Selection and Biosensor Application of Aptamers for Small Molecules

Pfeiffer, Franziska; Mayer, Günter

doi:10.3389/fchem.2016.00025

Cited by 193 publications

(148 citation statements)

References 294 publications

(305 reference statements)

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“…Notably, many of the same properties useful for metabolic production analysis, including inexpensive (<$0.40/reaction) and freeze-dryable components, and a rapid rate of signal generation, make kinetic ribosensors well-suited as point-of-care diagnostics. By assembling ribosensors from aptamers for small molecule or protein biomarkers, plate- or paper-based assays could be developed for applications in medicine, biodefense or global health 50,51 .…”

Section: Discussionmentioning

confidence: 99%

Multi-state design of kinetically-controlled RNA aptamer ribosensors

Burke

Sparkman-Yager

Carothers

2017

Preprint

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Metabolite-responsive RNA regulators with kinetically-controlled responses are widespread in nature. By comparison, very limited success has been achieved creating kinetic control mechanisms for synthetic RNA aptamer devices. Here, we show that kinetically-controlled RNA aptamer ribosensors can be engineered using a novel approach for multi-state, cotranscriptional folding design. The design approach was developed through investigation of 29 candidate p-aminophenylalanine-responsive ribosensors. We show that ribosensors can be transcribed in situ and used to analyze metabolic production directly from engineered microbial cultures, establishing a new class of cell-free biosensors. We found that kinetically-controlled ribosensors exhibited 5-10 fold greater ligand sensitivity than a thermodynamically-controlled device. And, we further demonstrated that a second aptamer, promiscuous for aromatic amino acid binding, could be assembled into kinetic ribosensors with 45-fold improvements in ligand selectivity. These results have broad implications for engineering RNA aptamer devices and overcoming thermodynamic constraints on molecular recognition through the design of kinetically-controlled responses.

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Section: Discussionmentioning

confidence: 99%

Multi-state design of kinetically-controlled RNA aptamer ribosensors

Burke

Sparkman-Yager

Carothers

2017

Preprint

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“…Aptamers usually single-stranded RNA or DNA, which consist of 2-60 nucleotides, which specifically bind to the target, including organic molecules and cells. Aptasensors referred to biosensors using aptamers as biorecognition element and aptasensor were described in 1996 [36] which had been used in multiple sensing applications. Advantages using aptamers are aptamers can provide high stability and affinity.…”

Section: Aptasensormentioning

confidence: 99%

Recent Biosensors Technologies for Detection of Mycotoxin in Food Products

Rovina¹,

Shaeera²,

Vonnie³

et al. 2020

Mycotoxins and Food Safety

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Mycotoxins are chemically diverse and capable of inducing a wide diversity of acute and chronic symptoms, ranging from feed refusal to rapid death. Accurate detection and monitoring of mycotoxins is an essential component of the prevention, diagnosis, and remediation of mycotoxin-related issues in livestock and human food. Current trends in food analysis are focusing on the application of fast, simple procedure needed, and low-cost biosensor technologies that can detect with high sensitivity and selectivity different compounds associated with food safety. This chapter discussed the recent analytical methods-based biosensor technology for quantification of mycotoxins in food products. Mainly focus on the biosensor technology based on the immobilization of antibodies onto various nanomaterials such as nanoparticles, graphite, carbon nanotubes, and quantum dots. The nanomaterials are able to be functionalized with various biomolecules such as enzymes, antibodies, nucleic acids, DNA/RNA aptamers, bio-or artificial receptors that make them suitable for detection of various substances such as food toxins, bacteria, and other compounds important in food analysis. All the nanomaterials provide an effective platform for achieving high sensitivity that is similar and, in some cases, even better than conventional analytical methods. We believe that future trends will be emphasized on improving biosensor properties toward practical application in the food industry.

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“…Aptamers are short oligomers consisting of either amino acids, DNA, or RNA, which are designed to bind to a variety of different biomolecules or whole cells. [49][50][51][52] The utility of aptamers has previously been demonstrated in a number of applications such as in vivo biosensors, biomarker discovery, clinical drug discovery, and diagnostics (reviewed in 53,54 ). The first FDA-approved nucleotide aptamer based drug (Pegaptanib) was used for the treatment of neovascular age related macular degeneration.…”

Section: Introductionmentioning

confidence: 99%

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

et al. 2020

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Aberrant expression of the transcription factor double homeobox protein 4 (DUX4) can lead to a number of diseases including facio‐scapulo‐humeral muscular dystrophy (FSHD), acute lymphoblastic leukemia, and sarcomas. Inhibition of DUX4 may represent a therapeutic strategy for these diseases. By applying Systematic Evolution of Ligands by EXponential Enrichment (SELEX), we identified aptamers against DUX4 with specific secondary structural elements conveying high affinity to DUX4 as assessed by fluorescence resonance energy transfer and fluorescence polarization techniques. Sequences analysis of these aptamers revealed the presence of two consensus DUX4 motifs in a reverse complementary fashion forming hairpins interspersed with bulge loops at distinct positions that enlarged the binding surface with the DUX4 protein, as determined by crystal structure analysis. We demonstrate that insertion of specific structural elements into transcription factor binding oligonucleotides can enhance specificity and affinity.

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Selection and Biosensor Application of Aptamers for Small Molecules

Cited by 193 publications

References 294 publications

Multi-state design of kinetically-controlled RNA aptamer ribosensors

Multi-state design of kinetically-controlled RNA aptamer ribosensors

Recent Biosensors Technologies for Detection of Mycotoxin in Food Products

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

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