Absolute configuration of a ribonucleic acid adduct formed in vivo by metabolism of benzo[a]pyrene.
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Benzopyrenes↗
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Results for “Circular RNA”
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Primer terminus recognition and highly processive replication by Epstein-Barr virus DNA polymerase.
The Epstein-Barr virus (EBV) DNA polymerase is essential for viral DNA replication in the lytic phase of the EBV life cycle. It efficiently extends RNA primers on the template DNA, suggesting the possible involvement of the EBV DNA polymerase in synthesizing Okazaki fragments from RNA primers on the lagging strand template. Competition experiments revealed that the EBV DNA polymerase had significantly higher affinity for primer termini hybridized to the template DNA than for the single-stranded DNA template or the single-stranded primer itself. ATP was not required either for primer terminus recognition or for sustainment of polymerization. The stimulation of the enzyme by (NH4)2SO4 was dependent on the template/primers utilized. These observations suggest that the primary and secondary structure of the template/primers are important factors for primer terminus recognition by the EBV DNA polymerase. The enzyme elongated synthetic RNA primer annealed to circular single-stranded M13 DNA coated with Escherichia coli single-stranded DNA-binding protein without dissociation. The processivity of the EBV DNA polymerase was strikingly high (greater than 7200 nucleotides) and the rate of polymerization was 12 nucleotides/s per polymerase molecule. The high processing capacity is a desirable feature in the synthesis of multiple copies of the EBV genome in rolling-circle DNA replication.
Adenosine Triphosphate↗
In vitro infection of human peripheral blood mononuclear cells by a defective hepatitis B virus with a deletion in the PreS1 region of the viral genome.
Previously, we identified a defective hepatitis B virus (HBV) which contains a 183 nucleotide deletion in the PreS1 region of the viral genome affecting the S gene promoter in sera from hepatitis B surface antigen (HBsAg)-negative patients with serum HBV-DNA. The aim of this study was to analyse the infectivity of this mutant. Peripheral blood mononuclear cells (PBMC) from a healthy donor were incubated with serum samples from 2 HBsAg-negative patients with serum HBV-DNA (infected with wild-type and deletion mutant HBV), from an HBsAg carrier (infected with wild-type HBV) and from a healthy donor. After 1 week, HBV-DNA was detected by polymerase chain reaction (PCR) in all supernatants and cells incubated with the HBV-DNA-positive inocula. DNase and trypsin pretreatment confirmed intracellular localization of HBV-DNA in cells. HBV-RNA and covalently closed circular HBV-DNA were also detected in PBMC, indicating that the viral DNA infecting these cells was transcriptionally active. Deletion mutant and wild-type HBV were detected in the supernatants and cells infected with the two HBsAg-negative sera, while only wild-type HBV was detected in the supernatant and cells incubated with the serum from the HBsAg-carrier. In conclusion, this HBV deletion mutant can infect, replicate and release viral particles in in vitro infected PBMC.
Cells, Cultured↗
Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.
Tumor-specific antigens, also known as neoantigens, have potential utility in anti-cancer immunotherapy, including immune checkpoint blockade (ICB), neoantigen-specific T cell receptor-engineered T (TCR-T), chimeric antigen receptor T (CAR-T), and therapeutic cancer vaccines (TCVs). After recognizing presented neoantigens, the immune system becomes activated and triggers the death of tumor cells. Neoantigens may be derived from multiple origins, including somatic mutations (single nucleotide variants, insertions/deletions, and gene fusions), circular RNAs, alternative splicing, RNA editing, and polymorphic microbiomes. An increasing amount of bioinformatics tools and algorithms are being developed to predict tumor neoantigens derived from different sources, which may require inputs from different multi-omics data. In addition, calculating the peptide-major histocompatibility complex (MHC) affinity can aid in selecting putative neoantigens, as high binding affinities facilitate antigen presentation. Based on these approaches and previous experiments, many resources have been developed to reveal the landscape of tumor neoantigens across multiple cancer types. Herein, we summarize these tools, algorithms, and resources to provide an overview of computational analysis for neoantigen discovery and prioritization, as well as the future development of potential clinical utilities in this field.
Humans↗
Repetitive DNA elements characteristic of pathogenic Entamoeba histolytica strains can also be detected after polymerase chain reaction in a cloned nonpathogenic strain.
Strains of Entamoeba histolytica which were isolated from symptomatic patients and which possess a characteristic pathogenic isoenzyme pattern (zymodeme) have extrachromosomal circular DNA molecules containing RNA genes and clusters of tandemly reiterated PvuI elements. The nucleotide sequence of comparable reiterated BamHI elements present in amebae with nonpathogenic zymodemes differs from that found in pathogenic ones. By using the polymerase chain reaction, it was demonstrated that the cloned, nonpathogenic E. histolytica strain SAW 1734R clAR also contains one or few of the tandemly repeated DNA PvuI elements characteristic of the pathogenic amebae. Sequences were detected by hybridization with the P-145 probe after in vitro amplification. Because of technical difficulties, it was impossible to resolve whether single copies of the nonpathogenic BamHI repetitive elements are present in pathogenic amebae. Our findings suggest that in the nonpathogenic amebae, the signal to start amplifying the PvuI-type elements may be induced during the process of elimination of bacterial associates from their growth environment.
Animals↗
Baboon endogenous virus genome. I. Restriction enzyme map of the unintegrated DNA genome of a primate retrovirus.
A detailed restriction map was deduced for the genome of an endogenous retrovirus of a higher primate, that of baboon. The cleavage sites for 12 restriction enzymes were mapped. The unintegrated linear viral DNA intermediate that is produced by infection of permissive cells with baboon endogenous virus was isolated. Hybridization with a strong-stop complementary DNA probe demonstrated presence of a terminal repetition in the linear viral DNA. The positions of restriction sites for two particular enzymes, SmaI and XhoI, near each end were consistent with this result and indicated that the length of the repetition is 0.55 +/- 0.01 kilobase. The linear viral DNA had a unique restriction map indicating that it is not a set of random circular permutations of the RNA genome. From hybridization with a 3'-specific probe, the DNA restriction map was aligned relative to the 5'-to-3' orientation of the viral RNA. We observed a minor heterogeneity in a BamHI recognition site 1.95 kilobases from the right end of the linear map.
Animals↗
Restriction endonuclease mapping of linear unintegrated proviral DNA of bovine leukemia virus.
A detailed restriction map was deduced for the genome of the exogenous bovine leukemia virus. The cleavage sites for nine restriction enzymes were mapped. The unintegrated linear viral DNA intermediate that is produced by infection of permissive cells with bovine leukemia virus was isolated. The linear viral DNA had a unique restriction map, indicating that it is not a set of random circular permutations of the RNA genome. From hybridization with a 3'-enriched probe, the DNA restriction map was aligned relative to the 5'-to-3' orientation of the viral RNA. Restriction enzyme analysis of integrated bovine leukemia virus information present in animals with enzootic bovine leukosis provided evidence for the existence of genetic variants of the virus.
Chromosome Mapping↗
A single antigenomic open reading frame of the hepatitis delta virus encodes the epitope(s) of both hepatitis delta antigen polypeptides p24 delta and p27 delta.
On the basis of the complete nucleotide sequence of the single-stranded, covalently closed circular hepatitis delta virus RNA genome (K.-S. Wang, Q.-L. Choo, A. J. Weiner, J.-H. Ou, R. C. Najarian, R. M. Thayer, G. T. Mullenbach, K. J. Denniston, J. L. Gerin, and M. Houghton, Nature [London] 323:508-514, 1986 [Author's correction, 328:456, 1987]), five long open reading frames (ORFs) encoding polypeptides containing a methionine proximal to the amino terminus were expressed in bacteria. Only polypeptides encoded by the antigenomic ORF5 cross-reacted with antisera obtained from patients with hepatitis delta virus infections. Immunological analysis of viral extracts and the recombinant ORF5 polypeptides synthesized in bacteria and yeast cells revealed that ORF5 encodes the immunogenic epitope(s) shared by both hepatitis delta viral polypeptides p27 delta and p24 delta and probably represents the complete structural gene for p27 delta and p24 delta. We also present evidence that ORF5 encodes the hepatitis delta antigen, an antigen originally found in the nuclei of hepatocytes of infected individuals (M. Rizzetto, M. G. Canese, S. Arico, O. Crivelli, F. Bonino, C. G. Trepo, and G. Verme, Gut 18:997-1003, 1977). A comparison of the primary structure of the predicted hepatitis delta antigen polypeptides with that of the core antigen of the hepatitis B virus shows that these polypeptides are very dissimilar.
Amino Acid Sequence↗
Molecular phylogenetic analyses indicate a wide and ancient radiation of African hepatitis delta virus, suggesting a deltavirus genus of at least seven major clades.
Hepatitis D virus (HDV) is a satellite of hepatitis B virus (HBV) for transmission and propagation and infects nearly 20 million people worldwide. The HDV genome is a compact circular single-stranded RNA genome with extensive intramolecular complementarity. Despite its different epidemiological and pathological patterns, the variability and geographical distribution of HDV are limited to three genotypes and two subtypes that have been characterized to date. Phylogenetic reconstructions based on the delta antigen gene and full-length genome sequence data show an extensive and probably ancient radiation of African lineages, suggesting that the genetic variability of HDV is much more complex than was previously thought, with evidence of additional clades. These results relate the geographic distribution of HDV more closely to the genetic variability of its helper HBV.
Adolescent↗
The molecular biology of hepatitis delta virus.
Hepatitis delta virus (HDV) contains a circular, viroid-like RNA genome, the only animal viral RNA of its kind. It possesses a ribozyme activity, which can autocatalytically cleave and ligate itself. The ribozyme has a unique structural requirement different from other known ribozymes. HDV RNA undergoes RNA-dependent RNA replication via a double rolling circle mechanism, which is probably mediated by cellular RNA polymerase II, utilizing modified cellular transcription machineries. HDV RNA encodes a single protein, hepatitis delta antigen, which is a nuclear, RNA-binding phosphoprotein and required for viral RNA replication. During replication, HDV RNA undergoes a specific RNA editing event to extend its open reading frame and produce a longer, isoprenylated delta antigen, which suppresses RNA replication and initiates viral particle assembly. Ribozyme, cell-mediated RNA-dependent RNA replication, and RNA editing are some of the unique properties and unresolved issues of the molecular biology of HDV.
Animals↗
Scarce adenylation in bacteriophage T4 mRNAs.
The degradation of mRNA is crucial for the rapid shift of bacteriophage T4 gene expression from early to late. The present study was conducted to investigate whether T4 mRNA is polyadenylated or not, because polyadenylation is known to facilitate the degradation of mRNA in Escherichia coli cells. Total RNA extracted from T4-infected cells was subjected to self-circularization or intermolecular ligation by T4 RNA ligase, and a region containing the 3'-5' junction was amplified by RT-PCR. Cloning and sequencing as well as the length distribution of amplified DNA fragments revealed no adenines at the 3'-ends of uvsY and soc RNAs. The present result suggests that T4 mRNA is not significantly adenylated.
Bacteriophage T4↗
Clevudine for the treatment of chronic hepatitis B virus infection.
Chronic hepatitis B virus (HBV) infection is a major health problem that is responsible for < or = 1 million deaths and 500,000 cases of hepatocellular carcinoma worldwide each year. Drugs that are currently approved by the FDA for the treatment of chronic HBV consist of two groups: the immunomodulators, such as conventional IFN-alpha and pegylated IFN-alpha2a; and nucleoside/nucleotide analogues, such as lamivudine, adefovir dipivoxil and entecavir. However, due to the limitations of these agents, newer agents with improved efficacy are currently being developed. One nucleoside/nucleotide analogue that is drawing a wide range of interest is clevudine, which is an analogue of the unnatural beta-L configuration. In the woodchuck hepatitis virus (WHV), clevudine 10 mg/kg has proven to be effective in suppressing viral replication with < or = 9 log10 decreases in WHV. At this dose, a significant reduction of intrahepatic WHV RNA and covalently closed circular WHV DNA levels can also be observed. Treatment with clevudine 10 mg/kg can confer additional antiviral benefit in the form of a more sustained reduction in WHV replication, serum woodchuck hepatitis surface antigen and intrahepatic woodchuck hepatitis core antigen expression following the withdrawal of clevudine. In humans, clevudine 10, 50, 100 or 200 mg/day for 28 days can reduce the median HBV DNA by -2.5, -2.7, -3 and -2.6 log10, respectively. More importantly, this suppression of antiviral activity is maintained at 12 and 24 weeks post treatment. Based on the early results of clevudine, more large-scale human studies with clevudine monotherapy or combination therapy is eagerly awaited.
Animals↗
Genesis and wanderings: origins and migrations in asymmetrically replicating mitochondrial DNA.
Mammalian mitochondria maintain a small circular genome that encodes RNA and polypeptides that are essential for the generation of ATP through oxidative phosphorylation. The mechanism of replication of mammalian mitochondrial DNA (mtDNA) has recently been a topic of controversy. New evidence has led to a modified strand-displacement model that reconciles much of the current data. This revision stems from a new appreciation for alternative light-strand origins. We consider here some of the potential mechanisms for light-strand origin initiation. We also consider further the susceptibility of branch migration within replicating mtDNA molecules. The existence of alternative light-strand origins and a propensity for branch migration in replicating mtDNA molecules exposes a new array of possible configurations of mtDNA. The assortment and assignment of these forms is relevant to the interpretation of experimental data and may also yield insight into the molecular basis of replication errors.
Animals↗
[CIRCULAR DICHROISM OF TRANSFERRED RIBONUCLEIC ACID IN AQUEOUS AND ALCOHOL SOLUTIONS].
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Alcohols↗
Co-inoculation with two non-infectious cDNA copies of potato spindle tuber viroid (PSTVd) leads to the appearance of novel fully infectious variants.
Potato spindle tuber viroid (PSTVd) is one of the smallest (about 360 nt) infectious plant agents. It is composed of a single-stranded circular non-coding RNA molecule. In the course of previous passage experiments with two intermediate PSTVd variants I2 and I4, three non-infectious clones (I2-50, I4-37 and I4 VI-17) were found. When inoculated separately as cDNAs on tomato "Rutgers" test plants these variants did not induce any visible disease symptoms and did not produce progeny. The presence of such non-infectious variants raises several questions about their origin and biology and to answer them, mixed co-infections with cDNA copies of two non-infectious variants (I2-50, I4-37) were performed. PSTVd infection was observed in seven out of 30 inoculated plants. The progeny isolated from three separate plants contained novel variants, together with the parental I2 and I4 sequences. It is conceivable that the appearance of repaired PSTVd molecules, clearly capable of cell-to-cell movement leading to the systemic infection, results from recombination events. An analysis of the recombinant molecules and comparison with databases identified the specific sites responsible for the restricted infectivity of the I2-50 and I4-37 PSTVd variants. In parallel experiments in which (+) strand PSTVd infectious transcripts were used, no recombinants were observed, and the original I2-50 and I4-37 non-infectious sequences were not detected in the progeny.
DNA, Complementary↗
A mode of action of RNase CI toward the various RNAs.
A mode of action of RNase CI toward the various native RNAs was examined. The mixture of tRNA from Thermus thermophilus HB8 were exhaustively cleaved by RNase CI to produce 90% of acid-soluble fraction. Among the minor nucleotides s2T were recognized by this enzyme. RNase CI generates a linear viroid molecule by introducing one single nick into viroid circular molecule. Double stranded RNA from RNA virus, such as Cytoplasmic polyhedrosis virus (CPV) from silk worm, was cleaved at some specific sites to produce more than ten of the discrete bands electrophoretically.
Animals↗
Structural studies of encephalomyocarditis virus RNA both in situ and in free solution.
The secondary structure of encephalomyocarditis (EMC) virus RNA has been studied in situ and in free solution by absorbance-temperature relationships and by circular dichroism (CD). Extracted EMC virus RNA melts reversibly and has a hypochromicity of about 20%; analysis of CD spectra and formaldehyde treatment suggests that approx. 60% of the nucleotides are involved in base-pairing at 25 degrees C. It is shown that the RNA within the virus particle is less structured than when it exists in free solution, being partially stabilized by capsid protein against melting until the virion is disrupted to release the intact RNA. Upon clarification to remove denatured capsid protein, the released RNA gives a melting profile identical with that of phenol-extracted virus RNA. The results suggest that the intact structure of the virus is dependent upon intimate non-covalent bonds between RNA and protein together with hydrophobic bonds between the protein subunits.
Circular Dichroism↗
Hybridization of complementary and homologous peptide nucleic acid oligomers to a guanine quadruplex-forming RNA.
Peptide nucleic acid (PNA) oligomers targeted to guanine quadruplex-forming RNAs can be designed in two different ways. First, complementary cytosine-rich PNAs can hybridize by the formation of Watson-Crick base pairs, resulting in hybrid PNA-RNA duplexes. Second, guanine-rich homologous PNAs can hybridize by the formation of G tetrads, resulting in hybrid PNA-RNA quadruplexes. UV thermal denaturation, circular dichroism, and fluorescence spectroscopy experiments were used to compare these two recognition modes and revealed 1:1 duplex formation for the complementary PNA and 2:1 (PNA2-RNA) quadruplex formation for the homologous PNA. Both hybrids were very stable, and hybridization was observed at low nanomolar concentrations. Hybrid quadruplex formation was equally efficient regardless of the PNA strand polarity, indicating a lack of interaction between the loop nucleobases on the PNA and RNA strands. The implications of this finding on sequence specificity as well as methods to improve affinity are also discussed.
Animals↗