Stabilizing structure-switching signaling RNA aptamers by entrapment in sol-gel derived materials for solid-phase assays

Long term storage of miRNA at room and elevated temperatures in a silica sol-gel matrix

Storage of biospecimens in their near native environment at room temperature can have a transformative global impact, however, this remains an arduous challenge to date due to the rapid degradation of biospecimens over time. Currently, most isolated biospecimens are refrigerated for short-term storage and frozen (-20 °C, -80 °C, liquid nitrogen) for long-term storage. Recent advances in room temperature storage of purified biomolecules utilize anhydrobiosis. However, a near aqueous storage solution that can preserve the biospecimen nearly "as is" has not yet been achieved by any current technology. Here, we demonstrate an aqueous silica sol-gel matrix for optimized storage of biospecimens. Our technique is facile, reproducible, and has previously demonstrated stabilization of DNA and proteins, within a few minutes using a standard benchtop microwave. Herein, we demonstrate complete integrity of miRNA 21, a highly sensitive molecule at 4, 25, and 40 °C over a period of ∼3 months. In contrast, the control samples completely degrade in less than 1 week. We attribute excellent stability to entrapment of miRNA within silica-gel matrices.

An Electrochemical Aptasensor Platform Based on Flower-Like Gold Microstructure-Modified Screen-Printed Carbon Electrode for Detection of Serpin A12 as a Type 2 Diabetes Biomarker

Purpose

In the present study, a highly sensitive and simple electrochemical (EC) aptasensor for the detection of serpin A12 as a novel biomarker of diabetes was developed on a platform where flower-like gold microstructures (FLGMs) are electrodeposited onto a disposable screen-printed carbon electrode. Meanwhile, serpin A12-specific thiolated aptamer was covalently immobilized on the FLGMs.

Methods

The electrochemical activity of a fabricated aptasensor under various conditions were examined by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). Aptamer concentration, deposition time, self-assembly time, and incubation time were optimized for assay of serpin A12. The differential pulse voltammetry (DPV) was implemented for quantitative detection of serpin A12 in K₃ [Fe (CN) ₆]/K₄ [Fe (CN) ₆] solution (redox probe).

Results

The label-free aptasensor revealed a linear range of serpin A12 concentration (0.039–10 ng/mL), detection limit of 0.020 ng/mL (S/N=3), and 0.031 ng/mL in solution buffer and plasma, respectively.

Conclusion

The results indicate that this aptasensor has a high sensitivity, selectivity, stability, and acceptable reproducibility for detection of serpin A12 in diabetic patients.

A universal aptasensing platform based on cryonase-assisted signal amplification and graphene oxide induced quenching of the fluorescence of labeled nucleic acid probes: application to the detection of theophylline and ATP

This study describes a universal fluorometric method for sensitive detection of analytes by using aptamers. It is based on the use of graphene oxide (GO) and cryonase-assisted signal amplification. GO is a strong quencher of FAM-labeled nucleic acid probes, while cryonase digests all types of nucleic acid probes. This makes the platform widely applicable to analytes for which the corresponding aptamers are available. Theophylline and ATP were chosen as model analytes. In the absence of targets, dye-labeled aptamers are in a flexible single strand state and adsorb on the GO. As a result, the probes are non-fluorescent due to the efficient quenching of dyes by GO. Upon the addition of a specific target, the aptamer/target complex desorbed from the GO surface and the probe becomes fluorescent. The released complex will immediately become a substrate for cryonase digestion and subsequently releasing the target to bind to another aptamer to initiate the next round of cleavage. This cyclic reaction will repeat again and again until all the related-probes are consumed and all fluorophores light up, resulting in significant fluorescent signal amplification. The detection limits are 47 nM for theophylline and 22.5 nM for ATP. This is much better than that of known methods. The assay requires only mix-and-measure steps that can be accomplished rapidly. In our perception, the detection scheme holds great promise for the design enzyme-aided amplification mechanisms for use in bioanalytical methods. Graphical abstract A cryonase-assisted signal amplification (CASA) method has been developed by using graphene oxide (GO) conjugated with a fluorophore-labeled aptamer for fluorescence signal generation. It has a large scope because it may be applied to numerous analytes.

Exploiting the application of l-aptamer with excellent stability: an efficient sensing platform for malachite green in fish samples

Effective monitoring of the content of malachite green (MG) in aquaculture is of great importance for food safety. Traditional methods for MG assay, such as chromatography and spectroscopy, have been criticized for expensive instrumentation and complicated pretreatments. An MG RNA aptamer (MGA) is a powerful tool for immediate and rapid detection of MG. However, RNA is easily degraded by nucleases and is unstable in the environment, making accurate and reliable detection of MG difficult. In order to address the problems, an innovative levo (l)-MGA with excellent stability is designed to perform the specific recognition function. Interestingly, the gel electrophoresis and fluorescence measurement results indicate that this unnaturally occurring l-aptamer is resistant to nuclease degradation and it can be kept intact in the standard buffer solution under room temperature for quite a long time. A label-free, simple, and efficient method has been developed for sensitive detection of MG in fish tissue, which holds promising potential in food analysis and environmental monitoring.

Detection of hexahydro-1,3-5-trinitro-1,3,5-triazine (RDX) with a microbial sensor

Explosives such as hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) are common contaminants found in soil and groundwater at military facilities worldwide, but large-scale monitoring of these contaminants at low concentrations is difficult. Biosensors that incorporate aptamers with high affinity and specificity for a target are a novel way of detecting these compounds. This work describes novel riboswitch-based biosensors for detecting RDX. The performance of the RDX riboswitch was characterized in Escherichia coli using a range of RDX concentrations from 0-44 μmol l^-1. Fluorescence was induced at RDX concentrations as low as 0.44 μmol l^-1. The presence of 4.4 μmol l^-1 RDX induced an 8-fold increase in fluorescence and higher concentrations did not induce a statistically significant increase in response.

Carbon nanoparticle-protected RNA aptasensor for amplified fluorescent determination of theophylline in serum based on nuclease-aided signal amplification

A carbon nanoparticle (CNP) and Cryonase-aided method that realizes the amplified fluorescent detection of theophylline was proposed.

Green synthesis of mesoporous γ-Al2O3 from coal fly ash with simultaneous on-site utilization of CO2

Mesoporous Al₂O₃ with crystalline framework walls has expanded all over the world due to the various potential applications especially in catalysis. Here, we develop a green and facile approach for the conversion of coal fly ash (CFA) into ordered mesoporous γ-Al₂O₃. The practical and promising lime-sinter method was comprehensively studied for the extraction of aluminum from CFA as a first step. The extraction efficiency of aluminum could reach up to 87.42%, through calcining with CaCO₃ at 1390°C for 1 h and then dissolving in Na₂CO₃ solution at 70°C for 0.5 h. Combined with the urgent demand for CO₂ emission reduction, simulated purified flue gas was introduced to precipitate the Al(OH)₃ precursors without structure-directing agents for just 1 h, followed by calcining at only 400°C or 550°C. A series of characterizations were conducted to discuss the effect of precipitation temperature and calcination temperature, resulting the superior product (Al₂O₃-65/550) with high surface area (230.3 m² g^-1), crystalline γ-Al₂O₃ phase and ordered mesostructure. This proposed strategy, integrating the on-site recycling of CFA and utilization of CO₂, appears to be promising for scalable production of mesoporous γ-Al₂O₃.

Bio-hybrid inorganic microparticles derived from CO2 for highly efficient and selective removal of antibiotics

BACKGROUND

Antibiotics, which are the most important medication in human history, have brought global concerns due to their potential risk to human health and environment by accelerating the development of drug-resistant bacteria, and accumulating in the food chain system. Among antibiotics, oxytetracycline (OTC) is widely used in aquaculture, and its potential risk of toxicity to human by bioaccumulation has been reported. Therefore, the effective removal of OTC is highly needed.

RESULTS

In this study, we report bio-hybrid inorganic microparticles (apt-mag-SiCC) for efficient capturing and facile magnet-based separation of oxytetracycline (OTC). These bio-hybrid inorganic microparticles are composed of magnetic separable silica coated calcium carbonate microparticles (mag-SiCC) derived from CO2, conjugated with oxytetracycline binding aptamers (OBA). These bio-hybrid inorganic microparticles were successfully synthesized, based on the characterization data obtained by SEM, FT-IR, EDAX, BET, and CLSM. About 6 μm sized bio-hybrid inorganic microparticles showed low non-specific adsorption to OTC and other molecules, and the selective capturing towards to the OTC in both buffer and tap water. Moreover, these bio-hybrid mineral microparticles were found to be stable, even after the repeated usages, maintaining the initial capturing efficiency.

CONCLUSION

Using the newly synthesized bio-hybrid inorganic microparticles, we could successfully capture OTC by facile magnet-based separation. With advantages of theses bio-hybrid inorganic microparticles such as easy fabrication, low-price, and environmental friendliness, this novel material could be utilized in the drinking water treatment, in vitro medicinal diagnostics, or in vitro removal of antibiotics lining out from the blood (blood purification).

Sol-Gel-Derived Biohybrid Materials Incorporating Long-Chain DNA Aptamers

Sol-gel-derived bio/inorganic hybrid materials have been examined for diverse applications, including biosensing, affinity chromatography and drug discovery. However, such materials have mostly been restricted to the interaction between entrapped biorecognition elements and small molecules, owing to the requirement for nanometer-scale mesopores in the matrix to retain entrapped biorecognition elements. Herein, we report on a new class of macroporous bio/inorganic hybrids, engineered through a high-throughput materials screening approach, that entrap micron-sized concatemeric DNA aptamers. We demonstrate that the entrapment of these long-chain DNA aptamers allows their retention within the macropores of the silica material, so that aptamers can interact with high molecular weight targets such as proteins. Our approach overcomes the major limitation of previous sol-gel-derived biohybrid materials by enabling molecular recognition for targets beyond small molecules.

Collagen Membranes with Ribonuclease Inhibitors for Long-Term Stability of Electrochemical Aptamer-Based Sensors Employing RNA

Electrochemical aptamer-based (E-AB) sensors offer advantageous analytical detection abilities due to their rapid response time (seconds to minutes), specificity to a target, and selectivity to function in complex media. Ribonucleic acid (RNA) aptamers employed in this class of sensor offer favorable binding characteristics resulting from the ability of RNA to form stable tertiary folds aided by long-range intermolecular interactions. As a result, RNA aptamers can fold into three-dimensional structures more complex than those of their DNA counterparts and consequently exhibit better binding ability to target analytes. Unfortunately, RNA aptamers are susceptible to degradation by nucleases, and for this reason, RNA-based sensors are scarce or require significant sample pretreatment before use in clinically relevant media. Here, we combine the usefulness of a collagen I hydrogel membrane with entrapped ribonuclease inhibitors (RI) to protect small molecule RNA E-AB sensors from endogenous nucleases in complex media. More specifically, the biocompatibility of the naturally polymerized hydrogel with encapsulated RI promotes the protection of an aminoglycoside-binding RNA E-AB sensor up to 6 h, enabling full sensor function in nuclease-rich environments (undiluted serum) without the need for prior sample preparation or oligonucleotide modification. The use of collagen as a biocompatible membrane represents a general approach to compatibly interface E-AB sensors with complex biological samples.

Construction of DNAzyme-Encapsulated Fibermats Using the Precursor Network Polymer of Poly(γ-glutamate) and 4-Glycidyloxypropyltrimethoxysilane

Here, we developed functional nucleic acid (FNA)-encapsulated electrospun fibermats. To facilitate stable FNA encapsulation in the γ-PGA/GPTMS fibermats, we used the FNA as an FNA/streptavidin complex, and as a representative FNA, we selected a DNAzyme, the DNA/hemin complex, which is composed of G-quadraplex-forming single-stranded DNA and hemin and exhibits oxidation activity with the aid of a cocatalyst, H₂O₂. Scanning electron microscopy and Fourier-transform infrared spectroscopy measurements revealed that encapsulation of the DNA/hemin complex (∼1 wt % against the γ-PGA/GPTMS hybrid) in the nanofibers of the γ-PGA/GPTMS fibermats did not affect the structure of the original nanofibers. However, because a unique MW-dependent molecular permeability originated from the 3D network structure of the γ-PGA/GPTMS hybrid, low-MW substrates such as 4-aminoantipyrine, N-ethyl-N-(2-hydroxy-3-sulfopropyl)-3-methylaniline, and luminol were able to reach the encapsulated DNA/hemin complex by permeating to the inside of the nanofibers from an immersion buffer and then underwent catalytic oxidation. Conversely, nucleases, which are proteins featuring high MWs (>5 kDa), could not penetrate the γ-PGA/GPTMS nanofibers, and the encapsulated DNA/hemin complex was therefore effectively protected against nuclease digestion. Thus, encapsulating FNAs on the inside of the nanofibers of fibermats offers clear advantages for the practical application of FNAs in sensors and drugs, particularly for use in the in vivo circumstances.

Generation of Biostable L-aptamers against Achiral Targets by Chiral Inversion of Existing D-aptamers

In this paper, based on reciprocal chiral substrate specificity, taking achiral molecules, ethanolamine (EA) and malachite green (MG) as two model targets, biostable L- DNA aptamers and L-RNA aptamers were generated respectively by chiral inversion of existing D-aptamers. In the detection of EA with L-DNA aptamer-based sensors, the feasibility of our strategy was confirmed, while in the detection of MG with L-RNA aptamers, linear calibration curves were obtained in the range from 0.1 to 5µm with the detection limit of 0.065µm under optimized experimental conditions. The results demonstrated that the mirror-image L-aptamers have identical recognition capability as D-aptamers. Meanwhile, L-aptamers have superior biostability to resist nuclease digestion, protein binding interference and off-target effects, enabling their applications in complex practical samples, such as lake water and fish tissue extractions. Our work provides a simple, yet universal and efficient way to develop biostable aptamers.

Engineering Signaling Aptamers That Rely on Kinetic Rather Than Equilibrium Competition

During the past decade, aptasensors have largely been designed on the basis of the notion that ligand-modulated equilibration between aptamer conformations could be exploited for sensing. One implementation of this strategy has been to denature the aptamer with an antisense oligonucleotide, wait for dissociation of the antisense oligonucleotide, and stabilize the folded, signaling conformer with a ligand. However, there is a large kinetic barrier associated with releasing the oligonucleotide from the aptamer to again obtain an active, binding conformation. If the length of the antisense oligonucleotide is decreased to make dissociation from the aptamer more favorable, higher background signals are observed. To improve the general methodology for developing aptasensors, we have developed a novel and robust strategy for aptasensor design in which an oligonucleotide kinetically competes with the ligand for binding rather than having to be released from a stable duplex. While the oligonucleotide can induce conformational change, it initially chooses between the aptamer and a molecular beacon (MB), a process that does not require a lengthy pre-equilibration. Using an anti-ricin aptamer as a starting point, we developed a "competitive" aptasensor with a measured limit of detection (LOD) of 30 nM with an optical readout and as low as 3 nM for ricin toxin A-chain (RTA) detection on an electrochemical platform.

Aptamer-based biosensors for biomedical diagnostics

Aptamers are single-stranded nucleic acids that selectively bind to target molecules. Most aptamers are obtained through a combinatorial biology technique called SELEX. Since aptamers can be isolated to bind to almost any molecule of choice, can be readily modified at arbitrary positions and they possess predictable secondary structures, this platform technology shows great promise in biosensor development. Over the past two decades, more than one thousand papers have been published on aptamer-based biosensors. Given this progress, the application of aptamer technology in biomedical diagnosis is still in a quite preliminary stage. Most previous work involves only a few model aptamers to demonstrate the sensing concept with limited biomedical impact. This Critical Review aims to summarize progress that might enable practical applications of aptamers for biological samples. First, general sensing strategies based on the unique properties of aptamers are summarized. Each strategy can be coupled to various signaling methods. Among these, a few detection methods including fluorescence lifetime, flow cytometry, upconverting nanoparticles, nanoflare technology, magnetic resonance imaging, electronic aptamer-based sensors, and lateral flow devices have been discussed in more detail since they are more likely to work in a complex sample matrix. The current limitations of this field include the lack of high quality aptamers for clinically important targets. In addition, the aptamer technology has to be extensively tested in a clinical sample matrix to establish reliability and accuracy. Future directions are also speculated to overcome these challenges.

Selective lighting up of epiberberine alkaloid fluorescence by fluorophore-switching aptamer and stoichiometric targeting of human telomeric DNA G-quadruplex multimer

Aptamers, that exist naturally in living cells as functional elements and can switch nonfluorescent natural targets to fluorophores, are very useful in developing highly sensitive and selective biosensors and screening functional agents. This work demonstrates that human telomeric G-quadruplex (HTG) can serve as a potential fluorophore-switching aptamer (FSA) to target a natural isoquinoline alkaloid. We found that, among the G-quadruplexes studied here and the various structurally similar alkaloids including epiberberine (EPI), berberine (BER), palmatine (PAL), jatrorrhizine (JAT), coptisine (COP), worenine (WOR), sanguinarine (SAN), chelerythrine (CHE), and nitidine (NIT), only the HTG DNA, especially with a 5'-TA-3' residue at the 5' end of the G-quadruplex tetrad (5'-TAG3(TTAG3)3-3', TA[Q]) as the minimal sequence, is the most efficient FSA to selectively light up the EPI fluorescence. Compared to the 5' end flanking sequences, the 3' end flanking sequences of the tetrad contribute significantly less to the recognition of EPI. The binding affinity of EPI to TA[Q] (K(d) = 37 nM) is at least 20 times tighter than those of the other alkaloids. The steady-state absorption, steady-state/time-resolved fluorescence, and NMR studies demonstrate that EPI most likely interact with the 5' end flanking sequence substructure beyond the core [Q] and the G-quadruplex tetrad in a much more specific manner than the other alkaloids. The highly selective and tight binding of EPI with the FSA and significantly enhanced fluorescence suggest the potential development of a selective EPI sensor (detection limit of 10 nM). More importantly, EPI, as the brightest FSA emitter among the alkaloids, can also serve as an efficient conformation probe for HTG DNA and discriminate the DNA G-quadruplex from the RNA counterpart. Furthermore, EPI can bind stoichiometrically to each G-quadruplex unit of long HTG DNA multimer with the most significant fluorescence enhancement, which has not been achieved by the previously reported probes. Our work suggests the potential use of EPI as a bioimaging probe and a therapeutic DNA binder.

Hydrophobic sol-gel channel patterning strategies for paper-based microfluidics

Hydrophobic sol-gel derived methylsilsesquioxane (MSQ) was compared to wax and alkylketene dimer (AKD) as barrier materials defining channels in paper-based microfluidic devices. While all three of the barrier types performed well with water, only the MSQ barriers were not breached by aggressive cell lysing solutions and surfactant solutions (SDS, CTAB, Triton X-100). The MSQ barriers also withstood glycerol, toluene and DMSO whereas all three barrier types were breached by alcohols. MSQ based devices could be prepared either by direct inkjet printing of the barriers or by base etching of MSQ impregnated paper. The functionality of MSQ based devices was demonstrated by formatting a colormetric sensor for Escherichia coli.

Incorporating mobile nanospheres in the lumen of hybrid microcapsules for enhanced enzymatic activity

Physical encapsulation of enzymes in microcapsules, as a mild, controllable method, has been widely utilized for enzyme immobilization. However, this method often suffers from the big mass transfer resistance from the capsule lumen. In this study, a novel biocatalysis system with enhanced catalytic activity is constructed through coencapsulating enzymes and nanospheres in the lumen of protamine/silica hybrid microcapsules, which are synthesized through the synergy of biomimetic silicification and layer-by-layer (LbL) assembly. When utilized as the host for catalase (CAT) encapsulation, the hybrid microcapsules maintain high mechanical stability, high enzyme loading, and low enzyme leaching. Particularly, because of the existence of mobile nanospheres, the mass transfer resistance in the microcapsules is significantly reduced because of the vigorous agitation, thus acquiring an enhanced catalytic activity. Our strategy may also find applications in drug delivery and biosensor fields.

Functional nucleic acid entrapment in sol-gel derived materials

Functional nucleic acids (FNAs) are single-stranded DNA or RNA molecules, typically generated through in vitro selection, that have the ability to act as receptors for target molecules (aptamers) or perform catalysis of a chemical reaction (deoxyribozymes and ribozymes). Fluorescence-signaling aptamers and deoxyribozymes have recently emerged as promising biological recognition and signaling elements, although little has been done to evaluate their potential for solid-phase assays, particularly with species made of RNA due to their lack of chemical stability and susceptibility to nuclease attack. Herein, we present a detailed overview of the methods utilized for solid-phase immobilization of FNAs using a sol-gel entrapment method that can provide protection from nuclease degradation and impart long-term chemical stability to the FNA reporter systems, while maintaining their signaling capabilities. This article will also provide a brief review of the results of such entrapment studies involving fluorescence-signaling versions of a DNA aptamer, selected RNA-cleaving deoxyribozymes, and two different RNA aptamers in a series of sol-gel derived composites, ranging from highly polar silica to hydrophobic methylsilsesquioxane-based materials. Given the ability to produce sol-gel derived materials in a variety of configurations, particularly as thin film coatings on electrodes, optical fibers, and other devices, this entrapment method should provide a useful platform for numerous solid-phase FNA-based biosensing applications.

Reversible switches of DNA nanostructures between "Closed" and "Open" states and their biosensing applications

A novel and versatile biosensing platform based on the structural conversion of 3D DNA nanostructures from ETDNA (Equilateral Triangle) to TPFDNA (Triangular Pyramid Frustum) was proposed for the first time. The inputs of aptamers and their relative targets made the DNA structure change from the "Open" to the "Closed" state, leading to the faradaic impedance changes as the output signals. The specific properties of excellent stability and specific rigid structure of 3D DNA nanostructures made the biosensor function as a regenerable, reusable and intelligent platform. The sensor exhibited excellent selectivity for IFN-γ detection with a wide linear range of 1.0 × 10(-9) to 2.0 × 10(-6) M and a low detection limit of 5.2 × 10(-10) M. The distinctive features of DNA nanostructures make them potentially advantageous for a broad range of biosensing, bionanoelectronics, and therapeutic applications.

Ultrasensitive electrochemical cocaine biosensor based on reversible DNA nanostructure

We proposed an ultrasensitive electrochemical cocaine biosensor based on the three-dimensional (3D) DNA structure conversion of nanostructure from Triangular Pyramid Frustum (TPFDNA) to Equilateral Triangle (ETDNA). The presence of cocaine triggered the aptamer-composed DNA nanostructure change from "Close" to "Open", leading to obvious faradaic impedance changes. The unique properties with excellent stability and specific rigid structure of the 3D DNA nanostructure made the biosensing functions stable, sensitive, and regenerable. The Faradaic impedance responses were linearly related to cocaine concentration between 1.0 nM and 2.0 μM with a correlation coefficient of 0.993. The limit of detection was calculated to be 0.21 nM following IUPAC recommendations (3Sb/b). It is expected that the distinctive features of DNA nanostructure would make it potentially advantageous for a broad range of biosensing, bionanoelectronics, and therapeutic applications.

Capillary electrophoresis-systematic evolution of ligands by exponential enrichment selection of base- and sugar-modified DNA aptamers: target binding dominated by 2'-O,4'-C-methylene-bridged/locked nucleic acid primer

Chemically modified DNA aptamers specific to human α-thrombin were obtained from oligodeoxyribonucleotide (ODN) libraries by using a capillary electrophoresis-systematic evolution of ligands by exponential enrichment (CE-SELEX) method. These libraries contained 2'-O,4'-C-methylene-bridged/linked bicyclic ribonucleotides (B/L nucleotides) in the primer region and/or C5-modified thymidine bearing N(6)-ethyladenine (t) in the nonprimer region. Modified DNA aptamers showed high binding affinities to the target, with dissociation constants (Kd) values in the range of subnanomolar to several ten nanomolar levels. The introduction of base modification significantly suppressed the frequency of G-quadruplex motifs, which are often seen in thrombin-binding DNA aptamers. The resulting alternatives contained the 10-mer consensus sequence t5Gt2G2, which is frequently found in modified DNA aptamers with subnanomolar protein binding affinities. Furthermore, some base- and sugar-modified DNA aptamers with the 12-mer consensus sequence t2G2tC(A/G)A2G2t displayed binding activities that were dependent on the presence of B/L nucleotides in the primer region. Such aptamers were interestingly not recovered from a natural DNA library or from DNA libraries modified with either B/L nucleotides or t's. This emerging characteristic binding property will enable the creation of a direct selection methodology for DNA-based molecular switches that are triggered by chemical conversion of B/L nucleotides introduced to constant sequence regions in ODN libraries.

Quality control certification of RNA aptamer-based detection

Aptamers are single-stranded DNA or RNA molecules with a defined tertiary structure for molecular recognition. Numerous RNA aptamers with excellent binding affinity and specificity have been reported; they constitute an attractive reservoir of molecular recognition elements for biosensor development. However, RNA is relatively unstable owing to spontaneous hydrolysis and nuclease degradation. Thus, RNA aptamer-based biosensors are prone to producing false-positive signals. Here, we present an RNA aptamer biosensor design strategy that utilises an internal control to distinguish target binding from false-positive signals. The sequence of a chosen RNA aptamer is expanded so that it can form three consecutive short RNA-DNA duplexes with 1) a quencher-labelled DNA strand (Q(1)DNA), 2) a dual-fluorophore-labelled DNA strand (F(1)DNAF(2)) and 3) another quencher-labelled DNA strand (Q(2)DNA). The addition of a target releases Q(2)DNA from the duplex assembly, and produces the expected positive signal from F(2). However, the authenticity of target recognition is validated only if no signal is generated from F(1). We have successfully engineered two fluorescent reporters by using an RNA aptamer that binds thrombin and one that binds theophylline. Both reporters show the expected binding affinity and specificity, and are capable of reporting system malfunction when treated with nucleases and chemical denaturants. This strategy provides a simple and reliable way to ensure high-quality detection when RNA aptamers are employed as molecular-recognition elements.

Preparation of aqueous sol-gel silica and titania multi-layered thin films and their evaluation as biomolecular encapsulation hosts

Multi-layered silica and titania thin films were prepared via an aqueous sol-gel route. The titania layers could efficiently entrap anti-HRP antibodies and showed increase in stability upon ageing, up to 2 months. Specific activity of the entrapped antibodies could be monitored in a reliable manner over one week. The silica films showed lower performances, as a probable consequence of large pore size. Increase in the titania precursor (TiBALDH) concentration and addition of glycerol allowed the design of tri-enzymatic multi-layered systems for the detection of lactose. The multilayer approach showed higher robustness than the co-immobilization of the enzymes in a single layer. This process is simple, solvent-free and flexible, opening the route to multi-biofunctional materials at the nanoscale.

Stabilization of ssRNA on graphene oxide surface: an effective way to design highly robust RNA probes

RNA probes constitute an important class of functional nucleic acids (FNAs). However, because of their notorious vulnerability to enzymatic degradation, extremely careful and special protocols must be followed when dealing with RNA probes. To fully use the large number of RNA FNAs available for bioanalysis and biomedicine, it is important to explore effective methods to protect RNA probes from enzymatic digestion. In this work, we systematically demonstrate that graphene oxide (GO) can effectively protect RNA probes from enzymatic digestion. Based on this finding, we propose an effective way to design robust RNA biosensors by simply mixing RNA probes with GO for analysis of nucleic acids, proteins, and small molecules. The entire assay is sensitive, selective, rapid, and more importantly, does not require any special protocols. The ability to protect ssRNA from enzymatic digestion by GO offers an exciting new way to stabilize ssRNA, which will not only provide new opportunities to utilize the large number of currently available, yet rarely explored, RNA FNAs for bioanalysis but also offer a new solution to protect important ssRNA molecules, such as microRNA and antisense ssRNA, for a great variety of biomedical applications.

Exploration of structure-switching in the design of aptamer biosensors

The process of "structure-switching" enables biomolecular switches to function as effective biosensing tools. Biomolecular switches can be activated or inactivated by binding to a specific target that triggers a precise conformational change in the biomolecules involved. Although many examples of aptamer-based biomolecular switches can be found in nature, substantial effort has been made in the last decade to engineer structure-switching aptamer sensors by coupling aptamers to a signal transduction method to generate a readout signal upon target binding to the aptamer domain. This chapter focuses on the progress of research on engineered structure-switching aptamer sensors. We begin by discussing the origin of the structure-switching aptamer design, highlight the key developments of structure-switching DNA aptamers for fluorescence-, electrochemistry-, and colorimetry-based detection, and introduce our recent efforts in exploring RNA aptamers to create structure-switching molecular sensors.

Challenges and opportunities for small molecule aptamer development

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.

Challenges and opportunities for small molecule aptamer development

Aptamers are single-stranded oligonucleotides that bind to targets with high affinity and selectivity. Their use as molecular recognition elements has emerged as a viable approach for biosensing, diagnostics, and therapeutics. Despite this potential, relatively few aptamers exist that bind to small molecules. Small molecules are important targets for investigation due to their diverse biological functions as well as their clinical and commercial uses. Novel, effective molecular recognition probes for these compounds are therefore of great interest. This paper will highlight the technical challenges of aptamer development for small molecule targets, as well as the opportunities that exist for their application in biosensing and chemical biology.