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DNA, Archaeal (0):
Recent article
DNA, Archaeal
ISME Journal (5)6 2011
Abstract
We describe the sediment metagenome from the oligotrophic Brazos-Trinity Basin (Site 1320) and show similarities and differences with the dataset from the Pacific Peru Margin (Site 1229) and other pyrosequenced datasets. The microbial community found at Integrated Ocean Drilling Program Site 1320 li...
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PMID: 21209666
PDF is available here.
PDF is available here.
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Abstract
To avoid the inhibition of methane production by ammonia that occurs during the degradation of garbage, anaerobic digestion with prior ammonia production and subsequent stripping was investigated. In the ammonia production phase, the maximum ammonia concentration was approximately 28...
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PMID: 21094085
PDF is available here.
PDF is available here.
Abstract
Viral and prokaryotic abundance, production and diversity were determined throughout the water column of the subtropical Atlantic Ocean to assess potential variations in the relation between viruses and prokaryotes. Prokaryotic abundance and heterotrophic activity decreased by one and three orders o...
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PMID: 20485386
PDF is available here.
PDF is available here.
Abstract
V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to fa...
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PMID: 20804791
PDF is available here.
PDF is available here.
Microbial Ecology (60)3 2010
Abstract
Communities of archaea, bacteria, and fungi were examined in forest soils located in the Oregon Coast Range and the inland Cascade Mountains. Soils from replicated plots of Douglas-fir (Pseudotsuga menziesii) and red alder (Alnus rubra) were characterized using fungal ITS (internal transcribed space...
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PMID: 20449582
PDF is available here.
PDF is available here.
Abstract
A haloalkaliphilic archaeon, strain JX313(T), was isolated from a saline-alkaline soil from Daqing, Heilongjiang Province, China. Its morphological, physiological and biochemical features and 16S rRNA gene sequence were determined. Colonies of the strain were orange-red and cells were non-motile coc...
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PMID: 19915113
PDF is available here.
PDF is available here.
Abstract
A halophilic archaeon, strain RO1-6(T), was isolated from a marine solar saltern in eastern China. Cells of strain RO1-6(T) were pleomorphic and motile and stained Gram-negative. Strain RO1-6(T) grew well on complex medium and colonies were red-pigmented. It was able to grow at 20-50°C (optimum 37...
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PMID: 19946053
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The in...
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PMID: 20434457
PDF is available here.
PDF is available here.
ISME Journal (4)6 2010
Abstract
These results suggest a model wherein functionally redundant microbial and viral taxa are cycling at the level of viral genotypes and virus-sensitive microbial strains. Microbial taxa, viral taxa, and metabolic function persist over time in stable ecosystems and both communities fluctuate in a Kill-...
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PMID: 20147985
PDF is available here.
PDF is available here.
Abstract
We compared four widely used methods, and found their DNA yields to vary up to 35-fold. Bacterial, archaeal and human DNA was quantified by real-time PCR, and a compositional analysis of different extracts was carried out using the Human Intestinal Tract Chip, a 16S rRNA gene-based phylogenetic micr...
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PMID: 20171997
PDF is available here.
PDF is available here.
Abstract
The archaeal community in the fermentative compartment and faeces of the cow and the rabbit were compared by analysis capillary electrophoresis single-stranded conformation polymorphism (CE-SSCP) profiles of 16S rRNA genes. Ruminal and faecal contents were sampled in five cows for th...
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PMID: 20417714
PDF is available here.
PDF is available here.
Abstract
The gene APE0743 encoding the superoxide dismutase (ApSOD) of a hyperthermophilic archaeon Aeropyrum pernix K1 was cloned and over-expressed as a GST fusion protein at a high level in Escherichia coli. The expressed protein was simply purified by the process of glutathione affinity chromatography an...
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PMID: 20467245
PDF is available here.
PDF is available here.
Abstract
These results suggest that ApCpnB has both foldase and holdase activities and can be used as a powerful molecular machinery for the production of recombinant proteins as soluble and active forms in E. coli....
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PMID: 20372025
PDF is available here.
PDF is available here.
Abstract
We investigated the abundance, community structure, and diversity of Bacteria and Archaea along these gradients to further distinguish the ecologies of these domains outside their established physiological range. Quantitative PCR was used to enumerate 16S rRNA gene abundances of Bacteria, Archaea, a...
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PMID: 19948847
PDF is available here.
PDF is available here.
Abstract
Phylogenetic analysis of 16S rRNA was used to investigate for the first time the structure of the microbial community that inhabits salt crystals retrieved from the bottom of a solar saltern, located in the coastal area of the Mediterranean Sea (Sfax, Tunisia). This community lives in an extremely s...
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PMID: 20130693
PDF is available here.
PDF is available here.
Genome Research (20)1 2010
Abstract
We have reconstructed the primary transcriptome of Sulfolobus solfataricus P2, one of the most widely studied model archaeal organisms. Analysis of 625 million bases of sequenced cDNAs yielded a single-base-pair resolution map of transcription start sites and operon structures for more than 1000 tra...
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PMID: 19884261
PDF is available here.
PDF is available here.
Abstract
We identified genes that may be involved in 1,2-dichloroethane degradation, naphthalene/anthracene degradation, gamma-hexachlorocyclohexane degradation, 1-/2-methylnaphthalene degradation and benzoate degradation via CoA ligation. Among the identified ORFs, gene homologs of (S)-2-haloacid dehalogena...
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PMID: 20662380
PDF is available here.
PDF is available here.
Abstract
Molecular characterization of subsurface microbial communities in the former Homestake gold mine, South Dakota, was carried out by 16S rDNA sequence analysis using a water sample and a weathered soil-like sample. Geochemical analyses indicated that both samples were high in sulphur, rich in nitrogen...
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PMID: 20662386
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
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PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
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PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2010
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Extremophiles (14)1 2009
Abstract
The accuracy of DNA synthesis by DNA polymerase B1 from the hyperthermophilic archaeon Sulfolobus solfataricus (Sso pol B1) at near the physiological temperature was investigated using M13-based mutational assays. Sso pol B1 showed replication fidelity similar to or higher than most...
|
PMID: 20012453
PDF is available here.
PDF is available here.
Acta Microbiologica Sinica (49)12 2009
Abstract
Five 16S rDNA sequences with the similarity between 93.2% and 99.2% to each other were obtained from Reticulitermes chinensis Snyder. Phylogenetic analysis showed that the five clones were clustered with Methanobrevibacter clones or isolates obtained from Reticulitermes speratus and Reticulitermes f...
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PMID: 20222453
PDF is available here.
PDF is available here.
Extremophiles (14)1 2009
Abstract
We have found that Cdc6/Orc1 binds to oriC and unwinds duplex DNA in the hyperthermophilic archaeon Pyrococcus furiosus, by means of a P1 endonuclease assay. A primer extension analysis further revealed that this localized unwinding occurs in the oriC region at a specific site, which is 12-bp long a...
|
PMID: 19787415
PDF is available here.
PDF is available here.
Abstract
Microbial diversity in Movile Cave (Romania) was studied using bacterial and archaeal 16S rRNA gene sequence and functional gene analyses, including ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), soxB (sulfate thioesterase/thiohydrolase) and amoA (ammonia monooxygenase). Sulfur oxidizers...
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PMID: 19474813
PDF is available here.
PDF is available here.
Abstract
The prokaryotic diversity associated with organic household waste (OHW), leachate (start-up inoculum), and mesophilic anaerobic digestion processes in the degradation of OHW for 44 and 90 days was investigated using a culture-independent approach. Bacterial and archaeal 16S rRNA and mcrA gene clone...
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PMID: 19551378
PDF is available here.
PDF is available here.
Biochemistry (Washington) (48)31 2009
Abstract
We report the kinetic parameters of several elementary steps for the forward polymerization reaction. PolB1 exo- binds tightly to DNA (K(d)(DNA) = 1.8 nM) and a correct incoming nucleotide (apparent K(d)(dTTP) = 11 microM). Moreover, several lines of kinetic evidence suggested that correct nucleotid...
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PMID: 19456143
PDF is available here.
PDF is available here.
Abstract
Phylogenetic analysis revealed archaea in the soil of Mila Mountain including the Crenarchaeota (71.7%) and unclassified-Archaea (28.3%) phyla. All the Crenarchaeota belong to the Thermoprotei. Phylogenetic analysis revealed AOA in the alp prairie soil of Mila Mountain belonged to the kingdom Crenar...
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PMID: 19835159
PDF is available here.
PDF is available here.
Abstract
Peptide tags containing tyrosines (Y-tag) were introduced at the C-terminus of a hyperthermophilic enzyme, alkaline phosphatase from Pyrococcus furiosus (PfuAP). Immobilization of the recombinant PfuAPs onto water-in-oil-in-water (W/O/W) type microcapsules was performed by an in situ polymerization...
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PMID: 19330489
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
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PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
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PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
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PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
|
PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
|
PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
|
PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
|
PMID: 19427858
PDF is available here.
PDF is available here.
FEBS Letters (583)12 2009
Abstract
We show that SSO1450 is a high-affinity nucleic acid binding protein. It binds DNA, RNA and DNA-RNA hybrid apparently sequence non-specific in a multi-site binding mode. Furthermore, SSO1450 promotes the hybridization of complementary nucleic acid strands....
|
PMID: 19427858
PDF is available here.
PDF is available here.