Among-Run Artifacts in DNA Hybridization

Background: Anthrax Lethal Factor (ANT) is the dominant virulence factor produced by B. anthracis and is the major cause of death of infected animals. In this paper, pencil graphite electrodes GE were modified with single-walled and multi-walled carbon nanotubes (CNTs) for the detection of hybridization related to the ANT DNA for the first time in the literature. Methods: The electrochemical monitoring of label-free DNA hybridization related to ANT DNA was explored using both SCNT and MCNT modified PGEs with differential pulse voltammetry (DPV). The performance characteristics of ANT-DNA hybridization on disposable GEs were explored by measuring the guanine signal in terms of optimum analytical conditions; the concentration of SCNT and MCNT, the concentrations of probe and target, and also the hybridization time. Under the optimum conditions, the selectivity of probe modified electrodes was tested and the detection limit was calculated. Results: The selectivity of ANT probes immobilized onto MCNT-GEs was tested in the presence of hybridization of probe with NC no response was observed and with MM, smaller responses were observed in comparison to full-match DNA hybridization case. Even though there are unwanted substituents in the mixture samples containing both the target and NC in the ratio 1:1 and both the target and MM in the ratio 1:1, it has been found that ANT probe immobilized CNT modified graphite sensor can also select its target by resulting with 20.9% decreased response in comparison to the one measured in the case of full-match DNA hybridization case Therefore, it was concluded that the detection of direct DNA hybridization was performed by using MCNT-GEs with an acceptable selectivity. Conclusion: Disposable SCNT/MCNT modified GEs bring some important advantages to our assay including easy use, cost-effectiveness and giving a response in a shorter time compared to unmodified PGE, carbon paste electrode and glassy carbon electrode developed for electrochemical monitoring of DNA hybridization. Consequently, the detection of DNA hybridization related to the ANT DNA by MCNT modified sensors was performed by using lower CNT, probe and target concentrations, in a shorter hybridization time and resulting in a lower detection limit according to the SCNT modified sensors. In conclusion, MCNT modified sensors can yield the possibilities leading to the development of nucleic acid sensors platforms for the improvement of fast and cost-effective detection systems with respect to DNA chip technology.

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A new method for the in situ assay of α-glucosidase activity and inhibitor screening through an enzyme substrate-mediated DNA hybridization chain reaction

New Journal of Chemistry ◽

10.1039/c9nj01868a ◽

2019 ◽

Vol 43 (24) ◽

pp. 9458-9465

Author(s):

Xiquan Yue ◽

Lihong Su ◽

Xu Chen ◽

Junfeng Liu ◽

Longpo Zheng ◽

...

Keyword(s):

Small Molecule ◽

Dna Hybridization ◽

New Method ◽

Hybridization Chain Reaction ◽

Chain Reaction ◽

Inhibitor Screening ◽

Glucosidase Activity ◽

Enzyme Substrate ◽

In Situ Assay

The strategy is based on small molecule-mediated hybridization chain reaction.

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Janthinobacterium tructae sp. nov., Isolated from Kidney of Rainbow Trout (Oncorhynchus mykiss)

Pathogens ◽

10.3390/pathogens10020229 ◽

2021 ◽

Vol 10 (2) ◽

pp. 229

Author(s):

Won Joon Jung ◽

Sang Wha Kim ◽

Sib Sankar Giri ◽

Hyoun Joong Kim ◽

Sang Guen Kim ◽

...

Keyword(s):

Rainbow Trout ◽

Dna Hybridization ◽

Biochemical Analysis ◽

Major Fatty Acid ◽

Phylogenetic Study ◽

Rainbow Trout Oncorhynchus Mykiss ◽

Close Relatives ◽

Rrna Sequences ◽

Fatty Acid Compositions ◽

Genome Distance

This study presents a novel Janthinobacterium strain, SNU WT3, isolated from the kidney of rainbow trout. A phylogenetic study using 16S rRNA sequences indicated that the strain is closely related to Janthinobacterium svalbardensis JA-1T. However, biochemical analysis found differences in D-xylose adonitol, N-acetylglucosamine, arbutin, and cellobiose. As for genome-to-genome distance and average nucleotide identity values calculated between strain SNU WT3 and other related strains such as J. lividum EIF1, J. svalbardensis PAMC 27463, and J. agaricidamnosum BHSEK were all below the cutoff value between species. DNA-DNA hybridization between strain SNU WT3 and other close relatives indicated the results of J. lividum DSM 1522T (47.11%) and J. svalbardensis JA-1T (38.88%) individually. The major fatty acid compositions of strain SNU WT3 were cylco-C17:0 (41.45%), C16:0 (33.86%) and C12:0 (5.87%). The major polar lipids were phosphatidylethanolamine, phosphatidylcholine, phosphatidylglycerol, and diphosphatidylglycerol. The quinone system was composed mainly of ubiquinone Q-8. The genome of strain SNU WT3 consists of 6,314,370 bp with a G + C content of 62.35%. Here, we describe a novel species of the genus Janthinobacterium, and the name Janthinobacterium tructae has been proposed with SNU WT3T (=KCTC 72518 = JCM 33613) as the type strain.

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Factors and methods to modulate DNA hybridization kinetics

Biotechnology Journal ◽

10.1002/biot.202000338 ◽

2021 ◽

pp. 2000338

Author(s):

Kingsley L. Wong ◽

Juewen Liu

Keyword(s):

Dna Hybridization

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INDUCTION OF INTRACHROMOSOMAL RECOMBINATION IN YEAST BY INHIBITION OF THYMIDYLATE BIOSYNTHESIS

Genetics ◽

10.1093/genetics/114.2.375 ◽

1986 ◽

Vol 114 (2) ◽

pp. 375-392

Author(s):

B A Kunz ◽

G R Taylor ◽

R H Haynes

Keyword(s):

Gene Conversion ◽

Dna Sequences ◽

Dna Hybridization ◽

Crossing Over ◽

Repeated Dna ◽

Yeast Saccharomyces Cerevisiae ◽

Haploid Strain ◽

Reciprocal Exchange ◽

Coli Plasmid ◽

Antifolate Drugs

ABSTRACT The biosynthesis of thymidylate in the yeast Saccharomyces cerevisiae can be inhibited by antifolate drugs. We have found that antifolate treatment enhances the formation of leucine prototrophs in a haploid strain of yeast carrying, on the same chromosome, two different mutant leu2 alleles separated by Escherichia coli plasmid sequences. That this effect is a consequence of thymine nucleotide depletion was verified by the finding that provision of exogenous thymidylate eliminates the increased production of Leu+ colonies. DNA hybridization analysis revealed that recombination, including reciprocal exchange, gene conversion and unequal sister-chromatid crossing over, between the duplicated genes gave rise to the induced Leu+ segregants. Although gene conversion unaccompanied by crossing over was responsible for the major fraction of leucine prototrophs, events involving reciprocal exchange exhibited the largest increase in frequency. These data show that recombination is induced between directly repeated DNA sequences under conditions of thymine nucleotide depletion. In addition, the results of this and previous studies are consistent with the possibility that inhibition of thymidylate biosynthesis in yeast may create a metabolic condition that provokes all forms of mitotic recombination.

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Pseudomonas eucalypticola sp. nov., a producer of antifungal agents isolated from Eucalyptus dunnii leaves

Scientific Reports ◽

10.1038/s41598-021-82682-7 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Yujing Liu ◽

Zhang Song ◽

Hualong Zeng ◽

Meng Lu ◽

Weiyao Zhu ◽

...

Keyword(s):

Dna Hybridization ◽

Antifungal Agents ◽

Novel Species ◽

Phytopathogenic Fungi ◽

Strictly Aerobic ◽

Rrna Sequence ◽

16S Rrna Sequence ◽

Eucalyptus Dunnii ◽

16S Rrna Sequence Analysis

AbstractPseudomonas are ubiquitously occurring microorganisms and are known for their ability to produce antimicrobials. An endophytic bacterial strain NP-1 T, isolated from Eucalyptus dunnii leaves, exhibits antifungal properties against five tested phytopathogenic fungi. The strain is a Gram-negative rod-shaped bacterium containing a single polar flagellum. It is strictly aerobic, grows at 4–37 °C, 2–5% NaCl, and pH 3–7. The 16S rRNA sequence analysis showed that NP-1 T belongs to the Pseudomonas genus. Phylogenetic analysis based on four concatenated partial genes (16S rDNA, gyrB, rpoB and rpoD) and the phylogenomic tree indicated that NP-1 T belongs to Pseudomonas fluorescens lineage but is distinct from any known Pseudomonas species. The G + C mol % of NP-1 T genome is 63.96, and the differences between NP-1 T and related species are larger than 1. The digital DNA-DNA hybridization and tetranucleotide signatures are 23.8 and 0.97, which clearly separates strain NP-1 T from its closest neighbours, Pseudomonas coleopterorum and Pseudomonas rhizosphaerae. Its phenotypic and chemotaxonomic features confirmed its differentiation from related taxa. The results from this polyphasic approach support the classification of NP-1 T as a novel species of Pseudomonas, and the name of Pseudomonas eucalypticola is thus proposed for this strain, whose type is NP-1 T (= CCTCC M2018494T = JCM 33572 T).

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