, Africans and Caucasians demonstrated that both haplotypes and genotypes for three height‐related SNPs (rs1042725, rs7968682 and rs7968902) in HMGA2 were distributed in an ethnicity‐dependent manner. This information will be useful for clarifying the genetic basis of human height.     

Binding studies of DNA with Co(III) coordination compound

The binding of Co(bpy)₂dppz³⁺ to calf thymus DNA was investigated by using absorption and emission spectroscopy, DNA melting techniques, cyclic voltammetry, viscosity and electro phoresis measurements, where bpy is 2,2′-bipyridyl, dppz is dipyrido[3,2-a:2′,3′-c] phenazine. The binding compound shm absorption hypochromicity, fluorescence enhancement, and increasing of DNA melting temperature and the specific viscosity. CV measurement shows the shifts in oxidation-reduction potential and change in peak current with addition of DNA. The compound ie also shown to be more efficient photosensitisers for strand breaks in plasmid DNA.     

Voltammetric Application of Polypyrrole-Modified Microelectrode Array for the Characterization of DNA Methylation in Glutathione S-Transferase Pi 1

Direct and efficient label-free voltammetric detection of glutathione S-transferase Pi 1 (GSTP1) hypermethylation is reported using a custom-developed 16-channel microelectrode array chip. The microelectrode array chip is used in a dipstick configuration allowing detection of DNA hybridization in a solution volume of only 0.35?mL. Platinum microelectrode disks (n?=?16) 30?µm in diameter have been modified with a polypyrrole bilayer before any contact with the oligonucleotides. The attachment of 15-mer Probe DNA to the bilayer is random but controlled by the presence of aliphatic tether groups allowing it to form a bidentate complex with the probe DNA. The voltammetric detection procedure of methylated GSTP1-specific target DNA is combined with bisulfite treatment of target DNA. Changes at the interface of the modified microelectrodes in an array configuration are used to record simultaneously cyclic voltammetry on all of the devices. The detection of hybridization is evaluated statistically by a yes or no event by comparing the changes in recorded cyclic voltammograms before and after exposure to the target DNA. All cyclic voltammograms of the methylated target show a greater percentage change than those with the nonmethylated target exposure and show a greater change in cyclic voltammogram area after methylated target exposure. We observe an average percentage difference of 25.6?±?4.9% with a variation of 19.1%. These results demonstrate that the fast sensing strategy possesses sensitivity and good specificity. Furthermore, this technology can potentially support rapid, accurate diagnosis and risk assessment of patients with prostate cancer.     

Effect of glutathione on lambda deoxyribonucleic acid strand breaks in the reaction system of glutathione-alloxan in the presence of Fe(3+)-ethylenediaminetetraacetic acid.

Alkaline sucrose density gradient and agarose gel electrophoresis methods were used to observe lambda deoxyribonucleic acid (DNA) strand breaks by the reaction system of reduced glutathione (GSH) with alloxan in the presence of Fe(3+)-ethylenediaminetetraacetic acid (EDTA). When DNA was incubated in the reaction system for 10 min, DNA strand breaks were easily induced. The increasing concentrations of GSH up to 1.0 mM in the reaction system in the presence of 1.0 mM alloxan caused DNA strand breaks in a concentration-dependent fashion and GSH beyond 2.0 mM caused in the strand breaks of DNA by which the fragments with multiple ranges of molecular weight were produced. The strand breaks of DNA in the reaction system containing low concentrations of GSH were protected by catalase and hydroxyl radical (HO.) scavengers but superoxide dismutase (SOD) did not, indicating that such breaks were induced by HO.generated from the Fenton reaction. On the other hand, the strand breaks of DNA at high concentrations of GSH were protected by ethanol and desferrioxamine, but not effectively by SOD and HO.scavengers, suggesting the possible participation of some oxidizing species of iron rather than HO.. These results indicate that HO.or oxidizing species of iron generated in the GSH-alloxan system depending on the concentration of GSH attacks DNA to produce strand breaks.     

Zeolites as model solids for investigations on the role of iron at the solid-liquid interface in particulate toxicity

In order to investigate the molecular mechanism whereby iron in asbestos and in other iron containing fibres plays a crucial role in fibre induced carcinogenicity, two Fe²⁺-exchanged zeolites (Y and H-ZSM-5) have been prepared and used as model solids. Fe-Y was active both in free radical generation via hydrogen abstraction and in single strand DNA damage, but lost both these properties when oxidized by hydrogen peroxide. Fe-ZSM-5, on the other hand, was nearly inactive. Iron chelators and reductants (ascorbate, citrate and EDTA) enhance the activity in DNA single strand breaks. Moreover, they reactivate oxidized Fe-Y and activate Fe-ZSM-5. Iron is mobilized and Fe³⁺ is partially reduced to Fe²⁺. The most pronounced effect was found when citrate was present together with ascorbate. H-abstraction turns out to be a rather general reaction, occurring also with peptides as target molecules. In this case EPR spectra show that more than one type of radical moiety is generated.     

Fluorescence and visual detection of single nucleotide polymorphism using cationic conjugated polyelectrolyte

We report a simple assay for visual detection of single nucleotide polymorphisms (SNPs) with good sensitivity and selectivity. The selectivity is determined by Escherichia coli (E. coli) DNA ligase mediated circular formation upon recognition of the point mutation on DNA targets. Rolling cycle amplification (RCA) of the perfect-matched DNA target is then initiated using the in situ formed circular template in the presence of Phi29 enzyme. Due to amplification of the DNA target, the RCA product has a tandem-repeated sequence, which is significantly longer than that for the SNP strand. Direct addition of a cationic conjugated polymer of poly[9,9'-bis(6'-(N,N,N-trimethylammonium)hexyl)fluorene-co-9,9'-bis(2-(2-(2-(N,N,N-trimethylammonium)ethoxyl)-ethoxy)-ethyl)fluorene tetrabromide] containing 20 mol% 2,1,3-benzothiadiazole (PFBT(20)) into the RCA solution leads to blue-whitish fluorescent color for SNP strand and yellowish fluorescent color for amplified DNA, due to PFBT(20)/DNA complexation induced intrachain/interchain energy transfer. To further improve the contrast for visual detection, FAM-labeled peptide nucleic acid (PNA) was hybridized to each amplified sequence, which is followed by the addition of poly{2,7-[9,9-bis(6'-N,N,N-trimethylammoniumhexyl)]fluorene-co-2,5-difluoro-1,4-phenylene dibromide} (PFP). The PNA/DNA hybridization brings PFP and FAM-PNA into close proximity for energy transfer, and the solution fluorescent color appears green in the presence of target DNA with a detection limit of 1 nM, which is significantly improved as compared to that for most reported visual SNP assay.     

Electroanalytical study of proflavine intercalation in 5-methyl or inosine-containing amplicons

Amplicons corresponding to the GC-rich p53 exon 5 and its analogues, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, or 60% of guanosine by inosine and GC-poor p53 exon 6 were synthesized and investigated electrochemically, in the presence and absence of proflavine, by differential pulse voltammetry (DPV). Incorporation of base analogues and the thermal stability of the resulting amplicons were tested in the presence of a fluorescent probe (Sybr–Green). Peak current at 1.0 V was lower for methylated than for unmethylated PCR amplicons and was similarly affected by proflavine intercalation. In contrast, considerable peak current differences were observed in the presence of proflavine for unmodified exon 5 v.s. exon 6 or inosine-containing amplicons. Thermal analysis verified the expected shifts in melting temperature (T _m) due to the base analogue incorporation and GC-content variations. In conclusion, methylated and unmethylated PCR amplicons could be distinguished in model DNA systems using differential pulse voltammetry (DPV) and use of proflavine could serve as an electrochemical probe for identifying different DNA conformations.     

Effects of direct radiation on deoxyribonucleic acid

It is argued that effects of ionizing radiation on DNA in cell nuclei may frequently be direct in the sense that many electron-gain and electron-loss centres become localised within the DNA molecules. The water of solvation that would also be present in the cell is presumed to pass on holes and electrons prior to the formation of OH· radicals and solvated electrons since these are not detected by ESR of in vitro model systems. Furthermore, a case is made that this direct damage may be particularly significant in that the cationic and anionic centres (G⁺ and T^- according to ESR results) are thought to be formed close enough together to lead, ultimately, to double strand breaks. Evidence that both G⁺ and T^- can lead to strand breaks is discussed. The presence of histone proteins modifies the yields of G⁺ and T^- to a significant extent. The effects of various additives are discussed. Oxygen has been shown by ESR spectroscopy to scavenge electrons in competition with DNA and also to react to form RO₂· radicals that are located on the DNA. It has been shown that this is accompanied by a significant enhancement of strand breaks. Nitroimidazoles act as efficient electron scavengers, their anions being clearly detected by ESR studies. The yield of T^- is consequently reduced and that of the protonated form, TH·, falls to zero. However, the initial yields of G⁺ are not greatly affected. This results in a reduction in the yield of single strand breaks and a proportionately greater decrease in the yield of double-strand breaks due to scavenging of only one of the radical centres. The origin of this is discussed in terms of a proposal for the mechanism of double-strand-break formation. Thus, at the molecular level these drugs protect the DNA against strand sission, in marked contrast with their radiosensitisation in vivo, particularly of hypoxic cells. Other additives studied include hydrogen peroxide and iodoacetamide. The studies on hydrogen peroxide have allowed us to assess the role of OH· radicals under the conditions used for ESR studies. Iodoacetamide gives ·CH₂CONH₂ radicals which are detected by ESR and, on annealing, these apparently attack the DNA to give species thought to be sugar radicals. This is associated with a significant increase in the yields of strand breaks. The ESR features assigned to sugar radicals have been shown to decay at temperatures below which the DNA radicals G⁺ and T^- are normally lost. This provides a good explanation of our failure to detect sugar radical intermediates by ESR spectroscopy on annealing samples in the absence of additives.     

DNA damage induced via independent generation of the radical resulting from formal hydrogen atom abstraction from the C1′-position of a nucleotide

Background: Deoxyribonucleotide radicals resulting from formal C1′-hydrogen atom abstraction are important reactive intermediates in a variety of DNA-damage processes. The reactivity of these radicals can be affected by the agents that generate them and the environment in which they are produced. As an initial step in determining the factors that control the reactivity of these important radical species, we developed a mild method for their generation at a defined site within a biopolymer.Results: Irradiation of oligonucleotides containing a photolabile nucleotide produced C1'-DNA radicals. In the absence of potential reactants other than O₂, approximately 90% of the damage events involve formation of alkaline-labile lesions, with the remainder resulting in direct strand breaks. The ratio of alkaline-labile lesions to direct strand breaks (∼ 9:1) is independent of whether the radical is generated in single-stranded DNA or double-stranded DNA. Strand damage is almost completely quenched under anaerobic conditions in the presence of low thiol concentrations. Competition studies with 02 indicate that the trapping rate of C1′-DNA radicals by β-mercaptoethanol is ∼ 1.1 x 10⁷ M⁻¹s⁻¹Conclusions: The mild generation of the C1'-DNA radical in the absence of exogenous oxidants makes it possible to examine their intrinsic reactivity. In the absence of other reactants, the formation of direct strand breaks from C1′-radicals is, at most, a minor pathway. Competition studies between β-mercaptoethanol and 02 indicate that significantly higher thiol concentrations than those in vivo or some means of increasing the effective thiol concentration near DNA are needed for these reagents to prevent the formation of DNA lesions arising from the C1'-radical under aerobic conditions.