Quantitation of gene-specific DNA damage by competitive PCR

Relationship Between Amplicon Size and Heat Conditions in Polymerase Chain Reaction Detection of DNA Degraded by Autoclaving

This study examined the influence of heat exposure on DNA samples during polymerase chain reaction (PCR) detection. In this study, λDNA samples, as model DNA, were exposed to 105°C for 3-90 minutes or to 105°C-115°C for 15 minutes by autoclaving. The exposed samples were subjected to real-time PCR using nine primer sets with amplicon sizes of 45-504 bp. Regarding DNA samples exposed to 105°C by autoclaving, the data showed negative correlations between the logarithm of λDNA concentration (log λDNA) calculated using real-time PCR and exposure duration and a good relationship between the slope of the regression line and amplicon size. Regarding λDNA samples exposed to heat for 15 minutes, the data showed negative correlations between the log λDNA and exposure temperature and a good relationship between the slope of the regression line and amplicon size. These results showed that the equations used in this study could predict the degree of degradation in λDNA samples by autoclaving, and the PCR detection levels of the DNA at each amplicon size.

Impaired integrity of DNA after recovery from inflammation causes persistent dysfunction of colonic smooth muscle

BACKGROUND & AIMS

Patients with inflammatory bowel disease who are in remission and those who developed irritable bowel syndrome after enteric infection continue to have symptoms of diarrhea or constipation in the absence of overt inflammation, indicating motility dysfunction. We investigated whether oxidative stress during inflammation impairs integrity of the promoter of Cacna1c, which encodes the pore-forming α1C subunit of Ca(v)1.2b calcium channels.

METHODS

We used long-extension polymerase chain reaction to evaluate DNA integrity in tissues from distal colons of rats; trinitrobenzene sulfonic acid was used to induce inflammation.

RESULTS

The H2O2 increased in the muscularis externa 1-7 days after inflammation was induced with trinitrobenzene sulfonic acid. The oxidative stress significantly impaired DNA integrity in 2 specific segments of the Cacna1c promoter: -506 to -260 and -2193 to -1542. The impairment peaked at day 3 and recovered partially by day 7 after induction of inflammation; expression of the products of Cacna1c followed a similar time course. Oxidative stress suppressed the expression of nuclear factor-erythroid-2-related factor 2 (Nrf2), an important regulator of anti-oxidant proteins. Intraperitoneal administration of sulforaphane significantly reversed the suppression of Nrf2, oxidative damage in the promoter of Cacna1c, and suppression of Cacna1c on day 7 of inflammation. The inflammation subsided completely by 56 days after inflammation was induced; however, impairment of DNA integrity, expression of Nrf2 and Cacna1c, and smooth muscle reactivity to acetylcholine remained suppressed at this time point.

CONCLUSIONS

Oxidative stress during inflammation impairs the integrity of the promoter of Cacna1c; impairment persists partially after inflammation has subsided. Reduced transcription of Cacna1c contributes to smooth muscle dysfunction in the absence of inflammation.

Quantification of damage in DNA recovered from highly degraded samples--a case study on DNA in faeces

BACKGROUND

Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (lambda) can be estimated by determining the rate of decline.

RESULTS

The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean lambda(predator) = 0.0106 per nucleotide; mean lambda(prey) = 0.0176 per nucleotide). This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples.

CONCLUSION

We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will allow researchers to measure template quality in order to evaluate alternate sources of DNA, different methods of sample preservation and different DNA extraction protocols. The technique could also be applied to study the process of DNA decay.

Quantitative analysis of total mitochondrial DNA: competitive polymerase chain reaction versus real-time polymerase chain reaction

An efficient and effective method for quantification of small amounts of nucleic acids contained within a sample specimen would be an important diagnostic tool for determining the content of mitochondrial DNA (mtDNA) in situations where the depletion thereof may be a contributing factor to the exhibited pathology phenotype. This study compares two quantification assays for calculating the total mtDNA molecule number per nanogram of total genomic DNA isolated from human blood, through the amplification of a 613-bp region on the mtDNA molecule. In one case, the mtDNA copy number was calculated by standard competitive polymerase chain reaction (PCR) technique that involves co-amplification of target DNA with various dilutions of a nonhomologous internal competitor that has the same primer binding sites as the target sequence, and subsequent determination of an equivalence point of target and competitor concentrations. In the second method, the calculation of copy number involved extrapolation from the fluorescence versus copy number standard curve generated by real-time PCR using various dilutions of the target amplicon sequence. While the mtDNA copy number was comparable using the two methods (4.92 +/- 1.01 x 10(4) molecules/ng total genomic DNA using competitive PCR vs 4.90 +/- 0.84 x 10(4) molecules/ng total genomic DNA using real-time PCR), both inter- and intraexperimental variance were significantly lower using the real-time PCR analysis. On the basis of reproducibility, assay complexity, and overall efficiency, including the time requirement and number of PCR reactions necessary for the analysis of a single sample, we recommend the real-time PCR quantification method described here, as its versatility and effectiveness will undoubtedly be of great use in various kinds of research related to mitochondrial DNA damage- and depletion-associated disorders.