scholarly journals Hydroxyapatite-Mediated Separation of Double-Stranded DNA, Single-Stranded DNA, and RNA Genomes from Natural Viral Assemblages

2010 ◽  
Vol 76 (15) ◽  
pp. 5039-5045 ◽  
Author(s):  
Cynthia Andrews-Pfannkoch ◽  
Douglas W. Fadrosh ◽  
Joyce Thorpe ◽  
Shannon J. Williamson
Keyword(s):  
Nucleic Acid ◽  
Significant Similarity ◽  
Metagenomic Sequence ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Marine Viruses ◽  
Viral Communities ◽  
Environmental Sequences ◽  
Dsdna Viruses

ABSTRACT Metagenomics can be used to determine the diversity of complex, often unculturable, viral communities with various nucleic acid compositions. Here, we report the use of hydroxyapatite chromatography to efficiently fractionate double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), dsRNA, and ssRNA genomes from known bacteriophages. Linker-amplified shotgun libraries were constructed to generate sequencing reads from each hydroxyapatite fraction. Greater than 90% of the reads displayed significant similarity to the expected genomes at the nucleotide level. These methods were applied to marine viruses collected from the Chesapeake Bay and the Dry Tortugas National Park. Isolated nucleic acids were fractionated using hydroxyapatite chromatography followed by linker-amplified shotgun library construction and sequencing. Taxonomic analysis demonstrated that the majority of environmental sequences, regardless of their source nucleic acid, were most similar to dsDNA viruses, reflecting the bias of viral metagenomic sequence databases.

scholarly journals Adintoviruses: A Proposed Animal-Tropic Family of Midsize Eukaryotic Linear dsDNA (MELD) Viruses

2020 ◽  
Author(s):  
Gabriel J Starrett ◽  
Michael J Tisza ◽  
Nicole L Welch ◽  
Anna K Belford ◽  
Alberto Peretti ◽  
...  
Keyword(s):  
Genome Packaging ◽  
Metagenomic Sequence ◽  
Dna Viruses ◽  
Diverse Range ◽  
Integrase Gene ◽  
Data Mining Approach ◽  
Double Stranded Dna ◽  
Wide Range ◽  
Linear Dsdna ◽  
Dsdna Viruses

Abstract Polintons (also known as Mavericks) were initially identified as a widespread class of eukaryotic transposons named for their hallmark type B DNA polymerase and retrovirus-like integrase genes. It has since been recognized that many polintons encode possible capsid proteins and viral genome-packaging ATPases similar to those of a diverse range of double-stranded DNA (dsDNA) viruses. This supports the inference that at least some polintons are actually viruses capable of cell-to-cell spread. At present, there are no polinton-associated capsid protein genes annotated in public sequence databases. To rectify this deficiency, we used a data-mining approach to investigate the distribution and gene content of polinton-like elements and related DNA viruses in animal genomic and metagenomic sequence datasets. The results define a discrete family-like clade of viruses with two genus-level divisions. We propose the family name Adintoviridae, connoting similarities to adenovirus virion proteins and the presence of a retrovirus-like integrase gene. Although adintovirus-class PolB sequences were detected in datasets for fungi and various unicellular eukaryotes, sequences resembling adintovirus virion proteins and accessory genes appear to be restricted to animals. Degraded adintovirus sequences are endogenized into the germlines of a wide range of animals, including humans.

Highly stable triple helix formation by homopyrimidine (l)-acyclic threoninol nucleic acids with single stranded DNA and RNA

2015 ◽  
Vol 13 (8) ◽  
pp. 2366-2374 ◽  
Author(s):  
Vipin Kumar ◽  
Venkitasamy Kesavan ◽  
Kurt V. Gothelf
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Triple Helix ◽  
Helical Structures ◽  
Single Stranded Dna ◽  
Dna And Rna ◽  
Helix Formation ◽  
Triple Helix Formation

Homopyrimidine acyclic (l)-threoninol nucleic acid (aTNA) was synthesized and found to form highly stable (l)-aTNA–DNA–(l)-aTNA and (l)-aTNA–RNA–(l)-aTNA triple helical structures.

scholarly journals The Nucleic Acid Binding Activity of Bleomycin Hydrolase Is Involved in Bleomycin Detoxification

1998 ◽  
Vol 18 (6) ◽  
pp. 3580-3585 ◽  
Author(s):  
Wenjin Zheng ◽  
Stephen Albert Johnston
Keyword(s):  
Nucleic Acid ◽  
Binding Activity ◽  
Dual Function ◽  
Nucleic Acid Binding ◽  
Peptide Cleavage ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Bleomycin Hydrolase ◽  
Nucleic Acid Binding Activity ◽  
Rna And Dna

ABSTRACT Yeast bleomycin hydrolase, Gal6p, is a cysteine peptidase that detoxifies the anticancer drug bleomycin. Gal6p is a dual-function protein capable of both nucleic acid binding and peptide cleavage. We now demonstrate that Gal6p exhibits sequence-independent, high-affinity binding to single-stranded DNA, nicked double-stranded DNA, and RNA. A region of the protein that is involved in binding both RNA and DNA substrates is delineated. Immunolocalization reveals that the Gal6 protein is chiefly cytoplasmic and thus may be involved in binding cellular RNAs. Variant Gal6 proteins that fail to bind nucleic acid also exhibit reduced ability to protect cells from bleomycin toxicity, suggesting that the nucleic acid binding activity of Gal6p is important in bleomycin detoxification and may be involved in its normal biological functions.

scholarly journals A Review of Marine Viruses in Coral Ecosystem

2021 ◽  
Vol 9 (7) ◽  
pp. 711
Author(s):  
Logajothiswaran Ambalavanan ◽  
Shumpei Iehata ◽  
Rosanne Fletcher ◽  
Emylia H. Stevens ◽  
Sandra C. Zainathan
Keyword(s):  
Marine Invertebrates ◽  
Marine Sponges ◽  
Detection Methods ◽  
Viral Diversity ◽  
Double Stranded Rna ◽  
Identification Methods ◽  
Double Stranded Dna ◽  
Marine Viruses ◽  
Coral Reef Ecosystems ◽  
Viral Communities

Coral reefs are among the most biodiverse biological systems on earth. Corals are classified as marine invertebrates and filter the surrounding food and other particles in seawater, including pathogens such as viruses. Viruses act as both pathogen and symbiont for metazoans. Marine viruses that are abundant in the ocean are mostly single-, double stranded DNA and single-, double stranded RNA viruses. These discoveries were made via advanced identification methods which have detected their presence in coral reef ecosystems including PCR analyses, metagenomic analyses, transcriptomic analyses and electron microscopy. This review discusses the discovery of viruses in the marine environment and their hosts, viral diversity in corals, presence of virus in corallivorous fish communities in reef ecosystems, detection methods, and occurrence of marine viral communities in marine sponges.

scholarly journals Facile synthesis and fundamental properties of an N-methylguanidine-bridged nucleic acid (GuNA[NMe])

2018 ◽  
Vol 16 (35) ◽  
pp. 6531-6536 ◽  
Author(s):  
Naohiro Horie ◽  
Shinji Kumagai ◽  
Yutaro Kotobuki ◽  
Takao Yamaguchi ◽  
Satoshi Obika
Keyword(s):  
Nucleic Acid ◽  
Modified Oligonucleotides ◽  
Facile Synthesis ◽  
Single Stranded Dna ◽  
Enzymatic Stability ◽  
Fundamental Properties ◽  
Dna And Rna

The GuNA[NMe]-modified oligonucleotides exhibited excellent duplex-forming ability towards the complementary single-stranded DNA and RNA, and showed robust enzymatic stability.

Two-dimensional strandness-dependent electrophoresis: A method to characterize single-stranded DNA, double-stranded DNA, and RNA–DNA hybrids in complex samples

2006 ◽  
Vol 350 (1) ◽  
pp. 120-127 ◽  
Author(s):  
Gudmundur H. Gunnarsson ◽  
Bjarki Gudmundsson ◽  
Hans G. Thormar ◽  
Arni Alfredsson ◽  
Jon J. Jonsson
Keyword(s):  
Two Dimensional ◽  
Single Stranded Dna ◽  
Complex Samples ◽  
Dna And Rna ◽  
Double Stranded Dna

scholarly journals Archaeal Nucleic Acid Ligases and Their Potential in Biotechnology

Archaea ◽  
2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Cecilia R. Chambers ◽  
Wayne M. Patrick
Keyword(s):  
Nucleic Acid ◽  
Pyrococcus Furiosus ◽  
Bacteriophage T4 ◽  
Biotechnological Applications ◽  
Dna Ligases ◽  
Dna And Rna ◽  
Double Stranded Dna ◽  
Current State ◽  
Methanothermobacter Thermautotrophicus

With their ability to catalyse the formation of phosphodiester linkages, DNA ligases and RNA ligases are essential tools for many protocols in molecular biology and biotechnology. Currently, the nucleic acid ligases from bacteriophage T4 are used extensively in these protocols. In this review, we argue that the nucleic acid ligases from Archaea represent a largely untapped pool of enzymes with diverse and potentially favourable properties for new and emerging biotechnological applications. We summarise the current state of knowledge on archaeal DNA and RNA ligases, which makes apparent the relative scarcity of information onin vitroactivities that are of most relevance to biotechnologists (such as the ability to join blunt- or cohesive-ended, double-stranded DNA fragments). We highlight the existing biotechnological applications of archaeal DNA ligases and RNA ligases. Finally, we draw attention to recent experiments in which protein engineering was used to modify the activities of the DNA ligase fromPyrococcus furiosusand the RNA ligase fromMethanothermobacter thermautotrophicus, thus demonstrating the potential for further work in this area.

scholarly journals Metagenomic Characterization of Chesapeake Bay Virioplankton

2007 ◽  
Vol 73 (23) ◽  
pp. 7629-7641 ◽  
Author(s):  
Shellie R. Bench ◽  
Thomas E. Hanson ◽  
Kurt E. Williamson ◽  
Dhritiman Ghosh ◽  
Mark Radosovich ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Chesapeake Bay ◽  
Low Frequency ◽  
Metagenomic Library ◽  
Marine Systems ◽  
Double Stranded Dna ◽  
Long Read ◽  
Environmental Sequences ◽  
Dsdna Viruses

ABSTRACT Viruses are ubiquitous and abundant throughout the biosphere. In marine systems, virus-mediated processes can have significant impacts on microbial diversity and on global biogeocehmical cycling. However, viral genetic diversity remains poorly characterized. To address this shortcoming, a metagenomic library was constructed from Chesapeake Bay virioplankton. The resulting sequences constitute the largest collection of long-read double-stranded DNA (dsDNA) viral metagenome data reported to date. BLAST homology comparisons showed that Chesapeake Bay virioplankton contained a high proportion of unknown (homologous only to environmental sequences) and novel (no significant homolog) sequences. This analysis suggests that dsDNA viruses are likely one of the largest reservoirs of unknown genetic diversity in the biosphere. The taxonomic origin of BLAST homologs to viral library sequences agreed well with reported abundances of cooccurring bacterial subphyla within the estuary and indicated that cyanophages were abundant. However, the low proportion of Siphophage homologs contradicts a previous assertion that this family comprises most bacteriophage diversity. Identification and analyses of cyanobacterial homologs of the psbA gene illustrated the value of metagenomic studies of virioplankton. The phylogeny of inferred PsbA protein sequences suggested that Chesapeake Bay cyanophage strains are endemic in that environment. The ratio of psbA homologous sequences to total cyanophage sequences in the metagenome indicated that the psbA gene may be nearly universal in Chesapeake Bay cyanophage genomes. Furthermore, the low frequency of psbD homologs in the library supports the prediction that Chesapeake Bay cyanophage populations are dominated by Podoviridae.

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