G-quadruplex DNA aptamers for zeatin recognizing

Artificial Riboswitch: Another Engine for a Whole-Cell Sensing System to Develop Biosensors for Heavy Metal Detection

Whole-cell biosensing systems has attracted increasing research attention as a new approach for on-site heavy metal detection. However, the design and application of whole-cell biosensing systems are limited by the unsatisfactory performance of the core sensing element ─ transcription factors. This paper proposed the development of artificial riboswitches for heavy metal identification based on their high sensitivity, specificity, and ease of modification, which can be used alone or combination with transcription factors to construct more efficient whole-cell biosensors. This article summarized the reported aptamers targeting heavy metals in the last 20 years, and presented methods for screening intracellularly folding aptamers and strategies for constructing and optimizing the performance of artificial riboswitches using these aptamers. Heavy-metal-induced artificial riboswitches can be used in multiple applications, significantly enhancing the design potential of whole-cell sensing systems. Artificial riboswitches can be considered as another "engine," alongside transcription factors, to drive the development and innovation of whole-cell sensing systems.

Emerging trends in nucleic acid and peptide aptamers in plant science research

MAIN CONCLUSION

Aptamer technology has significantly advanced the field of plant research, emerging as a tool for enhancing agricultural productivity, plant growth, and environmental monitoring. Aptamers are short nucleotide or amino acid sequences that can bind to a range of target molecules with high affinity and selectivity. In recent years, these affinity molecules have piqued the interest of researchers across various scientific fields, including pharmaceuticals, analytical chemistry, and plant science. Advancements in aptamer technology have significantly broadened the horizons of plant science, particularly in the areas of plant analyte detection, pathogen targeting, and protein function analysis. Despite the use of various other bioassays and molecular techniques for plant analyte detection, the small size, chemical stability, and cost-effective synthesis of aptamers make them invaluable tools for unravelling the complexities of plant cells. Here, we discuss the progress in the development of nucleic acid and peptide aptamers and summarize their applications in plant biotechnology. The principles and signalling methods of various aptamer-based biosensors and their prospects as biotechnological tools for functional genomic studies, pathogen resistance, and bioimaging are discussed. Finally, the present challenges and future perspectives of aptamer-based technology in plant research are also summarized.

In Silico Selection and Validation of High-Affinity ssDNA Aptamers Targeting Paromomycin

Glycans are promising for disease diagnosis since glycan biosynthesis is significantly affected by disease states, and glycosylation changes are probably more pronounced than protein expression during the transformation to the diseased condition. Glycan-specific aptamers can be developed for challenging applications such as cancer targeting; however, the high flexibility of glycosidic bonds and scarcity of studies on glycan-aptamer binding mechanisms increased the difficulty of screening. In this work, the model of interactions between glycans and ssDNA aptamers synthesized based on the sequence of rRNA genes was developed. Our simulation-based approach revealed that paromomycin as a representative example of glycans is preferred to bind base-restricted stem structures of aptamers because they are more critical in stabilizing the flexible structures of glycans. Combined experiments and simulations have identified two optimal mutant aptamers. Our work would provide a potential strategy that the glycan-binding rRNA genes could act as the initial aptamer pools to accelerate aptamer screening. In addition, this in silico workflow would be potentially applied in the more extensive in vitro development and application of RNA-templated ssDNA aptamers targeting glycans.

Nucleic acid aptamers as aptasensors for plant biology

Our knowledge of cell- and tissue-specific quantification of phytohormones is heavily reliant on laborious mass spectrometry techniques. Genetically encoded biosensors have allowed spatial and some temporal quantification of phytohormones intracellularly, but there is still limited information on their intercellular distributions. Here, we review nucleic acid aptamers as an emerging biosensing platform for the detection and quantification of analytes with high affinity and specificity. Options for DNA aptamer technology are explained through selection, sequencing analysis and techniques for evaluating affinity and specificity, and we focus on previously developed DNA aptamers against various plant analytes. We suggest how these tools might be applied in planta for quantification of molecules of interest both intracellularly and intercellularly.

Systematically Modulating Aptamer Affinity and Specificity by Guanosine-to-Inosine Substitution

Aptamers are widely used in small molecule detection applications due to their specificity, stability, and cost effectiveness. One key challenge in utilizing aptamers in sensors is matching the binding affinity of the aptamer to the desired concentration range for analyte detection. The most common methods for modulating affinity have inherent limitations, such as the likelihood of drastic changes in aptamer folding. Here, we propose that substituting guanosine for inosine at specific locations in the aptamer sequence provides a less perturbative approach to modulating affinity. Inosine is a naturally occurring nucleotide that results from hydrolytic deamination of adenosine, and like guanine, it base pairs with cytosine. Using the well-studied cocaine binding aptamer, we systematically replaced guanosine with inosine and were able to generate sequences having a range of binding affinities from 230 nM to 80 μM. Interestingly, we found that these substitutions could also modulate the specificity of the aptamers, leading to a range of binding affinities for structurally related analytes. Analysis of folding stability via melting temperature shows that, as expected, aptamer structure is impacted by guanosine-to-inosine substitutions. The ability to tune binding affinity and specificity through guanosine-to-inosine substitution provides a convenient and reliable approach for rapidly generating aptamers for diverse biosensing applications.

Selection and identification of high-affinity aptamer of Kunitz trypsin inhibitor and their application in rapid and specific detection

Kunitz trypsin inhibitor (KTI), a harmful protein, seriously affects food hygiene and safety. Therefore, a sensitive, efficient, and rapid method for KTI detection is urgently needed. Aptamers are short and single-stranded (ss) DNA that recognize target molecules with high affinity. This work used graphene oxide-SELEX (GO-SELEX) to screen KTI aptamers. The positive and reverse screening was designed to ensure the high specificity and affinity of the selected aptamers. After 10 rounds of screening, multiple nucleic acid chains were obtained, and the chains were sequenced. Three aptamers with better affinity were obtained, and the values of the dissociation constant (K d) were calculated to be 52.6 nM, 22.7 nM, and 67.9 nM, respectively. Finally, a colorimetric aptamer biosensor based on gold nanoparticles (AuNPs) was constructed. The biosensor exhibited a broader linear range of 30-750 ng/ml, with a lower detection limit of 18 ng/ml, and the spiked recovery rate was between 98.2% and 103.3%. This experiment preliminary demonstrated the potential of the application of KTI aptamer in the real sample tests.

Photo-activated aptamer-drug conjugates for targeted drug delivery

A photo-activated aptamer-drug conjugate, HG1-9-DNP was developed based on an aptamer HG1-9 and a photolabile naphthalimide derivative DNP. HG1-9-DNP could be internalized into cells mediated by TfR, then photocleaved and...

Selection and Characterization of Vimentin-Binding Aptamer Motifs for Ovarian Cancer

The application of aptamers in biomedicine is emerging as an essential technology in the field of cancer research. As small single-stranded DNA or RNA ligands with high specificity and low immunogenicity for their targets, aptamers provide many advantages in cancer therapeutics over protein-based molecules, such as antibodies. Vimentin is an intermediate filament protein that is overexpressed in endothelial cells of cancerous tissue. High expression levels of vimentin have been associated with increased capacity for migration and invasion of the tumor cells. We have selected and identified thioated aptamers with high specificity for vimentin using human ovarian cancer tissues. Tentative binding motifs were chosen for two vimentin aptamers based on predicted secondary structures. Each of these shorter, tentative binding motifs was synthesized, purified, and characterized via cell binding assays. Two vimentin binding motifs with high fidelity binding were selected and further characterized via cell and tissue binding assays, as well as flow cytometric analysis. The equilibrium binding constants of these small thioated aptamer constructs were also determined. Future applications for the vimentin binding aptamer motifs include conjugation of the aptamers to synthetic dyes for use in targeted imaging and therapy, and ultimately more detailed and precise monitoring of treatment response and tumor progression in ovarian pathology.

G-quadruplex: Flexible conformational changes by cations, pH, crowding and its applications to biosensing

G-quadruplex (G4) is a non-canonical structure that is formed in G-rich sequences of nucleic acids. G4s play important roles in vivo, such as telomere maintenance, transcription, and DNA replication. There are three typical topologies of G4: parallel, anti-parallel, and hybrid. In general, metal cations, such as potassium and sodium, stabilize G4s through coordination in the G-quartet. While G4s have some functions in vivo, there are many reports of developed applications that use G4s. As various conformations of G4s could form from one sequence depending on varying conditions, many researchers have developed G4-based sensors. Furthermore, G4 is a great scaffold of aptamers since many aptamers folded into G4s have also been reported. However, there are some challenges about its practical use due to the difference between practical sample conditions and experimental ones. G4 conformations are dramatically altered by the surrounding conditions, such as metal cations, pH, and crowding. Many studies have been conducted to characterize G4 conformations under various conditions, not only to use G4s in practical applications but also to reveal its function in vivo. In this review, we summarize recent studies that have investigated the effects of surrounding conditions (e.g., metal cations, pH, and crowding) on G4 conformations and the application of G4s mainly in biosensor fields, and in others.

Aptamer-Based Colorimetric Probe for trans-Zeatin Detection Using Unmodified Gold Nanoparticle

Trans-Zeatin is the major active phytohormone in immature corn kernels. Herein, a highly sensitive, good selective and simple aptamer-based colorimetric method for the detection of trans-zeatin was constructed. The selected aptamer sequence binds with trans-zeatin and induces a duplex-to-aptamer structure switching. The gold nanoparticles (AuNPs) solution is stable with high-concentration salt, which is protected by red complementary DNA. In the absence of trans-zeatin, the color of AuNPs changed from red to blue because aptamer DNA and complementary DNA form double-stranded DNA. Thus, the ratio of absorbance intensities (A522/A650) of AuNPs is changed with the concentration of trans-zeatin. The color change could be observed by the naked eye. The linear range of this method covers a large variation of trans-zeatin concentration from 0.05 to 0.75 μM. The detection limit is 0.037 μM. Moreover, this method was applied successfully to detect trans-zeatin in real plant samples.

Graphene/aptamer probes for small molecule detection: from in vitro test to in situ imaging

Small molecules are key targets in molecular biology, environmental issues, medicine and food industry. However, small molecules are challenging to be detected due to the difficulty of their recognition, especially in complex samples, such as in situ in cells or animals. The emergence of graphene/aptamer probes offers an excellent opportunity for small molecule quantification owing to their appealing attributes such as high selectivity, sensitivity, and low cost, as well as the potential for probing small molecules in living cells or animals. This paper (with 130 refs.) will review the application of graphene/aptamer probes for small molecule detection. We present the recent progress in the design and development of graphene/aptamer probes enabling highly specific, sensitive and rapid detection of small molecules. Emphasis is placed on the success in their development and application for monitoring small molecules in living cells and in vivo systems. By discussing the key advances in this field, we wish to inspire more research work of the development of graphene/aptamer probes for both on-site or in situ detection of small molecules and its applications for investigating the functions of small molecules in cells in a dynamic way. Graphical abstract Graphene/aptamer probes can be used to construct different platforms for detecting small molecules with high specificity and sensitivity, both in vitro and in situ in living cells and animals.

Aptamer-functionalized liposomes for targeted cancer therapy

Accumulation of chemotherapeutic agents in the tumor tissue while reducing adverse effects and drug resistance are among the major goals in cancer therapy. Among nanocarriers, liposomes have been found to be more effective in the passive targeting of cancer cells. A promising recent development in targeted drug delivery is the use of aptamer-functionalized liposomes for cancer therapy. Aptamer-targeted liposomes have enhanced uptake in tumor cells as shown in vitro and in vivo. Here, we discuss the aptamer-functionalized liposome platforms and review functionalization approaches as well as the factors affecting antitumor efficiency of aptamer-targeted liposomal systems. Finally, we provide a comprehensive overview of aptamer-targeted liposomes based on the molecular targets on the surface of cancer cells.

Graphene oxide-assisted non-immobilized SELEX of chiral drug ephedrine aptamers and the analytical binding mechanism

Here, we describe a study of screen characterization of aptamers targeting the chiral drug ephedrine using the non-immobilized graphene oxide (GO) SELEX. The improved method of long and short chains was here used to prepare the ssDNA library. The Resonance Rayleigh Scattering (RRS) method was first used to monitor the screening process. Through high-throughput sequencing, the genetic sequence data of 90,487 aptamers were obtained. Through the analysis of the parameters of free energy value and secondary structure prediction model of high repeatability sequence, the 10 candidate sequences were identified. Finally, a best-fit aptamer named EP08 was identified by combining the dissociation experiment. The binding affinity and binding mechanism of the aptamer and target were analyzed using an isothermal titration colorimetry (ITC) experiment and circular dichromatic (CD) experiment. The binding affinity (Kd) of the EP08 aptamer to ephedrine is approximately 2.86 ± 0.24 μM. This novel DNA aptamer will help in the future development of a new method for the identification and detection of chiral drug ephedrine.

Imaging of Neurite Network with an Anti-L1CAM Aptamer Generated by Neurite-SELEX

Neurite outgrowth is the critical step of nervous development. Molecular probes against neurites are essential for evaluation of the nervous system development, compound neurotoxicity, and drug efficacy on nerve regeneration. To obtain a neurite probe, we developed a neurite-SELEX strategy and generated a DNA aptamer, yly12, that strongly binds neurites. The molecular target of yly12 was identified to be neural cell adhesion molecule L1 (L1CAM), a surface antigen expressed in normal nervous system and various cancers. Here, yly12 was successfully applied to image the three-dimensional network of neurites between live cells, as well as the neurite fibers on normal brain tissue section. This aptamer was also found to have an inhibitory effect on neurite outgrowth between cells. Given the advantages of aptamers, yly12 hold great potential as a molecular tool in the field of neuroscientific research. The high efficiency of neurite-SELEX suggests that SELEX against a subcellular structure instead of the whole cells is more effective in obtaining the desired aptamers.

Oxidative degradation of polyamines by serum supplement causes cytotoxicity on cultured cells

Serum is a common supplement for cell culture due to it containing the essential active components for the growth and maintenance of cells. However, the knowledges of the active components in serum are incomplete. Apart from the direct influence of serum components on cultured cells, the reaction of serum components with tested drugs cannot be ignored, which usually results in the false conclusion on the activity of the tested drugs. Here we report the toxicity effect of polyamines (spermidine and spermine) on cultured cells, especially on drug-resistant cancer cell lines, which resulted from the oxidative degradation of polyamines by amine oxidases in serum supplement. Upon adding spermidine or spermine, high concentration of H₂O_2, an enzyme oxidation product of polyamines, was generated in culture media containing ruminant serum, such as fetal bovine serum (FBS), calf serum, bovine serum, goat serum or horse serum, but not in the media containing human serum. Drug-resistant cancer cell lines showed much higher sensitivity to the oxidation products of polyamines (H₂O₂ and acrolein) than their wild cell lines, which was due to their low antioxidative capacity.

In vitro selection and characterization of single stranded DNA aptamers for luteolin: A possible recognition tool

Distinctive bioactivities possessed by luteolin (3', 4', 5, 7-tetrahydroxy-flavone) are advantageous for sundry practical applications. This paper reports the in vitro selection and characterization of single stranded-DNA (ssDNA) aptamers, specific for luteolin (LUT). 76-mer library containing 1015 randomized ssDNA were screened via systematic evolution of ligands by exponential enrichment (SELEX). The recovered ssDNA pool from the 8th round was amplified with unlabeled primers and cloned into PSTBlue-1 vector prior to sequencing. 22 of LUT-binding aptamer variants were further classified into one of the seven groups based on their N40 random sequence regions, wherein one representative from each group was characterized. The dissociation constant of aptamers designated as LUT#28, LUT#20 and LUT#3 was discerned to be 107, 214 and 109 nM, respectively with high binding affinity towards LUT. Prediction analysis of the secondary structure suggested discrete features with typical loop and stem motifs. Furthermore, LUT#3 displayed higher specificity with insignificant binding toward kaempferol and quercetin despite its structural and functional similarity compared to LUT#28 and LUT#20. Further LUT#3 can detect free luteolin within 0.2-1 mM in solution. It was suggested that LUT#3 aptamer were the most suitable for LUT recognition tool at laboratory scale based on the condition tested.

Triplex-quadruplex structural scaffold: a new binding structure of aptamer

Apart from the canonical Watson-Crick duplex, nucleic acids can often form other structures, e.g. G-quadruplex and triplex. These structures give nucleic acid additional functions besides coding for genetic information. Aptamers are one type of functional nucleic acids that bind to specific targets with high selectivity and affinity by folding into special tertiary structures. Despite the fact that numerous aptamers have been reported, only a few different types of aptamer structures are identified. Here we report a novel triplex-quadruplex hybrid scaffold formed by a codeine binding aptamer (CBA). CBA and its derivatives are G-rich DNA sequences. Codeine binding can induce the formation of a complex structure for this aptamer containing a G-quadruplex and a G·GC triplex, while codeine is located at the junction of the triplex and quadruplex. When split CBA into two moieties, codeine does not bind either moieties individually, but can bind them together by inducing the formation of the triplex-quadruplex scaffold. This structure formation induced by codeine binding is shown to inhibit polymerase reaction, which shows a potential application of the aptamer sequence in gene regulations.

Selection of an aptamer against Muscovy duck parvovirus for highly sensitive rapid visual detection by label-free aptasensor

Muscovy duck parvovirus (MDPV) causes high mortality and morbidity in ducks. This study investigated a novel aptamer-based, label-free aptasensor detection of MDPV. In this study, we developed an ssDNA aptamer using the filtration partition and lambda exonuclease method with an affinity-based monitor and counter-screening process. After 15 rounds of SELEX (systematic evolution of ligands by exponential enrichment), the ssDNA aptamer Apt-10, which specifically bound to MDPV with high affinity (K_d = 467nM) was successfully screened, and the aptamer was also found to be good specific to MDPV. The selected Apt-10 aptamer can be used to distinguish MDPV and goose parvovirus (GPV). Three-dimensional structural analysis of the Apt-10 aptamer indicated that it folded into a compact stem-loop motif, which was related to its high affinity. Finally, a label-free detection method based on unmodified gold nanoparticles and Apt-10 aptamer was developed for MDPV determination. The concentration of Apt-10 aptamer at 5μM was optimal for MDPV determination in the label-free aptasensor. Excellent linearity was acquired and the lowest detection limit was 1.5 or 3 EID₅₀ (50% egg infection dose) of MDPV, respectively, depending upon spectrophotometry or the naked eye were used. These results show the potential of the aptamer for the rapid detection of MDPV and antiviral research.

Stepping Library-Based Post-SELEX Strategy Approaching to the Minimized Aptamer in SPR

When evolved from SELEX (systematic evolution of ligands by exponential enrichment), aptamers are generally about 70-130 nucleotides in length and needed to be effectively truncated for further diagnosis or therapeutic uses. Post-SELEX optimization is then aroused to simplify the aptamer sequence and improve the affinity property. In this work, we report a new post-SELEX strategy based on a stepping library for the first time. With a hypothesis that one nucleobase can influence the whole binding affinity through its adjacent base stacking and potential steric hydrogen bonding interaction, we designed a stepping library composed of all probable nucleotide truncation directions. We employed an aptamer 807-39nt toward EPO-α as a model, and surface plasmon resonance (SPR) as an efficient screening and evaluation method to optimize all label-free sequences in the library. We have successfully picked out In27 as the minimized aptamer from a mini library of only 35 sequences. Aptamer In27 has a sole loop, without the original stem portion of the initial aptamer, but retains the whole binding affinity. We have also defined the key nucleotide contribution by site mutagenesis with natural bases, and finally produced a degenerated sequence with higher or the same good affinities. Furthermore, we explored different binding behaviors between aptamer In27 and other recognition molecule such as agglutinin, monoclonal antibody, or receptor by competition or binding assays. Our work provides a new and efficient post-SELEX optimization strategy, as well as a minimized aptamer In27 with an explicit degenerated sequence and a defined binding behavior. That would enhance their great potential in future diagnosis and therapy.

Zooming In on Plant Hormone Analysis: Tissue- and Cell-Specific Approaches

Plant hormones are a group of naturally occurring, low-abundance organic compounds that influence physiological processes in plants. Our knowledge of the distribution profiles of phytohormones in plant organs, tissues, and cells is still incomplete, but advances in mass spectrometry have enabled significant progress in tissue- and cell-type-specific analyses of phytohormones over the last decade. Mass spectrometry is able to simultaneously identify and quantify hormones and their related substances. Biosensors, on the other hand, offer continuous monitoring; can visualize local distributions and real-time quantification; and, in the case of genetically encoded biosensors, are noninvasive. Thus, biosensors offer additional, complementary technologies for determining temporal and spatial changes in phytohormone concentrations. In this review, we focus on recent advances in mass spectrometry-based quantification, describe monitoring systems based on biosensors, and discuss validations of the various methods before looking ahead at future developments for both approaches.

Microbead-Based Platform for Multiplex Detection of DNA and Protein

We present a novel microbead-based detection platform as a simple and universal strategy for simultaneous determination of multiple biomolecules. This platform is composed of streptavidin coated uniform-sized polystyrene microbeads, dye and biotin-labeled ssDNA or aptamer probes, and quencher-labeled complementary sequences. By this method, upon target binding to the probes, quencher strand dissociation is triggered, which results in fluorescence reactivation of the microbead linked probes. The fluorescence variation is readily monitored by flow cytometry and with a high sensitivity. Explicitly, this microbead-based detection platform shows a high sensitivity for target DNA with a detection limit as low as 0.20 nM, alongside good selectivity from one-base mismatched DNA. This novel platform also shows good selectivity and high sensitivity for protein detection when aptamer is used as a probe. The detection limit for lysozyme is as low as 8.56 nM. Moreover, simultaneous detection of multiple targets has been achieved via incorporating different dye-labeled probes on the microbeads concurrently. We have also applied this developed strategy to the detection of target DNA in human serum. This strategy can be easily extended to other targets through simple probe and quencher variation.

Generating Cell Targeting Aptamers for Nanotheranostics Using Cell-SELEX

Detecting and understanding changes in cell conditions on the molecular level is of great importance for the accurate diagnosis and timely therapy of diseases. Cell-based SELEX (Systematic Evolution of Ligands by EXponential enrichment), a foundational technology used to generate highly-specific, cell-targeting aptamers, has been increasingly employed in studies of molecular medicine, including biomarker discovery and early diagnosis/targeting therapy of cancer. In this review, we begin with a mechanical description of the cell-SELEX process, covering aptamer selection, identification and identification, and aptamer characterization; following this introduction is a comprehensive discussion of the potential for aptamers as targeting moieties in the construction of various nanotheranostics. Challenges and prospects for cell-SELEX and aptamer-based nanotheranostic are also discussed.

Investigation of newly identified G-quadruplexes and their application to DNA detection

G-quadruplexes are guanine-rich nucleic acid sequences that can act as universal signal-transducers and generate colorimetric, fluorescence, and chemiluminescence signals when complexed with different ligands. Due to their merits including easy modification and low cost, it is of great importance to explore new G-quadruplexes with improved performance. Herein the properties of newly identified G-quadruplexes 9th-3-35 and 10th-2-40 were investigated in detail with UV-vis spectra, circular dichroism (CD) spectra and fluorescence spectra. The results indicated that 9th-3-35 and 10th-2-40 exhibited excellent peroxidase-like activity, as well as fluorescence enhancement of thioflavin T (ThT). Furthermore, the application of G-quadruplexes to DNA detection was performed on account of the ThT fluorescence enhancement, and the limit of detection was as low as 8 pM. This study implied that 9th-3-35 and 10th-2-40 are competitive candidates as signal-transducers in the design of bioassays.

Methods for Improving Aptamer Binding Affinity

Aptamers are single stranded oligonucleotides that bind a wide range of biological targets. Although aptamers can be isolated from pools of random sequence oligonucleotides using affinity-based selection, aptamers with high affinities are not always obtained. Therefore, further refinement of aptamers is required to achieve desired binding affinities. The optimization of primary sequences and stabilization of aptamer conformations are the main approaches to refining the binding properties of aptamers. In particular, sequence optimization using combined in silico sequence recombinations and in vitro functional evaluations is effective for the improvement of binding affinities, however, the binding affinities of aptamers are limited by the low hydrophobicity of nucleic acids. Accordingly, introduction of hydrophobic moieties into aptamers expands the diversity of interactions between aptamers and targets. Moreover, construction of multivalent aptamers by connecting aptamers that recognize distinct epitopes is an attractive approach to substantial increases in binding affinity. In addition, binding affinities can be tuned by optimizing the scaffolds of multivalent constructs. In this review, we summarize the various techniques for improving the binding affinities of aptamers.

Two-dimensional graphitic carbon nitride nanosheets for biosensing applications

Two-dimensional graphitic carbon nitride nanosheets (CNNSs) with planar graphene-like structure have stimulated increasingly research interest in recent years due to their unique physicochemical properties. CNNSs possess superior stability, high fluorescence quantum yield, low-toxicity, excellent biocompatibility, unique electroluminescent and photoelectrochemical properties, which make them appropriate candidates for biosensing. In this review, we first introduce the preparation and unique properties of CNNSs, with emphasis on their superior properties for biosensing. Then, recent advances of CNNSs in photoelectrochemical biosensing, electrochemiluminescence biosensing and fluorescence biosensing are highlighted. An additional attention is paid to the marriage of CNNSs and nucleic acids, which exhibits great potentials in both biosensing and intracellular imaging. Finally, current challenges and opportunities of this 2D material are outlined. Inspired by the unique properties of CNNSs and their advantages in biological applications, we expect that more attention will be drawn to this promising 2D material and extensive applications can be found in bioanalysis and diseases diagnosis.

Structural regulation by a G-quadruplex ligand increases binding abilities of G-quadruplex-forming aptamers

By the binding of a G4 ligand to G4-forming aptamers, their conformations became suitable for binding to the target and their binding ability increased.

Screening and identification of DNA aptamers against T-2 toxin assisted by graphene oxide

A high-affinity ssDNA aptamer that specifically binds to T-2 toxin was generated by the systemic evolution of ligands by exponential enrichment (SELEX) procedure assisted by graphene oxide (GO). After 10 rounds of selection against T-2 toxin, a highly enriched ssDNA pool was sequenced and the representative aptamers were subjected to binding assays to evaluate their affinity and specificity. Circular dichroism spectroscopy was also used to study the inherent interaction of T-2 toxin and the preferred aptamer Seq.16, which demonstrated a low dissociation constant (Kd) of 20.8 ± 3.1 nM and excellent selectivity for T-2 toxin. Using the selected aptamer Seq.16 as the recognition element, an aptamer-based fluorescent bioassay was developed for the measurement of T-2 in beer samples with a linear range from 0.5 to 37.5 μM (R(2) = 0.988) and a limit of detection (LOD) of 0.4 μM. The results indicate that GO-SELEX technology is appropriate for the screening of aptamers against small-molecule toxins, offering a promising application for aptamer-based biosensors.

Recent advances in aptasensors based on graphene and graphene-like nanomaterials

Graphene and graphene-like two-dimensional nanomaterials have aroused tremendous research interest in recent years due to their unique electronic, optical, and mechanical properties associated with their planar structure. Aptamers have exhibited many advantages as molecular recognition elements for sensing devices compared to traditional antibodies. The marriage of two-dimensional nanomaterials and aptamers has emerged many ingenious aptasensing strategies for applications in the fields of clinical diagnosis and food safety. This review highlights current advances in the development and application of two-dimensional nanomaterials-based aptasensors with the focus on two main signal-transducing mechanisms, i.e. electrochemical and optical. A special attention is paid to graphene, a one-atom thick layer of graphite with exceptional properties, representing a fastgrowing field of research. In view of the unique properties of two-dimensional nanostructures and their inherent advantages of synthetic aptamers, we expect that high-performance two-dimensional nanomaterials-based aptasensing devices will find extensive applications in environmental monitoring, biomedical diagnostics, and food safety.

Determination of free tryptophan in serum with aptamer--comparison of two aptasensors

Two aptasensors based on graphene oxide (GO) and molecular beacon were designed for the detection of L-tryptophan (L-Trp) using L-Trp aptamer (Trp3a-1). The fluorescein (FAM) labeled Trp3a-1 was absorbed by GO, which resulted in the fluorescence quenching, and exhibiting minimal background fluorescence. Upon the addition of L-Trp, Trp3a-1 was not absorbed quickly. This effect allows for a quantitative assay of L-Trp over the concentration range of 10-500 μM and with a detection limit of 6.84 μM. However, due to the unspecific adsorption of GO, the GO based aptasensor can't be applied in complex matrixes. In respect of molecular beacon based aptasensor, FRET between Trp3a-1 labeled with FAM and CS-Trp3a-1 labeled with BHQ-1(black hole quencher-1) which is partially complementary with the aptamer was used to detect L-Trp. L-Trp binding could induce the disassociation of CS-Trp3a-1, resulted in the enhancement of fluorescence in solution. With an excellent linear relationship in 10-500 μM and a detection limit of 6.97 μM in 25% serum, the aptasensor is expected to be improved for the detection of free L-Trp in other complex samples.

Exonuclease I aided enzyme-linked aptamer assay for small-molecule detection

A novel enzyme-linked aptamer assay (ELAA) with the aid of Exonuclease I (Exo I) for colorimetric detection of small molecules was developed. The fluorescein isothiocyanate (FITC)-labeled aptamer was integrated into a double-stranded DNA (dsDNA). In the presence of target, the binding of aptamer with target protected the aptamer from Exo I degradation, which resulted in the FITC tag remaining on the aptamer. Then, the anti-FITC-HRP conjugate was used to produce an optically observable signal. By monitoring the color change, we were able to detect two model molecules, ATP and L-argininamide, with high selectivity and high sensitivity even in the serum matrix. It is expected to be a simple and general ELAA method with wide applicability.