Single-stranded circular DNA theranostics

Gordon and Kleinschmidt have described a new preparative technique for visualizing DNA by electron microscopy. This procedure, which is a modification of Hall's “mica substrate technique”, consists of the following steps: (a) K+ ions on the cleavage surface of native mica are exchanged for Al3+ ions by ion exchange. (b) The mica, with Al3+ in the exchange sites on the surface, is placed in a dilute aqueous salt solution of DNA for several minutes; during this period DNA becomes adsorbed on the surface. (c) The mica with adsorbed DNA is removed from the DNA solution, rinsed, dried and visualized for transmission electron microscopy by Hall's platinum pre-shadow replica technique.In previous studies of circular DNA by this technique, most of the molecules seen were either broken to linears or extensively tangled; in general, it was not possible to obtain suitably large samples of open extended molecules for contour length measurements.

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Characterization of circular DNA molecules from cotton plants with leaf curl disease

Pakistan Journal of Botany ◽

10.30848/pjb2019-1(29) ◽

2018 ◽

Vol 51 (1) ◽

Author(s):

Sohail Akhtar ◽

Muhammad Nouman Tahir ◽

Imran Amin ◽

Rana Binyamin ◽

Shahid Mansoor

Keyword(s):

Dna Molecules ◽

Circular Dna ◽

Cotton Plants ◽

Leaf Curl Disease ◽

Leaf Curl

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Faculty Opinions recommendation of Biochemical analysis of the yeast condensin Smc2/4 complex: an ATPase that promotes knotting of circular DNA.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1014200.193052 ◽

2003 ◽

Author(s):

Tatsuya Hirano

Keyword(s):

Biochemical Analysis ◽

Circular Dna

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Mechanism of Hepatitis B Virus cccDNA Formation

Viruses ◽

10.3390/v13081463 ◽

2021 ◽

Vol 13 (8) ◽

pp. 1463

Author(s):

Lei Wei ◽

Alexander Ploss

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Medical Problem ◽

Circular Dna ◽

Critical Step ◽

Hbv Cccdna ◽

Double Stranded Dna ◽

Cellular Environment ◽

B Virus ◽

Comprehensive Picture

Hepatitis B virus (HBV) remains a major medical problem affecting at least 257 million chronically infected patients who are at risk of developing serious, frequently fatal liver diseases. HBV is a small, partially double-stranded DNA virus that goes through an intricate replication cycle in its native cellular environment: human hepatocytes. A critical step in the viral life-cycle is the conversion of relaxed circular DNA (rcDNA) into covalently closed circular DNA (cccDNA), the latter being the major template for HBV gene transcription. For this conversion, HBV relies on multiple host factors, as enzymes capable of catalyzing the relevant reactions are not encoded in the viral genome. Combinations of genetic and biochemical approaches have produced findings that provide a more holistic picture of the complex mechanism of HBV cccDNA formation. Here, we review some of these studies that have helped to provide a comprehensive picture of rcDNA to cccDNA conversion. Mechanistic insights into this critical step for HBV persistence hold the key for devising new therapies that will lead not only to viral suppression but to a cure.

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Excision of Oxidatively Generated Guanine Lesions by Competitive DNA Repair Pathways

International Journal of Molecular Sciences ◽

10.3390/ijms22052698 ◽

2021 ◽

Vol 22 (5) ◽

pp. 2698

Author(s):

Vladimir Shafirovich ◽

Nicholas E. Geacintov

Keyword(s):

Excision Repair ◽

Dna Lesions ◽

Dna Templates ◽

Circular Dna ◽

Damage Sensing ◽

Cell Extracts ◽

Dna Base ◽

Nucleotide Excision ◽

Repair Pathways ◽

Cellular Dna

The base and nucleotide excision repair pathways (BER and NER, respectively) are two major mechanisms that remove DNA lesions formed by the reactions of genotoxic intermediates with cellular DNA. It is generally believed that small non-bulky oxidatively generated DNA base modifications are removed by BER pathways, whereas DNA helix-distorting bulky lesions derived from the attack of chemical carcinogens or UV irradiation are repaired by the NER machinery. However, existing and growing experimental evidence indicates that oxidatively generated DNA lesions can be repaired by competitive BER and NER pathways in human cell extracts and intact human cells. Here, we focus on the interplay and competition of BER and NER pathways in excising oxidatively generated guanine lesions site-specifically positioned in plasmid DNA templates constructed by a gapped-vector technology. These experiments demonstrate a significant enhancement of the NER yields in covalently closed circular DNA plasmids (relative to the same, but linearized form of the same plasmid) harboring certain oxidatively generated guanine lesions. The interplay between the BER and NER pathways that remove oxidatively generated guanine lesions are reviewed and discussed in terms of competitive binding of the BER proteins and the DNA damage-sensing NER factor XPC-RAD23B to these lesions.

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Hepatitis B Core-Related Antigen as Surrogate Biomarker of Intrahepatic Hepatitis B Virus Covalently-Closed-Circular DNA in Patients with Chronic Hepatitis B: A Meta-Analysis

Diagnostics ◽

10.3390/diagnostics11020187 ◽

2021 ◽

Vol 11 (2) ◽

pp. 187

Author(s):

Gian Paolo Caviglia ◽

Angelo Armandi ◽

Chiara Rosso ◽

Davide Giuseppe Ribaldone ◽

Rinaldo Pellicano ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Hepatitis B Surface Antigen ◽

Meta Analysis ◽

Circular Dna ◽

Non Invasive ◽

Hbv Cccdna ◽

B Virus ◽

Chronic Hbv ◽

Intrahepatic Hbv

Hepatitis B virus (HBV) covalently-closed-circular (ccc)DNA is the key molecule responsible for viral persistence within infected hepatocytes. The evaluation of HBV cccDNA is crucial for the management of patients with chronic HBV infection and for the personalization of treatment. However, the need for liver biopsy is the principal obstacle for the assessment of intrahepatic HBV cccDNA. In the last decade, several studies have investigated the performance of hepatitis B core-related antigen (HBcrAg) as a surrogate of HBV cccDNA amount in the liver. In this meta-analysis, we collected 14 studies (1271 patients) investigating the correlation between serum HBcrAg and intrahepatic HBV cccDNA. Serum HBcrAg showed a high correlation with intrahepatic HBV cccDNA (r = 0.641, 95% confidence interval (CI) 0.510–0.743, p < 0.001). In a head-to-head comparison, we observed that the performance of HBcrAg was significantly superior to that of hepatitis B surface antigen (r = 0.665 vs. r = 0.475, respectively, p < 0.001). Subgroup analysis showed that the correlation between HBcrAg and intrahepatic HBV cccDNA was high, both in hepatitis B e antigen-positive and -negative patients (r = 0.678, 95% CI 0.403–0.840, p < 0.001, and r = 0.578, 95% CI 0.344–0.744, p < 0.001, respectively). In conclusion, the measurement of serum HBcrAg qualifies as a reliable non-invasive surrogate for the assessment of an intrahepatic HBV cccDNA reservoir.

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