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P Sachadyn

Publications and source records attributed to P Sachadyn.

9 recordsLinked to original sources
PubMed2000

One tube mutation detection using sensitive fluorescent dyeing of MutS protected DNA.

A novel, universal method for mutation detection utilising the ability of MutS protein to recognise DNA incomplementarities is proposed. The examined and reference DNA fragments are PCR amplified. The PCR products are purified, mixed, heated and cooled to form heteroduplexes. In the case of mutation the heteroduplex DNA containing mismatch is protected against exonuclease digestion by MutS, while the DNA without mismatches is degraded. The protection effect is visualised by the direct addition of a highly sensitive fluorescent dye (SYBR-Gold) selectively binding DNA. The Thermus thermophilus recombined His-tagged MutS and 3'-5' exonuclease activity of T4 DNA polymerase were used in the assay.

Adenosine Triphosphatases↗
PubMed2000

Purification to homogeneity of Candida albicans glucosamine-6-phosphate synthase overexpressed in Escherichia coli.

The Candida albicans GFA1 gene encoding glucosamine-6-phosphate synthase, an enzyme of cell wall biosynthesis pathway in fungi and bacteria, recently an object of interest as a target for the chemotherapy of systemic mycoses, was PCR amplified and cloned to an Escherichia coli expression vector pET23b. The activity of the enzyme in the lysates from the overproducing E. coli strain was approximately 50-100 times higher than in the lysates from the control E. coli strain. This abundant overproduction allows to purify milligram amounts of the enzyme to homogeneity.

Candida albicans↗
PubMed1999

Reducing the number of microlocations in oligonucleotide microchip matrices by the application of degenerate oligonucleotides.

The application of degenerate oligonucleotides to DNA Sequencing by Hybridisation with Oligonucleotide Matrix (SHOM) is proposed. The use of degenerate oligonucleotides is regarded as an example of pooling methods that are suitable for various laboratory procedures requiring numerous samples to be assayed. As each DNA sequence coded by four letters (A, G, C, T) may be defined by two sequences: a sequence coded by W and S (W-weak-A or T, S-strong-G or C) and a sequence coded by R and Y (R-purine-A or G, Y-pirymidine-T or C), n4n -nucleotide sequences may be defined with the help of 2xn2sequences. In the place of the originally described microchip matrix composed of all possible unambiguous octanucleotides (4(8)=65 536) attached to the equal number of 65 536 microlocations a matrix composed of 512 microlocations containing 256 2(8)-degenerate octanucleotides is proposed. The matrix contains all 256 possible octanucleotides coded by W and S variations and all 256 possible octanucleotides coded by R and Y variations. The 512 256-degenerate octanucleotides allows to retrieve the same information as 65 536 unambiguous octanucleotides. A variant of the DNA sequence reconstruction method applicable to this system is presented. The use of degenerate oligonucleotides also gives the possibility to apply matrices composed of longer oligonucleotides without increasing the number of microlocations in matrices, which would enable increasing the length of unambiguously reconstructed sequence, e.g. a matrix comprising 131 072 16-mer oligonucleotides i.e. 65 536 65 536-fold degenerate oligonucleotide coded by W and S variations and 65 536 65 536-fold degenerate oligonucleotide coded by R and Y variations could replace one matrix comprising all possible unambiguous 16-mer oligonucleotides (ca. 4.3x10(9)).

Animals↗
PubMed1998

The construction and use of a PCR internal control.

An example of the application and contruction of a polymerase chain reaction (PCR) internal control is presented. The internal control is synthesized in one PCR reaction. The primers used in this reaction possess 5' over-hanging ends which are identical to the primers used in the diagnostic reaction, whereas their 3' ends are complementary to a predetermined DNA sequence (pUC19 in this case) of defined length and sequence. As the sequence of the control except for primer sites, is not homologous to the PCR signal product, the formation of heteroduplexes and non-specific PCR products should not occur. Neither is there a risk that the target DNA will contaminate the internal control. However, the simultaneous amplification of two different DNA fragments flanked by the same primer sites resulted in either inhibition or enhancement of one or both products depending on the molar ratio of those DNA fragments. The presented method may be applied to construction of internal controls for quantitative PCR. The internal control was developed and tested for use in a PCR detection system for Agrobacterium tumefaciens.

Agrobacterium tumefaciens↗
PubMed1998

Cloning and sequence analysis of Histoplasma capsulatum glucosamine-6-phosphate synthase gene fragment.

The 3' part of the glucosamine-6-phosphate synthase gene from Histoplasma capsulatum was PCR amplified using degenerate primers designed from the known glucosamine-6-phosphate synthase gene sequences, cloned and sequenced. The computer analysis of the 676 bp sequence revealed the presence of two introns. The identities of the deduced amino acid sequence to the corresponding Saccharomyces cerevisiae and Candida albicans fragment are 65 and 63.8%, respectively.

Amino Acid Sequence↗
PubMed1998

Thermal profile with alternately raised and lowered annealing temperature improves the PCR amplification using highly degenerate primers.

The proposed here PCR thermal profile improves the specificity and efficiency of PCR using highly degenerate primers, especially in the case of larger PCR products (around 2000 bp and more). The improvement is achieved by the use of a specific annealing temperature in the beginning cycles and the alternate lowering and raising of the annealing temperature in the subsequent cycles.

DNA Primers↗
PubMed1997

A new PCR system for Agrobacterium tumefaciens detection based on amplification of T-DNA fragment.

The design of the PCR system presented in this work is based on the knowledge of the molecular character of the crown gall disease. The virulence of Agrobacterium tumefaciens requires the presence of a big (up to 235,000 bp) plasmid Ti (pTi-tumour inducing plasmid). This plasmid carries the so-called T-DNA fragment (T-DNA-transferred DNA), which integrates into cell chromosomes of the infected plants and subsequently changes the plant morphology nad metabolism. In cannot be excluded that after T-DNA integration the presence of Agrobacterium is not necessary for the development of pathological changes. Thus, T-DNA is the only sign that must be present both in virulent bacteria and in infected plants in any stadium of the disease and even before the infection. This is why T-DNA was chosen as the target region for PCR amplification. Primers flanking a 220 bp fragment of one of the conservative regions responsible for Agrobacterium pathogenicity, namely tms2 gene coding for indolacetamide amidohydrolase (the second step of auxin biosynthesis) were designed as the optimal for PCR amplification. The PCR amplification reactions were performed for matrixes isolated from cultures of reference strains giving one predicted product for each sample. First attempts of T-DNA detection in infected soils and plants were performed. We hope that the presented new PCR system for Agrobacterium tumefaciens detection will help to fight the crown gall disease in the nearest future.

Agrobacterium tumefaciens↗
PubMed1996

A proposal for using modified site-specific recombination systems for making insertions into a chosen chromosomal site in vivo based on the analysis of lambda phage integration.

A proposal is presented here to use modified mobile genetic elements for making chromosomal insertions in vivo, into any desired chromosomal site. The idea lies in replacing the sequences which direct specificity of integration of those elements with other DNA sequences, homologous to the desired target chromosomal site. The idea is analysed on the basis of a lambda phage integration system. A design for a universal system for making chromosomal insertions into any site of choice is proposed.

Bacteriophages↗