Acquisition of telomere repeat sequences by transfected DNA integrated at the site of a chromosome break.

Previous analysis of plasmid DNA transfected into 108 cell clones demonstrated extensive polymorphism near the integration site in one clone. This polymorphism was apparent by Southern blot analysis as diffuse bands that extended over 30 kb. In the present study, nucleotide sequence analysis of cloned DNA from the integration site revealed telomere repeat sequences at the ends of the integrated plasmid DNA. The telomere repeat sequences at one end were located at the junction between the plasmid and cell DNA. The telomere repeat sequences at the other end were located in the opposite orientation in the polymorphic region and were shown by digestion with BAL 31 to be at the end of the chromosome. Telomere repeat sequences were not found at this location in the plasmid or parent cell DNA. Although the repeat sequences may have been acquired by recombination, a more likely explanation is that they were added to the ends of the plasmid by telomerase before integration. Comparison of the cell DNA before and after integration revealed that a chromosome break had occurred at the integration site, which was shown by fluorescent in situ hybridization to be located near the telomere of chromosome 13. These results demonstrate that chromosome breakage and rearrangement can result in interstitial telomere repeat sequences within the human genome. These sequences could promote genomic instability, because short repeat sequences can be recombinational hotspots. The results also show that DNA rearrangements involving telomere repeat sequences can be associated with chromosome breaks. The introduction of telomere repeat sequences at spontaneous or ionizing radiation-induced DNA strand breaks may therefore also be a mechanism of chromosome fragmentation.

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Mechanistic insights into the R-loop formation and cleavage in CRISPR-Cas12i1

Nature Communications ◽

10.1038/s41467-021-23876-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Bo Zhang ◽

Diyin Luo ◽

Yu Li ◽

Vanja Perčulija ◽

Jing Chen ◽

...

Keyword(s):

Genome Editing ◽

Dna Cleavage ◽

Binary Complex ◽

Loop Formation ◽

Dna Duplex ◽

Target Dna ◽

Before And After ◽

Dna Strand ◽

Type V ◽

Functionally Diverse

AbstractCas12i is a newly identified member of the functionally diverse type V CRISPR-Cas effectors. Although Cas12i has the potential to serve as genome-editing tool, its structural and functional characteristics need to be investigated in more detail before effective application. Here we report the crystal structures of the Cas12i1 R-loop complexes before and after target DNA cleavage to elucidate the mechanisms underlying target DNA duplex unwinding, R-loop formation and cis cleavage. The structure of the R-loop complex after target DNA cleavage also provides information regarding trans cleavage. Besides, we report a crystal structure of the Cas12i1 binary complex interacting with a pseudo target oligonucleotide, which mimics target interrogation. Upon target DNA duplex binding, the Cas12i1 PAM-interacting cleft undergoes a remarkable open-to-closed adjustment. Notably, a zipper motif in the Helical-I domain facilitates unzipping of the target DNA duplex. Formation of the 19-bp crRNA-target DNA strand heteroduplex in the R-loop complexes triggers a conformational rearrangement and unleashes the DNase activity. This study provides valuable insights for developing Cas12i1 into a reliable genome-editing tool.

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Fragmentation of Plasmid DNA Produced by Gamma Radiation: A Theoretical Approach

ISRN Biophysics ◽

10.5402/2012/725350 ◽

2012 ◽

Vol 2012 ◽

pp. 1-6

Author(s):

R. A. S. Silva ◽

J. D. T. Arruda-Neto ◽

L. Nieto

Keyword(s):

Plasmid Dna ◽

Fragment Size ◽

Power Laws ◽

Double Strand Breaks ◽

Strand Breaks ◽

Starting Point ◽

Dna Strands ◽

High Let ◽

Fragment Distribution ◽

Dna Strand

Breaks in DNA, resulting in fragmented parts, can be produced by ionizing radiation which, in turn, is the starting point in the search for novel physical aspects of DNA strands. Double-strand breaks in particular cause disruption of the DNA strand, splitting it into several fragments. In order to study effects produced by radiation in plasmid DNA, a new simple mechanical model for this molecule is proposed. In this model, a Morse-like potential and a high-LET component are used to describe the DNA-radiation interaction. Two power laws, used to fit results of the model, suggest that, firstly, distribution of fragment size is nonextensive and, secondly, that a transition phase is present in the DNA fragment distribution pattern.

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Screen for Potential Candidate Alternatives of Sargentodoxa cuneata from Its Six Adulterants Based on Their Phenolic Compositions and Antioxidant Activities

International Journal of Molecular Sciences ◽

10.3390/ijms20215427 ◽

2019 ◽

Vol 20 (21) ◽

pp. 5427 ◽

Cited By ~ 4

Author(s):

Lingguang Yang ◽

Peipei Yin ◽

Xinxin Cao ◽

Yujun Liu

Keyword(s):

Plasmid Dna ◽

Antioxidant Activities ◽

Peroxyl Radicals ◽

Potential Candidate ◽

Total Phenols ◽

Polygonum Cuspidatum ◽

Caffeoylquinic Acids ◽

Phenolic Contents ◽

Hydroxybenzoic Acids ◽

Dna Strand

Daxueteng, the liana stem of Sargentodoxa cuneata, is a widely used Traditional Chinese Medicine facing the overflow of its commercial adulterants. A method for discriminating adulterants and screening potential candidate alternatives of S. cuneata was thus established. Total phenols and flavonoids of S. cuneata and its six adulterants and their abilities to scavenge DPPH• and ABTS•+, to absorb peroxyl radicals (ORAC), and to inhibit AAPH-induced supercoiled plasmid DNA strand scission were comprehensively assessed. Polygonum cuspidatum and Bauhinia championii, two of the six adulterants of S. cuneate, shared considerably higher antioxidant activities as well as phenolic contents and, therefore, were considered as potential candidate alternatives. Phenolic compositions of the two potential candidate alternatives and S. cuneata itself were further determined by UPLC-QTOF-MS/MS. Totally 38 phenolics, including four hydroxybenzoic acids, two tyrosols, two caffeoylquinic acids, seven flavanol or its oligomers, two lignans, three hydroxycinnamic acids, six stilbenes, seven anthraquinones, and five flavanones were determined from three species. Furthermore, contents of different phenolic categories were semi-quantified and the major antioxidant contributors of S. cuneata and the two potential candidate alternatives were subsequently determined. It is concluded that tyrosols and caffeoylquinic acids were unique categories making great antioxidant contributions in S. cuneata and thus were considered as effective biomarkers in distinguishing its potential candidate alternatives.

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Nucleotide-sequence analysis indicates that a DNA plasmid in a diseased isolate of Ophiostoma novo-ulmi is derived by recombination between two long repeat sequences in the mitochondrial large subunit ribosomal RNA gene

Current Genetics ◽

10.1007/bf00311881 ◽

1995 ◽

Vol 28 (1) ◽

pp. 54-59 ◽

Cited By ~ 26

Author(s):

S. N. Abu-Amero ◽

N. W. Charter ◽

K. W. Buck ◽

C. M. Brasier

Keyword(s):

Sequence Analysis ◽

Nucleotide Sequence ◽

Ribosomal Rna ◽

Large Subunit ◽

Nucleotide Sequence Analysis ◽

Ribosomal Rna Gene ◽

Repeat Sequences ◽

Dna Plasmid ◽

Large Subunit Ribosomal Rna

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Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

Biochemical Society Transactions ◽

10.1042/bst0370023 ◽

2009 ◽

Vol 37 (1) ◽

pp. 23-28 ◽

Cited By ~ 80

Author(s):

Shiraz Ali Shah ◽

Niels R. Hansen ◽

Roger A. Garrett

Keyword(s):

Plasmid Dna ◽

Genomic Dna ◽

Inhibitory Mechanism ◽

Archaeal Viruses ◽

Extrachromosomal Elements ◽

Dna Strand ◽

High Level

Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles, the chromosomal spacers show a high level of matches (∼30%) with viral or plasmid genomes. Moreover, their distribution along the virus/plasmid genomes, as well as their DNA strand specificity, appear to be random. This is consistent with the hypothesis that chromosomal spacers are taken up directly and randomly from virus and plasmid DNA and that the spacer transcripts target the genomic DNA of the extrachromosomal elements and not their transcripts.

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Influence of Acute Exercise on DNA Repair and PARP Activity before and after Irradiation in Lymphocytes from Trained and Untrained Individuals

International Journal of Molecular Sciences ◽

10.3390/ijms20122999 ◽

2019 ◽

Vol 20 (12) ◽

pp. 2999 ◽

Cited By ~ 5

Author(s):

Maria Moreno-Villanueva ◽

Andreas Kramer ◽

Tabea Hammes ◽

Maria Venegas-Carro ◽

Patrick Thumm ◽

...

Keyword(s):

Physical Activity ◽

Dna Damage ◽

Dna Repair ◽

Immune Cells ◽

Acute Exercise ◽

Dna Strand Breaks ◽

Strand Breaks ◽

Before And After ◽

Radiation Induced ◽

Dna Strand

Several studies indicate that acute exercise induces DNA damage, whereas regular exercise increases DNA repair kinetics. Although the molecular mechanisms are not completely understood, the induction of endogenous reactive oxygen species (ROS) during acute exhaustive exercise due to metabolic processes might be responsible for the observed DNA damage, while an adaptive increase in antioxidant capacity due to regular physical activity seems to play an important protective role. However, the protective effect of physical activity on exogenously induced DNA damage in human immune cells has been poorly investigated. We asked the question whether individuals with a high aerobic capacity would have an enhanced response to radiation-induced DNA damage. Immune cells are highly sensitive to radiation and exercise affects lymphocyte dynamics and immune function. Therefore, we measured endogenous and radiation-induced DNA strand breaks and poly (ADP-ribose) polymerase-1 (PARP1) activity in peripheral blood mononuclear cells (PBMCs) from endurance-trained (maximum rate of oxygen consumption measured during incremental exercise V’O2max > 55 mL/min/kg) and untrained (V’O2max < 45 mL/min/kg) young healthy male volunteers before and after exhaustive exercise. Our results indicate that: (i) acute exercise induces DNA strand breaks in lymphocytes only in untrained individuals, (ii) following acute exercise, trained individuals repaired radiation-induced DNA strand breaks faster than untrained individuals, and (iii) trained subjects retained a higher level of radiation-induced PARP1 activity after acute exercise. The results of the present study indicate that increased aerobic fitness can protect immune cells against radiation-induced DNA strand breaks.

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Detection of DNA strand breaks by comet assay in sputum leucocytes of bitumen-exposed workers: A pilot study

Human & Experimental Toxicology ◽

10.1177/0960327109359635 ◽

2010 ◽

Vol 29 (9) ◽

pp. 721-729 ◽

Cited By ~ 3

Author(s):

B. Marczynski ◽

M. Raulf-Heimsoth ◽

B. Pesch ◽

B. Kendzia ◽

HU Käfferlein ◽

...

Keyword(s):

Dna Damage ◽

Comet Assay ◽

Rank Correlation ◽

Dna Strand Breaks ◽

Strand Breaks ◽

Blood Lymphocytes ◽

Exposed Workers ◽

Before And After ◽

Dna Strand ◽

Post Shift

DNA strand breaks were determined in leucocytes of induced sputum (IS) and compared with DNA strand breaks in blood lymphocytes from 42 bitumen-exposed workers pre and post shift. Comet assay results were expressed in arbitrary units based on visual scoring (sputum leucocytes) and Olive tail moment (OTM, blood lymphocytes). DNA damage in IS leucocytes was overall high but did not change during shift. Level of DNA strand breaks in IS samples correlated with total cell count and neutrophil content (Spearman rank correlation coefficient rs = 0.47, p = 0.001, rs= 0.48, p = 0.001, respectively) and with IL-8 concentration before and after shift (rs = 0.31, P = 0.048, and rs = 0.43, P = 0.005). DNA damage in IS was not associated with DNA strand breaks in blood lymphocytes (rs = —0.04, p = 0.802 before shift, rs = 0.27, p = 0.088 after shift). A higher level of DNA strand breaks was measured in blood lymphocytes before shift (median OTM 1.7 before and 1.3 after shift, p = 0.023). A strong correlation was found between the number of neutrophils and IL-8 concentration in IS before and after shift (rs = 0.77 and rs= 0.75, p < 0.001). This study showed an association between genotoxic and inflammatory effects in the lower airways and compared simultaneously DNA strand breaks in IS and blood of bitumen-exposed workers.

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