Engineering a Synthetic Dopamine-Responsive Riboswitch for In Vitro Biosensing

The detection of chemicals using natural allosteric transcription factors is a powerful strategy for point-of-use molecular sensing, particularly using fieldable cell-free gene expression (CFE) systems. However, the reliance of detection schemes on characterized protein-based sensors limits the number of measurable analytes. One alternative solution to this issue is to develop new sensors by generating RNA aptamers against the target analyte and then incorporating them directly into a riboswitch scaffold for ligand-inducible genetic control of a reporter protein. However, this strategy has not generated more than a handful of successful portable cell-free molecular sensors. To address this gap, here we convert dopamine-binding aptamers into functional dopamine-sensing riboswitches that regulate gene expression in a freeze-dried CFE reaction. We then develop an assay for direct detection and semi-quantification of dopamine in human urine. We anticipate that this work will be broadly applicable for converting many in vitro-generated RNA aptamers into fieldable molecular diagnostics.

Current status and future directions for a neurotoxicity hazard assessment framework that integrates in silico approaches

Neurotoxicology is the study of adverse effects on the structure or function of the developing or mature adult nervous system following exposure to chemical, biological, or physical agents. The development of more informative alternative methods to assess developmental (DNT) and adult (NT) neurotoxicity induced by xenobiotics is critically needed. The use of such alternative methods including in silico approaches that predict DNT or NT from chemical structure (e.g., statistical-based and expert rule-based systems) is ideally based on a comprehensive understanding of the relevant biological mechanisms. This paper discusses known mechanisms alongside the current state of the art in DNT/NT testing. In silico approaches available today that support the assessment of neurotoxicity based on knowledge of chemical structure are reviewed, and a conceptual framework for the integration of in silico methods with experimental information is presented. Establishing this framework is essential for the development of protocols, namely standardized approaches, to ensure that assessments of NT and DNT based on chemical structures are generated in a transparent, consistent, and defendable manner.

In silico identification of protein targets for chemical neurotoxins using ToxCast in vitro data and read-across within the QSAR toolbox

This study evaluates the application of QSAR Toolbox and ToxCast screening data to identify neurological targets for pyrethroids.

There are many mechanisms of neurotoxicity that are initiated by the interaction of chemicals with different neurological targets. Under the U.S. Environmental Protection Agency's ToxCast program, the biological activity of thousands of chemicals was screened in biochemical and cell-based assays in a high-throughput manner. Two hundred sixteen assays in the ToxCast screening database were identified as targeting a total of 123 proteins having neurological functions according to the Gene Ontology database. Data from these assays were imported into the Organization for Economic Co-operation and Development QSAR Toolbox and used to predict neurological targets for chemical neurotoxins. Two sets of data were generated: one set was used to classify compounds as active or inactive and another set, composed of AC₅₀s for only active compounds, was used to predict AC₅₀ values for unknown chemicals. Chemical grouping and read-across within the QSAR Toolbox were used to identify neurologic targets and predict interactions for pyrethroids, a class of compounds known to elicit neurotoxic effects in humans. The classification prediction results showed 79% accuracy while AC₅₀ predictions demonstrated mixed accuracy compared with the ToxCast screening data.

Development of a 2,4-dinitrotoluene-responsive synthetic riboswitch in E. coli cells

Riboswitches are RNA sequences that regulate expression of associated downstream genes in response to the presence or absence of specific small molecules. A novel riboswitch that activates protein translation in E. coli cells in response to 2,4-dinitrotoluene (DNT) has been engineered. A plasmid library was constructed by incorporation of 30 degenerate bases between a previously described trinitrotoluene aptamer and the ribosome binding site. Screening was performed by placing the riboswitch library upstream of the Tobacco Etch Virus (TEV) protease coding sequence in one plasmid; a second plasmid encoded a FRET-based construct linked with a peptide containing the TEV protease cleavage site. Addition of DNT to bacterial culture activated the riboswitch, initiating translation of TEV protease. In turn, the protease cleaved the linker in the FRET-based fusion protein, causing a change in fluorescence. This new riboswitch exhibited a 10-fold increase in fluorescence in the presence of 0.5 mM DNT compared to the system without target.

A Comparison of 2-part and 3-part Nanoparticle-Based Sensors

There has long been a drive to produce sensors with ever-increasing sensitivity and selectivity, while also achieving robustness and ease of use. Nanoparticle-based sensing approaches have generated a great deal of attention and excitement, because they possess such qualities. For these assays to function properly, it requires the integration of molecular recognition motifs and materials with outstanding optical properties. Aptamers are DNA or RNA sequences that bind analytes with high specificity, which makes them a suitable choice as recognition elements. Changes in the surface plasmon resonance (SPR) of gold nanoparticles (AuNPS) as a function of interparticle distance, has been used as an optical signal to detect the presence of different species in solution by the naked eye. In this work, we coated gold nanoparticles with short oligonucleotides and aptamers for the design of sensors that can be used under different conditions, including salt concentration, pH and temperatures. Three aptamer sensors were developed using this approach 1) riboflavin, as a general indicator of biological activity, 2) ricin, a toxin that is of broad interest, and 3) theophylline, an adenosine antagonist. Our designs are based on two approaches, the first method consisted of the use of two sets of AuNPs, each coated with a short oligonucleotide complementary to a different part of the sequence of the aptamer of interest. Hybridization of the DNA-coated particles (DNA-AuNPs) with the free aptamer produced aggregates, i.e. 3-part design. The second approach consisted of the use of only two sets of DNA-AuNPs, one coated with an aptamer that contains a thiol group in its 5′ end, and the second set of AuNPs coated with a sequence complementary to part of the aptamer. Hybridization of these two sets of particles produced aggregates, i.e. 2-part design. In both cases, the presence of the analyte promoted a change in the conformation of the aptamer, which caused the dehybridization of the complementary sequences. This conformational change of the aptamer upon binding of the analyte produced the dissociation of the nanoparticle aggregates, which is translated into a change in the color of the suspensions from blue to red. In this presentation, we will compare the advantages and disadvantages associated with a 3-part versus a 2-part nanoparticle-oligonucleotide reporting assay.