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Article ; Online: Electrochemical Immuno- and Aptamer-Based Assays for Bacteria: Pros and Cons over Traditional Detection Schemes.

Jamal, Rimsha Binte / Shipovskov, Stepan / Ferapontova, Elena E

2020 Volume 20, Issue 19

Abstract: Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria ...

Abstract	Microbiological safety of the human environment and health needs advanced monitoring tools both for the specific detection of bacteria in complex biological matrices, often in the presence of excessive amounts of other bacterial species, and for bacteria quantification at a single cell level. Here, we discuss the existing electrochemical approaches for bacterial analysis that are based on the biospecific recognition of whole bacterial cells. Perspectives of such assays applications as emergency-use biosensors for quick analysis of trace levels of bacteria by minimally trained personnel are argued.
MeSH term(s)	Aptamers, Nucleotide ; Bacteria ; Biosensing Techniques ; Electrochemical Techniques ; Humans
Chemical Substances	Aptamers, Nucleotide
Language	English
Publishing date	2020-09-28
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2052857-7
ISSN	1424-8220 ; 1424-8220
ISSN (online)	1424-8220
ISSN	1424-8220
DOI	10.3390/s20195561
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Article ; Online: Cellulase-Linked Immunomagnetic Microbial Assay on Electrodes: Specific and Sensitive Detection of a Single Bacterial Cell.

Pankratov, Dmitrii / Bendixen, Mads / Shipovskov, Stepan / Gosewinkel, Ulrich / Ferapontova, Elena E

Analytical chemistry

2020 Volume 92, Issue 18, Page(s) 12451–12459

Abstract: Pathogen-associated infections represent one of the major threats to human health and require reliable methods for immediate and robust identification of pathogenic microorganisms. Here, an inexpensive cellulase-linked immunomagnetic methodology was ... ...

Abstract	Pathogen-associated infections represent one of the major threats to human health and require reliable methods for immediate and robust identification of pathogenic microorganisms. Here, an inexpensive cellulase-linked immunomagnetic methodology was developed for the specific and ultrasensitive analysis of bacteria at their single-cell levels within a 3 h procedure. Detection of a model bacterium,
MeSH term(s)	Bacillus subtilis/cytology ; Bacillus subtilis/isolation & purification ; Bacillus subtilis/metabolism ; Cellulase/chemistry ; Cellulase/metabolism ; Electrodes ; Enterobacter/cytology ; Enterobacter/isolation & purification ; Enterobacter/metabolism ; Escherichia coli/cytology ; Escherichia coli/isolation & purification ; Escherichia coli/metabolism ; Immunomagnetic Separation ; Pseudomonas putida/cytology ; Pseudomonas putida/isolation & purification ; Pseudomonas putida/metabolism ; Salmonella enteritidis/cytology ; Salmonella enteritidis/isolation & purification ; Salmonella enteritidis/metabolism ; Single-Cell Analysis ; Staphylococcus aureus/cytology ; Staphylococcus aureus/isolation & purification ; Staphylococcus aureus/metabolism
Chemical Substances	Cellulase (EC 3.2.1.4)
Language	English
Publishing date	2020-08-28
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.0c02262
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Article ; Online: Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

Kékedy-Nagy, László / Shipovskov, Stepan / Ferapontova, Elena E

Analytical chemistry

2016 Volume 88, Issue 16, Page(s) 7984–7990

Abstract: Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron ... ...

Abstract	Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. Clima , L. Gothelf , K. Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.
Language	English
Publishing date	2016-07-29
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.6b01020
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Article: Cellulase-Linked Immunomagnetic Microbial Assay on Electrodes: Specific and Sensitive Detection of a Single Bacterial Cell

Pankratov, Dmitrii / Bendixen, Mads / Shipovskov, Stepan / Gosewinkel, Ulrich / Ferapontova, Elena E

Analytical chemistry. 2020 Aug. 17, v. 92, no. 18

2020

Abstract	Pathogen-associated infections represent one of the major threats to human health and require reliable methods for immediate and robust identification of pathogenic microorganisms. Here, an inexpensive cellulase-linked immunomagnetic methodology was developed for the specific and ultrasensitive analysis of bacteria at their single-cell levels within a 3 h procedure. Detection of a model bacterium, Escherichia coli, was performed in a sandwich reaction with E. coli-specific either aptamer or antibody (Ab)-modified magnetic beads (MBs) and Ab/aptamer reporter molecules linked to cellulase. The cellulase-labeled immuno-aptamer sandwich applied onto nitrocellulose-film-modified electrodes digested the film and changed its electrical conductivity. Electrode’s chronocoulometric responses at 0.3 V, in the absence of any redox indicators, allowed a single E. coli cell detection and from 1 to 4 × 10⁴ CFU mL–¹ E. coli quantification. No interference/cross-reactivity from Salmonella enteritidis, Enterobacter agglomerans, Pseudomonas putida, Staphylococcus aureus, and Bacillus subtilis was observed when the assay was performed on Ab-modified MBs, and E. coli could be quantified in tap water and milk. This electrochemically label-free methodology is sufficiently fast, highly specific, and sensitive to be used in direct in-field applications. The assay can be adapted for specific detection of other bacterial strains of either the same or different species and offers new analytical tools for fast, specific, and reliable analysis of bacteria in the clinic, food, and environment.
Keywords	Bacillus subtilis ; Escherichia coli ; Pantoea agglomerans ; Pseudomonas putida ; Salmonella Enteritidis ; Staphylococcus aureus ; analytical chemistry ; antibodies ; bacteria ; electrical conductivity ; electrochemistry ; electrodes ; endo-1,4-beta-glucanase ; human health ; magnetism ; milk ; oligonucleotides ; tap water
Language	English
Dates of publication	2020-0817
Size	p. 12451-12459.
Publishing place	American Chemical Society
Document type	Article
Note	NAL-AP-2-clean
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021/acs.analchem.0c02262
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Article: Electrospray ionization mass spectrometry in enzymology: uncovering the mechanisms of two-substrate reactions.

Shipovskov, Stepan / Reimann, Curt T

The Analyst

2007 Volume 132, Issue 5, Page(s) 397–402

Abstract: The purpose of this review is to draw attention to the use of electrospray ionization mass spectrometry (ESI-MS) for monitoring the course of enzyme-substrate interactions, in the particular case of complex systems in which two substrates participate. ... ...

Abstract	The purpose of this review is to draw attention to the use of electrospray ionization mass spectrometry (ESI-MS) for monitoring the course of enzyme-substrate interactions, in the particular case of complex systems in which two substrates participate. The determination and characterization of intra-molecular reactions, especially those that occur in the enzyme active site, is not a trivial task in chemical kinetics, typically requiring long measurement times and relatively expensive techniques such as nuclear magnetic resonance (NMR), X-ray crystallography or electron microscopy (EM). However, nowadays almost all laboratories are equipped with or else have access to the ESI-MS technique. The aim of this review is to focus on the possibilities of employing even quite simple MS equipment to tackle different applications in studies of complex enzymatic systems.
MeSH term(s)	Biomarkers/analysis ; Catalysis ; Clinical Enzyme Tests ; Enzymes/analysis ; Humans ; Models, Molecular ; Spectrometry, Mass, Electrospray Ionization/methods ; Substrate Specificity
Chemical Substances	Biomarkers ; Enzymes
Language	English
Publishing date	2007-05
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	210747-8
ISSN	0003-2654
ISSN	0003-2654
DOI	10.1039/b615394c
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Article: Tyrosinase: polybrene noncovalent complexes in water-ethanol mixtures.

Shipovskov, Stepan / Levashov, Andrey

Biotechnology and bioengineering

2003 Volume 84, Issue 2, Page(s) 258–263

Abstract: Formation of noncovalent complexes between tyrosinase from mushrooms and a cationic polyelectrolyte, polybrene (PB, poly (1,5-dimethyl-1,5-diazaundecamethyelene) bromide), was shown to activate and stabilize tyrosinase in water-ethanol mixtures. In the ... ...

Abstract	Formation of noncovalent complexes between tyrosinase from mushrooms and a cationic polyelectrolyte, polybrene (PB, poly (1,5-dimethyl-1,5-diazaundecamethyelene) bromide), was shown to activate and stabilize tyrosinase in water-ethanol mixtures. In the reaction of catechol oxidation in aqueous solutions, catalytic activity (k(cat)) of tyrosinase-PB complex ([PB]/[tyrosinase] molar ratio 100:1, per mole of polymer) in a wide range of pH was higher than that of free tyrosinase. In aqueous solutions and in water-ethanol mixtures at moderate concentrations of ethanol (10-40% v/v), the value of k(cat) of tyrosinase-PB complex exceeded the activity of free enzyme, from 1.2-2-fold, accompanied by the essential (up to 10-fold) increase in the value of the specificity constant (k(cat)/K(m)). The results are of practical importance for the construction of biocatalysts working successfully in polar organic media.
MeSH term(s)	Agaricales/enzymology ; Catalysis ; Catechols/metabolism ; Enzymes, Immobilized/metabolism ; Ethanol/chemistry ; Hexadimethrine Bromide/chemistry ; Hydrogen-Ion Concentration ; Kinetics ; Monophenol Monooxygenase/chemistry ; Monophenol Monooxygenase/metabolism ; Oxidoreductases/chemistry ; Oxidoreductases/metabolism ; Protein Binding ; Solvents/chemistry ; Water/chemistry
Chemical Substances	Catechols ; Enzymes, Immobilized ; Solvents ; Water (059QF0KO0R) ; Ethanol (3K9958V90M) ; Hexadimethrine Bromide (4C905MSK4W) ; Oxidoreductases (EC 1.-) ; Monophenol Monooxygenase (EC 1.14.18.1) ; catechol (LF3AJ089DQ)
Language	English
Publishing date	2003-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	280318-5
ISSN	1097-0290 ; 0006-3592
ISSN (online)	1097-0290
ISSN	0006-3592
DOI	10.1002/bit.10762
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Article ; Online: A robust method of determination of high concentrations of peptides and proteins.

Levashov, Pavel A / Sutherland, Duncan S / Besenbacher, Flemming / Shipovskov, Stepan

Analytical biochemistry

2009 Volume 395, Issue 1, Page(s) 111–112

Abstract: In this paper, we pioneer application of a unique method of protein determination by coloring peptide bonds for analysis of a variety of biomolecules with different grades of purity (e.g., oligopeptides, membrane, and glycol proteins). We demonstrated ... ...

Abstract	In this paper, we pioneer application of a unique method of protein determination by coloring peptide bonds for analysis of a variety of biomolecules with different grades of purity (e.g., oligopeptides, membrane, and glycol proteins). We demonstrated that the calibration curve for all studied molecules is universal and linear within 0.1 to 1.2mg protein content range. The assay thus can be used to analyze peptides without preliminary dilutions and calibration in up to 1g/ml solutions of peptides, which is crucial for many biotechnological processes, such as development of coatings, scaffolds, and biocompatible materials.
MeSH term(s)	Calibration ; Colorimetry/methods ; Copper Sulfate ; Indicators and Reagents ; Peptides/analysis ; Proteins/analysis
Chemical Substances	Indicators and Reagents ; Peptides ; Proteins ; Copper Sulfate (LRX7AJ16DT)
Language	English
Publishing date	2009-12-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1110-1
ISSN	1096-0309 ; 0003-2697
ISSN (online)	1096-0309
ISSN	0003-2697
DOI	10.1016/j.ab.2009.08.017
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Article: Bioelectrocatalytic detection of theophylline at theophylline oxidase electrodes.

Ferapontova, Elena E / Shipovskov, Stepan / Gorton, Lo

Biosensors & bioelectronics

2007 Volume 22, Issue 11, Page(s) 2508–2515

Abstract: Bioelectrocatalytic oxidation of theophylline was studied at gold and graphite electrodes modified with microbial theophylline oxidase (ThOx), a multi-cofactor redox enzyme capable of selective oxidation of theophylline. Gold electrodes were additionally ...

Abstract	Bioelectrocatalytic oxidation of theophylline was studied at gold and graphite electrodes modified with microbial theophylline oxidase (ThOx), a multi-cofactor redox enzyme capable of selective oxidation of theophylline. Gold electrodes were additionally modified with self-assembled monolayers (SAMs) of (-OH)- and (-NH(2))-terminated alkanethiols of different chain lengths, to achieve compatibility between ThOx and the electrode surface. On graphite, ThOx was either physically co-adsorbed with a surfactant didodecyldimethylammonium bromide (DDAB), or entrapped within an Os-redox-polymer film. At all electrodes, ThOx was bioelectrocatalytically active; direct electrochemistry of ThOx in the absence of theophylline was followed only at the SAM-modified gold electrodes. Direct electrochemistry of ThOx correlated with redox transformations of the heme domain of ThOx, with a E(o/)of -110+/-2 mV versus Ag\|AgCl, at pH 7. Bioelectrocatalytic oxidation of theophylline was optimal at mixed (-OH)/(-NH(2))-terminated SAMs; co-adsorption of ThOx with DDAB improved the bioelectrocatalytic performance of the ThOx-electrode. In both cases, the response to theophylline was within the mM range. Alternatively, a reagentless ThOx-electrode based on ThOx cross-linked within the Os-redox-polymer matrix demonstrated a linear response to theophylline within the physiologically important 0.02-0.6mM (3.6-72 mg l(-1)) concentration range with a sensitivity of 52.1+/-7.8 mA cm(-2)M(-1).
MeSH term(s)	Biosensing Techniques/instrumentation ; Biosensing Techniques/methods ; Catalysis ; Coated Materials, Biocompatible/chemistry ; Electrochemistry/instrumentation ; Electrochemistry/methods ; Enzymes, Immobilized/chemistry ; Microelectrodes ; Oxidoreductases/chemistry ; Reproducibility of Results ; Sensitivity and Specificity ; Theophylline/analysis ; Theophylline/chemistry
Chemical Substances	Coated Materials, Biocompatible ; Enzymes, Immobilized ; Theophylline (C137DTR5RG) ; Oxidoreductases (EC 1.-) ; theophylline oxidase (EC 1.5.99.-)
Language	English
Publishing date	2007-05-15
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	1011023-9
ISSN	1873-4235 ; 0956-5663
ISSN (online)	1873-4235
ISSN	0956-5663
DOI	10.1016/j.bios.2006.09.034
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Article: Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes

KeÌkedy-Nagy, LaÌszloÌ / Ferapontova Elena E / Shipovskov Stepan

Analytical chemistry. 2016 Aug. 16, v. 88, no. 16

2016

Abstract	Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the âonâoffâ signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami, E.; Clima, L.; Gothelf, K.; Ferapontova, E. E. Anal. Chem. 2011, 83, 1594) providing the robust âoffâonâ nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.
Keywords	DNA ; electrochemistry ; electrodes ; electron transfer ; gold ; hybridization ; methylene blue
Language	English
Dates of publication	2016-0816
Size	p. 7984-7990.
Publishing place	American Chemical Society
Document type	Article
ZDB-ID	1508-8
ISSN	1520-6882 ; 0003-2700
ISSN (online)	1520-6882
ISSN	0003-2700
DOI	10.1021%2Facs.analchem.6b01020
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Article ; Online: Development of a lipase-based optical assay for detection of DNA.

Pinijsuwan, Suttiporn / Shipovskov, Stepan / Surareungchai, Werasak / Ferapontova, Elena E / Gothelf, Kurt V

Organic & biomolecular chemistry

2011 Volume 9, Issue 18, Page(s) 6352–6356

Abstract: A lipase-based assay for detection of specific DNA sequences has been developed. Lipase from Candida antarctica was conjugated to DNA and captured on magnetic beads in a sandwich assay, in which the binding was dependent on the presence of a specific ... ...

Abstract	A lipase-based assay for detection of specific DNA sequences has been developed. Lipase from Candida antarctica was conjugated to DNA and captured on magnetic beads in a sandwich assay, in which the binding was dependent on the presence of a specific target DNA. For amplification and to generate a detectable readout the captured lipase was applied to an optical assay that takes advantage of the enzymatic activity of lipase. The assay applies p-nitrophenol octanoate (NPO) as the substrate and in the presence of lipase the ester is hydrolyzed to p-nitrophenolate which has a strong absorbance at 405 nm. The method provides detection a detection limit of 200 fmol target DNA and it was able to distinguish single base mismatches from the fully complementary target.
MeSH term(s)	Base Pair Mismatch ; Biosensing Techniques/methods ; Candida/enzymology ; DNA/analysis ; Fungal Proteins ; Lipase/metabolism ; Nitrophenols/metabolism ; Sensitivity and Specificity
Chemical Substances	Fungal Proteins ; Nitrophenols ; DNA (9007-49-2) ; Lipase (EC 3.1.1.3) ; lipase B, Candida antarctica (EC 3.1.1.3) ; 4-nitrophenol (Y92ZL45L4R)
Language	English
Publishing date	2011-09-21
Publishing country	England
Document type	Evaluation Studies ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2097583-1
ISSN	1477-0539 ; 1477-0520
ISSN (online)	1477-0539
ISSN	1477-0520
DOI	10.1039/c0ob01165g
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