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Nucleic Acids Research Dec 1996A series of sequences of the DNA analog bicyclo-DNA, 6-12 nucleotides in length and containing all four natural nucleobases, were prepared and their Watson-Crick pairing...
A series of sequences of the DNA analog bicyclo-DNA, 6-12 nucleotides in length and containing all four natural nucleobases, were prepared and their Watson-Crick pairing properties with complementary RNA and DNA, as well as in its own series, were analyzed by UV-melting curves and CD-spectroscopy. The results can be summarized as follows: bicyclo-DNA forms stable Watson-Crick duplexes with complementary RNA and DNA, the duplexes with RNA generally being more stable than those with DNA. Pyrimidine-rich bicyclo-DNA sequences form duplexes of equal or slightly increased stability with DNA or RNA, whereas purine-rich sequences show decreased affinity to complementary DNA and RNA when compared with wild-type (DNA-DNA, DNA-RNA) duplexes. In its own system, bicyclo-DNA prefers antiparallel strand alignment and strongly discriminates for base mismatches. Duplexes are always inferior in stability compared with the natural ones. A detailed analysis of the thermodynamic properties was performed with the sequence 5'-GGATGGGAG-3'x 5'-CTCCCATCC-3' in both backbone systems. Comparison of the pairing enthalpy and entropy terms shows an enthalpic advantage for DNA association (delta deltaH = -18 kcal x (mol)-1)) and an entropic advantage for bicyclo-DNA association (delta deltaS = 49 cal x K(-1) x mol(-1), leading to a delta deltaG 25 degrees C of -3.4 kcal x mol(-1) in favor of the natural duplex. The salt dependence of Tm for this sequence is more pronounced in the case of bicyclo-DNA due to increased counter ion screening from the solvent. Furthermore bicyclo-DNA sequences are more stable towards snake venom phosphodiesterase by a factor of 10-20, and show increased stability in fetal calf serum by a factor of 8 compared with DNA.
Topics: Base Composition; Base Sequence; Circular Dichroism; DNA; Drug Stability; Nucleic Acid Conformation; Nucleic Acid Heteroduplexes; Phosphoric Diester Hydrolases; Purines; Pyrimidines; RNA, Complementary; Thermodynamics
PubMed: 8972851
DOI: 10.1093/nar/24.23.4660 -
Cell Proliferation Apr 2023Ste20-like kinase (SLK) is involved in cell proliferation and migration in somatic cells. This study aims to explore SLK expression and function in mouse oocyte meiosis....
Ste20-like kinase (SLK) is involved in cell proliferation and migration in somatic cells. This study aims to explore SLK expression and function in mouse oocyte meiosis. Western blot, immunofluorescence, Co-immunoprecipitation, drug treatment, cRNA construct and in vitro transcription, microinjection of morpholino oilgo (MO) and cRNA were performed in oocytes. High and stable protein expression of SLK was detected in mouse oocyte meiosis, with dynamic distribution in the nucleus, chromosomes and spindle apparatus. SLK phosphorylation emerges around meiotic resumption and reaches a peak during metaphase I (MI) and metaphase II. SLK knockdown with MO or expression of kinase-dead SLK K63R dramatically delays meiotic resumption due to sequentially suppressed phosphorylation of Polo-like kinase 1 (Plk1) and cell division cycle 25C (CDC25C) and dephosphorylation of cyclin-dependent kinase 1 (CDK1). SLK depletion promotes ubiquitination-mediated degradation of paxillin, an antagonist to α-tubulin deacetylation, and thus destroys spindle assembly and chromosome alignment; these phenotypes can be substantially rescued by exogenous expression of SLK kinase active fragment. Additionally, exogenous SLK effectively promotes meiotic progression and spindle assembly in aging oocytes with reduced SLK. Collectively, this study reveals SLK is required for meiotic resumption and spindle assembly in mouse oocyte meiosis.
Topics: Animals; Mice; RNA, Complementary; Oocytes; Cell Cycle Proteins; Meiosis; Microtubules; Spindle Apparatus; Protein Serine-Threonine Kinases
PubMed: 36579845
DOI: 10.1111/cpr.13391 -
FEBS Letters Jun 2013Klotho, a hormone and enzyme, is a powerful regulator of ageing and life span. Klotho deficiency leads to cardiac arrythmia and sudden cardiac death. We thus explored...
Klotho, a hormone and enzyme, is a powerful regulator of ageing and life span. Klotho deficiency leads to cardiac arrythmia and sudden cardiac death. We thus explored whether klotho modifies cardiac K(+)-channel hERG. Current was determined utilizing dual electrode voltage clamp and hERG protein abundance utilizing immunohistochemistry and chemiluminescence in Xenopus oocytes expressing hERG with or without klotho. Coexpression of klotho increased cell membrane hERG-protein abundance and hERG current at any given voltage without significantly modifying the voltage required to activate the channel. The effect of klotho coexpression was mimicked by recombinant klotho protein and reversed by β-glucuronidase-inhibitor D-saccharic acid-1,4-lactone.
Topics: Animals; Cells, Cultured; ERG1 Potassium Channel; Ether-A-Go-Go Potassium Channels; Glucaric Acid; Glucuronidase; Ion Channel Gating; Klotho Proteins; Lactones; Membrane Potentials; Oocytes; Patch-Clamp Techniques; RNA, Complementary; Xenopus
PubMed: 23603386
DOI: 10.1016/j.febslet.2013.04.011 -
Virology Mar 2000The terminal RNA regions of the genomic and antigenomic RNAs of the paramyxoviruses and rhabdoviruses are known to contain sequences essential for directing RNA...
The terminal RNA regions of the genomic and antigenomic RNAs of the paramyxoviruses and rhabdoviruses are known to contain sequences essential for directing RNA replication and transcription. The 3' terminus (leader region) of the negative-sense, genomic RNA of the rhabdoviruses and paramyxoviruses is known as the leader (Le) promoter and directs synthesis of positive-sense replication and transcription products. The 3' terminus of the antigenome is termed the trailer complementary (TrC) promoter and directs the synthesis of genomic RNA. By creating mutations in the corresponding regions of an HPIV3 minireplicon in which the viral protein coding sequences were replaced by the luciferase gene, we were able to precisely define the elements of the leader promoter involved in directing positive-strand replication of HPIV3. Nucleotides 1 through 12 (from the terminus) formed a domain critical for replication. The region from nucleotides 13 through 55 was important but not crucial for replication, while G residues at positions 79, 85, and 91 comprised another domain critical for replication. It was also shown that the TrC promoter is similar, though not identical, to the Le promoter. Nucleotides 1 through 12 of the TrC promoter were critical for synthesis of genomic RNA, though specific positions behaved differently from the corresponding positions of the Le promoter. While many of these mutations could not be analyzed for transcription because they completely abrogated genomic RNA synthesis (the template for transcription), we were surprised to find that no mutations in the leader promoter which decreased replication had any significant effect on transcription. However, mutations in the intergenic sequence and gene start signal following the leader and preceding the luciferase message severely decreased transcription, but not replication.
Topics: Base Sequence; Gene Expression Regulation, Viral; Genes, Reporter; Genome, Viral; HeLa Cells; Humans; Mutation; Parainfluenza Virus 3, Human; Physical Chromosome Mapping; Promoter Regions, Genetic; RNA, Complementary; RNA, Messenger; RNA, Viral; Replication Origin; Replicon; Sequence Alignment; Templates, Genetic; Transcription, Genetic; Transfection
PubMed: 10725212
DOI: 10.1006/viro.2000.0223 -
Nature Structural & Molecular Biology Jul 2008The evolutionary origin of human hepatitis delta virus (HDV) replication by RNA-directed transcription is unclear. Here we identify two species of 5'-capped,...
The evolutionary origin of human hepatitis delta virus (HDV) replication by RNA-directed transcription is unclear. Here we identify two species of 5'-capped, approximately 18-25-nucleotide small RNAs. One was of antigenomic polarity, corresponding to the 5' end of hepatitis delta antigen (HDAg) mRNA, and interacted with HDAg and RNA polymerase II (Pol II), whereas the other mapped to a structurally analogous region on the genomic RNA hairpin. An HDAg-interaction screen indicated that HDAg interacts with MOV10, the human homolog of the Arabidopsis thaliana RNA amplification factor gene SDE3 and Drosophila melanogaster RISC-maturation factor gene Armitage (armi). MOV10 knockdown inhibited HDV replication, but not HDAg mRNA translation, further supporting a role for MOV10 in RNA-directed transcription. Together, our studies define RNA hairpins as critical elements for the initiation of HDV-related, RNA-directed transcription. The identification of capped small RNAs and the involvement of MOV10 in HDV replication further suggest a conserved mechanism related to RNA-directed transcription in lower eukaryotes.
Topics: Base Sequence; Cell Line; Cloning, Molecular; DNA-Binding Proteins; Genome, Viral; Hepatitis Delta Virus; Hepatitis delta Antigens; Humans; Hydroxylation; Molecular Sequence Data; Nucleic Acid Conformation; Protein Binding; RNA Caps; RNA Helicases; RNA Transport; RNA, Complementary; RNA, Messenger; RNA, Viral; Sequence Analysis, DNA; Virus Replication
PubMed: 18552826
DOI: 10.1038/nsmb.1440 -
Viruses Sep 2022Some of the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are less susceptible to neutralization with post-vaccine sera and monoclonal...
Molecular Analyses of Clinical Isolates and Recombinant SARS-CoV-2 Carrying B.1 and B.1.617.2 Spike Mutations Suggest a Potential Role of Non-Spike Mutations in Infection Kinetics.
Some of the emerging severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants are less susceptible to neutralization with post-vaccine sera and monoclonal antibodies targeting the viral spike glycoprotein. This raises concerns of disease control, transmissibility, and severity. Numerous substitutions have been identified to increase viral fitness within the nucleocapsid and nonstructural proteins, in addition to spike mutations. Therefore, we sought to generate infectious viruses carrying only the variant-specific spike mutations in an identical backbone to evaluate the impact of spike and non-spike mutations in the virus life cycle. We used en passant mutagenesis to generate recombinant viruses carrying spike mutations of B.1 and B.1.617.2 variants using SARS-CoV-2- bacterial artificial chromosome (BAC). Neutralization assays using clinical sera yielded comparable results between recombinant viruses and corresponding clinical isolates. Non-spike mutations for both variants neither seemed to effect neutralization efficiencies with monoclonal antibodies nor the response to treatment with inhibitors. However, live-cell imaging and microscopy revealed differences, such as persisting syncytia and pronounced cytopathic effect formation, as well as their progression between BAC-derived viruses and clinical isolates in human lung epithelial cell lines and primary bronchial epithelial cells. Complementary RNA analyses further suggested a potential role of non-spike mutations in infection kinetics.
Topics: Antibodies, Monoclonal; Antibodies, Neutralizing; Antibodies, Viral; COVID-19; Glycoproteins; Humans; Mutation; RNA, Complementary; SARS-CoV-2; Spike Glycoprotein, Coronavirus
PubMed: 36146823
DOI: 10.3390/v14092017 -
Nucleic Acids Research Nov 1994An in vitro RNA synthesis system mimicking replication of genomic influenza virus RNA was developed with nuclear extracts prepared from influenza virus-infected HeLa...
An in vitro RNA synthesis system mimicking replication of genomic influenza virus RNA was developed with nuclear extracts prepared from influenza virus-infected HeLa cells using exogenously added RNA templates. The RNA synthesizing activity was divided into two complementing fractions, i.e. the ribonucleoprotein (RNP) complexes and the fraction free of RNP, which could be replaced with RNP cores isolated from virions and nuclear extracts from uninfected cells, respectively. When nuclear extracts from uninfected cells were fractionated by phosphocellulose column chromatography, the stimulatory activity for RNA synthesis was further separated into two distinct fractions. One of them, tentatively designated RAF (RNA polymerase activating factor), stimulated RNA synthesis with either RNP cores or RNA polymerase and nucleocapsid protein purified from RNP cores as the enzyme source. In contrast, the other, designated PRF (polymerase regulating factor), functioned as an activator only when RNP cores were used as the enzyme source. Biochemical analyses revealed that PRF facilitates dissociation of RNA polymerase from RNP cores. Of interest is that virus-coded non-structural protein 1 (NS1), which has been thought to be involved in regulation of replication, counteracted PRF function. Roles of cellular factors and viral proteins, NS1 in particular, are discussed in terms of regulation of influenza virus RNA genome replication.
Topics: Biological Factors; Cell Extracts; DNA-Directed RNA Polymerases; HeLa Cells; Humans; Influenza A virus; Models, Genetic; RNA, Complementary; RNA, Viral; Templates, Genetic; Viral Core Proteins; Viral Nonstructural Proteins; Virus Replication
PubMed: 7800498
DOI: 10.1093/nar/22.23.5047 -
European Journal of Biochemistry Apr 2003The transcription patterns of 64 linear double stranded DNA templates obtained with T7 RNA polymerase were investigated. These templates consisted of 17 nucleotide-long...
The transcription patterns of 64 linear double stranded DNA templates obtained with T7 RNA polymerase were investigated. These templates consisted of 17 nucleotide-long sequences under the control of the minimal bacteriophage T7 promoter and represented all possible combinations of nucleotides at positions +8, +10 and +11. Two clearly distinct types of template were identified, which produced the range of transcription patterns observed: (a) those that yielded 17-nucleotide-long RNA as the only detectable run-off product (only 15% of the total), and (b) templates that in addition to the expected full-length RNA, produced other products longer than 17 nucleotides. Self-complementarity analysis of the expected run-off transcripts showed that those obtained from the first type of template were able to form stable intermolecular duplexes with non-base-paired 3'-ends. However, the second type of template yielded RNAs able to generate energetically favorable intermolecular duplexes with 3'-end complementarity, therefore yielding an RNA-primed RNA-template. The gel-purified 17-nucleotide-long RNAs transcribed from the latter yielded longer products when incubated under in vitro transcription conditions in the absence of a DNA template. No extension was observed when assaying the 17-nucleotide RNA products resulting from the first type of template. We observed that just a single nucleotide change within the DNA template could convert the RNA product from an RNA-primed template into a nonextendible dimer thus leading to a drastic switch of the 17-nucleotide product yield from less than 10% to 100%. Further, two type B DNA templates were extended by two nucleotides at the 3'-end, to produce RNA transcripts theoretically unable to form 3'-end base-paired duplexes. The full-length products of these modified DNA templates were found to be nonextendible by T7 RNA polymerase under the standard in vitro transcription conditions.
Topics: Base Pairing; Catalysis; Cell-Free System; DNA; DNA-Directed RNA Polymerases; Gene Library; RNA; RNA, Catalytic; RNA, Complementary; Substrate Specificity; Templates, Genetic; Transcription, Genetic; Viral Proteins
PubMed: 12654001
DOI: 10.1046/j.1432-1033.2003.03510.x -
European Journal of Biochemistry Jun 1992U14 small nuclear RNA (snRNA) is an evolutionarily conserved RNA species that plays a role in rRNA processing. The conserved ability of fungal, amphibian and mammalian...
U14 small nuclear RNA (snRNA) is an evolutionarily conserved RNA species that plays a role in rRNA processing. The conserved ability of fungal, amphibian and mammalian U14 snRNAs to hybridize with both homologous and heterologous eukaryotic 18S rRNAs indicates a potential role for this intermolecular RNA/RNA interaction in U14 snRNA function. To understand better the possible role of this intermolecular base-pairing in rRNA processing, we have defined those nucleotide sequences in mouse U14 snRNA and 18S rRNA responsible for the observed in vitro hybridization. We have constructed, using synthetic DNA oligonucleotides, a U14 snRNA gene which has been positioned behind a T7 RNA polymerase promoter site and then inserted into a plasmid. The presence of natural or engineered restriction endonuclease sites within this construct has permitted the in vitro transcription of full-length mouse U14 snRNA transcripts (an 87-nucleotide mouse U14 snRNA minus 5' or 3' leader sequences) or 3' terminally truncated U14 snRNA fragments. Hybridization of full-length or truncated fragments of U14 snRNA to mouse 18S rRNA demonstrated the utilization of a previously proposed 18S rRNA complementary sequence located near the 3' end of mouse U14 snRNA (nucleotides 65-78) for intermolecular hybridization. Conversely, RNase-T1-generated fragments of 18S rRNA capable of hybrid-selection by U14 snRNA have been isolated and sequenced. A nested set of hybrid-selected 18S rRNA fragments define a mouse 18S rRNA sequence (nucleotides 459-472) which exhibits perfect complementarity to the defined U14 snRNA sequence 65-78. Primer-extension/chain-termination mapping of mouse U14-snRNA.18S-rRNA hybrids has confirmed the formation of the proposed hybrid structure. A second set of observed complementary sequences in mouse U14 snRNA (nucleotides 25-38) and mouse 18S rRNA (nucleotides 82-95) are not used for the in vitro hybridization of these two RNAs. Presumably the involvement of this second 18S-rRNA-complementary sequence in the secondary/tertiary folding of mouse U14 snRNA prevents its base-pairing with 18S rRNA. However, the strong evolutionary conservation of both U14-snRNA.18S-rRNA hybrid structures and their juxtapositioning within the folded secondary structure of 18S rRNAs argues for a biological role for each in U14 snRNA function.
Topics: Animals; Base Composition; Base Sequence; Blotting, Northern; Cloning, Molecular; DNA; Mice; Molecular Sequence Data; Nucleic Acid Hybridization; RNA; RNA, Complementary; RNA, Ribosomal, 18S; RNA, Small Nuclear; Terminator Regions, Genetic; Transcription, Genetic
PubMed: 1375913
DOI: 10.1111/j.1432-1033.1992.tb16939.x -
BMC Genomics Feb 2008DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is...
BACKGROUND
DNA microarrays provide a powerful method for global analysis of gene expression. The application of this technology to specific cell types and tissues, however, is typically limited by small amounts of available mRNA, thereby necessitating amplification. Here we compare microarray results obtained with two different methods of RNA amplification to profile gene expression in the C. elegans larval nervous system.
RESULTS
We used the mRNA-tagging strategy to isolate transcripts specifically from C. elegans larval neurons. The WT-Ovation Pico System (WT-Pico) was used to amplify 2 ng of pan-neural RNA to produce labeled cDNA for microarray analysis. These WT-Pico-derived data were compared to microarray results obtained with a labeled aRNA target generated by two rounds of In Vitro Transcription (IVT) of 25 ng of pan-neural RNA. WT-Pico results in a higher fraction of present calls than IVT, a finding consistent with the proposal that DNA-DNA hybridization results in lower mismatch signals than the RNA-DNA heteroduplexes produced by IVT amplification. Microarray data sets from these samples were compared to a reference profile of all larval cells to identify transcripts with elevated expression in neurons. These results were validated by the high proportion of known neuron-expressed genes detected in these profiles and by promoter-GFP constructs for previously uncharacterized genes in these data sets. Together, the IVT and WT-Pico methods identified 2,173 unique neuron-enriched transcripts. Only about half of these transcripts (1,044), however, are detected as enriched by both IVT and WT-Pico amplification.
CONCLUSION
We show that two different methods of RNA amplification, IVT and WT-Pico, produce valid microarray profiles of gene expression in the C. elegans larval nervous system with a low rate of false positives. However, our results also show that each method of RNA amplification detects a unique subset of bona fide neural-enriched transcripts and thus a wider array of authentic neural genes are identified by the combination of these data sets than by the microarray profiles obtained with either method of RNA amplification alone. With its relative ease of implementation and greater sensitivity, WT-Pico is the preferred method of amplification for cases in which sample RNA is limiting.
Topics: Animals; Caenorhabditis elegans; Gene Expression Profiling; Larva; Nervous System; Neurons; Nucleic Acid Amplification Techniques; Oligonucleotide Array Sequence Analysis; RNA, Complementary; Reproducibility of Results
PubMed: 18284693
DOI: 10.1186/1471-2164-9-84