Topic
Nuclear DNA
About: Nuclear DNA is a research topic. Over the lifetime, 3933 publications have been published within this topic receiving 185830 citations.
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TL;DR: This study quantitatively assess post-mortem DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA and suggests that reliable sequence data can be obtained from her barium specimens.
Abstract: Dried plant herbarium specimens are potentially a valuable source of DNA. Efforts to obtain genetic information from this source are often hindered by an inability to obtain amplifiable DNA as herbarium DNA is typically highly degraded. DNA post-mortem damage may not only reduce the number of amplifiable template molecules, but may also lead to the generation of erroneous sequence information. A qualitative and quantitative assessment of DNA post-mortem damage is essential to determine the accuracy of molecular data from herbarium specimens. In this study we present an assessment of DNA damage as miscoding lesions in herbarium specimens using 454-sequencing of amplicons derived from plastid, mitochondrial, and nuclear DNA. In addition, we assess DNA degradation as a result of strand breaks and other types of polymerase non-bypassable damage by quantitative real-time PCR. Comparing four pairs of fresh and herbarium specimens of the same individuals we quantitatively assess post-mortem DNA damage, directly after specimen preparation, as well as after long-term herbarium storage. After specimen preparation we estimate the proportion of gene copy numbers of plastid, mitochondrial, and nuclear DNA to be 2.4-3.8% of fresh control DNA and 1.0-1.3% after long-term herbarium storage, indicating that nearly all DNA damage occurs on specimen preparation. In addition, there is no evidence of preferential degradation of organelle versus nuclear genomes. Increased levels of CRT/GRA transitions were observed in old herbarium plastid DNA, representing 21.8% of observed miscoding lesions. We interpret this type of post-mortem DNA damage-derived modification to have arisen from the hydrolytic deamination of cytosine during long-term herbarium storage. Our results suggest that reliable sequence data can be obtained from herbarium specimens.
130 citations
TL;DR: Results show that ancient single-copy nuclear DNA can be recovered from warm, arid climates, showing that nuclear DNA preservation is not restricted to cold climates.
130 citations
TL;DR: DNA isolated from macronuclei of the ciliate, Tetrahymena pyriformis, has been found to contain [6N]methyl adenine (MeAde); this represents the first clear demonstration of significant amounts of MeAde in the DNA of a eucaryote.
Abstract: DNA isolated from macronuclei of the ciliate, Tetrahymena pyriformis, has been found to contain [6N]methyl adenine (MeAde); this represents the first clear demonstration of significant amounts of MeAde in the DNA of a eucaryote. The amounts of macronuclear MeAde differed slightly between different strains of Tetrahymena, with approximately 0.65–0.80% of the adenine bases being methylated. The MeAde content of macronuclear DNA did not seem to vary in different physiological states. The level of MeAde in DNA isolated from micronuclei, on the other hand, was quite low (at least tenfold lower than in macronuclear DNA).
129 citations
TL;DR: Elevated levels of circulating cell-free nuclear DNA and circulating Cell-free mitochondrial DNA in epithelial ovarian cancer may have diagnostic value, which suggests that the circulating molecules might be potential biomarkers in the disease.
129 citations
TL;DR: Autoradiography demonstrates that only half of the cells are labelled with [ 3 H]thymidine, and that many of the Cells showing cytoplasmic labelling have disintegrated nuclei, consistent with a hypothesis that in this system the DNA isolated from the cy toplasm is a degradation product of nuclear DNA.
128 citations