Ribonucleic Acid Fragments Research Articles

Mapping m6A Sites on HIV-1 RNA Using Oligonucleotide LC-MS/MS.

The biological significance of chemical modifications to the ribonucleic acid (RNA) of human immunodeficiency virus type-1 (HIV-1) has been recognized. However, our understanding of the site-specific and context-dependent roles of these chemical modifications remains limited, primarily due to the absence of nucleotide-resolution mapping of modification sites. In this study, we present a method for achieving nucleotide-resolution mapping of chemical modification sites on HIV-1 RNA using liquid chromatography and tandem mass spectrometry (LC-MS/MS). LC-MS/MS, a powerful tool capable of directly analyzing native RNAs, has proven effective for mapping RNA modifications in small RNA molecules, including ribosomal RNA and transfer RNA. However, longer RNAs have posed challenges, such as the 9 Kb HIV-1 virion RNA, due to the complexity of and ambiguity in mass differences among RNase T1-cleaved RNA fragments in LC-MS/MS data. Here, we introduce a new target RNA enrichment method to isolate small local RNA fragments of HIV-1 RNA that potentially harbor site-specific N6-methyladenosine (m6A) modifications. In our initial trial, we used target-specific DNA probes only and encountered insufficient RNA fragmentation due to inefficient S1 digestion near the target site. Recognizing that inefficient S1 digestion by HIV-1 RNA is likely due to the formation of secondary structures in proximity to the target site, we designed multiple DNA probes annealing to various sites of HIV-1 RNA to better control the structures of RNA substrates for S1 digestion. The use of these non-target DNA probes significantly improved the isolation of more homogeneous target RNA fragments of approximately 50 bases in length. Oligonucleotide LC-MS/MS analysis of these isolated target RNA fragments successfully separated and detected both m6A-methylated and non-methylated oligomers at the two m6A-predicted sites. The principle of this new target enrichment strategy holds promise and should be broadly applicable to the analysis of any lengthy RNA that was previously deemed infeasible for investigation using oligonucleotide LC-MS/MS.

Clearing the air on surgical plume.

Surgical smoke or plume is produced by a variety of surgical coagulators and dissectors. A number of jurisdictions have recently introduced policies to reduce the associated occupational health risks including WorkSafe Victoria and New South Wales Health. This paper is a narrative review of potential risks, including any associated with COVID-19, and options for mitigation. Surgical smoke or plume contains potentially toxic chemicals, some of which are carcinogens. Plume may also contain live virus, notably Human Papilloma and Hepatitis B, though any possible viral transmission is limited to a few case reports. Despite identifying COVID-19 ribonucleic acid fragments in various body tissues and fluids there are no current reports of COVID-19 transmission. Although plume is rapidly removed from the atmosphere in modern operating rooms, it is still inhaled by the operative team. Mitigation should include ensuring diathermy devices have evacuators while plume extraction should be standard for laparoscopic procedures. Consideration needs to be given to the potential to compromise the operating field of view, or the noise of the extractor impairing communication. There is an increasing range of suitable products on the market. The future includes pendant systems built into the operating room. The potential risks associated with surgical plume cannot be ignored. Health services should invest in plume extraction devices with a view to protecting their staff. The conduct of the operation should not be compromised by the devices chosen. Future operating theatres need to be designed to minimize exposure to plume.

Commentary: Potential transmissibility of SARS-CoV-2 infection via donor corneal tissue.

Commentary: Potential transmissibility of SARS-CoV-2 infection via donor corneal tissue.

RNA extraction for RNA sequencing of archival renal tissues

Background: Next generation sequencing (NGS) and especially ribonucleic acid (RNA) sequencing is a powerful tool to acquire insights into molecular disease mechanisms. Therefore, it is of interest to optimize methods for RNA extraction from archival, formalin fixed and paraffin embedded (FFPE) tissues. This is challenging due to RNA degradation and chemical modifications. The aim of this study was to find the most appropriate method to extract RNA from FFPE renal tissue to enable NGS.Method: We evaluated seven commercially available RNA extraction kits: High Pure FFPE RNA Isolation (Roche), ExpressArt Clear FFPE RNAready (Amsbio), miRNeasy FFPE, RNeasy FFPE (Qiagen), PureLink FFPE Total RNA (Invitrogen), RecoverAll Total Nucleic Acid Isolation (Ambion) and Absolutely RNA FFPE Kit (Agilent). RNA was obtained from tissue blocks of two healthy, male Wistar rats and from normal renal tissue of patients undergoing nephrectomy. Yield and quality of RNA extracted from rat whole kidney sections, human kidney core biopsies and laser capture microdissected (LCM) glomerular cross-sections were assessed: Analyses of RNA quantity were performed using NanoDrop and Qubit. RNA quality is reflected by DV200 values (% of RNA fragments >200 nucleotides) utilizing the Agilent 2100 BioAnalyzer. RNA of human LCM samples was subsequently sequenced using the Illumina TruSeq® RNA Access Library Preparation Kit.Conclusion: Total RNA can be extracted from archival renal biopsies in sufficient quality and quantity from one human kidney biopsy section and from around 100 LCM glomerular cross-sections to enable successful RNA library preparation and sequencing using commercially available RNA extraction kits.

Synthesis of DNA mimics representing HypNA-pPNA hetero-oligomers.

The methods for the synthesis and purification of negatively charged peptide nucleic acid (PNA)-relative deoxyribonucleic acid (DNA) mimics containing alternating residues of phosphono peptide nucleic acid (pPNA) monomers and PNA-like monomers on the base of trans-4-hydroxy-L-proline are described. Examples of the chimeric oligomers hybridization with complementary DNA and ribonucleic acid fragments are demonstrated.

Sequence of choline acetyltransferase temperature-sensitive mutants determined by the polymerase chain reaction

Two temperature-sensitive alleles of Drosophila melanogaster, Cha ts1 and Cha ts2, have been previously identified and are thought to be point mutations in the structural gene for the neurotransmitter biosynthetic enzyme choline acetyltransferase. In order to clarify the molecular nature of these alleles and characterize the presumed amino acid substitutions, we have used the polymerase chain reaction to amplify choline acetyltransferase messenger ribonucleic acid fragments from both mutant genotypes. Amplified mutant complementary deoxyribonucleic acid was cloned and used to construct chimeric complementary deoxyribonucleic acid clones containing approximately two-thirds of the wild-type sequence which would code for N-terminal amino acids and one-third of the mutant sequence coding for the C-terminal amino acids. After in vitro translation of complementary ribonucleic acid produced from the chimeric complementary deoxyribonucleic acid clones, choline acetyltransferase activity was determined and shown to be thermolabile. Sequence analyses of these clones showed that one amino acid substitution due to single base substitution is crucial in each chimeric choline acetyltransferase complementary deoxyribonucleic acid to generate a thermolabile choline acetyltransferase product. The point mutations of the structural gene for choline acetyltransferase are thus confirmed and shown to regulate the thermolability of the enzyme produced by Cha ts1 and Cha ts2.

Melting order of successively longer yeast phenylalanine-accepting transfer ribonucleic acid fragments with a common 5' end.

Temperature-jump methods were used to study the kinetics of the helix to coil transition in three fragments of yeast tRNAPhe that share a common 5' terminus (the 5' end of the mature tRNA). Correlation of the extrapolated helix dissociation time constants with NMR exchange broadening results allows assignment of the structural basis of the optical melting transition in the fragments. The results confirm nuclear magnetic resonance findings on these fragments: the 5' 1/4 fragment has no helical structure; the 5' 1/2 fragment contains the D stem; and the 5' 3/5 fragment contains the D stem and the anticodon stem. These are the structures expected if sequential folding of the tRNA during biosynthesis were to occur. The D stem is the last helix to melt in the 5' 3/5 fragment. We suggest that structural elements in addition to the four Watson-Crick base pairs of the D-stem helix are responsible for the anomalously high Tm of that hairpin.

Isolation of species-specific protein antigens of Rickettsia typhi and Rickettsia prowazekii for immunodiagnosis and immunoprophylaxis

A simple procedure for the selective isolation of the protective species-specific protein antigens (SPAs) of Rickettsia typhi and Rickettsia prowazekii was developed to permit use of the SPAs in the immunodiagnosis and immunoprophylaxis of typhus infections. Although the SPAs were readily extracted from lysozyme- or detergent-treated rickettsiae, as measured by rocket immunoelectrophoresis, other polypeptides were also present, as shown by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. In contrast, both water and seven buffers, each at a 10 mM concentration and pH 7.6, were nearly equally effective in the selective release of the SPAs from whole cells by extraction for 30 min at 45 degrees C. High-ionic-strength buffers and MgCl2 abolished this SPA release, thus suggesting that divalent cations were important in the binding of the SPAs to the cell envelope. The efficacy of the dilute buffer extraction procedure for isolation of large amounts of SPAs was tested by further characterization of the supernatants obtained by centrifugation (200,000 x g) of two successive tris-(hydroxymethyl)aminomethane-hydrochloride buffer (Tris) extracts. With this procedure, between 10 and 15 mg of SPA was obtained from 100 mg of purified rickettsiae. Although low-molecular-weight ribonucleic acid fragments were released into the Tris extracts in significant amounts, only the SPAs were detected, in significant quantities, as measured by polyacrylamide gel electrophoresis and rocket immunoelectrophoresis. The Tris extracts contained the same major and minor SPA polypeptides as those observed previously in SPA preparations obtained by extensive diethylaminoethyl-cellulose column chromatography, but the Tris SPAs were more satisfactory antigens in an enzyme-linked immunosorbent assay.

Mode of degradation of precursor-specific ribonucleic acid fragments by Bacillus subtilis

A precursor of 5S ribosomal ribonucleic acid (rRNA) from Bacillus subtilis was cleaved by ribonuclease (RNase) M5 in cell-free extracts from B. subtilis to yield the mature 5S rRNA plus RNA fragments derived from both termini of the precursor. The released, mature 5S rRNA was stable in these extracts; however, as occurred in vivo, the precursor-specific fragments were rapidly and completely destroyed. Such destruction was not observed in the presence of partially purified RNase M5, so fragment scavenging was not effected by the maturation nuclease itself. The selective destruction of the precursor-specific fragments was shown to occur through a 3'-exonucleolytic process with the release of nucleoside 5'-monophosphates; the responsible activity therefore had the character of RNAse II. Consideration of the primary and probable secondary structures of the precursor-specific fragments and mature 5S rRNA suggested that involvement of 3' termini in tight secondary structure may confer protection against the scavenging activity.

Amino Acid Incorporation into Transfer Ribonucleic Acid Fragments and into Heterologous Combinations of Fragments

Amino Acid Incorporation into Transfer Ribonucleic Acid Fragments and into Heterologous Combinations of Fragments

Biological activity of double-stranded ribonucleic acid fragments

Biological activity of double-stranded ribonucleic acid fragments

Synthesis and cleavage of influenza virus proteins.

The NWS strain of influenza virus grows rapidly in and kills the MDCK dog kidney cell strain. Within 1 to 2 hr, the virus inhibits host cell protein synthesis and for 3 to 4 hr more it directs the synthesis of influenza virus proteins at a rate about twice that of uninfected cell synthesis. The rates of virus ribonucleic acid (RNA) and protein synthesis reach a maximum within the first few hours after infection and then drop. Plaque assays exhibit a linear dose-response, indicating that only one virion is necessary for productive infection. We have confirmed earlier reports regarding the fragmented nature of the RNA genome of purified influenza virions. However, high resolution gel electrophoresis indicated that each size class of viral RNA is heterogenous, so that there are at least 10 and probably more fragment sizes of RNA in these virions. Repeated attempts to detect infectivity in preparations of extracted viral RNA were completely negative (over a 10(8)-fold loss of infectivity after extraction). Even infection of the "infectious" RNA-treated cells with intact, related, influenza viruses failed to support infectivity of the isolated RNA or to rescue a host range genetic marker of the RNA. Purified influenza virions exhibit only three major protein peaks based on separation according to molecular weights. These three major virion proteins are the only major virion proteins synthesized in infected cells. This is true throughout the infectious cycle from several hours after infection until the cells are dying. However, the molecular weight of these virion proteins differs slightly depending upon the cell type in which the virus is grown. No host membrane proteins are incorporated into the virions as they bud through the cell membrane. Pulse-chase labeling early after infection or prolonged chase experiments indicate that influenza virus proteins are cleaved from one or more precursor polypeptides. In fact, each of the three major peaks seems to be a heterogeneous mixture of polypeptides in various stages of cleavage. Peptide analysis confirms that the three major peaks share common peptides, but the exact precursor product relationships are not clear. There may be one or several precursor proteins. Also there could be overlapping messenger RNA molecules of varying length giving rise to polypeptides of various sizes and overlapping sequences. Late in infection, amino acid labeling shows a preponderance of internal nucleocapsid protein synthesis, indicating that either this protein is much more stable to cleavage in infection or it is made from a more stable messenger. There is no obvious relationship between virion RNA fragments and viral protein sizes, so these fragments may be artifacts.

SOLUBILIZATION AND HETEROGENEOUS NATURE OF PROTEINS FROM RIBOSOMES OF PEA-SEEDLING BUDS

The results of several procedures for solubilizing protein from pea-seedling ribosomes are described. Pancreatic ribonuclease (RNAase), alone at pH 8.0 and low ionic strength, solubilized 10%, whereas subsequent treatment with dilute HC1 solubilized a further 29%. RNAase in 8 M urea at pH 5.5 solubilized more than 90% of the ribosomal protein. After removal of ribonucleic acid fragments, all of this material, termed "total protein", remained in solution in 0.05 M acetate buffer at pH 5. Proteins solubilized by these three procedures were subjected to electrophoresis on starch–urea gels, amino acid analyses, and fingerprinting after digestion with trypsin and chymotrypsin. The protein soluble in RNAase probably contains only one or two components and is distinct in amino acid and peptide composition from the remainder of the ribosomal protein. Protein soluble in HC1 is representative of much of the "total protein" and both HC1-soluble and "total protein" are complex. Fingerprints showed that although RNAase-extracted protein and three fractions of "total protein" obtained by gel electrophoresis were different, they also possessed a number of peptides in common. It was concluded that the number of components in pea-ribosomal proteins is probably of the order of 16, the number of bands seen in gel-electrophoretic patterns.