Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering

Screening biotoxin aptamer and their application of optical aptasensor in food stuff: a review

Biotoxins are ranges of toxic substances produced by animals, plants, and microorganisms, which could contaminate foods during their production, processing, transportation, or storage, thus leading to foodborne illness, even food terrorism. Therefore, proposing simple, rapid, and effective detection methods for ensuring food free from biotoxin contamination shows a highly realistic demand. Aptamers are single-stranded oligonucleotides obtained from the systematic evolution of ligands by performing exponential enrichment (SELEX). They can specifically bind to wide ranges of targets with high affinity; thus, they have become important recognizing units in safety monitoring in food control and anti-terrorism. In this paper, we reviewed the technical points and difficulties of typical aptamer screening processes for biotoxins. For promoting the understanding of food control in the food supply chain, the latest progresses in rapid optical detection of biotoxins based on aptamers were summarized. In the end, we outlined some challenges and prospects in this field. We hope this paper could stimulate widespread interest in developing advanced sensing systems for ensuring food safety.

Equilibrium interactions of biomimetic DNA aptamers produce intrafibrillar calcium phosphate mineralization of collagen

Native and biomimetic DNA structures have been demonstrated to impact materials synthesis under a variety of conditions but have only just begun to be explored in this role compared to other biopolymers such as peptides, proteins, polysaccharides, and glycopolymers. One selected DNA aptamer has been explored in calcium phosphate and calcium carbonate mineralization, demonstrating sequence-dependent control of kinetics, morphology, and crystallinity. This aptamer is here applied to a biologically-relevant bone model system that uses collagen hydrogels. In the presence of the aptamer, intrafibrillar collagen mineralization is observed compared to negative controls and a positive control using well-studied poly-aspartic acid. The mechanism of interaction is explored through affinity measurements, kinetics of calcium uptake, and kinetics of aptamer uptake into the forming mineral. There is a marked difference observed between the selected aptamer containing a G-quadruplex secondary structure compared to a control sequence with no G-quadruplex. It is hypothesized that the equilibrium interaction of the aptamer with calcium-phosphate precursors and with the collagen itself leads to slow kinetic mineral formation and a morphology appropriate to bone. This points to new uses for DNA aptamers in biologically-relevant mineralization systems and the possibility of future biomedical applications. STATEMENT OF SIGNIFICANCE: Collagen is the protein structural component that mineralizes with calcium phosphate to form durable bone. Crystalline calcium phosphate must be infused throughout the collagen fiber structure to produce a strong material. This process is assisted by soluble proteins that interact with both calcium phosphate precursors and the collagen protein and has been proposed to follow a polymer-induce liquid precursor (PILP) model. Further understanding of this model and control of the process through synthetic, biomimetic molecules could have significant advantages in biomedical, restorative procedures. For the first time, synthetic DNA aptamers with specific secondary structures are here shown to influence and direct collagen mineralization. The mechanism of this process has been studied to demonstrate an important equilibrium between the DNA aptamer, calcium phosphate precursors, and collagen.

Unleashing the potential of tungsten disulfide: Current trends in biosensing and nanomedicine applications

The discovery of graphene ignites a great deal of interest in the research and advancement of two-dimensional (2D) layered materials. Within it, semiconducting transition metal dichalcogenides (TMDCs) are highly regarded due to their exceptional electrical and optoelectronic properties. Tungsten disulfide (WS2) is a TMDC with intriguing properties, such as biocompatibility, tunable bandgap, and outstanding photoelectric characteristics. These features make it a potential candidate for chemical sensing, biosensing, and tumor therapy. Despite the numerous reviews on the synthesis and application of TMDCs in the biomedical field, no comprehensive study still summarizes and unifies the research trends of WS2 from synthesis to biomedical applications. Therefore, this review aims to present a complete and thorough analysis of the current research trends in WS2 across several biomedical domains, including biosensing and nanomedicine, covering antibacterial applications, tissue engineering, drug delivery, and anticancer treatments. Finally, this review also discusses the potential opportunities and obstacles associated with WS2 to deliver a new outlook for advancing its progress in biomedical research.

Poly-thymine DNA templated MnO2 biomineralization as a high-affinity anchoring enabling tumor targeting delivery

Manganese oxide nanomaterials (MONs) are emerging as a type of highly promising nanomaterials for diseases diagnosis, and surface modification is the basis for colloidal stability and targeting delivery of the nanomaterials. Here, we report the in-situ functionalization of MnO₂ with DNA through a biomineralization process. Using adsorption-oxidation method, DNA templated Mn²⁺ precursor to biomineralize into nano-cubic seed, followed by the growth of MnO₂ to form cube/nanosheet hybrid nanostructure. Among four types of DNA homopolymers, poly-thymine (poly-T) was found to stably attach on MnO₂ surface to resist various biological displacements (phosphate, serum, and complementary DNA). Capitalized on this finding, a di-block DNA was rationally designed, in which the poly-T block stably anchored on MnO₂ surface, while the AS1411 aptamer block was not only an active ligand for tumor targeting delivery, but also a carrier for photosensitizer (Ce6) loading. Upon targeting delivery into tumor cells, the MnO₂ acted as catalase-mimic nanozyme for oxygenation to sensitize photodynamic therapy, and the released Mn²⁺ triggered chemodynamic therapy via Fenton-like reaction, achieving synergistic anti-tumor effect with full biocompatibility. This work provides a simple yet robust strategy to functionalize metal oxides nanomaterials for biological applications via DNA-templated biomineralization.

Secondary Structure of DNA Aptamer Influences Biomimetic Mineralization of Calcium Carbonate

Calcium materials, such as calcium carbonate, are produced in natural and industrial settings that range from oceanic to biomedical. An array of biological and biomimetic template molecules have been employed in controlling and understanding the mineralization reaction but have largely focused on small molecule additives or disordered polyelectrolytes. DNA aptamers are synthetic and programmable biomolecules with polyelectrolyte characteristics but with predictable and controllable secondary structure akin to native extracellular moieties. This work demonstrates for the first time the influence of DNA aptamers with known G-quadruplex structures on calcium carbonate mineralization. Aptamers demonstrate kinetic inhibition of mineral formation, sequence and pH-dependent uptake into the mineral, and morphological control of the primarily calcite material in controlled solution conditions. In reactions initiated from the complex matrix of ocean water, DNA aptamers demonstrated enhancement of mineralization kinetics and resulting amorphous material. This work provides new biomimetic tools to employ in controlled mineralization and demonstrates the influence that template secondary structure can have in material formation.

Competition-Enhanced Ligand Selection to Screen for DNA Aptamers for Spherical Gold Nanoparticles

The Competition-Enhanced Ligand Selection (CompELS) approach was used to identify aptamer candidates for spherical gold nanoparticles (AuNPs). This approach differs from conventional Systematic Evolution of Ligands by EXponential enrichment (SELEX)-based aptamer screening by eliminating repeated elution and polymerase chain reaction (PCR) amplification steps of bound candidate sequences between each selection round to continually enrich the candidate aptamer pool with oligonucleotides remaining from an earlier SELEX selection round. Instead, a new pool of unenriched oligonucleotides is added during each CompELS selection round to compete with existing target-bound oligonucleotides species for target binding sites. In this study, 24 aptamer candidates for AuNPs were identified using the CompELS approach and then compared to reveal similarities in their primary structures and their predicted secondary structures. No strong patterns in individual base identities (position-dependent) nor in segments of consecutive bases (independent of position) prevailed among the identified sequences. Motifs in predicted secondary structures, on the other hand, were shared among otherwise unrelated aptamer sequences. These motifs were revealed using a systematic classification and enumeration of distinct secondary structure elements, namely, hairpins, duplexes, single-stranded segments, interior loops, bulges, and multibranched loops.

Selected DNA aptamers as hydroxyapatite affinity reagents

DNA aptamers were selected for their ability to bind specifically and quickly to crystalline hydroxyapatite (Ca₁₀(PO₄)₆(OH)₂; HAP), the primary mineral component of enamel and bone. Aptamers were found to have an enhanced percent of G-nucleotides and a propensity for forming a G-quadruplex secondary structure. One aptamer was studied in comparison to control sequences and was found to bind with high affinity and at high loading capacity, with enhanced binding kinetics, and with specificity for crystalline HAP material over amorphous calcium phosphate (ACP) and β-tricalcium phosphate (TCP). The fluorescently-functionalized aptamer was demonstrated to specifically label HAP in a surface binding experiment and suggests the usefulness of this selected aptamer in biomedical or biotechnology fields where the labeling of specific calcium phosphate materials is required.

Plasmonic Selection of ssDNA Aptamers against Fibroblast Growth Factor Receptor

In this work, we describe the selection of ssDNA aptamers targeting fibroblast growth factor receptor binding protein 3 K650E, which has roles in cell division, growth, and differentiation through the kinase cascade. The selection process was based on the label-free, real-time monitoring of binding interactions by surface plasmon resonance, allowing for convenient manipulation of the selection rounds. Next generation sequencing data provided four major motif families from which nine individual sequences were selected based on their abundance levels. Electrophoretic mobility shift assays revealed binding of the selected aptamers to the target protein without significant interference from fibroblast growth factor receptor binding protein 2, indicating the selectivity of the aptamers. The dissociation constant at equilibrium for the best aptamer candidate, SU-3, was found to be (28.2 ± 19.6) × 10^-9 M (n = 5) using a single-cycle kinetic analysis method. Advantages of the experimental setup and potential applications of the selected aptamers are discussed.

Solidifying framework nucleic acids with silica

Soft matter can serve as a template to guide the growth of inorganic components with well-controlled structural features. However, the limited design space of conventional organic and biomolecular templates restricts the complexity and accuracy of templated growth. In past decades, the blossoming of structural DNA nanotechnology has provided us with a large reservoir of delicate-framework nucleic acids with design precision down to a single base. Here, we describe a DNA origami silicification (DOS) approach for generating complex silica composite nanomaterials. By utilizing modified silica sol-gel chemistry, pre-hydrolyzed silica precursor clusters can be uniformly coated onto the surface of DNA frameworks; thus, user-defined DNA-silica hybrid materials with ~3-nm precision can be achieved. More importantly, this method is applicable to various 1D, 2D and 3D DNA frameworks that range from 10 to >1,000 nm. Compared to pure DNA scaffolds, a tenfold increase in the Young's modulus (E modulus) of these composites was observed, owing to their soft inner core and solid silica shell. We further demonstrate the use of solidified DNA frameworks to create 3D metal plasmonic devices. This protocol provides a platform for synthesizing inorganic materials with unprecedented complexity and tailored structural properties. The whole protocol takes ~10 d to complete.

DNA Binding to Gold Nanoparticles through the Prism of Molecular Selection: Sequence-Affinity Relation

Native DNA strongly adsorbs to citrate-coated gold nanoparticles (AuNPs). The resulting composites (DNA/AuNPs) are valuable materials in many fields, especially in biomedicine. For this reason, the process of adsorption is a focus for intensive research. In this work, DNA adsorption to gold nanoparticles was studied using a molecular selection procedure followed by high-throughput DNA sequencing. The chemically synthesized DNA library containing a central N₂₆ randomized fragment was sieved through four cycles of adsorption to AuNPs in a tree-like selection-amplification scheme (SELEX (Selective Evolution of Ligands by EXponential enrichment)). The frequencies of occurrence of specific oligomeric DNA motifs, k-mers ( k = 1-6), in the initial and selected pools were calculated. Distribution of secondary structures in the pools was analyzed. A large set of diverse A, T, and G enriched k-mers undergo a pronounced positive selection, and these sequences demonstrate faster and strong binding to the AuNPs. For facile binding, such structural motifs should be located in the loop regions of weak intramolecular complexes-hairpins with imperfect stem, or other portion of the structure, which is unpaired under selection conditions. Our data also show that, under the conditions employed in this study, cytosine is significantly depleted during the selection process, although guanine remains unchanged. These regularities were confirmed in a series of binding experiments with a set of synthetic DNA oligonucleotides. The detailed analysis of DNA binding to AuNPs shows that the sequence specificity of this interaction is low due to its nature, although the presence and the number of specific structural motifs in DNA affect both the rate of formation and the strength of the formed noncovalent associates with AuNPs.

SAROTUP: a suite of tools for finding potential target-unrelated peptides from phage display data

SAROTUP (Scanner And Reporter Of Target-Unrelated Peptides) 3.1 is a significant upgrade to the widely used SAROTUP web server for the rapid identification of target-unrelated peptides (TUPs) in phage display data. At present, SAROTUP has gathered a suite of tools for finding potential TUPs and other purposes. Besides the TUPScan, the motif-based tool, and three tools based on the BDB database, i.e., MimoScan, MimoSearch, and MimoBlast, three predictors based on support vector machine, i.e., PhD7Faster, SABinder and PSBinder, are integrated into SAROTUP. The current version of SAROTUP contains 27 TUP motifs and 823 TUP sequences. We also developed the standalone SAROTUP application with graphical user interface (GUI) and command line versions for processing deep sequencing phage display data and distributed it as an open source package, which can perform perfectly locally on almost all systems that support C++ with little or no modification. The web interfaces of SAROTUP have also been redesigned to be more self-evident and user-friendly. The latest version of SAROTUP is freely available at http://i.uestc.edu.cn/sarotup3.

Rapidly Neutralizable and Highly Anticoagulant Thrombin-Binding DNA Aptamer Discovered by MACE SELEX

We present a rapidly neutralizable and highly anticoagulant thrombin-binding aptamer with a short toehold sequence, originally discovered by systematic evolution of ligands by exponential enrichment (SELEX) with microbead-assisted capillary electrophoresis (MACE). MACE is a novel CE-partitioning method for SELEX and able to separate aptamers from a library of unbound nucleic acids, where the aptamer and target complexes can be detected reliably and partitioned with high purity even in the first selection cycle. Three selection rounds of MACE-SELEX discovered several TBAs with a nanomolar affinity (K_d = 4.5-8.2 nM) that surpasses previously reported TBAs such as HD1, HD22, and NU172 (K_d = 118, 13, and 12 nM, respectively). One of the obtained aptamers, M08, showed a 10- to 20-fold longer prolonged clotting time than other anticoagulant TBAs, such as HD1, NU172, RE31, and RA36. Analyses of the aptamer and thrombin complexes using both bare and coated capillaries suggested that a large number of efficient aptamers are missed in conventional CE-SELEX because of increased interaction between the complex and the capillary. In addition, the toehold-mediated rapid antidote was designed for safe administration. The efficient aptamer and antidote system developed in the present study could serve as a new candidate for anticoagulant therapy.

Sequence-Specific Control of Inorganic Nanomaterials Morphologies by Biomolecules

Controlling morphologies of nanomaterials such as their shapes and surface features has been a major endeavor in the field of nanoscale science and engineering, because the morphology is a major determining factor for functional properties of nanomaterials. Compared with conventional capping ligands based on organic molecules or polymers, the programmability of biomolecules makes them attractive alternatives for morphology-controlled nanomaterials synthesis. Towards the goal of predictable control of the synthesis, many studies have been performed on using different sequences of biomolecules to generate specific nanomaterial morphology. In this review, we summarize recent studies in the past few years on using DNA and peptide sequences to control inorganic nanomaterial morphologies, focusing on both case studies and mechanistic investigations. The functional properties resulting from such a sequence-specific control are also discussed, along with strengths and limitations of different approaches to achieving the goal.

Competition-Enhanced Ligand Selection to Identify DNA Aptamers

Competition-enhanced ligand screening (CompELS) was employed to rapidly screen through large DNA libraries to identify single-stranded, oligonucleotide-based ligands called aptamers that bind to a nonbiological target. This previously unreported aptamer screening approach involves the repeated introduction of unenriched random sequence populations during the biopanning process, but avoids iterative elution and polymerase chain reaction (PCR) amplification steps inherent to traditional SELEX (systematic evolution of ligands by exponential enrichment) screening. In this study, 25 aptamers were identified against a gold surface via CompELS and evaluated to identify patterns in primary structures and predicted secondary structures. Following a final one-round competition experiment with the 25 identified aptamers, one particular aptamer sequence (1N) emerged as the most competitive adsorbate species for the gold substrate. Binding analysis indicated at least an order of magnitude difference in the binding affinity of 1N ( K_d = 5.6 × 10^-10 M) compared to five other high affinity aptamer candidates ( K_d = 10^-8-10^-9 M) from identical secondary structure families. Collectively, these studies introduce a rapid, reliable screening and ranking platform along with a classification scheme well-suited for identifying and characterizing aptamers for nonbiological as well as biological targets.

Elimination terminal fixed region screening and high-throughput kinetic determination of aptamer for lipocalin-1 by surface plasmon resonance imaging

A highly efficient method for eliminating terminal fixed region interference of aptamer with real-time monitoring of the SELEX process was described by silver decahedra nanoparticles probe (Ag₁₀-A₁₀-RP(15)) capture and block the terminal fixed region candidates. A microarray chip was developed by immobilization of target protein (lipocalin-1 (LCN-1)) and control proteins (Human serum albumin (HSA), Bovine serum albumin (BSA) and Holo-transferrin) on the biochip surface. The nucleic acid pool was first incubated with target and then captured by hybridization with Ag₁₀-A₁₀-RP(15). The work allows rapid screening of aptamer elimination fixed-region interference, and the kinetic constants of candidate sequences can be quickly determined using SPRi technology. Eventually, ten aptamers with high affinity and specific for LCN-1 after only fifth-round of selection was acquired.

Precipitation SELEX: identification of DNA aptamers for calcium phosphate materials synthesis

DNA aptamers that enhance calcium phosphate mineral formation were identified using a novel precipitation SELEX method. The evolved DNA library was substantially enriched in G nucleotides and in predicted G-quadruplex structures, suggesting their importance in the mechanism of mineralization. This work could readily be extended to provide additional novel DNA aptamers for materials synthesis.

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

Searching for DNA sequences that can strongly and selectively bind to inorganic surfaces is a long-standing topic in bionanotechnology, analytical chemistry and biointerface research. This can be achieved either by aptamer selection starting with a very large library of ≈10¹⁴ random DNA sequences, or by careful screening of a much smaller library (usually from a few to a few hundred) with rationally designed sequences. Unlike typical molecular targets, inorganic surfaces often have quite strong DNA adsorption affinities due to polyvalent binding and even chemical interactions. This leads to a very high background binding making aptamer selection difficult. Screening, on the other hand, can be designed to compare relative binding affinities of different DNA sequences and could be more appropriate for inorganic surfaces. The resulting sequences have been used for DNA-directed assembly, sorting of carbon nanotubes, and DNA-controlled growth of inorganic nanomaterials. It was recently discovered that poly-cytosine (C) DNA can strongly bind to a diverse range of nanomaterials including nanocarbons (graphene oxide and carbon nanotubes), various metal oxides and transition-metal dichalcogenides. In this Concept article, we articulate the need for screening and potential artifacts associated with traditional aptamer selection methods for inorganic surfaces. Representative examples of application are discussed, and a few future research opportunities are proposed towards the end of this article.

DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays

Zinc oxide (ZnO) is a highly important material, and Zn(2+) is a key metal ion in biology. ZnO and Zn(2+) interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry. Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 μg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred, indicating DNA adsorption. Then, fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5 > T5 > C5. Dissolution was slower with longer DNA. The adsorption affinity was also measured by a displacement assay to be G5 > C5 > T5 > A5, suggesting that tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption because ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in situ formation of ZnO from Zn(2+) was studied. First, titrating Zn(2+) into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn(2+). At pH 6, quenching occurred linearly with the Zn(2+) concentration, suggesting the effect of Zn(2+) precipitation at pH 7.5. Second, a Zn(2+)-dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn(2+), attributable to Zn(2+) precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn(2+), and ZnO. This understanding can avoid misinterpretation of DNA assay results and adds knowledge to DNA immobilization.

Trends in aptamer selection methods and applications

Aptamers are target specific ssDNA, RNA or peptide sequences generated by an in vitro selection and amplification method called SELEX (Systematic Evolution of Ligands by EXponential Enrichment), which involves repetitive cycles of binding, recovery and amplification steps. Aptamers have the ability to bind with a variety of targets such as drugs, proteins, heavy metals, and pathogens with high specificity and selectivity. Aptamers are similar to monoclonal antibodies regarding their binding affinities, but they offer a number of advantages over the existing antibody-based detection methods, which make the aptamers promising diagnostic and therapeutic tools for future biomedical and analytical applications. The aim of this review article is to provide an overview of the recent advancements in aptamer screening methods along with a concise description of the major application areas of aptamers including biomarker discovery, diagnostics, imaging and nanotechnology.

Replacing antibodies with aptamers in lateral flow immunoassay

Aptamers have been identified against various targets as a type of chemical or nucleic acid ligand by systematic evolution of ligands by exponential enrichment (SELEX) with high sensitivity and specificity. Aptamers show remarkable advantages over antibodies due to the nucleic acid nature and target-induced structure-switching properties and are widely used to design various fluorescent, electrochemical, or colorimetric biosensors. However, the practical applications of aptamer-based sensing and diagnostics are still lagging behind those of antibody-based tests. Lateral flow immunoassay (LFIA) represents a well established and appropriate technology among rapid assays because of its low cost and user-friendliness. The antibody-based platform is utilized to detect numerous targets, but it is always hampered by the antibody preparation time, antibody stability, and effect of modification on the antibody. Seeking alternatives to antibodies is an area of active research and is of tremendous importance. Aptamers are receiving increasing attention in lateral flow applications because of a number of important potential performance advantages. We speculate that aptamer-based LFIA may be one of the first platforms for commercial use of aptamer-based diagnosis. This review first gives an introduction to aptamer including the selection process SELEX with its focus on aptamer advantages over antibodies, and then depicts LFIA with its focus on aptamer opportunities in LFIA over antibodies. Furthermore, we summarize the recent advances in the development of aptamer-based lateral flow biosensing assays with the aim to provide a general guide for the design of aptamer-based lateral flow biosensing assays.

Experimental fitness landscapes to understand the molecular evolution of RNA-based life

In evolutionary biology, the relationship between genotype and Darwinian fitness is known as a fitness landscape. These landscapes underlie natural selection, so understanding them would greatly improve quantitative prediction of evolutionary outcomes, guiding the development of synthetic living systems. However, the structure of fitness landscapes is essentially unknown. Our ability to experimentally probe these landscapes is physically limited by the number of different sequences that can be identified. This number has increased dramatically in the last several years, leading to qualitatively new investigations. Several approaches to illuminate fitness landscapes are possible, ranging from tight focus on a single peak to random speckling or even comprehensive coverage of an entire landscape. We discuss recent experimental studies of fitness landscapes, with a special focus on functional RNA, an important system for both synthetic cells and the origin of life.