BACKGROUND: Clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. Although DNA is commonly extracted from fixed tissues and amplified by PCR, the effects of formalin fixation are relatively unknown. Formalin fixation is known to impair PCR, presumably through damage that blocks polymerase elongation, but an insidious possibility is error prone translesion synthe...

The highly thermostable DNA polymerase from Thermus aquaticus (Taq) is ideal for both manual and automated DNA sequencing because it is fast, highly processive, has little or no 3'-exonuclease activity, and is active over a broad range of temperatures. Sequencing protocols are presented that produce readable extension products greater than 1000 bases having uniform band intensities. A combinati...

The use of glass–silicon chips for PCR analysis has been widely reported in the last decade, but there have been few systematic efforts to pin down the biochemical problems such systems bring forth. Here we report a systematic analysis of material-related inhibition and adsorption phenomena in glass–silicon PCR-chips. The results suggest that the previously reported inhibition of PCR by silicon...

We previously described in a paper published in BIOS an undergraduate lab activity involving the gene cloning, expression, and purification of Thermus aquaticus (Taq) DNA polymerase, an enzyme used in the polymerase chain reaction (PCR). Based on the large number of requests for biological materials and questions about the protocols this paper invoked, we explored methods to simplify the protei...

Kary B. Mullis developed a revolutionary method name polymerase chain reaction (PCR) in 1983, which can synthesize new strand of DNA complementary to the template and produce billions copies fragment only few hours. Denaturation, annealing, extension are three primary steps involved PCR process, generally requires thermocyclers, template, pair primers, Taq polymerase, nucleotides, buffers, etc....

Few techniques are available to detect DNA lesions in cultured cells at the nucleotide level (8). One such method is primer extension of genomic DNA (5) that may be improved using linear amplification by repeated PCR cycles (1,11). This method has been used successfully to map the genomic sites of topoisomerase II (2,3,7) and topoisomerase I activity (10). DNA topoisomerases modulate DNA struct...

The polymerase chain reaction (PCR) and dideoxy DNA sequencing are frequently used techniques of molecular biology which utilise DNA polymerases. The high temperatures required for PCR necessitate a thermostable enzyme for DNA amplification, and DNA polymerase derived from the thermophilic microorganism, Thermus aquaticus, is used most commonly. The high optimal polymerisation temperature of th...

We describe a photochemical procedure for the sterilization of polynucleotides that are created by the Polymerase Chain Reaction (PCR). The procedure is based upon the blockage of Taq DNA polymerase when it encounters a photochemically modified base in a polynucleotide strand. We have discovered reagents that can be added to a PCR reaction mixture prior to amplification and tolerate the thermal...

It is generally believed that sequence heterogeneity in PCR products from fossil remains are due to regular DNA polymerase errors as well as miscoding lesions compounded by damage in the template DNA (Pääbo 1990; Handt et al. 1994b, 1996; Höss et al. 1996; Krings et al. 1997). However, it has been difficult to test the frequency with which this assumption holds. First, DNA extractions from foss...

The polymerase chain reaction (PCR) method is widely used for the reproduction and amplification of specific DNA segments, and a novel PCR method using nanomaterials such as gold nanoparticles has recently been reported. This paper reports on the effects of superparamagnetic nanoparticles on PCR amplification without an external magnetic field, and clarifies the mechanism behind the effects of ...