Engineering biosensors with extended, narrowed, or arbitrarily edited dynamic range

Label-free electrochemiluminescent detection of DNA by hybridization with a molecular beacon to form hemin/G-quadruplex architecture for signal inhibition

A facile label-free electrochemiluminescent (ECL) DNA sensor was designed using a molecular beacon with a guanine-rich stem as a recognition probe. The ECL emission was produced from surface unpassivated CdTe quantum dots (QDs) co-immobilized with colloidal gold nanoparticles (AuNPs) on a chitosan-modified electrode surface. The molecular beacon was adsorbed onto the AuNPs by the thiolated stem. Upon the hybridization of the molecular beacon with target DNA to open the cycle in the presence of hemin, the dissociated guanine-rich sequence could conjugate hemin to form a G-quadruplex architecture. The formed DNAzyme then catalyzed the reduction of dissolved oxygen, the endogenous coreactant for ECL emission of QDs, leading to a decrease in ECL signal. The variations in surface morphology during the fabrication and recognition processes of the ECL sensor were characterized by atomic force microscopy and electrochemical impedance spectroscopy. The ECL signal inhibition depended linearly on the logarithmic value of DNA concentration ranging from 5.0 fM to 0.1 nM, with a detection limit of 0.9 fM. This proposed label-free method is a promising application of QDs-based ECL emission for ultrasensitive DNA assay.

Enzymatic AND logic gate with sigmoid response induced by photochemically controlled oxidation of the output

We report a study of a system which involves an enzymatic cascade realizing an AND logic gate, with an added photochemical processing of the output, allowing the gate's response to be made sigmoid in both inputs. New functional forms are developed for quantifying the kinetics of such systems, specifically designed to model their response in terms of signal and information processing. These theoretical expressions are tested for the studied system, which also allows us to consider aspects of biochemical information processing such as noise transmission properties and control of timing of the chemical and physical steps.

Using distal-site mutations and allosteric inhibition to tune, extend, and narrow the useful dynamic range of aptamer-based sensors

Here we demonstrate multiple, complementary approaches by which to tune, extend, or narrow the dynamic range of aptamer-based sensors. Specifically, we employ both distal-site mutations and allosteric control to tune the affinity and dynamic range of a fluorescent aptamer beacon. We show that allosteric control, achieved by using a set of easily designed oligonucleotide inhibitors that competes against the folding of the aptamer, allows rational fine-tuning of the affinity of our model aptamer across 3 orders of magnitude of target concentration with greater precision than that achieved using mutational approaches. Using these methods, we generate sets of aptamers varying significantly in target affinity and then combine them to recreate several of the mechanisms employed by nature to narrow or broaden the dynamic range of biological receptors. Such ability to finely control the affinity and dynamic range of aptamers may find many applications in synthetic biology, drug delivery, and targeted therapies, fields in which aptamers are of rapidly growing importance.

Wanted: a positive control for anomalous subdiffusion

Anomalous subdiffusion in cells and model systems is an active area of research. The main questions are whether diffusion is anomalous or normal, and if it is anomalous, its mechanism. The subject is controversial, especially the hypothesis that crowding causes anomalous subdiffusion. Anomalous subdiffusion measurements would be strengthened by an experimental standard, particularly one able to cross-calibrate the different types of measurements. Criteria for a calibration standard are proposed. First, diffusion must be anomalous over the length and timescales of the different measurements. The length-scale is fundamental; the time scale can be adjusted through the viscosity of the medium. Second, the standard must be theoretically well understood, with a known anomalous subdiffusion exponent, ideally readily tunable. Third, the standard must be simple, reproducible, and independently characterizable (by, for example, electron microscopy for nanostructures). Candidate experimental standards are evaluated, including obstructed lipid bilayers; aqueous systems obstructed by nanopillars; a continuum percolation system in which a prescribed fraction of randomly chosen obstacles in a regular array is ablated; single-file diffusion in pores; transient anomalous subdiffusion due to binding of particles in arrays such as transcription factors in randomized DNA arrays; and computer-generated physical trajectories.

Rational design of allosteric inhibitors and activators using the population-shift model: in vitro validation and application to an artificial biosensor

The population-shift mechanism can be used for rational re-engineering of structure-switching biosensors to enable their allosteric inhibition and activation. As a proof-of-principle example of this, we have introduced distal allosteric sites into molecular beacons, which are optical sensors for the detection of specific nucleic acid sequences. The binding of inhibitors and activators to these sites enabled the rational modulation of the sensor's target affinity-and thus its useful dynamic range-over 3 orders of magnitude. The convenience with which this was done suggests that the population-shift mechanism may prove to be a useful method by which allosteric regulation can be introduced into biosensors, "smart" biomaterials, and other artificial biotechnologies.

Re-engineering electrochemical biosensors to narrow or extend their useful dynamic range

Here we demonstrate two convenient methods to extend and narrow the useful dynamic range of a model electrochemical DNA sensor. We did so by combining DNA probes of different target affinities but with similar specificity on the same electrode. We were able to achieve an extended dynamic response spanning 3 orders of magnitude in target concentration. Using a different strategy we have also narrowed the useful dynamic range of an E-DNA sensor to only an 8-fold range of target concentrations.

Protein conformational switches: from nature to design

Protein conformational switches alter their shape upon receiving an input signal, such as ligand binding, chemical modification, or change in environment. The apparent simplicity of this transformation--which can be carried out by a molecule as small as a thousand atoms or so--belies its critical importance to the life of the cell as well as its capacity for engineering by humans. In the realm of molecular switches, proteins are unique because they are capable of performing a variety of biological functions. Switchable proteins are therefore of high interest to the fields of biology, biotechnology, and medicine. These molecules are beginning to be exploited as the core machinery behind a new generation of biosensors, functionally regulated enzymes, and "smart" biomaterials that react to their surroundings. As inspirations for these designs, researchers continue to analyze existing examples of allosteric proteins. Recent years have also witnessed the development of new methodologies for introducing conformational change into proteins that previously had none. Herein we review examples of both natural and engineered protein switches in the context of four basic modes of conformational change: rigid-body domain movement, limited structural rearrangement, global fold switching, and folding-unfolding. Our purpose is to highlight examples that can potentially serve as platforms for the design of custom switches. Accordingly, we focus on inducible conformational changes that are substantial enough to produce a functional response (e.g., in a second protein to which it is fused), yet are relatively simple, structurally well-characterized, and amenable to protein engineering efforts.

A fluorescent molecular switch for room temperature operation based on oligonucleotide hybridization without labeling of probes or targets

A molecular switch was prepared by self-assembly. Neutravidin served as a template that allowed for a biotinylated probe oligonucleotide to be placed adjacent to a biotinylated long-chain linker that was terminated with thiazole orange (TO). Hybridization of probe oligonucleotide with target to form double-stranded DNA resulted in intercalation of the adjacent TO probe. This was a reversible process that could be tracked by fluorescence intensity changes. Formamide was used as a denaturant for double-stranded DNA, and could be used to depress thermal denaturation temperatures. In this work formamide had a dual function, providing for control of hybridization selectivity at room temperature, while concurrently ameliorating non-specific adsorption to improve signal-to-noise when using thiazole orange as a fluorescence signalling agent to determine oligonucleotide hybridization. Room temperature single nucleotide polymorphism (SNP) discrimination for oligonucleotide targets was achieved both in solution and for molecular switches that were immobilized onto optical fibers. In solution, a concentration of 18.5% formamide provided greater than 40-fold signal difference between single-stranded DNA and double-stranded DNA, in contrast to only a 2-fold difference in the absence of formamide. Selectivity for SNP determination in solution was demonstrated using targets of varying lengths including a 141-base PCR amplicon. The improved signal-to-noise achieved by use of formamide is likely due to preferential displacement of dye molecules that are otherwise electrostatically bound to the polyanionic nucleic acid backbone.

Quantitation of femtomolar protein levels via direct readout with the electrochemical proximity assay

We have developed a separation-free, electrochemical assay format with direct readout that is amenable to highly sensitive and selective quantitation of a wide variety of target proteins. Our first generation of the electrochemical proximity assay (ECPA) is composed of two thrombin aptamers which form a cooperative complex only in the presence of target molecules, moving a methylene blue (MB)-conjugated oligonucleotide close to a gold electrode. Without washing steps, electrical current is increased in proportion to the concentration of a specific target protein. By employing a DNA-based experimental model with the aptamer system, we show that addition of a short DNA competitor can reduce background current of the MB peak to baseline levels. As such, the detection limit of aptamer-based ECPA for human thrombin was 50 pM via direct readout. The dual-probe nature of ECPA gave high selectivity and 93% recovery of signal from 2.5 nM thrombin in 2% bovine serum albumin (BSA). To greatly improve the flexibility of ECPA, we then proved the system functional with antibody-oligonucleotide conjugates as probes; the insulin detection limit was 128 fM with a dynamic range of over 4 orders of magnitude in concentration, again with high assay selectivity. ECPA thus allows separation-free, highly sensitive, and highly selective protein detection with a direct electrochemical readout. This method is extremely flexible, capable of detecting a wide variety of protein targets, and is amenable to point-of-care protein measurement, since any target with two aptamers or antibodies could be assayed via direct electrochemical readout.

Graphene-based wireless bacteria detection on tooth enamel

Direct interfacing of nanosensors onto biomaterials could impact health quality monitoring and adaptive threat detection. Graphene is capable of highly sensitive analyte detection due to its nanoscale nature. Here we show that graphene can be printed onto water-soluble silk. This in turn permits intimate biotransfer of graphene nanosensors onto biomaterials, including tooth enamel. The result is a fully biointerfaced sensing platform, which can be tuned to detect target analytes. For example, via self-assembly of antimicrobial peptides onto graphene, we show bioselective detection of bacteria at single-cell levels. Incorporation of a resonant coil eliminates the need for onboard power and external connections. Combining these elements yields two-tiered interfacing of peptide-graphene nanosensors with biomaterials. In particular, we demonstrate integration onto a tooth for remote monitoring of respiration and bacteria detection in saliva. Overall, this strategy of interfacing graphene nanosensors with biomaterials represents a versatile approach for ubiquitous detection of biochemical targets.