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Rational Design of Allosteric Inhibitors and Activators Using the Population-Shift Model: In Vitro Validation and Application to an Artificial Biosensor.(1)

The population-shift mechanism allows for the re-engineering of biosensors utilizing the concept of allosterism to allow for a structure-based switching on/off capacity into biosensors, “smart-biomaterials, and other artificial biotechnologies.  A fundamental problem in the design of valuable biosensors has been limited number of biomolecules that produce enough signal (for example emission of light, etc.) upon binding to its target.  However this issue has been resolved with the development of biosensors in which target binding is transduced into a quantifiable optical or electrochemical signal after coupling with conformational changes in the receptor (for review see (2)).

There are a few advantages to this biosensor design:

• Works well in complex samples, such as blood, serum; Low background noise from nonspecific adsorption from interfering biomolecules
• Supports real-time monitoring- allosteric biosensors do not rely on additional reagents and are rapidly reversible
• Binding of the receptors is dependent on an unfavorable conformational change, so there is possibility to fine tune this conformational switch.

Concept of allosterism

Allosterism is generally defined as a change in the activity and conformation of an enzyme/protein resulting from the binding of a compound at a site on the enzyme other than the active binding site.  Allosterism plays a critical role in the control and integration of molecular events in biological systems.  Frequently, allosterism is seen with multisubunit proteins/enzymes, where subunit interaction is necessary for allosteric effects, and is distal to the binding site.  Examples of allosteric systems include hemoglobin, phosphofructose kinase and many

NAD⁺ -dependent dehydrogenases.  For example, the binding of O₂ to hemoglobin is enhanced the binding of addition O₂, the Bohr effect (the affinity of hemoglobin to O₂ depends on H⁺), and the metabolic product diphosphoglycerate regulates O₂ binding.

Types of DNA Biosensors

DNA-based biosensors rely on the hybridization of complementary DNA.  Many optical biosensors based on the phenomenon of surface plasmon resonance (SPR) utilize a property of and other materials; specifically that a thin layer of gold on a high refractive index glass surface can absorb laser light, producing electron waves (surface plasmons) on the gold surface. This occurs only at a specific angle and wavelength of incident light and is highly dependent on the surface of the gold, such that binding of a target analyte to a receptor on the gold surface produces a measurable signal.

Electrochemical biosensors are normally based on enzymatic catalysis of a reaction that produces or consumes electrons (such enzymes are rightly called redox enzymes). The sensor substrate usually contains three electrodes; a reference electrode, a working electrode and a counter electrode. The target analyte is involved in the reaction that takes place on the active electrode surface, and the reaction may cause either electron transfer across the double layer (producing a current) or can contribute to the double layer potential (producing a voltage). We can either measure the current (rate of flow of electrons is now proportional to the analyte concentration) at a fixed potential or the potential can be measured at zero current (this gives a logarithmic response). The label-free and direct electrical detection of small peptides and proteins is possible by their intrinsic charges using bio-functional ion-sensitive field-effect transistors.

Piezoelectric sensors utilize crystals which undergo an elastic deformation when an electrical potential is applied to them. An alternating potential produces a standing wave in the crystal at a characteristic frequency. This frequency is highly dependent on the elastic properties of the crystal, such that if a crystal is coated with a biological recognition element the binding of a (large) target analyte to a receptor will produce a change in the resonance frequency, which gives a binding signal. In a mode that uses surface acoustic waves (SAW), the sensitivity is greatly increased.

Type	Biological Element	Transducer
OpticalFiber Optics Surface plasmon resonance Biomolecular interactionAnalysis Raman spectroscopy	DNA	Optical fiberResonant mirror BIAcore SERG probe
Electrochemical	DNA	Carbon paste electrodes
Piezoelectric     FrequencyAcoustics	DNA	CrystalsCrystals

The most popular of optical DNA biosensors is molecular beacons, DNA probes containing a fluorescent moiety and a quencher of on the same DNA strand. This probe has an internal complementary sequence so as the DNA folds into a secondary structure, most likely a stem-loop or hairpin structure, so the fluor and quencher are held in close proximity, quenching the fluorescent signal.  Target hybridization opens up the stem-loop structure, thereby emitting the fluorescent signal. A typical molecular beacon probe is 25 nucleotides long. A typical molecular beacon structure can be divided in 4 parts:

• Loop: This is the 18–30 base pair region of the molecular beacon which is complementary to the target sequence.

• Stem: The beacon stem is formed by the attachment, to both termini of the loop, of two short (5 to 7 nucleotide residues) oligonucleotides that are complementary to each other.

• 5′ fluorophore: At the 5′ end of the molecular beacon, a fluorescent dye is covalently attached.
• 3′ quencher (non fluorescent): The quencher dye is covalently attached to the 3′ end of the molecular beacon. When the beacon is in closed loop shape, the quencher resides in proximity to the fluorophore, which results in quenching the fluorescent emission of the latter.

Structure of a molecular beacon. Description and figure from Wikipedia (5).

Common applications of DNA biosensors include cDNA microarray and Affymetrix GeneChip™ technology.

Ricci et al. provide a proof-of –principle paper to demonstrate how allosteric switching can be introduced into biosensors(1). The authors engineered allosteric inhibition into a molecular beacon by the addition of two single-stranded tails that serve as an allosteric site where binding of an inhibitor sequence would bridge the two tails and prevent target binding (holding the probe in the inactivated state).  Using this approach the authors demonstrated over a three-fold increase in the dynamic range of the beacon.

The authors also demonstrated this effect, with an allosterically activated biosensor in which “allosteric activation was engineered into a molecular beacon using one single-stranded tail as an allosteric binding site.  The activator sequence binding to this tail partially invades the stem, destabilizing the nonbinding state and thus improving the target affinity.”  Thus this population-shift mechanism allows for the design of sensors that can be allosterically activated using activators that destabilize the beacon’s nonbinding conformation, increasing the beacon’s dynamic range without compromising target specificity. Finally the authors suggest that population-shift mechanisms can be engineered into many different types of “switching” biosensors including aptamer-based and protein-based sensors (3,4).

1.            Ricci, F., Vallee-Belisle, A., Porchetta, A., and Plaxco, K. W. (2012) Journal of the American Chemical Society 134, 15177-15180

2.            Vallee-Belisle, A., and Plaxco, K. W. (2010) Current opinion in structural biology 20, 518-526

3.            White, R. J., Rowe, A. A., and Plaxco, K. W. (2010) The Analyst 135, 589-594

4.            Kohn, J. E., and Plaxco, K. W. (2005) Proceedings of the National Academy of Sciences of the United States of America 102,   10841-10845

5.            http://en.wikipedia.org/wiki/Molecular_beacon

Other research papers on Biosensors were published on this Scientific Web site as follows:

Measuring glucose without needle pricks: nano-sized biosensors made the test easy

New Definition of MI Unveiled, Fractional Flow Reserve (FFR)CT for Tagging Ischemia

New Drug-Eluting Stent Works Well in STEMI

Sensor detects glucose in saliva, tears for diabetes testing

Synthesizing Synthetic Biology: PLOS Collections

Competition in the Ecosystem of Medical Devices in Cardiac and Vascular Repair: Heart Valves, Stents, Catheterization Tools and Kits for Open Heart and Minimally Invasive Surgery (MIS)