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Nucleic Acids
Published in Danilo D. Lasic, LIPOSOMES in GENE DELIVERY, 2019
The tertiary structure distinguishes between linear and cyclic forms. Open or linear forms are produced by double-strand breaks, while nicked DNA is cyclic with one strand broken. Cyclic forms can have a supercoiled (superhelical) conformation. Catenated circles are linked dimers or trimers in which closed rings are interlocked. Large-scale conformational properties also include supercoiling, looping, catenation, and knotting and strongly depend on ionic conditions in the solution. Additionally, supercoiling causes twist (sometimes called writhe and twist) which can lead to the formation of sequence-specific binding sites for various proteins (Trifonov, 1991). While the majority of the extrachromosomal DNA in living cells is circular, some viruses have linear plasmids typically ~2000 bp in length. Figure 3-6 shows some of the possible DNA forms in solution.
Premature Aging
Published in Nate F. Cardarelli, The Thymus in Health and Senescence, 2019
WS fibroblasts in vitro exhibited chromosome instability.124,126,128–134 Variegated translocation mosaicism (pseudoploidy with multiple structure rearrangements that are clonal) is observed.124,129,132,134,135 WS fibroblast proliferation seems to be proportional to the degree of chromosomal mutation.129 Late passage fibroblasts exhibit transfer RNA alterations.131 Chromosome breakage level is somewhat elevated relative to normal cells.132 Cultured WS lymphocytes show an average of 0.15 chromosome breaks per cell, compared to the normal control value of 0.03 to 0.04 breaks per cell.114 Extrachromosomal DNA appears in chronological young WS patients as it does normally in the chronologically old.133 Premature centromere dysjunction in the X chromosome is observed in WS patients, and also characteristically seen in lymphocyte cultures of elderly women.114,136 WS skin fibroblasts show no detectable effect in chromosome repair capability.137
Optimal Detection of and Effect of Vitamin D3 on Extrachromosomal Oncogene Sequences
Published in Maryce M. Jacobs, Vitamins and Minerals in the Prevention and Treatment of Cancer, 2018
Daniel D. Von Hoff, Donald R. VanDevanter
Previous work by our group has demonstrated that once episomes are formed (presumably by a deletion event5) they multimerize to form double minutes.6,7 If cells are carried further in passage, the extrachromosomally located double minutes can integrate into a chromosomal site. Once the amplified oncogenes or drug resistance genes are moved from the extrachromosomal (episome or DM) locations (where they are vulnerable to loss from the cell) to an intrachromosomal site, they no longer can be lost from the cell. Therefore, any strategy for elimination of extrachromosomal DNA (in the form of episomes or DMs) from the cell must rely on the amplified genes remaining in that extrachromosomal site(s).
Fatty acids, esters, and biogenic oil disinfectants: novel agents against bacteria
Published in Baylor University Medical Center Proceedings, 2023
Aruna Lamba, Jonathan Kopel, David Westenberg, Shubhender Kapila
Different microorganisms vary in their response to antiseptics and disinfectants. This is hardly surprising in view of their different cellular structure, composition, and physiology. Traditionally, microbial susceptibility to disinfectants has been classified based on these differences. In recent years, considerable progress has been made in understanding more fully the responses of different types of bacteria (Mycobacterium, nonsporulating bacteria, and bacterial spores) to antibacterial agents. As a result, resistance can either be a natural property of an organism (intrinsic) or acquired through mutation or through acquisition of plasmids (self-replicating, extrachromosomal DNA) or transposons (chromosomal or plasmid integrating, transmissible DNA cassettes).12–15 Intrinsic resistance is demonstrated by many gram-negative bacteria, bacterial spores, Mycobacterium, and Staphylococci. Resistance acquired through plasmid mediation is most widely associated with resistance to mercury compounds and other metallic salts. In recent years, acquired resistance to certain other types of biocides has been observed, notably in Staphylococci. As such, there is growing interest in investigating new disinfectants, such as fatty acid esters and biogenic oil vapors, to address this limitation.
Large extracellular vesicles carry most of the tumour DNA circulating in prostate cancer patient plasma
Published in Journal of Extracellular Vesicles, 2018
Tatyana Vagner, Cristiana Spinelli, Valentina R. Minciacchi, Leonora Balaj, Mandana Zandian, Andrew Conley, Andries Zijlstra, Michael R. Freeman, Francesca Demichelis, Subhajyoti De, Edwin M. Posadas, Hisashi Tanaka, Dolores Di Vizio
We questioned whether the amount of DNA in circulating L-EVs is proportional to disease progression in patients. We observed a pronounced variability in the amount of L-EV DNA from mCRPC patient plasma, with no correlation with disease progression. This might be due to technical limitations or intra-individual variability or to the small number of patient specimens examined in our study. This result is in apparent contrast with previous reports indicating that the number of L-EVs correlates with tumour progression [7]. However, an increased number of circulating L-EVs does not necessarily correspond to an increased DNA content, because perhaps not all L-EVs contain DNA. Furthermore, factors such as genomic instability [47,48], rather than EV number, might have a bigger impact on the amount of DNA in circulating EVs. Highly unstable tumour genomes would provide extrachromosomal DNA, which can then be loaded into L-EVs, ultimately resulting in a subpopulation highly enriched in DNA.
CRISPR/Cas: from adaptive immune system in prokaryotes to therapeutic weapon against immune-related diseases
Published in International Reviews of Immunology, 2020
Juan Esteban Garcia-Robledo, María Claudia Barrera, Gabriel J. Tobón
In 2005, three research articles reported evidence that CRISPR spacers sequences are similar to various exogenic elements [22, 35]. Bolotinda et al. demonstrated that the majority of the nucleotide sequences forming CRISPR spacers in different bacterial genomes have substantial homology with extrachromosomal DNA, mainly with sequences belonging to bacteriophage viruses and plasmids [31]. In the same year, a Spanish research group reported multiple conserved sequences with close homology to various bacteriophage and plasmid DNAs among 4500 different CRISPR spacers from 67 strains of 36 prokaryote genera [34].