Quantitative and qualitative profiling of mitochondrial DNA length heteroplasmy

Quantitative and qualitative analysis of mitochondrial DNA length heteroplasmy for the first hypervariable segment (HV1) and second hypervariable segment (HV2) regions were performed using size-based separation of fluorescently-labeled polymerase chain reaction (PCR) products by capillary electrophoresis. In this report, the relative proportions of length heteroplasmies in individuals were determined, and each length variant in the heteroplasmic mtDNA mixture was identified. The study demonstrated that 36% and 69% of Koreans show length heteroplasmy in the HV1 and HV2 regions, respectively. Electropherograms revealed that length heteroplasmy in the HV1 region resulted in over 5 length variants in an individual. The peak patterns of length heteroplasmy in the HV1 region were classified into five major types. In the HV2 region, length heteroplasmy resulted in 3-6 length variants in an individual, and showed seven variant peak patterns. The increased knowledge concerning mtDNA length heteroplasmy is believed to not only offer a useful means of determining genetic identity due to increased mitochondrial DNA haplotype diversity by allowing mtDNAs to be classified into several peak patterns, but also represent a promising tool for the diagnosis of several common diseases which are etiologically or prognostically associated with mtDNA polymorphisms.     

Dielectrophoretic isolation of DNA and nanoparticles from blood

The ability to effectively detect disease-related DNA biomarkers and drug delivery nanoparticles directly in blood is a major challenge for viable diagnostics and therapy monitoring. A DEP method has been developed which allows the rapid isolation, concentration and detection of DNA and nanoparticles directly from human and rat whole blood. Using a microarray device operating at 20 V peak-to-peak and 10 kHz, a wide range of high molecular weight (HMW)-DNA and nanoparticles were concentrated into high-field regions by positive DEP, while the blood cells were concentrated into the low-field regions by negative DEP. A simple fluidic wash removes the blood cells while the DNA and nanoparticles remain concentrated in the DEP high-field regions where they can be detected by fluorescence. HMW-DNA could be detected at 260 ng/mL, which is a detection level suitable for analysis of disease-related cell-free circulating DNA biomarkers. Fluorescent 40 nm nanoparticles could be detected at 9.5 × 10(9) particles/mL, which is a level suitable for monitoring drug delivery nanoparticles. The ability to rapidly isolate and detect DNA biomarkers and nanoparticles from undiluted whole blood will benefit many diagnostic applications by significantly reducing sample preparation time and complexity.     

Complete mitochondrial DNA sequence of a tadpole shrimp (Triops cancriformis) and analysis of museum samples

The complete mitochondrial DNA (mtNDA) of the tadpole shrimp Triops cancriformis was sequenced. The sequence consisted of 15,101 bp with an A+T content of 69%. Its gene arrangement was identical with those sequences of the water flea (Daphnia pulex) and giant tiger prawn (Penaeus monodon), whereas it differed from that of the brine shrimp (Artemia franciscana) in the arrangement of its genes for tRNAs. Phylogenetic analysis revealed T. cancriformis to be more closely related to the water flea than to the brine shrimp and giant tiger prawn. We also compared the 16S rRNA sequences of five formalin-fixed tadpole shrimps that had been collected in five different locations and stored in a museum. The sequence divergence was in the range of 0-1.51%, suggesting that those samples were closely related to each other.     

Electrophoretic analysis of sequence variability in three mitochondrial DNA regions for ascaridoid parasites of human and animal health significance

Sequence variability in three mitochondrial DNA (mtDNA) regions, namely cytochrome c oxidase subunit 1 (cox1), NADH dehydrogenase subunits 1 and 4 (nad1 and nad4), among and within Toxocara canis, T. cati, T. malaysiensis, T. vitulorum and Toxascaris leonina from different geographical origins was examined by a mutation-scanning approach. A portion of the cox1 gene (pcox1), a portion of the nad1 and nad4 genes (pnad1 and pnad4) were amplified separately from individual ascaridoid nematodes by polymerase chain reaction and the amplicons analyzed by single-strand conformation polymorphism (SSCP). Representative samples displaying sequence variation in SSCP profiles were subjected to sequencing in order to define genetic markers for their specific identification and differentiation. While the intra-specific sequence variations within each of the five ascaridoid species were 0.2-3.7% for pcox1, 0-2.8% for pnad1 and 0-2.3% for pnad4, the inter-specific sequence differences were significantly higher, being 7.9-12.9% for pcox1, 10.7-21.1% for pnad1 and 12.9-21.7% for pnad4, respectively. Phylogenetic analyses based on the combined sequences of pcox1, pnad1 and pnad4 revealed that the recently described species T. malaysiensis was more closely related to T. cati than to T. canis. These findings provided mtDNA evidence for the validity of T. malaysiensis and also demonstrated clearly the usefulness and attributes of the mutation-scanning sequencing approach for studying the population genetic structures of these and other nematodes of socio-economic importance.     

Ferrite supports for isolation of DNA from complex samples and polymerase chain reaction amplification

The influence of cobalt ferrite particles, with non-modified or modified surface, on the course of polymerase chain reaction (PCR) was investigated. DNA isolated from bacterial cells of Bifidobacterium bifidum was used in PCR evaluation of magnetic microspheres. The presence of cobalt ferrite particles inhibits PCR amplification. The effect is not dependent on the functional groups of the modifying reagents used (none, amino, carboxyl). Amplification was improved after the magnetic separation of magnetic particles. Proposed indirect method enabled verification of the suitability of designed particles for their application in PCR assays. Magnetic particles coated with alginic acid under high PEG and sodium chloride concentration were used for the isolation of PCR-ready bacterial DNA from various dairy products. DNA was isolated from crude bacterial cell lysates without phenol extraction of samples. Bifidobacterium and Lactobacillus DNAs were identified in dairy products using PCR.     

Desorption of plasmid DNA from anion exchangers: Salt concentration at elution is independent of plasmid size and load

Detailed studies on the sorption behavior of plasmids on anion exchangers are rare compared to proteins. In this study, we systematically compare the elution behavior of plasmid DNA on three common anion exchange resins using linear gradient and isocratic elution experiments. Two plasmids of different lengths, 8 and 20 kbp, were studied and their elution characteristics were compared to a green fluorescent protein. Using established methods for determining retention characteristics of biomolecules in ion exchange chromatography lead to remarkable results. In contrast to the green fluorescent protein, plasmid DNA consistently elutes at one characteristic salt concentration in linear gradient elution. This salt concentration was the same independent of plasmid size but differed slightly for different resins. The behavior is consistent also at preparative loadings of plasmid DNA. Thus, only a single linear gradient elution experiment is sufficient to design elution in a process scale capture step. At isocratic elution conditions, plasmid DNA elutes only above this characteristic concentration. Even at slightly lower concentrations most plasmids remain tightly bound. We hypothesize, that the desorption is accompanied by a conformational change leading to a reduced number of available negative charges for binding. This explanation is supported by structural analysis before and after elution.     

Mutation scanning-coupled analysis of haplotypic variability in mitochondrial DNA regions reveals low gene flow between human and porcine Ascaris in endemic regions of China

Haplotypic variation within and among the Ascaris populations representing six provinces in China was investigated. Mitochondrial DNA regions in the cytochrome c oxidase subunit 1 (cox1) and NADH dehydrogenase subunit 1 (nad1) genes were amplified by PCR from total genomic DNA samples (n > 720) from Ascaris individuals from humans and pigs, and subjected to mutation scanning and subsequent selective sequencing. For the cox1, ten different electrophoretic profiles were recorded for human Ascaris, and the same number for pig Ascaris, one of them being common to both host species. For the nad1, 11 different profiles were detected for human Ascaris, and 15 for pig Ascaris. Having defined all haplotypes (20 for pcox1 and 26 for pnad1) by sequencing, their frequencies were estimated in each of the two host species and each of the six provinces. For each mitochondrial region, the frequency of the different haplotypes varied considerably, depending on host species and geographical origin. Analysis of the sequence data (representing all haplotypes for each mitochondrial locus) by F-statistics indicated restricted gene flow between human Ascaris and pig Ascaris, and supported the conclusions from previous molecular epidemiological investigations that pigs are not a significant source of Ascaris infection in humans in endemic regions.     

Specific and genotypic identification of Cryptosporidium from a broad range of host species by nonisotopic SSCP analysis of nuclear ribosomal DNA

The accurate identification of Cryptosporidium (Protozoa: Apicomplexa) species and genotypes is central to the understanding of the transmission and to the diagnosis and control of cryptosporidiosis. In this study, we demonstrate the effectiveness of nonisotopic SSCP analysis of a approximately 300 bp region of the small subunit (pSSU) of ribosomal DNA for the specific identification of and delineation among 18 different Cryptosporidium species and genotypes from a wide range of hosts. This mutation scanning approach allowed the rapid and reliable differentiation between species/genotypes differing by as little as 1.3% in the pSSU sequence, with the capacity to detect point mutations. The present findings confirm the usefulness of this tool for the rapid genetic screening of Cryptosporidium samples from any host species, providing a foundation for detailed systematic, epidemiological and ecological studies. Although applied herein to pSSU, this low cost approach should be applicable to a wide range of genetic loci for population genetic investigations of Cryptosporidium.     

Synthesis,crystal structures and characterization of late first row transition metal complexes derived from thiosemicarbazone hub: DNA binding/cleavage studies

Air‐ and moisture‐stable coordination compounds of late first row transition metals, i.e. Co(III), Ni(II), Cu(II) and Zn(II), derived from the ligand (E)‐4‐(4‐chlorophenyl)‐1‐(1‐hydroxypropan‐2‐ylidene)thiosemicarbazide were prepared and successfully characterized using various spectro‐analytical techniques. The molecular structures of the ligand LH and complexes C1 and C2 were determined using single‐crystal X‐ray diffraction. The complexes C1 and C2 are stabilized by weak intermolecular CH???π stacking interactions: C1 between phenyl rings (C2–H21???C2) with a contact distance of 2.855 Å and C2 between phenyl ring and thione sulfur (C13???S1) with a contact distance of 3.366(6) Å. Complex C3 is found to be electrochemically active in the working potential range, showing a quasi‐reversible redox process. The interactions of all the compounds with calf thymus DNA were comprehensively investigated using electronic absorption spectroscopy, viscosity and thermal denaturation studies. Cleavage studies of Escherichia coli DNA were monitored using agarose gel electrophoresis. The results show that LH and complex C4 bind to calf thymus DNA through partial intercalation, while remaining complexes bind electrostatically. Further, C1, C2 and C4 complexes show better cleavage potential towards E. coli DNA. Copyright © 2015 John Wiley & Sons, Ltd.     

Electrostatic complex of didodecyldimethylammonium and DNA: Langmuir monolayer, Langmuir–Blodgett film and dye recognition at air/water interface

DNA–didodecyldimethylammonium (DNA–DDDA) electrostatic complex was prepared and characterized through Fourier transformation infrared (FT-IR), ¹H NMR and circular dichroism (CD) spectroscopy. When the dye molecule aqueous solutions were used as the subphase, the interaction between three dye molecules, acridine orange (AO), ethidium bromide (EB) and 5,10,15,20-tetrakis(4-N-methylpyridyl)porphine tetra(p-toluenesulfonate) (TMPyP) and the complex at air/solution interface were investigated through the surface pressure–area (π–A) isotherms, Brewster angle microscopy and UV-Vis spectroscopy, respectively. Our investigation indicates that the interaction capabilities of the three dyes to DNA–DDDA complex are different and present an order of TMPyP>AO>EB. For the interaction forms, we believe that TMPyP intercalates into the double helix of DNA, and AO adsorbs onto the surface of the DNA. As for EB, the measured signal is too weak to give a definite interaction form in the present experiment.     

Real light emitter in the bioluminescence of the calcium-activated photoproteins aequorin and obelin: light emission from the singlet-excited state of coelenteramide phenolate anion in a contact ion pair

Fluorescence of the phenolate anion (3(O)⁻) and the amide anion (5(N)⁻) of coelenteramide analogues in ion pairs with various counter cations was systematically investigated to elucidate the ionic structure of the light emitter in the bioluminescence of the calcium-activated photoproteins aequorin and obelin. The fluorescent properties of 3(O)⁻ in an ion pair with a conjugate acid of an organic base (BASE-H⁺) were varied depending on the structural variation of the ion pair and the solvent polarity. In particular, the fluorescence of 3(O)⁻ in the ion pair with the conjugate acid of n-butylamine (NBA-H⁺) indicates that the singlet-excited state of 3(O)⁻ (¹3(O)^−∗) and NBA-H⁺ make a contact ion pair in which the fluorescence emission maxima of 3(O)⁻ is sensitive to the solvent polarity and the fluorescence quantum yields of 3(O)⁻ increase in a less polar solvent. The results also confirm that ¹3(O)^−∗ is a twisted intramolecular charge transfer state. By contrast, the fluorescence of 5(N)⁻ in an ion pair depends little on the BASE-H⁺ or the solvent polarity. Based on these results, we conclude that the light emitter in aequorin and obelin bioluminescences is the singlet-excited state of coelenteramide phenolate anion 2(O)⁻ (¹2(O)^−∗) in a contact ion pair with an imidazolium side chain of a histidine residue, which is located at the less polar active sites of the photoproteins. We also propose a mechanism for the bioluminescence reaction, including the chemiexcitation process to give ¹2(O)^−∗.     

Exploring STR signal in the single‐ and multicopy number regimes: Deductions from an in silico model of the entire DNA laboratory process

Short tandem repeat (STR) profiling from DNA samples has long been the bedrock of human identification. The laboratory process is composed of multiple procedures that include quantification, sample dilution, PCR, electrophoresis, and fragment analysis. The end product is a short tandem repeat electropherogram comprised of signal from allele, artifacts, and instrument noise. In order to optimize or alter laboratory protocols, a large number of validation samples must be created at significant expense. As a tool to support that process and to enable the exploration of complex scenarios without costly sample creation, a mechanistic stochastic model that incorporates each of the aforementioned processing features is described herein. The model allows rapid in silico simulation of electropherograms from multicontributor samples and enables detailed investigations of involved scenarios. An implementation of the model that is parameterized by extensive laboratory data is publically available. To illustrate its utility, the model was employed in order to evaluate the effects of sample dilutions, injection time, and cycle number on peak height, and the nature of stutter ratios at low template. We verify the model's findings by comparison with experimentally generated data.     

Staring at the Naked Goddess: Unraveling the Structure and Reactivity of Artemis Endonuclease Interacting with a DNA Double Strand

Artemis is an endonuclease responsible for breaking hairpin DNA strands during immune system adaptation and maturation as well as the processing of potentially toxic DNA lesions. Thus, Artemis may be an important target in the development of anticancer therapy, both for the sensitization of radiotherapy and for immunotherapy. Despite its importance, its structure has been resolved only recently, and important questions concerning the arrangement of its active center, the interaction with the DNA substrate, and the catalytic mechanism remain unanswered. In this contribution, by performing extensive molecular dynamic simulations, both classically and at the hybrid quantum mechanics/molecular mechanics level, we evidenced the stable interaction modes of Artemis with a model DNA strand. We also analyzed the catalytic cycle providing the free energy profile and key transition states for the DNA cleavage reaction.     

Metal based pharmacologically active agents: Synthesis,structural elucidation,DNA interaction,in vitro antimicrobial and in vitro cytotoxic screening of copper(II) and zinc(II) complexes derived from amino acid based pyrazolone derivatives

The paper presents the synthesis of complex combinations of Cu(II) and Zn(II) with Schiff base obtained by the condensation reaction of 4-aminoantipyrine with benzaldehyde and 2-amino-3-methyl-butanoicacid. Structural features of synthesized compounds were determined by analytical and spectral techniques. Binding of synthesized complexes with calf thymus DNA (CT DNA) was studied by spectroscopic methods and viscosity measurements. Experimental results indicated the ability of the complexes to form adducts with DNA and to distort the double helix by changing the base stacking. Oxidative DNA cleavage activities of the complexes were studied with supercoiled (SC) pUC19 DNA using gel electrophoresis. The in vitro antimicrobial screening effects of the investigated compounds were monitored by the disk diffusion method. The synthesized Schiff base complexes exhibited higher antimicrobial activity than the respective free Schiff base. The in vitro cytotoxicity of synthesized complexes against Ehrlich ascites carcinoma (EAC) tumor model was investigated using trypan blue dye exclusion assay. The complexes possessed significant cytotoxic activity.     

New potential DNA intercalators of the carbazole series from indole-2,3-quinodimethanes: Synthesis,crystal structure,and molecular modeling with a watson-crick mini-helix

Summary 1-Alkylpyrano[3,4-b]indol-3-ones3 react via a Diels-Alder step with an aryne or N-phenylmaleimide to furnish the new [b]annellated carbazoles4–10 in a one-pot process. In an analogous procedure, the in situ generated N-benzoylindole-2,3-quinodimethane (13) reacted with quinones to furnish the dioxocarbazoles14–16. Compounds4–8 and14–16 with a coplanar skeleton are members of a class of potential DNA intercalators, as has been shown for5 and8 by X-ray structural analysis. On the basis of the geometries determined by X-ray crystallography, the intercalative binding of these molecules with a Watson-Crick mini-helix was predicted by molecular modeling methods.

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Neue potentielle DNA-Interkalatoren der Carbazol-Reihe aus Indol-2,3-chinodimethanen: Synthese, Kristallstruktur und Molecular Modeling mit einer Watson-Crick Minihelix

Zusammenfassung 1-Alkylpyrano[3,4-b]indol-3-one3 reagieren über einen Diels-Alder-Schritt mit Arin oder N-Phenylmaleinimid zu [b]annellierten Carbazolen4–10 in einer Einstufenreaktion. In analoger Weise reagiert ein in situ erzeugtes N-Benzoylindol-2,3-chinodimethan13 mit Chinonen zu den Dioxocarbazolen14–16. Die Verbindungen4–8 und14–16 gehören infolge ihrer coplanaren Struktur zur Klasse potentieller DNA-Interkalatoren. Auf der Basis von Röntgenstrukturanalysen von5 und8 wird die interkalative Bindung mit einer Watson-Crick Minihelix durch Molecular Modeling vorhergesagt.

     

Synthesis and spectroscopic characterization of transition metal complexes derived from novel benzofuran hydrazone chelating ligand: DNA cleavage studies and antimicrobial activity with special emphasis on antituberculosis

Mononuclear divalent complexes of Co, Ni, Cu and Zn derived from a benzofuran‐based novel hydrazone tridentate ligand were synthesized and characterized using various spectroscopic methods. Elemental analysis reveals that the metal‐to‐ligand ratio is 1:2 which is supported by mass spectrometry results. Conductivity measurements suggest that all the complexes are non‐electrolytic in nature. The ligand and complexes were evaluated for their antimicrobial potency. Bioassay of all hydrazone chelates shows enhanced activity as compared to that of the ligand. The complex with cobalt ion as the metal centre shows better activity against fungi than the standard. Also, ligand and complexes were screened for antituberculosis activity; some analogues (Ni, Cu, Zn) are eight times more active than the standard. Both ligand and complexes show moderate ability to cleave calf thymus DNA. Copyright © 2015 John Wiley & Sons, Ltd.     

DNA修饰电极的研究: VIII. 1, 10-菲咯啉存在时钴离子在ssDNA 修饰金电极上 的电化学行为及痕量钴的检测

发现在过量1,10-菲咯啉存在时,Co^3^+^/^2^+在单链DNA(ssDNA)修饰金电极上的电化学响应显著增强。采用紫外光谱和循环伏安法考察了Co^3^+^/^2^+/1,10-菲咯啉体系与sSDNA的相互作用,并利用Co^3^+^/^2^+在1,10-菲咯啉存在时在ssDNA修饰金电极上的高灵敏电化学响应对痕量钴离子进行了测定。