A simple and accurate genomic primer extension method has been developed to detect ultraviolet footprinting patterns of regulatory protein-DNA interactions in mammalian genomic DNA. The technique can also detect footprinting or sequencing patterns introduced into genomic DNA by other methods. Purified genomic DNA, containing either damaged bases or strand breaks introduced by footprinting or se...

This paper describes the use of real-time PCR for the confirmation of microarray data. Current publication guidelines require that all microarray results are confirmed by an independent gene expression profiling method. Real-time PCR is the method of choice for most researchers but it is not without drawbacks. The first step in confirming array results by real-time PCR is selection of gene-spec...

The Polα/primase complex assembles the short RNA-DNA fragments for priming of lagging and leading strand DNA replication in eukaryotes. As such, the Polα polymerase subunit encounters two types of substrates during primer synthesis: an RNA:DNA helix and a DNA:DNA helix. The engagement of the polymerase subunit with the DNA:DNA helix has been suggested as the of basis for primer termination in e...

In search of a primer set that could be used to study Planctomycetes dynamics in lakes and especially via fingerprinting methods, e.g. denaturing gradient gel electrophoresis (DGGE), three existing specific primer sets, developed for marine and soil systems, have been tested on water samples from four freshwater ecosystems. The first primer set (PLA46F/PLA886R) allowed PCR amplification of Plan...

BACKGROUND Complex PCR applications for large genome-scale projects require fast, reliable and often highly sophisticated primer design software applications. Presently, such applications use pipelining methods to utilise many third party applications and this involves file parsing, interfacing and data conversion, which is slow and prone to error. A fully integrated suite of software tools for...

background: infestation of the skin by the “itch mite” sarcoptes scabiei var. hominis results in a contagious skin infection in humans called “sca-bies”. by resolving morphology issues, the present study was designed to be acquainted with itch mite by molecular markers. methods: the mite samples were collected from scabies patients by visiting government hospitals of twin city, pakistan. for su...

Many protocols in methylation studies utilize one primer set to generate a PCR product from bisulfite modified template regardless of its methylation status (methylation independent amplification MIP). However, proportional amplification of methylated and unmethylated alleles is hard to achieve due to PCR bias favoring amplification of unmethylated relatively GC poor sequence. Two primer design...

INTRODUCTION In this method, an oligodeoxynucleotide primer hybridized to mRNA is extended by an RNA-dependent DNA polymerase to create a cDNA copy that can be amplified by PCR. Depending on the purpose of the experiment, the primer for first-strand cDNA synthesis can be specifically designed to hybridize to a particular target gene, or a general primer such as oligo(dT) can be used to prime cD...

SUMMARY BEsTRF (Best Estimated T-RF) provides a standalone environment for analyzing primers-enzymes-gene section combinations used in terminal-restriction fragment length polymorphism (T-RFLP) for its optimal resolution. User-defined sequence databases of several hundred thousand DNA sequences can be explored and the resolution of user-specified sets of primers and restriction endonucleases ca...

Analysis of fractions containing purified DNA polymerase epsilon from calf thymus has revealed the presence of a 5' to 3' exonuclease activity that is specific for a single strand of duplex DNA. This activity is capable of degrading a 3'-labeled oligonucleotide hybridized to M13mp18 DNA. When a second oligonucleotide primer is annealed 3 bases upstream, degradation of the downstream primer is s...