Biochemical and molecular characterization of a restriction endonuclease Tvu2HI from Thermoactinomyces vulgaris 2H and study of its R-M system

A bacterial strain 2H isolated from soil and identified as Thermoactinomyces vulgaris produce a potent Type II restriction endonuclease activity that has been extracted by a PEG/dextran aqueous two-phase system. Optimal temperature for the restriction endonuclease activity was 55-65°C. Specific DNA cleavage was obtained at pH range 7-10 and 10-20mM MgCl₂. Restriction cleavage analysis followed by sequencing confirms GG^CC as the recognition sequence. This enzyme, named Tvu2HI, is a thermostable isoschizomer of the mesophilic prototype restriction endonuclease HaeIII. Sequencing of the complete Thermoactinomyces vulgaris 2H genome revealed the presence of two adjacent ORFs coding for the restriction endonuclease Tvu2HI and the corresponding methyltransferase; an ORF coding for a putative Vsr nicking enzyme was found close to those coding for the Tvu2HI restriction-modification system. Phylogenetic analysis based on sequence alignment suggests a common origin of Tvu2HI R-M system with HaeIII-like R-M systems. This is the first investigation dealing with a Type II restriction endonuclease identified in a natural isolate of the genus Thermoactinomyces.

RFLP analysis of forensic DNA samples with single-locus VNTR genetic markers

This unit covers the many and varied methods for extracting DNA from such diverse specimens as blood, tissue, stamps and envelopes, and cigarette butts, among others. Modifications to the methods that allow the DNA to be used for either PCR or Southern blotbased analyses are also included.

Genotyping for DQA1 and PM loci in urine using PCR-based amplification: effects of sample volume, storage temperature, preservatives, and aging on DNA extraction and typing

Urine is often the sample of choice for drug screening in aviation/general forensic toxicology and in workplace drug testing. In some instances, the origin of the submitted samples may be challenged because of the medicolegal and socioeconomic consequences of a positive drug test. Methods for individualization of biological samples have reached a new boundary with the application of the polymerase chain reaction (PCR) in DNA profiling, but a successful characterization of the urine specimens depends on the quantity and quality of DNA present in the samples. Therefore, the present study investigated the influence of storage conditions, sample volume, concentration modes, extraction procedures, and chemical preservations on the quantity of DNA recovered, as well as the success rate of PCR-based genotyping for DQA1 and PM loci in urine. Urine specimens from male and female volunteers were divided and stored at various temperatures for up to 30 days. The results suggested that sample purification by dialfiltration, using 3000-100,000 molecular weight cut-off filters, did not enhance DNA recovery and typing rate as compared with simple centrifugation procedures. Extraction of urinary DNA by the organic method and by the resin method gave comparable typing results. Larger sample volume yielded a higher amount of DNA, but the typing rates were not affected for sample volumes between 1 and 5 ml. The quantifiable amounts of DNA present were found to be greater in female (14-200 ng/ml) than in male (4-60 ng/ml) samples and decreased with the elapsed time under both room temperature (RT) and frozen storage. Typing of the male samples also demonstrated that RT storage samples produced significantly higher success rates than that of frozen samples, while there was only marginal difference in the DNA typing rates among the conditions tested using female samples. Successful assignment of DQA1 + PM genotype was achieved for all samples of fresh urine, independent of gender, starting sample volume, or concentration method. Preservation by 0.25% sodium azide was acceptable for sample storage at 4 degrees C during a period of 30 days. For longer storage duration, freezing at -70 degrees C may be more appropriate. Thus, the applicability of the DQA1 + PM typing was clearly demonstrated for individualization of urine samples.

AMPFLP analysis of the VNTR loci D1S80 and ApoB in Hungary

Population data studies for D1S80 and ApoB were carried out on a caucasian population sample from Hungary of 229 and 222 unrelated individuals, respectively. We observed 26 different alleles for D1S80 and 13 for ApoB. The allele frequencies found are similar to those reported in the literature for European caucasians. No evidence of significant deviations from Hardy-Weinberg equilibrium were observed for both AMPFLP systems.

Application of dual internal standards for precise sizing of polymerase chain reaction products using capillary electrophoresis

Capillary electrophoresis (CE) is an analytical technique which provides rapid, high resolution analysis of amplified DNA fragments produced by the polymerase chain reaction (PCR). In this study, two internal standards are used as size markers to bracket und precisely size PCR products. The technique is applied to typing PCR products from the short tandem repeat locus HUMTH01. HUMTH01 consists of five to seven major alleles in the size range of 179-203 bp, with each allele four bp apart. Using this genetic marker, a population containing 97 individuals was examined with both polyacrylamide gel electrophoresis and CE. Identical genotypes were obtained with both techniques demonstrating the reliability of CE in DNA typing applications. The DNA analysis took place in sets of 10 with a calibration of the CE being performed between each set of samples. For the 97 samples examined, the pooled standard deviation was 0.3 bp. The observed genotype frequencies determined from the sample set did not deviate significantly from Hardy-Weinberg expectations. From these CE results, we conclude that HUMTH01 PCR products can be accurately and precisely sized by capillary electrophoresis using the method described.

DNA investigations on fetal material from paternity cases

Three paternity cases have been investigated where DNA was extracted from fetuses (age: 8-10 weeks old) after interruption of pregnancy. In each case it was possible to clearly identify the putative father using 5 or 6 single locus probes (SLP's). Fetal bands (SLP) could be clearly identified from mixtures of placental and fetal DNA by comparison with the maternal and paternal bands. However, it was very difficult to resolve the fragment patterns of tissue mixtures with one multi locus probe (MLP), because of band overlap. Another advantage of using SLP's was that biostatistical calculations could be carried out and very informative Essen-Möller values for the probability of paternity were obtained.

Problems associated with the DNA analysis of stains

Selected stain cases are presented which highlight various problems associated with DNA investigations on stain materials, especially risks of artefacts. These cases involve stain materials (blood, semen) which were exposed to different external conditions so that the DNA was partially degraded and of variable quantity. One multi locus probe (MLP) and 4-6 single locus probes (SLP's) were used for individualisation but artefacts such as extra bands, band deficiencies or shifts only occurred with the MLP. In one case where only a few spermatozoa were present in the vaginal swab, DNA extraction was carried out without preferential lysis to avoid loss of sperm DNA. The resulting mixed band pattern could be clearly attributed to the bands from the corresponding blood samples after SLP hybridisation.

Extraction strategy for obtaining DNA from bloodstains for PCR amplification and typing of the HLA-DQ alpha gene

A simple, practical approach for the extraction of PCR-amplifiable DNA for the HLA-DQ alpha gene from bloodstains deposited on various substrates is described. DNA from bloodstains is purified using Chelex 100 ion-exchange resin and then amplified. If amplification is not achieved, the extract is washed through a Centricon 100 dialysis/concentration tube. If the second amplification of this extract produces a negative result, the extract is processed with Chelex 100 again. This approach has been found to be reliable, safe, efficient and economical.