Zero-Length Protein–Nucleic Acid Crosslinking by Radical-Generating Coordination Complexes as a Probe for Analysis of Protein–DNA Interactionsin Vitroandin Vivo

Gavin, Igor M.; Melnik, Svitlana; Yurina, N. P.; Khabarova, M. I.; Bavykin, Sergei G.

doi:10.1006/abio.1998.2827

Cited by 16 publications

(8 citation statements)

References 29 publications

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“…Treatment of DNA or RNA with (OP) 2 Cu results in abstraction of a hydrogen atom from the sugar moiety, producing a carbon-based radical that can rearrange to an abasic site as a result of deglycosylation followed by fragmentation of the nucleic acid (39). Aldehydes and lactones formed at the site of scission may be used for conjugation of amino derivatives with the nucleic acid fragments (19,42). We recently used this idea to create a new method for sequence- 2 Cu chemistry for sample preparation on the silica minicolumn.…”

Section: Discussionmentioning

confidence: 99%

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

Bavykin

Akowski

Zakhariev

et al. 2001

Appl Environ Microbiol

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105

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We have developed a three-component system for microbial identification that consists of (i) a universal syringe-operated silica minicolumn for successive DNA and RNA isolation, fractionation, fragmentation, fluorescent labeling, and removal of excess free label and short oligonucleotides; (ii) microarrays of immobilized oligonucleotide probes for 16S rRNA identification; and (iii) a portable battery-powered device for imaging the hybridization of fluorescently labeled RNA fragments with the arrays. The minicolumn combines a guanidine thiocyanate method of nucleic acid isolation with a newly developed hydroxyl radical-based technique for DNA and RNA labeling and fragmentation. DNA and RNA can also be fractionated through differential binding of double-and single-stranded forms of nucleic acids to the silica. The procedure involves sequential washing of the column with different solutions. No vacuum filtration steps, phenol extraction, or centrifugation is required. After hybridization, the overall fluorescence pattern is captured as a digital image or as a Polaroid photo. This three-component system was used to discriminate Escherichia coli, Bacillus subtilis, Bacillus thuringiensis, and human HL60 cells. The procedure is rapid: beginning with whole cells, it takes approximately 25 min to obtain labeled DNA and RNA samples and an additional 25 min to hybridize and acquire the microarray image using a stationary image analysis system or the portable imager.Traditional methods of bacterial identification are usually based on morphological and/or physiological features of a microorganism or on analysis of 16S rRNA gene sequences (59). These methods can require considerable amounts of time. Recently, PCR and other amplification technologies were introduced for bacterial identification (33). Immunological methods (16) and mass spectrometry (18) have also been adapted for this purpose but are expensive or cumbersome. DNA microchip technology (37) advantageously combines a rapid, highthroughput platform for nucleic acid hybridization with low cost and the potential for automation, although sample preparation procedures, including DNA and RNA isolation, fragmentation, and labeling, are still limiting steps (32,44). Another limitation of microarray technology is the lack of portable and inexpensive devices for the acquisition of hybridization patterns (5). We have addressed these shortcomings through the development of a rapid and simple system for sample preparation and microarray analysis. MATERIALS AND METHODSPreparation of silica syringe-operated columns. A silica suspension (50 l) was prepared as described previously (4) and loaded into a 25-mm-long sterile centrifuge device containing a polysulfone filter with a diameter of 6.5 mm and a pore size of 0.2 m (Whatman, Fairfield, N.J.). The column was sealed against the end of a 10-ml syringe without any glue, using the O-ring from a 1.5-ml screw-cap microcentrifuge tube introduced between the syringe and the top of the column, and washed once with 500 l of diethylpyro...

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Section: Discussionmentioning

confidence: 99%

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

Bavykin

Akowski

Zakhariev

et al. 2001

Appl Environ Microbiol

Self Cite

105

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“…In addition to the production of antioxidative enzymes, microorganisms have a non-enzymatic oxidative stress defense mechanism relying on the chelation of metal ions. 76 Fe 2+ and Cu 2+ are the most prevalent and active ions generated in free-radical formation. Fe 2+ can produce HO• through the Fenton reaction, and Cu 2+ released from chromatin can also catalyze HO• generation.…”

Section: Metal Ion Chelationmentioning

confidence: 99%

Oxidative stress tolerance and antioxidant capacity of lactic acid bacteria as probiotic: a systematic review

2020

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Lactic acid bacteria (LAB) are the most frequently used probiotics in fermented foods and beverages and as food supplements for humans or animals, owing to their multiple beneficial features, which appear to be partially associated with their antioxidant properties. LAB can help improve food quality and flavor and prevent numerous disorders caused by oxidation in the host. In this review, we discuss the oxidative stress tolerance, the antioxidant capacity related herewith, and the underlying mechanisms and signaling pathways in probiotic LAB. In addition, we discuss appropriate methods used to evaluate the antioxidant capacity of probiotic LAB. The aim of the present review is to provide an overview of the current state of the research associated with the oxidative stress tolerance and antioxidant capacity of LAB.

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“…In the present study, it was found that ferric ion chelating activity of all LABs was 58.96% on average and there was no statistical difference between the species. It was demonstrated that the studied microorganisms exhibited non-enzymatic (Gavin et al 1998) defense mechanisms such as metal ion chelation. The result of this study showed that the strains from LAB fermented sucuk can chelate metal ions like ferrous ions and inhibiting the catalysis of oxidation by metal ions.…”

Section: Fe +2 Ion Chelating Activitymentioning

confidence: 99%

Antioxidant activitiy of Lactobacillus plantarum , Lactobacillus sake and Lactobacillus curvatus strains isolated from fermented Turkish Sucuk

Düz

Doğan

2020

An. Acad. Bras. Ciênc.

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Zero-Length Protein–Nucleic Acid Crosslinking by Radical-Generating Coordination Complexes as a Probe for Analysis of Protein–DNA Interactionsin Vitroandin Vivo

Cited by 16 publications

References 29 publications

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

Portable System for Microbial Sample Preparation and Oligonucleotide Microarray Analysis

Oxidative stress tolerance and antioxidant capacity of lactic acid bacteria as probiotic: a systematic review

Antioxidant activitiy of Lactobacillus plantarum , Lactobacillus sake and Lactobacillus curvatus strains isolated from fermented Turkish Sucuk

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