Template Purification Research Articles

Modular Synthesis of Tetraurea and Octaurea Macrocycles Encoded with Specific Monomer Sequences

Modular Synthesis of Tetraurea and Octaurea Macrocycles Encoded with Specific Monomer Sequences

Unexpected Link between the Template Purification Solvent and the Structure of Titanium Dioxide Hollow Spheres

Carbon spheres were applied as templates to synthesize titanium dioxide hollow spheres. The templates were purified with either ethanol or acetone, and the effects of this treatment on the properties of the resulting titania were investigated. The photocatalytic activity of the catalysts was measured via the decomposition of phenol model pollutant under visible light irradiation. It was found that the solvent used for the purification of the carbon spheres had a surprisingly large impact on the crystal phase composition, morphology, and photocatalytic activity. Using ethanol resulted in a predominantly rutile phase titanium dioxide with regular morphology and higher photocatalytic activity (r0,phenol = 3.9 × 10−9 M∙s−1) than that containing mainly anatase phase prepared using acetone (r0,phenol = 1.2 × 10−9 M∙s−1), surpassing the photocatalytic activity of all investigated references. Based on infrared spectroscopy measurements, it was found that the carbon sphere templates had different surface properties that could result in the appearance of carbonate species in the titania lattice. The presence or absence of these species was found to be the determining factor in the development of the titania’s properties.

Validation of the Microreader 40Y ID System: a Y-STR multiplex for casework and database samples.

Y-chromosome-specific short tandem repeat loci (Y-STRs) are commonly analysed in forensic science for paternity testing, familial searches, and, in sexual assault cases, to determine male DNA identity from mixed sources with high background female DNA content. The Microreader 40Y ID System is a six-dye multiplex amplification kit that contains 17 Y-STR loci from the Yfiler Plus PCR Amplification Kit and the powerplex Y23 system (DYS19, DYF385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS549, DYS635(Y GATA C4), DYS643, Y GATA H4, DYS460, DYS481, DYS533, DYF387S1, DYS449, DYS518, DYS570, DYS576, and DYS627), plus six high polymorphic loci (DYS444, DYS447, DYS557, DYS596, DYS527 a/b) as well as 4 additional candidate Y-STR loci (DYS593, DYF404S1, DYS645) and a Y-Indel loci (Rs2032678), thereby providing greater efficiency, compatibility, and accuracy. The Microreader 40Y ID System can directly amplify markers from blood or saliva on filter paper or FTA cards, without template extraction or purification, and can also be used for extracted DNA templates. To verify the efficiency and accuracy of the kit, the Microreader 40Y ID System was validated by investigating sensitivity, amplification conditions, male-male and male-female mixtures, PCR inhibition, species specificity, reproducibility, and efficacy with degraded samples. The Y-STR loci were also tested using 437 male samples from Tibet, Han, and Yi. The Microreader 40Y ID System was able to compensate for some of the shortcomings of Y-STR markers in practical applications, such as cost and profile interpretation, and fully meets the domestic Y chromosome database construction specifications and requirements.

4C-seq from beginning to end: A detailed protocol for sample preparation and data analysis.

Chromosome conformation capture (3C) methods measure DNA contact frequencies based on nuclear proximity ligation, to uncover in vivo genomic folding patterns. 4C-seq is a derivative 3C method, designed to search the genome for sequences contacting a selected genomic site of interest. 4C-seq employs inverse PCR and next generation sequencing to amplify, identify and quantify its proximity ligated DNA fragments. It generates high-resolution contact profiles for selected genomic sites based on limited amounts of sequencing reads. 4C-seq can be used to study multiple aspects of genome organization. It primarily serves to identify specific long-range DNA contacts between individual regulatory DNA modules, forming for example regulatory chromatin loops between enhancers and promoters, or architectural chromatin loops between cohesin- and CTCF- associated domain boundaries. Additionally, 4C-seq contact profiles can reveal the contours of contact domains and can identify the structural domains that co-occupy the same nuclear compartment. Here, we present an improved step-by-step protocol for sample preparation and the generation of 4C-seq sequencing libraries, including an optimized PCR and 4C template purification strategy. In addition, a data processing pipeline is provided which processes multiplexed 4C-seq reads directly from FASTQ files and generates files compatible with standard genome browsers for visualization and further statistical analysis of the data such as peak calling using peakC. The protocols and the pipeline presented should readily allow anyone to generate, visualize and interpret their own high resolution 4C contact datasets.

From Supramolecular Species to Self-Templated Porous Carbon and Metal-Doped Carbon for Oxygen Reduction Reaction Catalysts.

The preparation of carbon materials usually involves the decomposition of precursors and the reorganization of the as-generated fragments. However, the cleavage of bonds and the simultaneous formation of new bonds at nearly the same positions prevents effective yet precise fabrication. Herein, a supramolecular precursor, cucurbit[6]uril, that contains multiple bonds with distinct bond strengths is proposed to decouple the twin problem of simultaneous bond cleavage and formation, allowing multistage transformations to hierarchical porous carbon and metal-doped carbon in a single yet effective pyrolysis step without the need of a template or additional purification. As a proof-of-concept, the Fe-doped carbon electrocatalysts realized a Pt/C-like half-wave potential of 0.869 V vs. RHE and small Tafel slope of 51.3 mV dec-1 in oxygen reduction reaction.

From Supramolecular Species to Self‐Templated Porous Carbon and Metal‐Doped Carbon for Oxygen Reduction Reaction Catalysts

AbstractThe preparation of carbon materials usually involves the decomposition of precursors and the reorganization of the as‐generated fragments. However, the cleavage of bonds and the simultaneous formation of new bonds at nearly the same positions prevents effective yet precise fabrication. Herein, a supramolecular precursor, cucurbit[6]uril, that contains multiple bonds with distinct bond strengths is proposed to decouple the twin problem of simultaneous bond cleavage and formation, allowing multistage transformations to hierarchical porous carbon and metal‐doped carbon in a single yet effective pyrolysis step without the need of a template or additional purification. As a proof‐of‐concept, the Fe‐doped carbon electrocatalysts realized a Pt/C‐like half‐wave potential of 0.869 V vs. RHE and small Tafel slope of 51.3 mV dec−1 in oxygen reduction reaction.

Integrated DNA purification, PCR, sample cleanup, and capillary electrophoresis microchip for forensic human identification

A fully integrated microdevice and process for forensic short tandem repeat (STR) analysis has been developed that includes sequence-specific DNA template purification, polymerase chain reaction (PCR), post-PCR cleanup and inline injection, and capillary electrophoresis (CE). Fragmented genomic DNA is hybridized with biotin-labeled capture oligos and pumped through a fluidized bed of magnetically immobilized streptavidin-coated beads in microchannels where the target DNA is bound to the beads. The bead-DNA conjugates are then transferred into a 250 nL PCR reactor for autosomal STR amplification using one biotin and one fluorescence-labeled primer. The resulting biotin-labeled PCR products are electrophoretically injected through a streptavidin-modified capture gel where they are captured to form a concentrated and purified injection plug. The thermally released sample plug is injected into a 14 cm long CE column for fragment separation and detection. The DNA template capture efficiency provided by the on-chip sequence-specific template purification is determined to be 5.4% using K562 standard DNA. This system can produce full 9-plex STR profiles from 2.5 ng input standard DNA and obtain STR profiles from oral swabs in about 3 hours. This fully integrated microsystem with sample-in-answer-out capability is a significant advance in the development of rapid, sensitive, and reliable micro-total analysis systems for on-site human identification.

Routine human papillomavirus genotyping by DNA sequencing in community hospital laboratories

BackgroundHuman papillomavirus (HPV) genotyping is important for following up patients with persistent HPV infection and for evaluation of prevention strategy for the individual patients to be immunized with type-specific HPV vaccines. The aim of this study was to optimize a robust "low-temperature" (LoTemp™) PCR system to streamline the research protocols for HPV DNA nested PCR-amplification followed by genotyping with direct DNA sequencing. The protocol optimization facilitates transferring this molecular technology into clinical laboratory practice. In particular, lowering the temperature by 10°C at each step of thermocycling during in vitro DNA amplification yields more homogeneous PCR products. With this protocol, template purification before enzymatic cycle primer extensions is no longer necessary.ResultsThe HPV genomic DNA extracted from liquid-based alcohol-preserved cervicovaginal cells was first amplified by the consensus MY09/MY11 primer pair followed by nested PCR with GP5+/GP6+ primers. The 150 bp nested PCR products were subjected to direct DNA sequencing. The hypervariable 34–50 bp DNA sequence downstream of the GP5+ primer site was compared to the known HPV DNA sequences stored in the GenBank using on-line BLAST for genotyping. The LoTemp™ ready-to-use PCR polymerase reagents proved to be stable at room temperature for at least 6 weeks. Nested PCR detected 107 isolates of HPV in 513 cervicovaginal clinical samples, all validated by DNA sequencing. HPV-16 was the most prevalent genotype constituting 29 of 107 positive cases (27.2%), followed by HPV-56 (8.5%). For comparison, Digene HC2 test detected 62.6% of the 107 HPV isolates and returned 11 (37.9%) of the 29 HPV-16 positive cases as "positive for high-risk HPV".ConclusionThe LoTemp™ ready-to-use PCR polymerase system which allows thermocycling at 85°C for denaturing, 40°C for annealing and 65°C for primer extension can be adapted for target HPV DNA amplification by nested PCR and for preparation of clinical materials for genotyping by direct DNA sequencing. HPV genotyping is performed by on-line BLAST algorithm of a hypervariable L1 region. The DNA sequence is included in each report to the physician for comparison in following up patients with persistent HPV infection, a recognized tumor promoter in cancer induction.

Methylation status of the p16 tumor-supressor and DAP-kinase genes in colon biopsies from normal and ulcerative colitis samples

Backgroud and Aims: The normal methylation patterns in tumor tissues are altered in numerous genes. Some of these like p16 and DAP-kinase genes may show a hypermethylation pattern in the CpG islands of their promoter regions in colorectal cancer. The aim of the study was to examine the methylation status of these genes in ulcerative colitis. Methods: DNA was extracted from frozen colon biopsies of 5 healthy patients and from 5 with ulcerative colitis, using High Pure PCR Template Purification Kit. Bisulfite conversion of the samples was perfomed with CpGenome DNA Modification Kit. Methylation-specific PCR was carried out using CpGWIZ p16 Amplification Kit and CpGWIZ DAP-kinase Amplification Kit, to check the conversion and to visualize the changes. Each kit contains three primers and three control DNA for unmethylated, methylated and wild-type allele sequences. Results: Methylation status was determined in 10 samples, for both p16 and DAP- kinase genes. The results showed unmethylated homozygous state for methylation in normal samples both at the p16 locus and the DAP-kinase locus. No methylation was found in the p16 promoter region in the ulcerative colitis samples, but two cases displayed heterozygous state for methylation in the DAP-kinase promoter region. Conclusions: The DAP-kinase hypermethylation in ulcerative colitis samples can refer to the startpoint the further malignant alteration.

Removal of PCR inhibitors using dielectrophoresis as a selective filter in a microsystem

Diagnostic PCR has been used to analyse a wide range of biological materials. Conventional PCR consists of several steps such as sample preparation, template purification, and PCR amplification. PCR is often inhibited by contamination of DNA templates. To increase the sensitivity of the PCR, the removal of PCR inhibitors in sample preparation steps is essential and several methods have been published. The methods are either chemical or based on filtering. Conventional ways of filtering include mechanical filters or washing e.g. by centrifugation. Another way of filtering is the use of electric fields. It has been shown that a cell will experience a force when an inhomogeneous electric field is applied. The effect is called dielectrophoresis (DEP). The resulting force depends on the difference between the internal properties of the cell and the surrounding fluid. DEP has been applied to manipulate cells in many microstructures. In this study, we used DEP as a selective filter for holding cells in a microsystem while the PCR inhibitors were flushed out of the system. Haemoglobin and heparin - natural components of blood - were selected as PCR inhibitors, since the inhibitory effects of these components to PCR have been well documented. The usefulness of DEP in a microsystem to withhold baker's yeast (Saccharomyces cerevisiae) cells while the PCR inhibitors haemoglobin and heparin are removed will be presented and factors that influence the effect of DEP in the microsystem will be discussed. This is the first time dielectrophoresis has been used as a selective filter for removing PCR inhibitors in a microsystem.

Molecular evidence for multiple Toxoplasmagondii infections in individual patients in England and Wales: public health implications

We sought to determine the SAG2 genotypes of Toxoplasma gondii associated with cases of acute human toxoplasmosis in England and Wales. The samples examined were collected from a wide range of cases including congenital infections, AIDS and immunosuppressed patients and were derived from a number of different tissues. Parasite DNA was detected by PCR amplification without the need for prior template purification, and SAG2 genotype was determined by both restriction enzyme analysis and direct DNA sequencing of the PCR amplification products. Parasites of both SAG2 type I and type II genotypes were seen with approximately equal frequency amongst the samples examined. Neither of these genotypes was found to be more frequently associated with a particular clinical presentation or sample tissue. Unexpectedly, we found clear evidence of mixed ( SAG2 type I+type II) infections in approximately the same number of samples as were seen to be associated with either type I or II alone. Our use of direct DNA sequencing rather than simple restriction analysis was essential for the detection of mixed infections since incomplete restriction digestion of samples containing a single parasite type was occasionally observed. It is possible that the presence of more than one type of parasite in single samples might be related to our recent demonstration that mixtures of SAG2 type I and type II parasites are present in a significant proportion of commercial meat preparations. Moreover, the presence of mixed infections in single patients might offer a direct molecular method of assessing risk factors for infection.

Polymerase Chain Reaction-Based Methods for Detection of Listeria monocytogenes: Toward Real-Time Screening for Food and Environmental Samples

A review is presented of nucleic acid amplification-based methodology, specifically polymerase chain reaction (PCR)-based assays, for the detection of Listeria monocytogenes in food and environmental samples. Until recently, developmental challenges including poor sensitivity, due in part to reaction inhibition by components of the sample matrix, and the potential for false-positive reactions have limited routine application of PCR-based screening assays. Commercial assays address these challenges while offering convenient, standardized protocols, a high level of automation, and results within 2 days after the sampling date. Although sample enrichment is necessary to achieve desired detection limits, continued efforts toward template purification will facilitate the development of assays offering real-time, quantitative results. The development of ribonucleic acid (RNA) amplification-based assays may increase in importance, particularly if end-product testing is prioritized by regulatory agencies, as messenger RNA appears to serve as an accurate indicator of cell viability. Further, the increase in target copy number may improve assay sensitivity. PCR-based screening methods offer efficient, reliable results and are ideal for monitoring the presence of L. monocytogenes in foods and in the food processing environment.

A Fully Automated High-throughput Nucleic Acid Purification System Using Silica Coated Magnetic Bead Technology

The design of a fully automated high-throughput system for the purification of sequencing templates is described. Hardware, software, and chemistries have been optimized to suit the needs of high-throughput laboratories involved in genome sequencing projects. Using this system, up to 5760 samples (60 times 96-well plates) can be purified in less than 16 hours during a single unattended run. The system can also be configured to perform sequencing reaction setup for all 60 plates following template purification, extending total run times to < 24 hours. Final sequencing reactions are prepared in 384-well microplates.

A Fully Automated High-Throughput Nucleic Acid Purification System Using Silica Coated Magnetic Bead Technology

The design of a fully automated high-throughput system for the purification of sequencing templates is described. Hardware, software, and chemistries have been optimized to suit the needs of high-throughput laboratories involved in genome sequencing projects. Using this system, up to 5760 samples (60 times 96-well plates) can be purified in less than 16 hours during a single unattended run. The system can also be configured to perform sequencing reaction setup for all 60 plates following template purification, extending total run times to &lt; 24 hours. Final sequencing reactions are prepared in 384-well microplates.

Multiplex automated primer extension analysis: simultaneous genotyping of several polymorphisms.

Accurate and fast genotyping of single nucleotide polymorphisms (SNPs) is of significant scientific importance for linkage and association studies. We report here an automated fluorescent method we call multiplex automated primer extension analysis (MAPA) that can accurately genotype multiple known SNPs simultaneously. This is achieved by substantially improving a commercially available protocol (SNaPshot). This protocol relies on the extension of a primer that ends one nucleotide 5'of a given SNP with fluorescent dideoxy-NTPs (minisequencing), followed by analysis on an ABI PRisMS 377 Semi-Automated DNA Sequencer Our modification works by multiplexing the initial reaction that produces the DNA template for primer extension and/or multiplexing several primers (corresponding to several SNPs) in the same primer extension reaction. Then, we run each multiplexed reaction on a single gel lane. We demonstrate that MAPA can be used to genotype up to four SNPs simultaneously, even in compound heterozygote samples, with complete accuracy (based on concordance with sequencing results). We also show that primer design, unlike the DNA template purification method, can significantly affect genotyping accuracy, and we suggest useful guidelines for quick optimization.

Detection of genetically modified organisms in food: critical points for quality assurance

The detection of genetically modified organisms (GMOs) by the polymerase chain reaction (PCR) is a complex multiparameter problem. Therefore, a number of critical issues in respect to quality control need to be considered. For practical purposes, the PCR process itself can be divided into three subprocesses: template isolation and reaction setup (pre-PCR), PCR reaction and detection of amplification products, and data evaluation (post-PCR). Crucial factors for the pre-PCR process are the following: homogeneity of the sample to be analysed, performance of template isolation and purification in terms of yield and purity, standardized process for the estimation of concentrations of genomic DNA and all reagents used in the reaction. For the PCR itself, crucial factors to be controlled are: setup of reactions, batch to batch variations of reagents, temperature-time programs used for the PCR amplification, and the performance of different types of hardware (e.g. different brands of thermocyclers). The crucial factor for the post-PCR process is the detection of the amplification products of the PCR. The tremendous sensitivity of PCR methods requires a careful and consequent separation of the three processes in terms of hardware, laboratory space and sample handling. The avoidance of contamination is one of the most critical factors. The goal of quality assurance measures must be to ensure appropriate results at maximum sensitivity. The complexity of any PCR system used for the detection of GMOs leads to the requirement of a careful validation process for any laboratory using such methods. For qualitative analyses crucial validation parameters are: specificity, selectivity, repeatability, intermediate precision, reproducibility, limit of detection and robustness.

Preparation of PCR products for DNA sequencing.

We demonstrate that routine PCR product analytical agarose gels can also serve as preparative gels for quick DNA template purification before sequencing. The band of interest is excised, placed into a Gel Nebulizer inside a Micropure separator and rapidly purified in a single centrifugation step. Gel-purified PCR product, suitable for manual and automated sequencing, is delivered within 10 min.

Snapback SSCP analysis: engineered conformation changes for the rapid typing of known mutations.

Several approaches may be applied to detect known mutations, including restriction enzyme cleavage, allele-specific oligonucleotide (ASO) hybridization or amplification, dideoxy fingerprinting, and direct DNA sequencing. All these approaches require several extra steps after PCR and may involve radioactive isotopes, time-consuming hybridization, template purification, or digestion steps. The ease and simplicity of the SSCP test make it a popular choice for mutation detection, but a significant limitation is that some DNA changes will not alter the overall conformation of either single strand and are thus not amenable to SSCP typing. We describe Snapback SSCP to genotype normal and mdx mice (an animal model of Duchenne muscular dystrophy) that previously could not be differentiated by conventional SSCP analysis. A snapback primer was designed with additional bases at the 5' terminus, which were complementary to the normal sequence flanking the mdx mutation and used under the original amplification conditions. Each single strand of these snapback PCR products now had one terminus capable of re-annealing or "snapping back" to the normal sequence but not the mdx mutation. In this manner, a conformation change was engineered into the normal strand that could be readily distinguished from the mdx allele on a SSCP gel. This approach could be applied to the routine screening of other known mutations that are not amenable to detection by simple SSCP analysis.

35] Automated sequencing of mitochondrial DNA

This chapter describes a method for direct sequencing of mitochondrial DNA (mtDNA) fragments amplified from genomic DNA without using cloning procedures, radioisotopes, or columns for template purification. A manual method for direct sequencing of mtDNA is reported. The protocol discussed in the chapter describes methods for fully automated sequencing of mtDNA with a combination of a chemical robot and a fluorescence-based automated DNA sequencer. This method permits rapid, accurate, and easy determination of entire sequence of mitochondrial genome. Several methods for direct sequencing of polymerase chain reaction (PCR)- amplified DNA are discussed in the chapter. For the cycle sequencing method both double-stranded and single-stranded DNA can serve as templates. The main purpose of the asymmetric PCR is not to obtain single-stranded DNA template but to deplete the FL 2 primer. In the sequencing results, large peaks are sometimes observed at 40–50 nucleotides from the primer peak. These are caused by the primer dimers formed between primer FL 2 and primer H 2.

39] Mapping DNA-protein interactions in cells and nuclei: Genomic sequencing by template purification

Publisher Summary This chapter presents a procedure for analyzing DNA-protein interactions on genomic DNA using template purification and genomic sequencing. The principles of the purification method and genomic sequencing are discussed in the chapter. Precise protocols for the treatment of cells with dimethyl sulfate (DMS) or KMnO4, and the isolation of nuclei for DNase I footprinting are presented. A number of genomic sequencing procedures, principally aimed at determining at the nucleotide level DNA-protein interactions on genomic DNA, have been developed. Although these sequencing procedures depend on different approaches, they all are difficult to carry out. The principal limitation is that a sequencing signal must be generated from a single-copy sequence which, for man, or mouse, is present in a total of about 3 × 109 bp of genomic DNA. Finally, protocols for the purification of a specific sequence from whole genomic DNA followed by detection of a sequence ladder using primer extension are also described.