China
Africa
Explore chapters and articles related to this topic
Mutagenic Consequences Of Chemical Reaction with DNA
Published in Philip L. Grover, Chemical Carcinogens and DNA, 2019
The most detailed study of the mechanism of repair has been made by Cole,116 who used trimethylpsoralen and E. coli. Cole has shown that the basic repair process involves the coordinate action of excision and recombination repair. The process is shown in Figure 5. The initial step is recognition of the cross-link and an incision by uvr endonuclease. Next, a second incision releases the end of the cross-link. Possibly the 5′ to 3′ exonuclease activity of DNA polymerase 1 can perform this step, possibly an unknown enzyme is involved. Cole goes on to demonstrate that, although the resulting gap cannot be filled by simple polymerization, it appears to be filled by recombination with a preexisting intact duplex elsewhere in the cell. Whether excision-deficient bacteria can survive any cross-links is uncertain. Bacteria deficient in both excision and recombination repair are considerably more sensitive than the corresponding single mutants, but this difference could relate to repair of monoadducts.
DNA-Binding Proteins and DNA-Synthesizing Enzymes in Eukaryotes
Published in Lubomir S. Hnilica, Chromosomal Nonhistone Proteins, 2018
Cells characteristically contain multiple forms of DNA polymerases. In prokaryotic cells, three activities are known: DNA polymerase I, II, and III.13,35 Eukaryotic cells have also at least three enzymes: DNA polymerase α, β, and γ.10–14 These DNA polymerases can easily be distinguished from one another by their size, chromatographic behavior, primer template specificities, optimal ion conditions, sensitivity to N-ethylmaleimide,10–14 and immunological comparison.14a A new type of polymerase activity called δ was recently described. This enzyme has properties similar to DNA polymerase a, but has associated exonuclease activity.36 The classification and some properties of eukaryotic DNA polymerases are listed in Table 1.
Antiviral Drugs
Published in Thomas T. Yoshikawa, Shobita Rajagopalan, Antibiotic Therapy for Geriatric Patients, 2005
Acyclovir is an analog of 2×-deoxyguanosine. It is transformed to the active acyclovir triphosphate form, first by monophosphorylation by the viral thymidine kinase present in infected cells, and then by di- and triphosphorylation by host cell enzymes. The concentration of acyclovir triphosphate is 40-100-fold higher in herpes virus infected cells than noninfected cells. Acyclovir triphosphate competitively inhibits viral DNA polymerase and results in termination of viral replication. It has minimal effect on human cellular DNA polymerase (1). Acyclovir activity is limited to the herpes virus group; the minimum inhibitory concentration (MIC)so is 0.1 nM for herpes simplex type 1, 0.4 |iM for herpes simplex type 2, and 2.6 pM against varicella zoster virus (VZV). The oral bioavailability of acyclovir is low, »10-30%, but is adequate for treatment of herpes simplex. Higher and more frequent dosing is needed for the treatment of VZV. Acyclovir is available in both oral (tablet and suspension) and intravenous forms.
Potential therapeutic targets for Mpox: the evidence to date
Published in Expert Opinion on Therapeutic Targets, 2023
Siddappa N Byrareddy, Kalicharan Sharma, Shrikesh Sachdev, Athreya S. Reddy, Arpan Acharya, Kaylee M. Klaustermeier, Christian L Lorson, Kamal Singh
VACV DNA genome replication is conducted by a holoenzyme consisting of multiple proteins [25]. An essential component of this holoenzyme is E9, the DNA-dependent DNA polymerase belonging to B family DNA polymerases. The MPXV genome encodes F8L (OPG71) [2], also a B family DNA-dependent DNA polymerase [27], which shares ~ 98% identity with VACV E9. The first B family DNA polymerase (RB69) structure showed an overall architecture of this class of enzymes [28]. This structure showed a canonical polymerase domain consisting of the Thumb, Palm, and Fingers subdomains, as seen in the structure of the Klenow Fragment (KF) of E. coli DNA polymerase I [29]. A notable difference between these polymerases is the relative position of the 3’ − 5’ exonuclease domain, which is ~ 180° opposite to that in KF relative to the polymerase active site. Subsequent crystal structures of the RB69 polymerase showed that residues of a β-hairpin positioned in the major groove of the template-primer played a role in the partitioning of primer to the 3’ − 5’ exonuclease site upon mismatch nucleotide incorporation [28,30–32]. Indeed, a resistance mutation on topologically similar β-hairpin in poxviruses’ DNA polymerase showed the relevance of the resistance mechanism of nucleotide analogs mediated by 3’ − 5’ exonuclease function (discussed below).
Gut microbiota modulate radiotherapy-associated antitumor immune responses against hepatocellular carcinoma Via STING signaling
Published in Gut Microbes, 2022
Zongjuan Li, Yang Zhang, Weifeng Hong, Biao Wang, Yixing Chen, Ping Yang, Jian Zhou, Jia Fan, Zhaochong Zeng, Shisuo Du
Total RNA was extracted from samples, purified, and their concentrations and purity determined by nanodrop nd-1000 (NanoDrop, Wilmington, DE, USA). The integrity of RNA was detected by Bioanalyzer 2100 (Agilent, CA, USA). Concentration >50 ng/μL, Rin value > 7.0, OD260/280 > 1.8, total RNA >1 μg met the downstream test. Oligo (DT) magnetic beads (Dynabeads, oligo (DT), Thermo Fisher, USA) were used to specifically capture mRNA with poly A. Captured mRNA was fragmented (NEBNext® Magnesium RNA Fragmentation Module, USA). Fragmented RNA was reversed to synthesize cDNA. Then, E. coli DNA polymerase I (NEB, USA) and RNase H (NEB, USA) were used for two strand synthesis. These DNA and RNA were transformed into DNA double strands. At the same time, the dUTP solution (Thermo Fisher, CA, USA) was added into the ends of the double stranded DNA to fill the flat ends. Then, an A deoxynucleotide was added at both ends to connect it with the connector with T deoxynucleotides at the end. The fragment was retrieved and purified by magnetic beads. The second strand was digested using the UDG enzyme (NEB, Ma, US), after which a library with fragment size of 300 bp ± 50 bp was formed by PCR. Finally, Illumina Novaseq™ 6000 (LC Bio Technology CO., Ltd. Hangzhou, China) was used to perform pair-end sequencing according to standard operations. The sequencing mode was PE150.
Repair mechanism of Wuwei Fuzheng Yijing formula in di-2-ethylhexyl phthalate-induced sperm DNA fragmentation in mice
Published in Pharmaceutical Biology, 2022
Chenming Zhang, Shiqi Wang, Zulong Wang, Qi Zhang, Rubing Chen, Hao Zhang, Zhong Hua, Sicheng Ma
After 60 d of intervention, nine mice were randomly selected from the control, DEHP and WFYH groups (three from each group) for transcriptomic analysis. According to the kit instructions, total RNA was isolated with the TRIzol reagent (Invitrogen, Carlsbad, CA). The quality of the isolated RNA was examined using an Agilent 2100 Bioanalyzer Platform (Agilent Technologies, Inc., Santa Clara, CA), and no RNase agarose gel electrophoresis was used for confirmation. The eukaryotic mRNA was aggregated with Oligo (dT) spheres, and the aggregated prokaryotic mRNA was eliminated with the Ribo-Zero™ magnetic kit (Epicenter, Moraga, CA). The aggregated mRNA fractions were split into short fractions by scrap buffer and were then converted into cDNA using arbitrary primers. Generation of the cDNA was performed using DNA polymerase I, RNase H and dNTPs along with the buffer. The cDNA was purified using the QIAQuick PCR isolation kit (Qiagen, Venlo, Netherlands), the ends were repaired, the base was introduced, and ligation of the cDNA was performed with the Illumina sequencing appendage. The linked products were sequenced by an Illumina Novaseq 6000.