Aptamers against pathogenic microorganisms

Davydova, Anna; Vorobjeva, M. A.; Pyshnyi, D. V.; Altman, Sidney; Vlassov, Valentin V.; Venyaminova, Alya G.

doi:10.3109/1040841x.2015.1070115

Cited by 89 publications

(59 citation statements)

References 194 publications

(247 reference statements)

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“…Advances in generating synthetic riboswitches have accelerated their application as genetic controllers in the areas of molecular sensors, metabolic pathway optimization (Cress et al, ; Dietrich et al, ; Liu et al, ; McKeague et al, ; Rogers et al, ) and therapeutic applications (Davydova et al, ; Lee et al, ). In the past decade, several natural and artificial RNA‐based sensors have been engineered to respond to a wide range of metabolites, including folinic acid (Trausch et al, ), theophylline (Beisel et al, ; Lynch et al, ; Michener and Smolke, ; Topp et al, ; Wachsmuth et al, ), xanthine (Beisel et al, ), tetracycline (Beisel et al, ; Weigand and Suess, ), ammeline (Dixon et al, ), cyclic‐di‐GMP (Kellenberger et al, ; Lynch et al, ), cyclic‐di‐AMP (Kellenberger et al, ), β‐catenin (Bloom et al, ), thiamine 5′‐pyrophosphate (TPP) (You et al, ), guanine (Paige et al, ; You et al, ), adenine (You et al, ), S‐adenosyl‐methionine (SAM) (Paige et al, ; You et al, ), adenosine 5‐diphosphate (ADP) (Paige et al, ), guanosine 5‐triphosphate (GTP) (Paige et al, ), flavin mononucleotide (FMN) (Meyer et al, ), lysine (Yang et al, ; Zhou and Zeng, ), glucosamine 6‐phosphate (Lee and Oh, ) in prokaryotic, eukaryotic, and mammalian cells through various mechanisms.…”

Section: Introductionmentioning

confidence: 99%

Naringenin‐responsive riboswitch‐based fluorescent biosensor module for Escherichia coli co‐cultures

Xiu

Jang

Jones

et al. 2017

Biotech & Bioengineering

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The ability to design and construct combinatorial synthetic metabolic pathways has far exceeded our capacity for efficient screening and selection of the resulting microbial strains. The need for high-throughput rapid screening techniques is of upmost importance for the future of synthetic biology and metabolic engineering. Here we describe the development of an RNA riboswitch-based biosensor module with dual fluorescent reporters, and demonstrate a high-throughput flow cytometry-based screening method for identification of naringenin over producing Escherichia coli strains in co-culture. Our efforts helped identify a number of key operating parameters that affect biosensor performance, including the selection of promoter and linker elements within the sensor-actuator domain, and the effect of host strain, fermentation time, and growth medium on sensor dynamic range. The resulting biosensor demonstrates a high correlation between specific fluorescence of the biosensor strain and naringenin titer produced by the second member of the synthetic co-culture system. This technique represents a novel application for synthetic microbial co-cultures and can be expanded from naringenin to any metabolite if a suitable riboswitch is identified. The co-culture technique presented here can be applied to a variety of target metabolites in combination with the SELEX approach for aptamer design. Due to the compartmentalization of the two genetic constructs responsible for production and detection into separate cells and application as independent modules of a synthetic microbial co-culture we have subsequently reduced the need for re-optimization of the producer module when the biosensor is replaced or removed. Biotechnol. Bioeng. 2017;114: 2235-2244. © 2017 Wiley Periodicals, Inc.

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Section: Introductionmentioning

confidence: 99%

Naringenin‐responsive riboswitch‐based fluorescent biosensor module for Escherichia coli co‐cultures

Xiu

Jang

Jones

et al. 2017

Biotech & Bioengineering

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“…Nowadays, synthetic fluorescently-labeled NA-aptamers have gained increasing attention as prospective tools in nanobiotechnology, diagnostics, and therapy [ 124 , 125 , 126 , 127 , 128 , 129 , 130 ]. Pyrene-labeled aptamers integrated into various biosensing systems are used for the detection of a broad range of biologically-relevant targets, such as proteins, small molecules, and metal ions (IgE, PDGF, lysozyme, thrombin, cocaine, l -argininamide, ATP, GTP, adenosine, potassium ions, and others).…”

Section: Fluorescent Biosensorsmentioning

confidence: 99%

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

et al. 2017

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In this review, we summarize the recent advances in the use of pyrene-modified oligonucleotides as a platform for functional nucleic acid-based constructs. Pyrene is of special interest for the development of nucleic acid-based tools due to its unique fluorescent properties (sensitivity of fluorescence to the microenvironment, ability to form excimers and exciplexes, long fluorescence lifetime, high quantum yield), ability to intercalate into the nucleic acid duplex, to act as a π-π-stacking (including anchoring) moiety, and others. These properties of pyrene have been used to construct novel sensitive fluorescent probes for the sequence-specific detection of nucleic acids and the discrimination of single nucleotide polymorphisms (SNPs), aptamer-based biosensors, agents for binding of double-stranded DNAs, and building blocks for supramolecular complexes. Special attention is paid to the influence of the design of pyrene-modified oligonucleotides on their properties, i.e., the structure-function relationships. The perspectives for the applications of pyrene-modified oligonucleotides in biomolecular studies, diagnostics, and nanotechnology are discussed.

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“…So far,o ver 48 different aptamers against different microorganisms have been screened by in vitro SELEX in different laboratories. [90] The targets range from bacteria (S. enterica serovar Typhimurium, [91] Staphylococcus aureus, [92] E. coli [93] ), viruses (HIV-1, [94,95] influenza viruses, [37,96,97] hepatitis viruses [98][99][100] )t ou nicellular parasites( Trypanosoma brucei, [101,102] Plasmodium falciparum [103] ). Aptamers can be used as recognizing elements for microorganism detection by specifically binding to the surface determinants.T he high affinity ands electivity allow aptamerst od istinguish similarp roteins.…”

Section: Aptamers For Capture and Detectionofmicroorganismsmentioning

confidence: 99%

Recent Progress in Aptamer‐Based Functional Probes for Bioanalysis and Biomedicine

Zhang

Zhou

Zhu

et al. 2016

Chemistry A European J

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Nucleic acid aptamers are short synthetic DNA or RNA sequences that can bind to a wide range of targets with high affinity and specificity. In recent years, aptamers have attracted increasing research interest due to their unique features of high binding affinity and specificity, small size, excellent chemical stability, easy chemical synthesis, facile modification, and minimal immunogenicity. These properties make aptamers ideal recognition ligands for bioanalysis, disease diagnosis, and cancer therapy. This review highlights the recent progress in aptamer selection and the latest applications of aptamer-based functional probes in the fields of bioanalysis and biomedicine.

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Aptamers against pathogenic microorganisms

Cited by 89 publications

References 194 publications

Naringenin‐responsive riboswitch‐based fluorescent biosensor module for Escherichia coli co‐cultures

Naringenin‐responsive riboswitch‐based fluorescent biosensor module for Escherichia coli co‐cultures

Recent Advances in Nucleic Acid Targeting Probes and Supramolecular Constructs Based on Pyrene-Modified Oligonucleotides

Recent Progress in Aptamer‐Based Functional Probes for Bioanalysis and Biomedicine

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