Thermodynamic basis for the optimization of binding-induced biomolecular switches and structure-switching biosensors

Photocurrent switchable dual-target bioassay: Signal distinction and interface reconfiguration via pH-responsive triplex DNA programming

Most multiplexed photoelectrochemical (PEC) sensors require additional instrumentation and cumbersome electrode modification and surface partitioning, which limits their portability and instrument miniaturization. Herein, a pH-responsive programmable triple DNA nanomachine was developed for constructing a reconfigurable multiplex PEC sensing platform. By programming the base sequence, T-A·T-riched triple DNA was designed to construct integrated nano-controlled release machine (INCRM) for simultaneous recognition of multiple targets. The INCRM enables to recognize two targets in one step, and sequentially separate the signal labels by pH adjustment. The detached signal label catalyzes glucose to produce gluconic acid, causing the C-riched DNA fold into a triple structure on the electrode surface. As a result, one target can be detected relying on the enhanced photocurrent due to accelerated electron transfer between the CdS QD labeled at the end of C-riched DNA and the electrode. The triplex DNA dissociation in pH 7.4 buffer reconfigures the electrode interface, which can be continued to detect another target. The feasibility of the multiplexed sensor is verified by the detection of extensively coexisting antibiotics enrofloxacin (ENR) and ciprofloxacin (CIP). Under the optimal conditions, wide linear range (10 fg/mL ∼ 1 μg/mL) and low detection limit (3.27 fg/mL and 9.60 fg/mL) were obtained. The pH-regulated programmable triplex DNA nanomachine-based sensing platform overcomes the technical difficulties of conventional multiplexed PEC assay, which may open the way for miniaturization of multiplexed PEC sensors.

Thermodynamic Allosteric Switch-Actuated 3D DNA Nanomachine for Ultrasensitive Electrochemical/Fluorescent Dual-Mode Biosensing of a Transcription Factor

Herein, we reported an innovative thermodynamic allosteric switch-actuated 3D DNA nanomachine for selective, sensitive, and accurate electrochemical (EC)/fluorescent (FL) dual-mode biosensing of a microphthalmia-associated transcription factor (MITF). The thermodynamic allosteric switch was ingeniously customized as a hairpin probe (HP) that was in dynamic equilibrium but rapidly interconverting conformations. At the "inactive state", the MITF-binding region and the switch part were "sequestered". Upon the introduction of MITF, an MITF-HP complex promptly formed, and the equilibrium of HP thermodynamically inclined from the "inactive state" toward the "active state" conformation. Immediately, the exposed switch on HP effectively actuated the 3D DNA nanomachine and synchronously produced the restriction site for Nb.BbvCI nicking endonuclease. After the autonomous conveying of the 3D DNA nanomachine by means of the high-efficiency circularly nicking endonuclease signal amplification (NESA), not only was MB-S1 in the supernatant used for FL measurements but also MB-SP/MNs/S2 in the precipitate was adapted for EC analysis, significantly improving the utilization of output products derived from the 3D DNA nanomachine. Accordingly, benefiting from the efficient DNA nanomachine signal amplification manner and the self-calibration function of a dual-mode bioassay, the constructed biosensor exhibits superior sensitivity and accuracy for MITF determination.

Rationally Designed DNA-Based Scaffolds and Switching Probes for Protein Sensing

The detection of a protein analyte and use of this type of information for disease diagnosis and physiological monitoring requires methods with high sensitivity and specificity that have to be also easy to use, rapid and, ideally, single step. In the last 10 years, a number of DNA-based sensing methods and sensors have been developed in order to achieve quantitative readout of protein biomarkers. Inspired by the speed, specificity, and versatility of naturally occurring chemosensors based on structure-switching biomolecules, significant efforts have been done to reproduce these mechanisms into the fabrication of artificial biosensors for protein detection. As an alternative, in scaffold DNA biosensors, different recognition elements (e.g., peptides, proteins, small molecules, and antibodies) can be conjugated to the DNA scaffold with high accuracy and precision in order to specifically interact with the target protein with high affinity and specificity. They have several advantages and potential, especially because the transduction signal can be drastically enhanced. Our aim here is to provide an overview of the best examples of structure switching-based and scaffold DNA sensors, as well as to introduce the reader to the rational design of innovative sensing mechanisms and strategies based on programmable functional DNA systems for protein detection.

Programing Chemical Communication: Allostery vs Multivalent Mechanism

The emergence of life has relied on chemical communication and the ability to integrate multiple chemical inputs into a specific output. Two mechanisms are typically employed by nature to do so: allostery and multivalent activation. Although a better understanding of allostery has recently provided a variety of strategies to optimize the binding affinity, sensitivity, and specificity of molecular switches, mechanisms relying on multivalent activation remain poorly understood. As a proof of concept to compare the thermodynamic basis and design principles of both mechanisms, we have engineered a highly programmable DNA-based switch that can be triggered by either a multivalent or an allosteric DNA activator. By precisely designing the binding interface of the multivalent activator, we show that the affinity, dynamic range, and activated half-life of the molecular switch can be programed with even more versatility than when using an allosteric activator. The simplicity by which the activation properties of molecular switches can be rationally tuned using multivalent assembly suggests that it may find many applications in biosensing, drug delivery, synthetic biology, and molecular computation fields, where precise control over the transduction of binding events into a specific output is key.

Functional DNA Superstructures Exhibit Positive Homotropic Allostery in Ligand Binding

Inspired by intrinsically disordered proteins in nature, DNA aptamers can be engineered to display strongly homotropic allosteric (or cooperative) ligand binding, representing a unique feature that could be of great utility in applications such as biosensing, imaging and drug delivery. The use of an intrinsic disorder mechanism, however, comes with an inherent drawback of significantly reduced overall binding affinity. We hypothesize that it could be addressed via the design of multivalent supramolecular aptamers. We built functional DNA superstructures (denoted as 3D DNA), made of long-chain DNA containing tandem repeating DNA aptamers (or concatemeric aptamers). The 3D DNA systems exhibit highly cooperative binding to both small molecules and proteins, without loss of binding affinities of their parent aptamers. We further produced a highly responsive sensor for fluorescence imaging of glutamate stimulation-evoked adenosine triphosphate (ATP) release in neurons, as well as force stimulus-triggered ATP release in astrocytes.

Enthalpy and entropy synergistic regulation-based programmable DNA motifs for biosensing and information encryption

Deoxyribonucleic acid (DNA) provides a collection of intelligent tools for the development of information cryptography and biosensors. However, most conventional DNA regulation strategies rely solely on enthalpy regulation, which suffers from unpredictable stimuli-responsive performance and unsatisfactory accuracy due to relatively large energy fluctuations. Here, we report an enthalpy and entropy synergistic regulation-based pH-responsive A⁺/C DNA motif for programmable biosensing and information encryption. In the DNA motif, the variation in loop length alters entropic contribution, and the number of A⁺/C bases regulates enthalpy, which is verified through thermodynamic characterizations and analyses. On the basis of this straightforward strategy, the performances, such as pK_a, of the DNA motif can be precisely and predictably tuned. The DNA motifs are finally successfully applied for glucose biosensing and crypto-steganography systems, highlighting their potential in the field of biosensing and information encryption.

Programming the dynamic range of nanobiosensors with engineering poly-adenine-mediated spherical nucleic acid

Spherical nucleic acid (SNA) conjugates consisting of gold cores functionalized with a densely packed DNA shells are of great significance in the field of medical detection and intracellular imaging. Especially, poly adenine (polyA)-mediated SNAs can improve the controllability and reproducibility of DNA assembly on the nanointerface, showing the tunable hybridization ability. However, due to the physics of single-site binding, the biosensor based on SNA usually exhibits a dynamic range spanning a fixed 81-fold change in target concentration, which limits its application in disease monitoring. To address this problem, we report a tri-block DNA-based approach to assemble SNA for nucleic acid detection based on structure-switching mechanism with programmable dynamic range. The tri-block DNA is a FAM-labeled stem-loop structure, which contains three blocks: polyA block as an anchoring block for tunable surface density, stem block with different GC base pair content for varying the structure stability, and the fixed loop block for target recognition. We find that varying the polyA block, the reaction temperature, and the GC base pair, SNA shows different target binding affinity and detection limit but with normally 81-fold dynamic range. We can extend the dynamic range to 1000-fold by using the combination of two SNAs with different affinity, and narrow the dynamic range to 5-fold by sequestration mechanism. Furthermore, the tunable SNA enables sensitive detection of mRNA in cells. Given its tunable dynamic range, such nanobiosensor based on SNA offers new possibility for various biomedical and clinical applications.

An enzyme-responsive electrochemical DNA biosensor achieving various dynamic range by using only-one immobilization probe

Developing a simple and easy-to-operate biosensor with tunable dynamic range would provide enormous opportunities to promote the diagnostic applications. Herein, an enzyme-responsive electrochemical DNA biosensor is developed by using only-one immobilization probe. The immobilization probe was designed with a two-loop hairpin-like structure that contained the mutually independent target recognition and enzyme (EcoRI restriction endonuclease) responsive domains. The target recognition was based on a toehold-mediated strand displacement reaction strategy. The toehold region was initially caged in the loop of the immobilization probe and showed a relatively low binding affinity with target, which was improved via EcoRI cleavage of immobilization probe to liberate the toehold region. The EcoRI cleavage operation for immobilization probe demonstrated the well regulation ability in detection performance. It showed a largely extended dynamic range, a significantly lowered detection limit and better discrimination ability toward the mismatched sequences whether in two buffers (with high or low salt concentrations) or in the serum system. The advantages also includes simplicity in probe design, and facile biosensor fabrication and operation. It thus opens a new avenue for the development of the modulated DNA biosensor and hold a great potential for the diagnostic applications and drug monitoring.

Functional advantages of building nanosystems using multiple molecular components

Over half of all the natural nanomachines in living organisms are multimeric and likely exploit the self-assembly of their components to provide functional benefits. However, the advantages and disadvantages of building nanosystems using multiple molecular components remain relatively unexplored at the thermodynamic, kinetic and functional levels. In this study we used theory and a simple DNA-based model that forms the same nanostructures with different numbers of components to advance our knowledge in this area. Despite its lower assembly rate, we found that a system built with three components may undergo a more cooperative assembly transition from less preorganized components, which facilitates the emergence of functionalities. Using simple variations of its components, we also found that trimeric nanosystems display a much higher level of programmability than their dimeric counterparts because they can assemble with various levels of cooperativity, self-inhibition and time-dependent properties. We show here how two simple strategies (for example, cutting and adding components) can be employed to efficiently programme the regulatory function of a more complex, artificially selected, RNA-cleaving catalytic nanosystem.

Using Spectroscopy to Guide the Adaptation of Aptamers into Electrochemical Aptamer-Based Sensors

Electrochemical aptamer-based (EAB) sensors utilize the binding-induced conformational change of an electrode-attached, redox-reporter-modified aptamer to transduce target recognition into an easily measurable electrochemical output. Because this signal transduction mechanism is single-step and rapidly reversible, EAB sensors support high-frequency, real-time molecular measurements, and because it recapitulates the reagentless, conformation-linked signaling seen in vivo among naturally occurring receptors, EAB sensors are selective enough to work in the complex, time-varying environments found in the living body. The fabrication of EAB sensors, however, requires that their target-recognizing aptamer be modified such that (1) it undergoes the necessary binding-induced conformational change and (2) that the thermodynamics of this "conformational switch" are tuned to ensure that they reflect an acceptable trade-off between affinity and signal gain. That is, even if an "as-selected" aptamer achieves useful affinity and specificity, it may fail when adapted to the EAB platform because it lacks the binding-induced conformational change required to support EAB signaling. In this paper we reveal the spectroscopy-guided approaches we use to modify aptamers such that they support the necessary binding-induced conformational change. Specifically, using newly reported aptamers, we demonstrate the systematic design of EAB sensors achieving clinically and physiologically relevant specificity, limits of detection, and dynamic range against the targets methotrexate and tryptophan.

DNA mechanical flexibility controls DNA potential to activate cGAS-mediated immune surveillance

DNA is well-documented to stimulate immune response. However, the nature of the DNA to activate immune surveillance is less understood. Here, we show that the activation of cyclic GMP-AMP synthase (cGAS) depends on DNA mechanical flexibility, which is controlled by DNA-sequence, -damage and -length. Consistently, DNA-sequence was shown to control cGAS activation. Structural analyses revealed that a conserved cGAS residue (mouse R222 or human R236) contributed to the DNA-flexibility detection. And the residue substitution neutralised the flexibility-controlled DNA-potential to activate cGAS, and relaxed the DNA-length specificity of cGAS. Moreover, low dose radiation was shown to mount cGAS-mediated acute immune surveillance (AIS) via repairable (reusable) DNAs in hrs. Loss of cGAS-mediated AIS decreased the regression of local and abscopal tumours in the context of focal radiation and immune checkpoint blockade. Our results build a direct link between immunosurveillance and DNA mechanical feature.

Programmable self-regulated molecular buffers for precise sustained drug delivery

Unlike artificial nanosystems, biological systems are ideally engineered to respond to their environment. As such, natural molecular buffers ensure precise and quantitative delivery of specific molecules through self-regulated mechanisms based on Le Chatelier's principle. Here, we apply this principle to design self-regulated nucleic acid molecular buffers for the chemotherapeutic drug doxorubicin and the antimalarial agent quinine. We show that these aptamer-based buffers can be programmed to maintain any specific desired concentration of free drug both in vitro and in vivo and enable the optimization of the chemical stability, partition coefficient, pharmacokinetics and biodistribution of the drug. These programmable buffers can be built from any polymer and should improve patient therapeutic outcome by enhancing drug activity and minimizing adverse effects and dosage frequency.

Critical Design Factors for Electrochemical Aptasensors Based on Target-Induced Conformational Changes: The Case of Small-Molecule Targets

Nucleic-acid aptamers consisting in single-stranded DNA oligonucleotides emerged as very promising biorecognition elements for electrochemical biosensors applied in various fields such as medicine, environmental, and food safety. Despite their outstanding features, such as high-binding affinity for a broad range of targets, high stability, low cost and ease of modification, numerous challenges had to be overcome from the aptamer selection process on the design of functioning biosensing devices. Moreover, in the case of small molecules such as metabolites, toxins, drugs, etc., obtaining efficient binding aptamer sequences proved a challenging task given their small molecular surface and limited interactions between their functional groups and aptamer sequences. Thus, establishing consistent evaluation standards for aptamer affinity is crucial for the success of these aptamers in biosensing applications. In this context, this article will give an overview on the thermodynamic and structural aspects of the aptamer-target interaction, its specificity and selectivity, and will also highlight the current methods employed for determining the aptamer-binding affinity and the structural characterization of the aptamer-target complex. The critical aspects regarding the generation of aptamer-modified electrodes suitable for electrochemical sensing, such as appropriate bioreceptor immobilization strategy and experimental conditions which facilitate a convenient anchoring and stability of the aptamer, are also discussed. The review also summarizes some effective small molecule aptasensing platforms from the recent literature.

Enhancement of CRISPR/Cas12a trans-cleavage activity using hairpin DNA reporters

The RNA programmed non-specific (trans) nuclease activity of CRISPR-Cas Type V and VI systems has opened a new era in the field of nucleic acid-based detection. Here, we report on the enhancement of trans-cleavage activity of Cas12a enzymes using hairpin DNA sequences as FRET-based reporters. We discover faster rate of trans-cleavage activity of Cas12a due to its improved affinity (K_m) for hairpin DNA structures, and provide mechanistic insights of our findings through Molecular Dynamics simulations. Using hairpin DNA probes we significantly enhance FRET-based signal transduction compared to the widely used linear single stranded DNA reporters. Our signal transduction enables faster detection of clinically relevant double stranded DNA targets with improved sensitivity and specificity either in the presence or in the absence of an upstream pre-amplification step.

Dissipative DNA nanotechnology

DNA nanotechnology has emerged as a powerful tool to precisely design and control molecular circuits, machines and nanostructures. A major goal in this field is to build devices with life-like properties, such as directional motion, transport, communication and adaptation. Here we provide an overview of the nascent field of dissipative DNA nanotechnology, which aims at developing life-like systems by combining programmable nucleic-acid reactions with energy-dissipating processes. We first delineate the notions, terminology and characteristic features of dissipative DNA-based systems and then we survey DNA-based circuits, devices and materials whose functions are controlled by chemical fuels. We emphasize how energy consumption enables these systems to perform work and cyclical tasks, in contrast with DNA devices that operate without dissipative processes. The ability to take advantage of chemical fuel molecules brings dissipative DNA systems closer to the active molecular devices that exist in nature.

The Mechanistic Integration and Thermodynamic Optimality of a Nanomotor

The performance of artificial nanomotors is still far behind nature-made biomolecular motors. A mechanistic disparity between the two categories exists: artificial motors often rely on a single mechanism to rectify directional motion, but biomotors integrate multiple mechanisms for better performance. This study proposes a design for a motor-track system and shows that by introducing asymmetric compound foot-track interactions, both selective foot detachment and biased foot-track binding arise from the mechanics of the system. The two mechanisms are naturally integrated to promote the motility of the motor towards being unidirectional, while each mechanism alone only achieves 50% directional fidelity at most. Based on a reported theory, the optimization of the motor is conducted via maximizing the directional fidelity. Along the optimization, the directional fidelity of the motor is raised by parameters that concentrate more energy on driving selective-foot detachment and biased binding, which in turn promotes work production due to the two energies converting to work via a load attached. However, the speed of the motor can drop significantly after the optimization because of energetic competition between speed and directional fidelity, which causes a speed-directional fidelity tradeoff. As a case study, these results test thermodynamic correlation between the performances of a motor and suggest that directional fidelity is an important quantity for motor optimization.

Real-Time Tunable Dynamic Range for Calibration-Free Biomolecular Measurements with a Temperature-Modulated Electrochemical Aptamer-Based Sensor in an Unprocessed Actual Sample

The sensing technologies for monitoring molecular analytes in biological fluids with high frequency and in real time could enable a broad range of applications in personalized healthcare and clinical diagnosis. However, due to the limited dynamic range (less than 81-fold), real-time analysis of biomolecular concentration varying over multiple orders of magnitude is a severe challenge faced by this class of analytical platforms. For the first time, we describe here that temperature-modulated electrochemical aptamer-based sensors with a dynamically adjustable calibration-free detection window could enable continuous, real-time, and accurate response for the several-hundredfold target concentration changes in unprocessed actual samples. Specifically, we could regulate the electrode surface temperature of sensors to obtain the corresponding dynamic range because of the temperature-dependent affinity variations. This temperature modulation method relies on an alternate hot and cold electrode reported by our group, whose surface could actively be heated and cooled without the need for altering ambient temperature, thus likewise applying for the flowing system. We then performed dual-frequency calibration-free measurements at different interface temperatures, thus achieving an extended detection window from 25 to 2500 μM for procaine in undiluted urine, 1-500 μM for adenosine triphosphate, and 5-2000 μM for adenosine in undiluted serum. The resulting sensor architecture could drastically expand the real-time response range accessible to these continuous, reagent-less biosensors.

Rational Design of Allosteric Nanodevices Based on DNA Triple Helix

Inspired by allosteric regulation of natural molecules, we present a rational design scheme to build synthetic nucleic acid allosteric nanodevices. The clearly specified conformational states of switches obtained from systematic screening and analyses make the ON-OFF transition clear-cut and quantification ready. Under the rational design scheme, we have developed a series of DNA switches with triplex-forming oligos as allosteric modulators and implemented designated allosteric transitions, allosteric coregulation, and reaction pathway control. In conjunction with toehold-mediated strand displacement, our design scheme has also been applied to synthetic nucleic acid computing including a set of logic operations and complex algorithm.

DNA-Based Nanoswitches: Insights into Electrochemiluminescence Signal Enhancement

Electrochemiluminescence (ECL) is a powerful transduction technique that has rapidly gained importance as a powerful analytical technique. Since ECL is a surface-confined process, a comprehensive understanding of the generation of ECL signal at a nanometric distance from the electrode could lead to several highly promising applications. In this work, we explored the mechanism underlying ECL signal generation on the nanoscale using luminophore-reporter-modified DNA-based nanoswitches (i.e., molecular beacon) with different stem stabilities. ECL is generated according to the "oxidative-reduction" strategy using tri-n-propylamine (TPrA) as a coreactant and Ru(bpy)₃²⁺ as a luminophore. Our findings suggest that by tuning the stem stability of DNA nanoswitches we can activate different ECL mechanisms (direct and remote) and, under specific conditions, a "digital-like" association curve, i.e., with an extremely steep transition after the addition of increasing concentrations of DNA target, a large signal variation, and low preliminary analytical performance (LOD 22 nM for 1GC DNA-nanoswtich and 16 nM for 5GC DNA-nanoswitch). In particular, we were able to achieve higher signal gain (i.e., 10 times) with respect to the standard "signal-off" electrochemical readout. We demonstrated the copresence of two different ECL generation mechanisms on the nanoscale that open the way for the design of customized DNA devices for highly efficient dual-signal-output ratiometric-like ECL systems.

Unraveling the effect of the aptamer complementary element on the performance of duplexed aptamers: a thermodynamic study

Duplexed aptamers (DAs) are widespread aptasensor formats that simultaneously recognize and signal the concentration of target molecules. They are composed of an aptamer and aptamer complementary element (ACE) which consists of a short oligonucleotide that partially inhibits the aptamer sequence. Although the design principles to engineer DAs are straightforward, the tailored development of DAs for a particular target is currently based on trial and error due to limited knowledge of how the ACE sequence affects the final performance of DA biosensors. Therefore, we have established a thermodynamic model describing the influence of the ACE on the performance of DAs applied in equilibrium assays and demonstrated that this relationship can be described by the binding strength between the aptamer and ACE. To validate our theoretical findings, the model was applied to the 29-mer anti-thrombin aptamer as a case study, and an experimental relation between the aptamer-ACE binding strength and performance of DAs was established. The obtained results indicated that our proposed model could accurately describe the effect of the ACE sequence on the performance of the established DAs for thrombin detection, applied for equilibrium assays. Furthermore, to characterize the binding strength between the aptamer and ACEs evaluated in this work, a set of fitting equations was derived which enables thermodynamic characterization of DNA-based interactions through thermal denaturation experiments, thereby overcoming the limitations of current predictive software and chemical denaturation experiments. Altogether, this work encourages the development, characterization, and use of DAs in the field of biosensing.

Aptamer Switches Regulated by Post-Transition/Transition Metal Ions

We introduced an aptamer switch design that relies on the ability of post-transition/transition metal ions to trigger, through their coordination to nucleobases, substantial DNA destabilization. In the absence of molecular target, the addition of one such metal ion to usual aptamer working solutions promotes the formation of an alternative, inert DNA state. Upon exposure to the cognate compound, the equilibrium is shifted towards the competent DNA form. The switching process was preferentially activated by metal ions of intermediate base over phosphate complexation preference (i.e. Pb²⁺ , Cd²⁺ ) and operated with diversely structured DNA molecules. This very simple aptamer switch scheme was applied to the detection of small organics using the fluorescence anisotropy readout mode. We envision that the approach could be adapted to a variety of signalling methods that report on changes in the surface charge density of DNA receptors.

Strategies for Biomolecular Analysis and Continuous Physiological Monitoring

Portable devices capable of rapid disease detection and health monitoring are crucial to decentralizing diagnostics from clinical laboratories to the patient point-of-need. Although technologies have been developed targeting this challenge, many require the use of reporter molecules or reagents that complicate the automation and autonomy of sensors. New work in the field has targeted reagentless approaches to enable breakthroughs that will allow personalized monitoring of a wide range of biomarkers on demand. This Perspective focuses on the ability of reagentless platforms to revolutionize the field of sensing by allowing rapid and real-time analysis in resource-poor settings. First, we will highlight advantages of reagentless sensing techniques, specifically electrochemical detection strategies. Advances in this field, including the development of wearable and in situ sensors capable of real-time monitoring of biomarkers such as nucleic acids, proteins, viral particles, bacteria, therapeutic agents, and metabolites, will be discussed. Reagentless platforms which allow for wash-free, calibration free-detection with increased dynamic range are highlighted as a key technological advance for autonomous sensing applications. Furthermore, we will highlight remaining challenges which must be overcome to enable widespread use of reagentless devices. Finally, future prospects and potential breakthroughs in precision medicine that will arise as a result of further development of reagentless sensing approaches are discussed.

Folding-upon-Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes

We present a new class of DNA-based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding-upon-repair DNA nanoswitches are synthetic DNA sequences containing O6 -methyl-guanine (O6 -MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of the O6 -MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding-upon-repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors.

Thermodynamic analysis of cooperative ligand binding by the ATP-binding DNA aptamer indicates a population-shift binding mechanism

The ATP-binding DNA aptamer is often used as a model system for developing new aptamer-based biosensor methods. This aptamer follows a structure-switching binding mechanism and is unusual in that it binds two copies of its ligand. We have used isothermal titration calorimetry methods to study the binding of ATP, ADP, AMP and adenosine to the ATP-binding aptamer. Using both individual and global fitting methods, we show that this aptamer follows a positive cooperative binding mechanism. We have determined the binding affinity and thermodynamics for both ligand-binding sites. By separating the ligand-binding sites by an additional four base pairs, we engineered a variant of this aptamer that binds two adenosine ligands in an independent manner. Together with NMR and thermal stability experiments, these data indicate that the ATP-binding DNA aptamer follows a population-shift binding mechanism that is the source of the positive binding cooperativity by the aptamer.

Expanding detection windows for discriminating single nucleotide variants using rationally designed DNA equalizer probes

Combining experimental and simulation strategies to facilitate the design and operation of nucleic acid hybridization probes are highly important to both fundamental DNA nanotechnology and diverse biological/biomedical applications. Herein, we introduce a DNA equalizer gate (DEG) approach, a class of simulation-guided nucleic acid hybridization probes that drastically expand detection windows for discriminating single nucleotide variants in double-stranded DNA (dsDNA) via the user-definable transformation of the quantitative relationship between the detection signal and target concentrations. A thermodynamic-driven theoretical model was also developed, which quantitatively simulates and predicts the performance of DEG. The effectiveness of DEG for expanding detection windows and improving sequence selectivity was demonstrated both in silico and experimentally. As DEG acts directly on dsDNA, it is readily adaptable to nucleic acid amplification techniques, such as polymerase chain reaction (PCR). The practical usefulness of DEG was demonstrated through the simultaneous detection of infections and the screening of drug-resistance in clinical parasitic worm samples collected from rural areas of Honduras.

Downhill (Un)Folding Coupled to Binding as a Mechanism for Engineering Broadband Protein Conformational Transducers

Canonical proteins fold and function as conformational switches that toggle between their folded (on) and unfolded (off) states, a mechanism that also provides the basis for engineering transducers for biosensor applications. One of the limitations of such transducers, however, is their relatively narrow operational range, limited to ligand concentrations 20-fold below or above their C₅₀. Previously, we discovered that certain fast-folding proteins lose/gain structure gradually (downhill folding), which led us to postulate their operation as conformational rheostats capable of processing inputs/outputs in analog fashion. Conformational rheostats could make transducers with extended sensitivity. Here we investigate this hypothesis by engineering pH transducing into the naturally pH insensitive, downhill folding protein gpW. Particularly, we engineered histidine grafts into its hydrophobic core to induce unfolding via histidine ionization. We designed and tested the effects of ionization via computational modeling and studied experimentally the four most promising single grafts and two double grafts. All tested mutants become reversible pH transducers in the 4-9 range, and their response increases proportionally to how buried the histidine graft is. Importantly, the pH-dependent reversible (un)folding occurs in rheostatic fashion, so the engineered transducers can detect up to 6 orders of magnitude in [H⁺] for single grafts, and even more for double grafts. Our results demonstrate that downhill (un)folding coupled to binding produces the gradual, analog responses to the ligand (here H⁺) that are expected of conformational rheostats, and which make them a powerful mechanism for engineering transducers with sensitivity over many orders of magnitude in ligand concentration (broadband).

Protein-Controlled Actuation of Dynamic Nucleic Acid Networks by Using Synthetic DNA Translators*

Integrating dynamic DNA nanotechnology with protein-controlled actuation will expand our ability to process molecular information. We have developed a strategy to actuate strand displacement reactions using DNA-binding proteins by engineering synthetic DNA translators that convert specific protein-binding events into trigger inputs through a programmed conformational change. We have constructed synthetic DNA networks responsive to two different DNA-binding proteins, TATA-binding protein and Myc-Max, and demonstrated multi-input activation of strand displacement reactions. We achieved protein-controlled regulation of a synthetic RNA and of an enzyme through artificial DNA-based communication, showing the potential of our molecular system in performing further programmable tasks.

Programming Biomimetically Confined Aptamers with DNA Frameworks

Active sites of proteins are generally encapsulated within three-dimensional peptide scaffolds that provide the molecular-scale confinement microenvironment. Nevertheless, the ability to tune thermodynamic stability in biomimetic molecular confinement relies on the macromolecular crowding effect of lack of stoichiometry and reconfigurability. Here, we report a framework nucleic acid (FNA)-based strategy to increase thermodynamic stability of aptamers. We demonstrate that the molecular-scale confinement increases the thermodynamic stability of aptamers via facilitated folding kinetics, which is confirmed by the single-molecule FRET (smFRET). Unfavorable conformations of aptamers are restricted as revealed by the Monte Carlo simulation. The binding affinity of the DNA framework-confined aptamer is improved by ∼3-fold. With a similar strategy we improve the catalytic activity of hemin-binding aptamer. Our approach thus shows high potential for designing protein-mimicking DNA nanostructures with enhanced binding affinity and catalytic activity for biosensing and biomedical engineering.

Optimizing the Specificity Window of Biomolecular Receptors Using Structure-Switching and Allostery

To ensure maximum specificity (i.e., minimize cross-reactivity with structurally similar analogues of the desired target), most bioassays invoke "stringency", the careful tuning of the conditions employed (e.g., pH, ionic strength, or temperature). Willingness to control assay conditions will fall, however, as quantitative, single-step biosensors begin to replace multistep analytical processes. This is especially true for sensors deployed in vivo, where the tuning of such parameters is not just inconvenient but impossible. In response, we describe here the rational adaptation of two strategies employed by nature to tune the affinity of biomolecular receptors so as to optimize the placement of their specificity "windows" without the need to alter measurement conditions: structure-switching and allosteric control. We quantitatively validate these approaches using two distinct, DNA-based receptors: a simple, linear-chain DNA suitable for detecting a complementary DNA strand and a structurally complex DNA aptamer used for the detection of a small-molecule drug. Using these models, we show that, without altering assay conditions, structure-switching and allostery can tune the concentration range over which a receptor achieves optimal specificity over orders of magnitude, thus optimally matching the specificity window with the range of target concentrations expected to be seen in a given application.

Real-Time Monitoring of a Protein Biomarker

The ability to monitor protein biomarkers continuously and in real-time would significantly advance the precision of medicine. Current protein-detection techniques, however, including ELISA and lateral flow assays, provide only time-delayed, single-time-point measurements, limiting their ability to guide prompt responses to rapidly evolving, life-threatening conditions. In response, here we present an electrochemical aptamer-based sensor (EAB) that supports high-frequency, real-time biomarker measurements. Specifically, we have developed an electrochemical, aptamer-based (EAB) sensor against Neutrophil Gelatinase-Associated Lipocalin (NGAL), a protein that, if present in urine at levels above a threshold value, is indicative of acute renal/kidney injury (AKI). When deployed inside a urinary catheter, the resulting reagentless, wash-free sensor supports real-time, high-frequency monitoring of clinically relevant NGAL concentrations over the course of hours. By providing an "early warning system", the ability to measure levels of diagnostically relevant proteins such as NGAL in real-time could fundamentally change how we detect, monitor, and treat many important diseases.

Re-Evaluating the Conventional Wisdom about Binding Assays

Analytical technologies based on binding assays have evolved substantially since their inception nearly 60 years ago, but our conceptual understanding of molecular recognition has not kept pace. Contemporary technologies, such as single-molecule and digital measurements, have challenged, or even rendered obsolete, core concepts behind conventional binding assay design. Here, we explore the fundamental principles underlying molecular recognition systems, which we consider in terms of signals generated through concentration-dependent shifts in equilibrium. We challenge certain orthodoxies related to binding-based detection assays, including the primary importance of a low dissociation constant (K_D) and the extent to which this parameter constrains dynamic range and limit of detection. Lastly, we identify key principles for designing binding assays that are optimally suited for a given detection application.

Computational Design of an Allosteric Antibody Switch by Deletion and Rescue of a Complex Structural Constellation

Therapeutic monoclonal antibodies have transformed medicine, especially with regards to treating cancers and disorders of the immune system. More than 50 antibody-derived drugs have already reached the clinic, the majority of which target cytokines or cell-surface receptors. Unfortunately, many of these targets have pleiotropic functions: they serve multiple different roles, and often not all of these roles are disease-related. This can be problematic because antibodies act throughout the body, and systemic neutralization of such targets can lead to safety concerns. To address this, we have developed a strategy whereby an antibody's ability to recognize its antigen is modulated by a second layer of control, relying on addition of an exogenous small molecule. In previous studies, we began to explore this idea by introducing a deactivating tryptophan-to-glycine mutation in the domain-domain interface of a single-chain variable fragment (scFv), and then restoring activity by adding back indole to fit the designed cavity. Here, we now describe a novel computational strategy for enumerating larger cavities that can be formed by simultaneously introducing multiple adjacent large-to-small mutations; we then carry out a complementary virtual screen to identify druglike compounds to match each candidate cavity. We first demonstrate the utility of this strategy in a fluorescein-binding single-chain variable fragment (scFv) and experimentally characterize a triple mutant with reduced antigen-binding (Rip-3) that can be rescued using a complementary ligand (Stitch-3). Because our design is built upon conserved residues in the antibody framework, we then show that the same mutation/ligand pair can also be used to modulate antigen-binding in an scFv build from a completely unrelated framework. This set of residues is present in many therapeutic antibodies as well, suggesting that this mutation/ligand pair may serve as a general starting point for introducing ligand-dependence into many clinically relevant antibodies.

Designed Alteration of Binding Affinity in Structure-Switching Aptamers through the Use of Dangling Nucleotides

The ability to change binding affinity in a controlled fashion is a key step in the rational design of biomolecules in general and functional nucleic acids in particular. Here, we use dangling nucleotides to alter the binding affinity of structure-switching aptamers. Dangling nucleotides can stabilize or destabilize a nucleic acid structure with a known ΔG°₃₇. When the dangling nucleotide stabilizes the structure, less free energy from ligand binding is needed to fold the molecule and hence the ligand is observed to bind tighter than in the absence of the unpaired nucleotide. For a destabilizing dangling nucleotide, the opposite occurs, and the observed binding is weaker. We demonstrate this concept using both the cocaine-binding aptamer and the ATP-binding aptamer systems. We find that for both aptamers there is a direct, but different, relationship between the predicted stabilization and the change in the observed binding free energy.

Independent control of the thermodynamic and kinetic properties of aptamer switches

Molecular switches that change their conformation upon target binding offer powerful capabilities for biotechnology and synthetic biology. Aptamers are useful as molecular switches because they offer excellent binding properties, undergo reversible folding, and can be engineered into many nanostructures. Unfortunately, the thermodynamic and kinetic properties of the aptamer switches developed to date are intrinsically coupled, such that high temporal resolution can only be achieved at the cost of lower sensitivity or high background. Here, we describe a design strategy that decouples and enables independent control over the thermodynamics and kinetics of aptamer switches. Starting from a single aptamer, we create an array of aptamer switches with effective dissociation constants ranging from 10 μM to 40 mM and binding kinetics ranging from 170 ms to 3 s. Our strategy is broadly applicable to other aptamers, enabling the development of switches suitable for a diverse range of biotechnology applications.

Aptamer switches are promising biotechnological tools but coupling of their affinity and temporal response limits their versatility. Here, the authors developed an intramolecular strand-displacement strategy that allows for independent fine-tuning of thermodynamics and kinetics of aptamer switches.

Precise Cross-Dimensional Regulation of the Structure of a Photoreversible DNA Nanoswitch

In this study, an accurately and digitally regulated allosteric nanoswitch based on the conformational control of two DNA hairpins was developed. By switching between UV irradiation and blue light conditions, the second molecular beacon (H#2) would bind/separate with a repression sequence (RES) via the introduced PTG molecules (a photosensitive azobenzene derivative), resulting in the target aptamer sequence in the first molecular beacon (H#1) not being able/being able to hold the stem-loop configuration, hence losing/regaining the ability to bind with the target. Importantly, we successfully monitor conformation changes of the nanoswitch by an elegant mathematical model for connecting K_i (the dissociation constant between RES and H#2) with K_d (the overall equilibrium constant of the nanoswitch binding the target), hence realizing "observing" DNA structure across dimensions from "structural visualization" to digitization and, accurately, digitally regulating DNA structure from digitization to "structural visualization".

Tethered imidazole mediated duplex stabilization and its potential for aptamer stabilization

Previous investigations of the impact of an imidazole-tethered thymidine in synthetic DNA duplexes, monitored using UV and NMR spectroscopy, revealed a base context dependent increase in thermal stability of these duplexes and a striking correlation with the imidazolium pK_a. Unrestrained molecular dynamics (MD) simulations demonstrated the existence of a hydrogen bond between the imidazolium and the Hoogsteen side of a nearby guanosine which, together with electrostatic interactions, form the basis of the so-called pK_a-motif responsible for these duplex-stabilizing and pK_a-modulating properties. Here, the robustness and utility of this pK_a-motif was explored by introducing multiple imidazole-tethered thymidines at different positions on the same dsDNA duplex. For all constructs, sequence based expectations as to pK_a-motif formation were supported by MD simulations and experimentally validated using NOESY. Based on the analysis of the pK_a values and melting temperatures, guidelines are formulated to assist in the rational design of oligonucleotides modified with imidazolium-tethered thymidines for increased thermal stability that should be generally applicable, as demonstrated through a triply modified construct. In addition, a proof-of-principle study demonstrating enhanced stability of the l-argininamide binding aptamer modified with an imidazole-tethered thymidine in the presence and absence of ligand, demonstrates its potential for the design of more stable aptamers.

Duplexed aptamers: history, design, theory, and application to biosensing

Nucleic acid aptamers are single stranded DNA or RNA sequences that specifically bind a cognate ligand. In addition to their widespread use as stand-alone affinity binding reagents in analytical chemistry, aptamers have been engineered into a variety of ligand-specific biosensors, termed aptasensors. One of the most common aptasensor formats is the duplexed aptamer (DA). As defined herein, DAs are aptasensors containing two nucleic acid elements coupled via Watson-Crick base pairing: (i) an aptamer sequence, which serves as a ligand-specific receptor, and (ii) an aptamer-complementary element (ACE), such as a short DNA oligonucleotide, which is designed to hybridize to the aptamer. The ACE competes with ligand binding, such that DAs generate a signal upon ligand-dependent ACE-aptamer dehybridization. DAs possess intrinsic advantages over other aptasensor designs. For example, DA biosensing designs generalize across DNA and RNA aptamers, DAs are compatible with many readout methods, and DAs are inherently tunable on the basis of nucleic acid hybridization. However, despite their utility and popularity, DAs have not been well defined in the literature, leading to confusion over the differences between DAs and other aptasensor formats. In this review, we introduce a framework for DAs based on ACEs, and use this framework to distinguish DAs from other aptasensor formats and to categorize cis- and trans-DA designs. We then explore the ligand binding dynamics and chemical properties that underpin DA systems, which fall under conformational selection and induced fit models, and which mirror classical SN1 and SN2 models of nucleophilic substitution reactions. We further review a variety of in vitro and in vivo applications of DAs in the chemical and biological sciences, including riboswitches and riboregulators. Finally, we present future directions of DAs as ligand-responsive nucleic acids. Owing to their tractability, versatility and ease of engineering, DA biosensors bear a great potential for the development of new applications and technologies in fields ranging from analytical chemistry and mechanistic modeling to medicine and synthetic biology.

Exploiting the conformational-selection mechanism to control the response kinetics of a "smart" DNA hydrogel

The sequence-specific hybridization and molecular recognition properties of DNA support the construction of stimulus-responsive hydrogels with precisely controlled crosslink geometry. Here we show that, as predicted by the conformational selection mechanism, the response kinetics of such a hydrogel can be tuned over orders of magnitude by modulating the thermodynamic stability of its crosslinks.

Optogenetic Navigation of Routes Leading to Protein Amyloidogenesis in Bacteria

Modulation of liquid-liquid and liquid-hydrogel phase transitions is central to avoid the cytotoxic aggregation of proteins in eukaryotic cells, but knowledge on its relevance in bacteria is limited. Here the power of optogenetics to engineer proteins as light-responsive switches has been used to control the balance between solubility and aggregation for LOV2-WH1, a chimera between the plant blue light-responsive domain LOV2 and the bacterial prion-like protein RepA-WH1. These proteins were first linked by fusing, as a continuous α-helix, the C-terminal photo-transducer Jα helix in LOV2 with the N-terminal domain-closure α1 helix in RepA-WH1, and then improved for light-responsiveness by including mutations in the Jα moiety. In the darkness and in a crowded solution in vitro, LOV2-WH1 nucleates the irreversible assembly of amyloid fibers into a hydrogel. However, under blue light illumination, LOV2-WH1 assembles as soluble oligomers. When expressed in Escherichia coli, LOV2-WH1 forms in the darkness large intracellular amyloid inclusions compatible with bacterial proliferation. Strikingly, under blue light, LOV2-WH1 aggregates decrease in size, while they become detrimental for bacterial growth. LOV2-WH1 optogenetics governs the assembly of mutually exclusive inert amyloid fibers or cytotoxic oligomers, thus enabling the navigation of the conformational landscape of protein amyloidogenesis to generate potential photo-activated anti-bacterial devices (optobiotics).

Expanded Interactome of the Intrinsically Disordered Protein Dss1

Dss1 (also known as Sem1) is a conserved, intrinsically disordered protein with a remarkably broad functional diversity. It is a proteasome subunit but also associates with the BRCA2, RPA, Csn12-Thp1, and TREX-2 complexes. Accordingly, Dss1 functions in protein degradation, DNA repair, transcription, and mRNA export. Here in Schizosaccharomyces pombe, we expand its interactome further to include eIF3, the COP9 signalosome, and the mitotic septins. Within its intrinsically disordered ensemble, Dss1 forms a transiently populated C-terminal helix that dynamically interacts with and shields a central binding region. The helix interfered with the interaction to ATP-citrate lyase but was required for septin binding, and in strains lacking Dss1, ATP-citrate lyase solubility was reduced and septin rings were more persistent. Thus, even weak, transient interactions within Dss1 may dynamically rewire its interactome.

Detecting transcription factors with allosteric DNA-Silver nanocluster switches

Sensitive and efficient detection of protein markers, such as transcription factors (TFs), is an important issue in postgenomic era. In this paper, we report a DNA nanodevice, allosteric DNA-silver nanocluster switches (AgSwitches), for TFs detection. The mechanism of this nanodevice is based on the binding-induced allostery whereby the binding between AgSwitches and TFs alters the conformation of AgSwitches. This alteration brings DNA-silver nanocluster (DNA-AgNCs) and guanine-rich enhancer sequences (GRS) into close proximity, generating fluorescent enhancement for quantifications. Our results revealed that the sequence design of AgSwitches can be rationally optimized according to stimulated free energy, and we demonstrated that this method can not only be used for detecting TFs in nuclear extracts of cells, but also be developed as a tool for screening inhibitors of TFs. Overall, this work expanded the category allosteric DNA nanodevices by first introducing DNA-AgNCs into this area, and the obtained method was efficient for TFs-related investigations.