Mechanism of DNA adsorption and desorption on graphene oxide

Graphene Oxide-Modified Resin for Selective dsRNA Removal from In Vitro-Transcribed mRNA

Messenger RNA (mRNA) has proven to be an effective vaccine agent against unexpected pandemics, offering the advantage of rapidly producing customized therapeutics targeting specific pathogens. However, undesired byproducts, such as double-stranded RNA (dsRNA), generated during in vitro transcription (IVT) reactions may impede translation efficiency and trigger inflammatory cytokines in cells after mRNA uptake. In this study, we developed a facile method using PEGylated polystyrene resins that were further surface-modified with graphene oxide (GO@PEG-PS) for the removal of dsRNA from IVT mRNA. The GO@PEG-PS resin adsorbed mRNA due to the property of graphene oxide (GO), which preferentially adsorbs single-stranded nucleic acids over double-stranded nucleic acids in the presence of Mg2+. The resin-bound single-stranded (ss) RNA was readily desorbed with a mixture of EDTA and urea, possibly by chelating Mg2+ and disrupting hydrogen bonding, respectively. Spin-column chromatography with GO@PEG-PS for IVT mRNA eliminated at least 80% of dsRNA, recovering approximately 85% of mRNA. Furthermore, this procedure precluded the salt precipitation step after the IVT reaction, which fractionates mRNAs from the IVT components, including nucleotides and enzymes. The purified mRNA exhibited enhanced protein translation with reduced secretion of interferon (IFN)-β upon mRNA transfection. We anticipate that the mRNA purification chromatography system employing GO@PEG-PS resin will facilitate the removal of dsRNA contamination during mRNA production.

Efficient solid-phase extraction of oligo-DNA from complex media using a nitrocellulose membrane modified with carbon nanotubes and aminated reduced graphene oxide

Oligonucleotides are essential for gene regulation, expression, and disease biomarker identification, yet their small size presents challenges due to lower abundance and increased susceptibility to degradation in biological samples. Addressing these challenges, a novel approach was developed for effective oligonucleotide extraction, consisting of a commercially available nitrocellulose (NC) membrane non-covalently modified with a combination of single-walled carbon nanotubes (SWCNTs) and polyethylene glycol (PEG) aminated reduced graphene oxide (GA). The membrane was evaluated for the extraction of a fluorescent labelled single-stranded deoxyribonucleic acid (ssDNA), with fewer than 30 nucleotides, from complex solutions containing various ionic species (MnCl2, MgCl2, and MnCl2/MgCl2). Fourier transform infrared spectroscopy confirmed successful modification, revealing characteristic peaks of NC, SWCNT, and GA. Raman spectroscopy and X-ray photoelectron spectroscopy showed distinctive changes after the membrane interaction with divalent cations and ssDNA. Scanning electron microscopy revealed morphological changes in the SWCNTs/GA-NC hybrid membrane, showing a smoother surface compared to the porous structure of the unmodified NC membrane. Wettability assays indicated hydrophobic properties for the SWCNT/GA-NC hybrid membrane, with a water contact angle exceeding 110°, contrasting with the hydrophilic nature of the NC membrane, which exhibits a contact angle of 26.7°. Optimal performance of the SWCNTs/GA-NC hybrid membrane was observed when incubated in MgCl2, demonstrating the highest fluorescence emission at approximately 670 relative fluorescence units. This corresponded to the extraction of approximately 781 pg (≈ 16%) of the total oligo-DNA, highlighting the enhanced efficacy of the hybrid material compared to the unmodified NC membrane, which extracted only 318 pg (≈ 7%) of oligo-DNA.

Antibody and Aptamer-Based Magnetic-Graphene Oxide Desorption (M-GOD) Quantum Dot Assays for Rapid and Sensitive Detection of SAR-CoV-2

Rapid detection of respiratory diseases using a noninvasive bind-and-detect breath test could shift the future of rapid diagnostics. Commercially available biotinylated anti-SARS-CoV-2 spike (S) protein antibody was conjugated to streptavidin-coated quantum dots, purified, and adsorbed onto magnetic-graphene oxide (M-GO) flakes to quench the conjugate. When inactivated SARS-CoV-2 was added at increasing levels, the antibody-quantum dot conjugates desorbed from the M-GO as a function of virus concentration with an apparent limit of detection ~ 9,600 inactivated virus particles within 2-5 min in phosphate-buffered saline (PBS) plus 10 mM Mg2+ assessed by a spectrofluorometer. A similar fluorescence response was obtained using a published biotinylated DNA aptamer sequence designated MSA52 and inactivated SARS-CoV-2 in PBS plus 5 mM Mg2+. Concentrations of Mg2+ greater than 5 mM diminished the aptamer magnetic-graphene oxide desorption (M-GOD) assay performance, perhaps by altering the aptamer's 3-dimensional conformation and ability to bind the virus. As reported previously, the MSA52 aptamer assay demonstrated reasonable specificity for variants of SARS-CoV-2 and significantly less intense detection of inactivated Influenza A and Respiratory Syncytial Virus (RSV) in the M-GOD assay format. This rapid and sensitive detection of inactivated SARS-CoV-2 in clear PBS buffer bodes well for the ultimate goal of rapid homogeneous bind-and-detect detection of COVID and other viral respiratory pathogens in human breath condensates and other easily accessible body fluids.

How a mixture of microRNA-29a (miR-29a) and microRNA-144 (miR-144) cancer biomarkers interacts with a graphene quantum dot

MicroRNAs (miRNAs) which are small non-coding RNAs have been reported to be potential cancer biomarker. However, it is difficult to extract such short RNA from a sample matrix. New effective strategies are required. Recently, graphene quantum dots (GQDs) have been used to detect nucleotides in many biosensor platforms, but their applications for miRNA extraction remain limited. GQD was reported to be able to collect short miRNA, but its performance to collect miRNAs with different structure remains unknown. Thus, in this work, the capability of GQD to interact with two different miRNAs is investigated. A mixture of hairpin-like miR-29a and circular miR-144 molecules are used as a representative of two miRNA morphologies. Two systems (a miRNA mixture, comprising 4 of miR-29a and 4 of miR-144, with (miR_GQD) and without GQD (miR)) were studied in comparison. MiRNAs in a mixture (miR) can aggregate, but no permanent miRNA assembly is captured. In contrast, the presence of GQD can rapidly and spontaneously activate the permanent miRNA/GQD clustering. This finding highlights the ability of GQD to be a miRNA collector. Interestingly, all GQD-bound miRNAs do not unfold. This allows the easy accessibility for probes. Also, nano-sized GQD seems to prefer hairpin miR-29a. The free 5' terminus of miR-29a acts as the sticky end to adhere on GQD. This work highlights the importance of RNA secondary structure on GQD/miRNA aggregation capability. An insight obtained here will be useful for further design of miRNA isolation strategies.

Ultra-Tough Graphene Oxide/DNA 2D Hydrogel with Intrinsic Sensing and Actuation Functions

Hydrogel devices with mechanical toughness and tunable functionalities are highly desirable for practical long-term applications such as sensing and actuation elements for soft robotics. However, existing hydrogels have poor mechanical properties, slow rates of response, and low functionality. In this work, two-dimensional hydrogel actuators are proposed and formed on the self-assembly of graphene oxide (GO) and deoxynucleic acid (DNA). The self-assembly process is driven by the GO-induced transition of double stranded DNA (dsDNA) into single stranded DNA (ssDNA). Thus, the hydrogel's structural unit consists of two layers of GO covered by ssDNA and a layer of dsDNA in between. Such heterogeneous architectures stabilized by multiple hydrogen bondings have Young's modulus of up to 10 GPa and rapid swelling rates of 4.0 × 10-3 to 1.1 × 10-2 s-1, which surpasses most types of conventional hydrogels. It is demonstrated that the GO/DNA hydrogel actuators leverage the unique properties of these two materials, making them excellent candidates for various applications requiring sensing and actuation functions, such as artificial skin, wearable electronics, bioelectronics, and drug delivery systems.

Electron videography of a lipid-protein tango

Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.

Development of Optical Differential Sensing Based on Nanomaterials for Biological Analysis

The discrimination and recognition of biological targets, such as proteins, cells, and bacteria, are of utmost importance in various fields of biological research and production. These include areas like biological medicine, clinical diagnosis, and microbiology analysis. In order to efficiently and cost-effectively identify a specific target from a wide range of possibilities, researchers have developed a technique called differential sensing. Unlike traditional "lock-and-key" sensors that rely on specific interactions between receptors and analytes, differential sensing makes use of cross-reactive receptors. These sensors offer less specificity but can cross-react with a wide range of analytes to produce a large amount of data. Many pattern recognition strategies have been developed and have shown promising results in identifying complex analytes. To create advanced sensor arrays for higher analysis efficiency and larger recognizing range, various nanomaterials have been utilized as sensing probes. These nanomaterials possess distinct molecular affinities, optical/electrical properties, and biological compatibility, and are conveniently functionalized. In this review, our focus is on recently reported optical sensor arrays that utilize nanomaterials to discriminate bioanalytes, including proteins, cells, and bacteria.

A highly selective and sensitive electrochemical sensor for tetracycline resistant genes detection based on the non-covalent interaction of graphene oxide and nucleobase

Antibiotic resistance genes (ARGs) are causing worldwide environmental problems, however, the traditional analytical methods and test equipment for them are time-consuming and expensive. The electrochemical sensor using the non-covalent bond between graphene oxide (GO) and single-stranded tet (ss-tet) was established for specific tetracycline resistance genes (tet, composed of ss-tet and complementary ss-tet (ss-tet') in water) detection, which preparation time was only 35 min and far less than most reported sensors based on covalent bond. As the result of the detection for tet, the developed sensor not only had the low detection limit of 50.0 pM (8.1 × 102 copies·mL-1), the short detection time within 42 min, but also had satisfactory stability, excellent reproducibility, and highly selectivity (RSD < 4.43 %). Besides, it also had acceptable accuracy comparing to the real-time quantitative polymerase chain reaction (RT-qPCR) and PCR array in tet detection. Noticeably, it also had been successfully applied to tetA detection in different water samples. In brief, the prepared non-covalent bond sensor is simple, rapid, and suitable for highly selective and sensitive detection of the ARGs in actual water.

Selection of Highly Specific DNA Aptamer for the Development of QCM-Based Arsenic Sensor

Heavy metal arsenic is a water pollutant that affects millions of lives worldwide. A novel aptamer candidate for specific and sensitive arsenic detection was identified using Graphene Oxide-SELEX (GO-SELEX). Eleven rounds of GO-SELEX were performed to screen As(III) specific sequences. The selected aptamer sequences were evaluated for their binding affinity. The dissociation constant of the best aptamer candidate, As-06 was estimated by fluorescence recovery upon target addition, and it was found to be 8.15 nM. A QCM-based biosensing platform was designed based on the target-triggered release of aptamer from the QCM electrode. An rGO-SWCNT nanocomposite was adsorbed on the gold surface, and the single-stranded probe was stacked on the rGO-CNT layer. Upon addition of the target to the solution, a concentration-dependent release of the ssDNA probe was observed and recorded as the change in the electrode frequency. The developed QCM sensor showed a dynamic linear range from 10 nM to 100 nM and a low detection limit of 8.6 nM. The sensor exhibited excellent selectivity when challenged with common interfering anions and cations.

The Use of Crystalline Carbon-Based Nanomaterials (CBNs) in Various Biomedical Applications

This review study aims to present, in a condensed manner, the significance of the use of crystalline carbon-based nanomaterials in biomedical applications. Crystalline carbon-based nanomaterials, encompassing graphene, graphene oxide, reduced graphene oxide, carbon nanotubes, and graphene quantum dots, have emerged as promising materials for the development of medical devices in various biomedical applications. These materials possess inorganic semiconducting attributes combined with organic π-π stacking features, allowing them to efficiently interact with biomolecules and present enhanced light responses. By harnessing these unique properties, carbon-based nanomaterials offer promising opportunities for future advancements in biomedicine. Recent studies have focused on the development of these nanomaterials for targeted drug delivery, cancer treatment, and biosensors. The conjugation and modification of carbon-based nanomaterials have led to significant advancements in a plethora of therapies and have addressed limitations in preclinical biomedical applications. Furthermore, the wide-ranging therapeutic advantages of carbon nanotubes have been thoroughly examined in the context of biomedical applications.

Label-Free DNA Biosensor Based on Reduced Graphene Oxide and Gold Nanoparticles

Currently available DNA detection techniques frequently require compromises between simplicity, speed, accuracy, and cost. Here, we propose a simple, label-free, and cost-effective DNA detection platform developed at screen-printed carbon electrodes (SPCEs) modified with reduced graphene oxide (RGO) and gold nanoparticles (AuNPs). The preparation of the detection platform involved a two-step electrochemical procedure based on GO reduction onto SPCEs followed by the electrochemical reduction of HAuCl4 to facilitate the post-grafting reaction with AuNPs. The final sensor was fabricated by the simple physical adsorption of a single-stranded DNA (ssDNA) probe onto a AuNPs-RGO/SPCE electrode. Each preparation step was confirmed by morphological and structural characterization using scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy, respectively. Furthermore, the electrochemical properties of the modified electrodes have been investigated by cyclic voltammetry (CV) and electrochemical impedance spectroscopy (EIS). The results demonstrated that the introduction of AuNPs onto RGO/SPCEs led to an enhancement in surface conductivity, a characteristic that favored an increased sensitivity in detection. The detection process relied on the change in the electrochemical signal induced by the binding of target DNA to the bioreceptor and was particularly monitored by the change in the charge transfer resistance of a [Fe(CN)6]4-/3- redox couple added in the test solution.

Graphene Oxide/Nitrocellulose Non-Covalent Hybrid as Solid Phase for Oligo-DNA Extraction from Complex Medium

A nitrocellulose-graphene oxide hybrid that consists of a commercially nitrocellulose (NC) membrane non-covalently modified with graphene oxide (GO) microparticles was successfully prepared for oligonucleotide extraction. The modification of NC membrane was confirmed by Fourier Transform Infrared Spectroscopy (FTIR), which highlighted the principal absorption bands of both the NC membrane at 1641, 1276, and 835 cm^-1 (NO₂) and of GO in the range of 3450 cm^-1 (CH₂-OH). The SEM analysis underlined the well-dispersed and uniform coverage of NC membrane with GO, which displayed thin spider web morphology. The wettability assay indicated that the NC-GO hybrid membrane exhibited slightly lower hydrophilic behavior, with a water contact angle of 26.7°, compared to the 15° contact angle of the NC control membrane. The NC-GO hybrid membranes were used to separate oligonucleotides that had fewer than 50 nucleotides (nt) from complex solutions. The features of the NC-GO hybrid membranes were tested for extraction periods of 30, 45, and 60 min in three different complex solutions, i.e., an aqueous medium, an α-Minimum Essential Medium (αMEM), and an αMEM supplemented with fetal bovine serum (FBS). The oligonucleotides were desorbed from the surface of the NC-GO hybrid membrane using Tris-HCl buffer with a pH of 8.0. Out of the three media utilized, the best results were achieved after 60 min incubation of the NC-GO membranes in αMEM, as evidenced by the highest fluorescence emission of 294 relative fluorescence units (r.f.u.). This value corresponded to the extraction of approximately 330-370 pg (≈7%) of the total oligo-DNA. This method is an efficient and effortless way to purify short oligonucleotides from complex solutions.

Facilitation of Dye-Based Quantitative Real-Time Polymerase Chain Reaction with Poly(ethylene glycol)-Engrafted Graphene Oxide

Quantitative real-time polymerase chain reaction (qPCR) is an important and extensively utilized technique in medical and biotechnological applications. qPCR enables the real-time detection of nucleic acid during amplification, thus surpassing the necessity of post-amplification gel electrophoresis for amplicon detection. Despite being widely employed in molecular diagnostics, qPCR exhibits limitations attributed to nonspecific DNA amplification that compromises the efficiency and fidelity of qPCR. Herein, we demonstrate that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly improve the efficiency and specificity of qPCR by adsorbing single-stranded DNA (ssDNA) without affecting the fluorescence of double-stranded DNA binding dye during DNA amplification. PEG-nGO adsorbs surplus ssDNA primers in the initial phase of PCR, having lower concentrations of DNA amplicons and thus minimizing the nonspecific annealing of ssDNA and false amplification due to primer dimerization and erroneous priming. As compared to conventional qPCR, the addition of PEG-nGO and the DNA binding dye, EvaGreen, in the qPCR setup (dubbed as PENGO-qPCR) significantly enhances the specificity and sensitivity of DNA amplification by preferential adsorption of ssDNA without inhibiting DNA polymerase activity. The PENGO-qPCR system for detection of influenza viral RNA exhibited a 67-fold higher sensitivity than the conventional qPCR setup. Thus, the performance of a qPCR can be greatly enhanced by adding PEG-nGO as a PCR enhancer as well as EvaGreen as a DNA binding dye to the qPCR mixture, which exhibits a significantly improved sensitivity of the qPCR.

Carbon-based nanostructures for cancer therapy and drug delivery applications

Synthesis, design, characterization, and application of carbon-based nanostructures (CBNSs) as drug carriers have attracted a great deal of interest over the past half of the century because of their promising chemical, thermal, physical, optical, mechanical, and electrical properties and their structural diversity. CBNSs are well-known in drug delivery applications due to their unique features such as easy cellular uptake, high drug loading ability, and thermal ablation. CBNSs, including carbon nanotubes, fullerenes, nanodiamond, graphene, and carbon quantum dots have been quite broadly examined for drug delivery systems. This review not only summarizes the most recent studies on developing carbon-based nanostructures for drug delivery (e.g. delivery carrier, cancer therapy and bioimaging), but also tries to deal with the challenges and opportunities resulting from the expansion in use of these materials in the realm of drug delivery. This class of nanomaterials requires advanced techniques for synthesis and surface modifications, yet a lot of critical questions such as their toxicity, biodistribution, pharmacokinetics, and fate of CBNSs in biological systems must be answered.

A Bioluminescent Protein-Graphene Oxide Donor-Quencher Pair in DNA Hybridization Assays

Despite fluorescent quenching with graphene oxide (GO) having shown great success in various applications - bioluminescent quenching has not yet been demonstrated using GO as a quencher. To explore the ability of GO to quench bioluminescence, we used Gaussia luciferase (Gluc) as a donor and GO as a quencher and demonstrated its application in sensing of two target analytes, HIV-1 DNA and IFN-γ. We demonstrated that the incubation of Gluc conjugated HIV-1 and IFN-γ oligonucleotide probes with GO provided for monitoring of probe-target interactions based on bioluminescence measurement in a solution phase sensing system. The limits of detection obtained for IFN-γ and HIV-1 DNA detection were 17 nM and 7.59 nM, respectively. Both sensing systems showed selectivity toward the target analyte. The detection of IFN-γ in saliva matrix was demonstrated. The use of GO as a quencher provides for high sensitivity while maintaining the selectivity of designed probes to their respective targets. The use of GO as a quencher provides for an easy assay design and low cost, environmentally friendly reporter.

The aggregation of multiple miR-29a cancer biomarkers induced by graphene quantum dots: Molecular dynamics simulations

MicroRNAs (miRNAs) are small non-coding RNAs that play a role in regulating gene expression. MiRNAs are focused on as potential cancer biomarkers due to their involvement in the cancer development. New effective techniques for extracting miRNA from a biological matrix is important. Recently, graphene quantum dots (GQDs) have been used to detect DNA/RNA in many sensor platforms, but the application in miRNA extraction remains limited. To extract miRNAs, the miRNA adsorption and desorption on GQD are the key. Thus, in this work, the adsorption mechanism of excess miRNA on GQD in solution is revealed using Molecular dynamics simulations. The miRNA assemblies on one and two GQDs were studied to explore the possibility of using GQD for miRNA extraction. The folded miR-29a molecule, one of key cancer biomarkers, is used as an miRNA model. Three systems with one (6miR) and two GQDs (with parallel (6miR_2GP) and sandwich (6miR_2GS) organisations) in six-miR-29a solution were set. The data show excess miR-29a can reduce the miR-29a-GQD binding efficiency. The opening of intrabase pairing of GQD-absorbed miR-29a facilitates the interbase coupling resulting in the self-aggregation of miR-29a. The GQD organisation also affects the miR-29a adsorption ability. The additional GQDs result in the tighter miR-29a adsorption which can retard the miR-29a desorption. The proper GQD concentration is thus important to successfully collect all miR-29a and accommodate the easy miR-29a dissociation. Our results can be useful for a design of DNA probe and choosing decent nanosized GRA concentration for experimental setups.

Graphene oxide-mediated fluorescence turn-on GO-FAM-FRET aptasensor for detection of sterigmatocystin

Sterigmatocystin (STC) is a toxic fungal secondary metabolite recognized by the FAO and WHO as a genotoxic and carcinogenic substance. STC contaminates several foods and feed commodities, posing a health risk to humans. The present study proposes to develop a graphene oxide-mediated aptasensor platform for the one-step detection of STC. In this study, DNA aptamers were generated against STC by using a target immobilization-free graphene oxide (GO)-SELEX protocol. The champion aptamers were subjected to in silico maturation using a genetic algorithm to improve binding affinity. Further, MSA-C6 and STC interactions were characterized by MD simulation, bio-layer interferometry (KD 27.9 nM) and flow cytometry. GO was immobilized on a polypropylene surface and functionalized with FAM labelled MSA-C6 to develop a simple one-step fluorescence turn-on aptasensor. The linear detection range of the aptasensor was found to be 80-720 ppb with LOD 23.56 ± 4.93 ppb and LOQ 132.43 ± 3.25 ppb. Insignificant interference of salts and detergents as well as negligible cross-reactivity with other structurally similar mycotoxins were observed. Recovery studies in simulated contaminated samples indicated appreciable recoveries (71-89%) using aptasensing assay. The results of the study indicate the successful development of a simple one-step detection platform for STC, useful for the measurement and monitoring of samples for the presence of STC. It also reports a high-affinity aptamer, which can be exploited in other sensing platforms.

Molecular Dynamics Simulations of Interactions between Human Telomeric i-Motif Deoxyribonucleic Acid and Functionalized Graphene

The work deals with molecular dynamics (MD) simulations of protonated, human telomeric i-motif deoxyribonucleic acid (DNA) with functionalized graphene. We studied three different graphene sheets: unmodified graphene with hydrogen atoms attached to their edges and two functionalized ones. The functionalization of graphene edge consists in attaching partially protonated or dissociated amine and carboxyl groups. We found that in all cases the protonated i-motif adsorbs strongly on the graphene surface. The biased MD simulations showed that the work necessary to drag the i-motif out from amine-doped graphene is about twice larger than that in other cases. In general, the system i-motif/amine-doped graphene stands out from the rest, e.g., in this case, the i-motif adsorbs its side with 3' and 5' ends oriented in the opposite to surface direction. In other cases, the DNA fragment is adsorbed to graphene by 3' and 5' ends. In all cases, the adsorption on graphene influences the i-motif internal structure by changing the distances between i-motif strands as well as stretching or shortening the DNA chain, but only in the case of amine-doped graphene the adsorption affects internal H-bonds formed between nucleotides inside the i-motif structure.

Enhanced Specificity in Loop-Mediated Isothermal Amplification with Poly(ethylene glycol)-Engrafted Graphene Oxide for Detection of Viral Genes

Loop-mediated isothermal amplification (LAMP) is a nucleic acid amplification method that allows the simple, quick, and low-cost detection of various viral genes. LAMP assays are susceptible to generating non-specific amplicons, as high concentrations of DNA primers can give rise to primer dimerization and mismatched hybridizations, resulting in false-positive signals. Herein, we reported that poly(ethylene glycol)-engrafted nanosized graphene oxide (PEG-nGO) can significantly enhance the specificity of LAMP, owing to its ability to adsorb single-stranded DNA (ssDNA). By adsorbing surplus ssDNA primers, PEG-nGO minimizes the non-specific annealing of ssDNAs, including erroneous priming and primer dimerization, leading to the enhanced specificity of LAMP. The detection of complementary DNAs transcribed from the hepatitis C virus (HCV) RNA was performed by the PEG-nGO-based LAMP. We observed that the inclusion of PEG-nGO significantly enhances the specificity and sensitivity of the LAMP assay through the augmented difference in fluorescence signals between the target and non-target samples. The PEG-nGO-based LAMP assay greatly facilitates the detection of HCV-positive clinical samples, with superior precision to the conventional quantitative real-time PCR (RT-qPCR). Among the 20 clinical samples tested, all 10 HCV-positive samples are detected as positive in the PEG-nGO-based LAMP, while only 7 samples are detected as HCV-positive in the RT-qPCR. In addition, the PEG-nGO-based LAMP method significantly improves the detection precision for the false-positive decision by 1.75-fold as compared to the LAMP without PEG-nGO. Thus, PEG-nGO can significantly improve the performance of LAMP assays by facilitating the specific amplification of target DNA with a decrease in background signal.

Phenol/Chloroform-Free TiO2-Based miRNA Extraction from Cell Lysate

While microRNAs are considered as excellent biomarkers of various diseases, there are still several remaining challenges regarding their isolation. In this study, we aimed to design a novel RNA isolation method that would help to overcome those challenges. Therefore, we present a novel phenol/chloroform-free, low-cost method for miRNA extraction. Within this method, RNA is extracted from cell lysate with an isopropanol/water/NaCl system, followed by solid-phase extraction using TiO2 microspheres to effectively separate short RNAs from long RNA molecules. We also demonstrated the pH-dependent selectivity of TiO2 microspheres towards different sizes of RNA. We were able to regulate the size range of extracted RNAs with simple adjustments in binding conditions used during the solid-phase extraction.

Accurate, rapid and highly sensitive detection of African swine fever virus via graphene oxide-based accelerated strand exchange amplification

African swine fever is an acute, severe and highly contagious infectious disease caused by African swine fever virus (ASFV), posing a huge threat to the global swine industry. Rapid and accurate diagnostic methods are of great significance for the effective prevention and control of ASFV transmission. In this work, we established and evaluated a graphene oxide-based accelerated strand exchange amplification (GO-ASEA) method for rapid, highly sensitive, and quantitative detection of ASFV. The use of GO provided a novel solution reference for improving the specificity of strand exchange amplification and solving the potential false positive problem caused by primer dimers. The detection limit of the GO-ASEA assay was 5.8 × 10^-1 copies per μL of ASFV (equal to 2.9 copies per reaction) or 5.8 × 10⁰ copies per μL of ASFV in spiked swine nasal swabs. The selectivity of the GO-ASEA assay was supported by the ASFV DNA reference material and another seven porcine-derived viruses with similar clinical symptoms. The GO-ASEA assay took only about 29 minutes and was validated with 6 inactivated specimens and 52 swine nasal swabs, showing excellent clinical applicability. The novel assay is an accurate and practical method for rapid, highly sensitive detection of ASFV, and can potentially serve as a robust tool in epidemic prevention and point-of-care diagnosis.

Isolation and Characterization of a ssDNA Aptamer against Major Soluble Antigen of Renibacterium salmoninarum

Bacterial kidney disease (BKD) is a major health problem of salmonids, affecting both wild and cultured salmon. The disease is caused by Renibacterium salmoninarum (Rs), a fastidious, slow-growing and strongly Gram-positive diplobacillus that produces chronic, systemic infection characterized by granulomatous lesions in the kidney and other organs, often resulting in death. Fast detection of the pathogen is important to limit the spread of the disease, particularly in hatcheries or aquaculture facilities. Aptamers are increasingly replacing conventional antibodies as platforms for the development of rapid diagnostic tools. In this work, we describe the first instance of isolating and characterizing a ssDNA aptamer that binds with high affinity to p57 or major soluble antigen (MSA), the principal antigen found on the cell wall surface of Rs. Specifically, in this study a construct of the full-length protein containing a DNA binding domain (MSA-R2c) was utilized as target. Aptamers were isolated from a pool of random sequences using GO-SELEX (graphene oxide-systematic evolution of ligands by exponential enrichment) protocol. The selection generated multiple aptamers with conserved motifs in the random region. One aptamer with high frequency of occurrence in different clones was characterized and found to display a strong binding affinity to MSA-R2c with a Kd of 3.0 ± 0.6 nM. The aptamer could be potentially utilized for the future development of a sensor for rapid and onsite detection of Rs in water or in infected salmonids, replacing time-consuming and costly lab analyses.

Exploring graphene oxide intrinsic electroactivity to elucidate the non-covalent interactions with DNA oligonucleotides

We show here how the electrochemical reduction signal of graphene oxide nanocolloids is inhibited upon the formation of non-covalent interactions with single stranded DNA oligonucleotides. The drop in the reduction current intensity is strongly influenced by the nucleobase sequence, and can therefore be directly correlated to the specific DNA homo-oligonucleotide.

Enhancing Peptide Nucleic Acid-Nanomaterial Interaction and Performance Improvement of Peptide Nucleic Acid-Based Nucleic Acid Detection by Using Electrostatic Effects

Single-stranded peptide nucleic acid (PNA) probes interact strongly with several nanomaterials, and the interaction was diminished in the presence of complementary nucleic acid targets which forms the basis of many nucleic acid sensing platforms. As opposed to the negatively charged DNA probes, the charges on the PNA probes may be fine-tuned by incorporating amino acids with charged side chains. The contribution of electrostatic effects to the interaction between PNA probes and nanomaterials has been largely overlooked. This work reveals that electrostatic effects substantially enhanced the quenching of dye-labeled conformationally constrained pyrrolidinyl PNA probes by several nanomaterials including graphene oxide (GO), reduced graphene oxide, gold nanoparticles (AuNPs), and silver nanoparticles. The fluorescence quenching and the color change from red to purple in the case of AuNPs because of aggregation were inhibited in the presence of complementary nucleic acid targets. Thus, fluorescence and colorimetric assays for DNA and RNA that can distinguish even single-base-mismatched nucleic acids with improved sensitivity over conventional DNA probes were established. Both the GO- and AuNP-based sensing platforms have been successfully applied for the detection of real DNA and RNA samples in vitro and in living cells. This study emphasizes the active roles of electrostatic effects in the PNA-nanomaterial interactions, which paves the way toward improving the performance of PNA-nanomaterial based assays of nucleic acids.

In Situ Growth of MOFs Crystals to Synthesis Graphene Oxide /ZIF-7 Gel with Enhanced Adsorption Capacity for Methylene Blue

Graphene oxide gel containing ZIF-7 (Zx@GoG) was synthesized by immersing graphene oxide gel (GoG) in DMF solution of Zn2+ and DMF solution of organic ligands, respectively, and characterized by powder...

Exploiting the optical sensing of fluorophore-tagged DNA nucleobases on hexagonal BN and Al-doped BN sheets: a computational study

Hexagonal boron nitride (h-BN) sheets possess high fluorescence quenching ability and high affinity towards DNA/RNA, and they can be used as a sensing platform for rapid detection. We report the absorption and emission properties of DNA nucleobases such as adenine (A), cytosine (C), guanine (G), and thymine (T) tagged with benzoxazole on h-BN and aluminium-doped h-BN (Al_hBN) sheets. The binding affinity of studied nucleobases on h-BN sheets at the M062X/6-31G* level of theory showed the following adsorption trend: G ≥ T ≥ A > C, which is in good agreement with the previous results. The calculated stability trend of nucleobases on the Al_hBN sheet follows as C > G > A > T at the same level of theory. The physically adsorbed behavior of nucleobases to h-BN sheets was confirmed by the non-covalent interactions (NCIs) and the total density of states (TDOS) plots. The NCI results indicated that van der Waals interactions contribute significantly to the adsorption of nucleobases on h-BN sheets. Atoms in molecules (AIM) calculations revealed the electrostatic interactions between nucleobases and the Al_hBN sheet. The quenching phenomenon of nucleobase-tagged fluorophores on h-BN and Al_hBN sheets was investigated by TD-DFT calculations using the same level of theory. The thymine-tagged fluorophore upon adsorption to the pristine h-BN sheet was found to be blue-shifted (∼43 nm); however, the guanine-tagged fluorophore with Al_hBN showed a remarkable difference from other nucleobase-tagged fluorophores in the absorption and emission spectrum. Guanine-tagged fluorophores showed a smaller blue shift (∼7 nm) in the absorption spectrum; however, it showed a larger red shift (∼55 nm) than the other nucleobase-tagged fluorophores on Al_hBN sheets and can be useful in recognizing a sequence-specific phenomenon as a fluorescent biosensor of DNA and RNA to ascertain the presence of such nucleobases.

What Happens When a Complementary DNA Meets miR-29a Cancer Biomarker in Complex with a Graphene Quantum Dot

MicroRNAs (miRNAs), short single-stranded noncoding RNA molecules, serve as potential cancer biomarkers due to their involvement in cancer development. One of the strategies to extract miRNAs is to perform the miRNA adsorption on nanomaterials and dissociation by a complementary DNA strand (DNA probe). Recently, graphene quantum dots (GQDs) were found to show a good ability to absorb miRNAs. Thus, in this work, the mechanism of the GQD-adhered miRNA capture by its complementary DNA is revealed using molecular dynamics simulations. miR-29a, a potential cancer biomarker, is used as a miRNA model. Three systems containing one and four chains of miR-29a in addition to one and four complementary DNA probes (1R1D, 1R4D, and 4R4D) were studied. GQDs are the prime targets of a DNA attack. The full coverage of GQDs is required to protect the adsorption of DNA probes on the GQD face. The nucleobase-backbone interactions are the main contributors to miR-DNA interactions in this work. The interbase paring becomes small because most nucleobases of miR-29a and their probe are stacked to maintain their secondary structures, and some are absorbed on the GQD surface. Apparently, weakening of the nucleobase-GQD π-π stacking and the intrabase-pairing strength is needed for extracting miR-29a by a probe. Although no GQD-absorbed miR-29a desorption is found here, the basic principles obtained can be useful for further utilization of GQDs and their derivatives for miRNA extraction and detection.

Ten Years Progress of Electrical Detection of Heavy Metal Ions (HMIs) Using Various Field-Effect Transistor (FET) Nanosensors: A Review

Heavy metal pollution remains a major concern for the public today, in line with the growing population and global industrialization. Heavy metal ion (HMI) is a threat to human and environmental safety, even at low concentrations, thus rapid and continuous HMI monitoring is essential. Among the sensors available for HMI detection, the field-effect transistor (FET) sensor demonstrates promising potential for fast and real-time detection. The aim of this review is to provide a condensed overview of the contribution of certain semiconductor substrates in the development of chemical and biosensor FETs for HMI detection in the past decade. A brief introduction of the FET sensor along with its construction and configuration is presented in the first part of this review. Subsequently, the FET sensor deployment issue and FET intrinsic limitation screening effect are also discussed, and the solutions to overcome these shortcomings are summarized. Later, we summarize the strategies for HMIs' electrical detection, mechanisms, and sensing performance on nanomaterial semiconductor FET transducers, including silicon, carbon nanotubes, graphene, AlGaN/GaN, transition metal dichalcogenides (TMD), black phosphorus, organic and inorganic semiconductor. Finally, concerns and suggestions regarding detection in the real samples using FET sensors are highlighted in the conclusion.

Graphene oxide-based fluorescent biosensors and their biomedical applications in diagnosis and drug discovery

Graphene oxide (GO), an oxidized derivative of graphene, has received much attention for developing novel fluorescent bioanalytic platforms due to its remarkable optical properties and biocompatibility. The reliable performance and robustness of GO-based biosensors have enabled various applications in the biomedical field including diagnosis and drug discovery. Here, recent advances in the development of GO-based fluorescent biosensors are overviewed, particularly nucleic acid detection and enzyme activity assay. In addition, practical applications in biomarker detection and high-throughput screening are also examined. Lastly, basic design principles and remaining challenges of these types of biosensors are discussed for further progress.

Modeling the Adsorption of the miR-29a Cancer Biomarker on a Graphene Quantum Dot

MicroRNAs (miRNAs) are small noncoding RNA molecules associated with the regulation of gene expression in organisms. MiRNAs are focused on as potential cancer biomarkers due to their involvement in cancer development. New potential techniques for miRNA detection are rapidly developed, while there is a lack of effective extraction approaches, especially for miRNAs. Recently, graphene quantum dots (GQDs) have been involved in many disease biosensor platforms including miRNA detection, but no application in miRNA extraction is studied. To extract miRNAs, miRNA adsorption and desorption on GQDs are the key. Thus, in this work, the adsorption mechanism of miRNA on GQDs in solution is revealed using molecular dynamics simulations. The aim is to explore the possibility of using GQDs for miRNA extraction. The folded miR-29a molecule, one of the key cancer biomarkers, is used as a miRNA model. Two systems with one (1miR) and four (4miR) chains of miR-29a were set. MiR-29a molecules in all systems are simultaneously adsorbed on the GQD surface. Our finding highlights the ability of the GQD in collecting miRNAs in solution. In 1miR, the whole miR-29a chain sits on the GQD face, whereas all miR-29a molecules in 4miR show the "clamping" conformation. No "lying flat" orientation of miR-29a is observed due to the existence of the preserved hairpin region. Interestingly, the 5' end shows tighter binding than the 3' terminus. A design of complementary DNA with the recognition segment involving the sequences close to the 3' end can promote effective miR-29a desorption.

A naturally fluorescent protein C-phycoerythrin and graphene oxide bio-composite as a selective fluorescence 'turn off/on' probe for DNA quantification and characterization

Highly specific graphene-DNA interactions have been at the forefront of graphene-based sensor design for various analytes, including DNA itself. However, in addition to its detection, DNA also needs to be characterized according to its size and concentration in a sample, which is an additional analytical step. Designing a highly sensitive and selective DNA sensing and characterization platform is, thus, of great interest. The present study demonstrates that a bio-derived, naturally fluorescent protein C-phycoerythrin (CPE) - graphene oxide (GO) bio-composite can be used to detect dsDNA in nanomolar quantities efficiently via fluorescent "turn off/on" mechanism. Interaction with GO temporarily quenches CPE fluorescence in a dose-dependent manner. Analytical characterization indicates an indirect charge transfer with a corresponding loss of crystalline GO structure. The fluorescence is regained with the addition of DNA, while other biomolecules do not pose any hinderance in the detection process. The extent of regain is DNA length dependent, and the corresponding calibration curve successfully quantifies the size of an unknown DNA. The incubation time for detection is ~3-5 min. The bio-composite platform also works successfully in a complex biomolecule matrix and cell lysate. However, the presence of serum albumin poses a hinderance in the serum sample. Particle size analysis proves that CPE displacement from GO surface by the incoming DNA is the reason for the 'turn on' response, and that the sensing process is exclusive to dsDNA. This new platform could be an exciting and rapid DNA sensing and characterization tool.

Computational Insights into Molecular Adsorption Characteristics of Methylated DNA on Graphene Oxide for Multicancer Early Detection

DNA methylation is an epigenetic modification involving the transfer of a methyl group to cytosine residues of a DNA molecule. Altered DNA methylation of certain genes is associated with several diseases including cancer. Nanomaterials, such as graphene oxide (GO), offer great potential as sensing elements for methylated DNA (mDNA) detection due to their distinct properties. Understanding molecular interactions between mDNA and GO can make provision for developing a universal cancer screening test. Molecular dynamics (MD) simulation and density functional theory (DFT) calculation have been employed for investigating their detailed macro- and microscale interactions. Based upon the MD simulation, different adsorption levels of methylated and unmethylated DNAs on GO were represented by a contacting surface area (CSA), which depends on surrounding conditions (in water or a MgCl₂ solution). In water, the CSAs of the methylated and unmethylated single-stranded DNA (ssDNA) were ≈13 and ≈5 nm², respectively, representing more preferable adsorption on GO for the methylated ssDNA. In the presence of divalent ions (Mg²⁺), the CSAs of both methylated and unmethylated DNA molecules were ≈8 nm², suggesting that there was no significant difference in adsorption in a saline solution. To reveal the electrical property of GO covered by either methylated or unmethylated DNA, its electronic structure was investigated by the DFT calculation. The energy gaps of pristine graphene (pG) and GO adsorbed by 5-methylcytosine (5mC) were 1.6 and 12.9 meV, respectively, while cytosine adsorption resulted in lower energy gaps (1.2 meV for pG and 9.5 meV for GO). When comparing methylated DNA-covered GO with that covered with unmethylated DNA, remarkable differences in electrical conductivity, which were caused by the electronic structure of GO, were observed. These findings will provide a new route for an efficient detection method of DNA methylation, which can further be used to develop a universal cancer test.

A facile aptasensor based on polydopamine nanospheres for high-sensitivity sensing of T-2 toxin

A facile fluorescent aptasensor based on polydopamine nanospheres (PDANSs) has been proposed for the rapid and high sensitive sensing of T-2 toxin. PDANSs are dopamine-derived synthetic eumelanin polymers with excellent fluorescence quenching ability, dispersibility and biocompatibility. In the assay, 6-carboxyfluorescein (FAM)-labeled aptamers (FAM-aptamers) were adsorbed onto PDANSs via noncovalent bonding, resulting in quenching fluorescence. In the presence of T-2, the binding of T-2 to the aptamers could promote the formation of the A-form duplex hairpin structure, which was used as a sensing platform to detect T-2 on the basis of fluorescence recovery. The results showed that the aptasensor was rapid and sensitive for the detection of T-2 toxin with a linear detection range of 10-180 μg L-1 and a detection limit of 7.23 μg L-1. The performance of the proposed method was comparable with that of the liquid chromatography-mass spectrometry method (LC-MS). Thus, the aptasensor could be used for the determination of real samples. The design method proposed in this study provides a strategy for the development of PDANS-based toxin biosensors.

Graphene-Based FRET Aptasensors

Graphene-based FRET aptasensors can be realized only by unique combinations of aptamer that can be freely functionalized by chemical modification, and graphene/graphene oxide that works as an excellent fluorescence acceptor at the same time as aptamer adsorbates. This review describes the principles of the sensor, several applications to microchannel devices, improvement of the sensing performance by molecular design of the aptamer and remarks on future prospects based on an introduction of recent works and achievements, including the author's paper. The sensor employs DNA modified with graphene/graphene oxide at the terminal as the molecular probe. This system is supported by the excellent property of DNA that does not lose the molecular recognition ability even due to a chemical modification at the terminal. I hope that this review will be useful for developing research on higher performance of graphene aptasensors in the future.

Isothermal Detection of Canine Blood Parasite (Ehrlichia canis) Utilizing Recombinase Polymerase Amplification Coupled with Graphene Oxide Quenching-Based Pyrrolidinyl Peptide Nucleic Acid

Canine monocytic ehrlichiosis (CME), caused by transmitted Ehrlichia canis infection, is a major disease in dogs with worldwide distribution. Herein, a nucleic acid assay was established for the identification of E. canis infection employing a fluorescently labeled conformationally constrained pyrrolidinyl PNA probe (Flu-acpcPNA) designed to sequence-specifically target the 16S rRNA gene. The sensing principle is based on the excellent quenching ability of graphene oxide (GO) of the free PNA probe, that was diminished upon binding to the DNA target. The addition of DNase I improved the performance of the detection system by eliminating the nonspecific quenching capability of long-chain dsDNA and thus enhancing the fluorescence signaling. The assay was coupled with a recombinase polymerase amplification (RPA) technique, which could be performed under isothermal conditions (37 °C) without DNA denaturation and purification steps. The established method is simple to set up and execute, proving a rapid, specific, and sensitive detection of 16S rRNA gene of E. canis with a limit of detection at least 11.1 pM. This technique shows good potential for the visual detection of double-stranded DNA targets without the need for PCR or complicated instruments, which shows great promise for practical usage in resource limited areas.

Nanomaterial and Aptamer-Based Sensing: Target Binding versus Target Adsorption Illustrated by the Detection of Adenosine and ATP on Metal Oxides and Graphene Oxide

Target molecule-induced desorption of aptamer probes from nanomaterials has been a very popular sensing method, taking advantage of the fluorescence quenching or catalytic activity of nanomaterials for signal generation. While it is generally conceived that aptamers desorb due to binding to target molecules, in this work, we examined the effect of competitive target adsorption. From five metal oxide nanoparticles including CeO₂, ZnO, NiO, Fe₃O₄, and TiO₂, only ATP was able to induce desorption of its aptamer. Adenosine could not, even though it had an even higher affinity than ATP to the aptamer. The same conclusion was also observed with a random DNA that cannot bind ATP, indicating that the desorption of DNA was due to competitive adsorption of ATP instead of aptamer binding. On graphene oxide, however, adenosine produced slightly more aptamer desorption than ATP under most of the conditions, and this can be partially attributed to the weaker interaction of negatively charged ATP with negatively charged graphene oxide. For such surface-based biosensors, it is recommended that a nonaptamer control DNA be tested side-by-side to ensure the sensing mechanism to be related to aptamer binding instead of target adsorption.

Graphene/MoS2 Nanohybrid for Biosensors

Graphene has been studied a lot in different scientific fields because of its unique properties, including its superior conductivity, plasmonic property, and biocompatibility. More recently, transition metal dicharcogenide (TMD) nanomaterials, beyond graphene, have been widely researched due to their exceptional properties. Among the various TMD nanomaterials, molybdenum disulfide (MoS2) has attracted attention in biological fields due to its excellent biocompatibility and simple steps for synthesis. Accordingly, graphene and MoS2 have been widely studied to be applied in the development of biosensors. Moreover, nanohybrid materials developed by hybridization of graphene and MoS2 have a huge potential for developing various types of outstanding biosensors, like electrochemical-, optical-, or surface-enhanced Raman spectroscopy (SERS)-based biosensors. In this review, we will focus on materials such as graphene and MoS2. Next, their application will be discussed with regard to the development of highly sensitive biosensors based on graphene, MoS2, and nanohybrid materials composed of graphene and MoS2. In conclusion, this review will provide interdisciplinary knowledge about graphene/MoS2 nanohybrids to be applied to the biomedical field, particularly biosensors.

Pesticide Aptasensors-State of the Art and Perspectives

Contamination by pesticides in the food chain and the environment is a worldwide problem that needs to be actively monitored to ensure safety. Unfortunately, standard pesticide analysis based on mass spectrometry takes a lot of time, money and effort. Thus, simple, reliable, cost-effective and field applicable methods for pesticide detection have been actively developed. One of the most promising technologies is an aptamer-based biosensor or so-called aptasensor. It utilizes aptamers, short single-stranded DNAs or RNAs, as pesticide recognition elements to integrate with various innovative biosensing technologies for specific and sensitive detection of pesticide residues. Several platforms for aptasensors have been dynamically established, such as colorimetry, fluorometry, electrochemistry, electrochemiluminescence (ECL) and so forth. Each platform has both advantages and disadvantages depending on the purpose of use and readiness of technology. For example, colorimetric-based aptasensors are more affordable than others because of the simplicity of fabrication and resource requirements. Electrochemical-based aptasensors have mainly shown better sensitivity than others with exceedingly low detection limits. This paper critically reviews the progression of pesticide aptasensors throughout the development process, including the selection, characterization and modification of aptamers, the conceptual frameworks of integrating aptamers and biosensors, the ASSURED (affordable, sensitive, specific, user-friendly, rapid and robust, equipment-free and deliverable to end users) criteria of different platforms and the future outlook.

Designing signal-on sensors by regulating nanozyme activity

Nanozymes are nanomaterials with enzyme-like activities. Compared to natural enzymes, nanozymes are more stable and cost-effective, and they have unique properties due to their nanoscale size and surface chemistry. In this review, we summarize 'signal-on' nanozyme-based sensors for detecting metal ions, anions, small molecules and proteins. Since protein-based enzymes are already highly active, they were used to detect their inhibitors, resulting in 'signal-off' sensors. On the other hand, for nanozymes, target molecules were detected either as a promotor of nanozyme activity or for its ability to selectively remove nanozyme inhibitors. In both cases, 'signal-on' detection was achieved. We classify the commonly used nanozymes based on their composition such as metal oxide, gold nanoparticles and other nanomaterials, most of which belong to the oxidase, peroxidase and catalase mimics. The nanozymes can catalyze the oxidation of colorless or non-fluorescent substrates to produce a visual or fluorescent signal. Based on this, this article presents some typical 'turn-on' and 'turn-off-on' sensors, and we critically review their design principles. At the end, further perspectives for the nanozyme-based sensors are outlined.

Promoting DNA Adsorption by Acids and Polyvalent Cations: Beyond Charge Screening

Adsorbing DNA oligonucleotides onto nanoparticles is the first step in developing DNA-based biosensors, drug delivery systems, and smart materials. Since DNA is a polyanion, it is repelled by negatively charged nanoparticles, which constitute the majority of commonly used nanomaterials. Adding salt such as NaCl to screen charge repulsion is a standard method of promoting DNA adsorption. However, Na⁺ does not supply additional attractive forces. In addition, adding a high concentration of NaCl can cause the aggregation of nanomaterials. In this feature article, we mainly summarize the methods developed in our laboratory to promote DNA adsorption by lowering the pH and by adding polyvalent metal ions, especially transition-metal ions. Various materials including noble metals (gold, silver, and platinum), 2D materials (graphene oxide, MoS₂, WS₂, and MXene), polydopamine, and several metal oxides are discussed. In general, low pH can protonate DNA bases and nanoparticle surfaces, reducing charge repulsion and even leading to attraction, although DNA folding at low pH can sometimes be detrimental to adsorption. Polyvalent metal ions can bridge additional interactions to achieve otherwise impossible adsorption. On the basis of the current understanding, a few future research directions are proposed to further improve DNA adsorption.

Effects of graphene oxide on PCR amplification for microbial community survey

BACKGROUND

Graphene oxide (GO) has been suggested as an efficient assistant additive to eliminate non-specific amplification of the polymerase chain reaction (PCR). Although many studies have focused on exploring its molecular mechanism, the practice of GO on the quantitation of microbial community has not been implemented yet. In this study, GO was added in PCR system to explore the changes on removing typical amplification errors, such as chimera and mismatches on two kinds of mock communities (an evenly mixed and a staggered mock communities) and environmental samples.

RESULTS

High-throughput sequencing of bacterial and fungal communities, based on 16S rRNA genes and internal transcribed spacers (ITS) respectively, showed that GO could significantly increase large segmental error (chimeric sequence) in PCR procedure while had no specific effect on point error (mismatched sequence). Besides, GO reduced the α-diversity of community, and changed the composition of fungal community more obviously than bacterial community.

CONCLUSIONS

Our study provides the first quantitative data on microbial community level to prove the negative effect of GO, and also indicates that there may be a more complex interaction between GO and comprehensive DNA fragments in PCR process.

Biodistribution of Graphene Oxide Determined through Postadministration Labeling with DNA-Conjugated Gold Nanoparticles and ICPMS

Recent research has revealed the use of graphene oxide (GO) and its derivatives as a potential biomaterial because of their attractive physicochemical characteristics and functional properties. However, if GO and related derivatives are to become useful materials for biomedical applications, it will be necessary to evaluate their biodistribution for health and safety considerations. To obtain a more accurate biodistribution for GO, we (i) developed a postadministration labeling strategy employing DNA-conjugated gold nanoparticles (DNA-AuNPs) to selectively label administered GO in Solvable-treated tissue samples and (ii) constructed an automatic sample pretreatment scheme (using a C₁₈-packed minicolumn) to effectively separate the DNA-AuNP-labeled GO from the unbound DNA-AuNPs and the dissolved tissue matrices, thereby enabling ultrasensitive, interference-free quantification of GO through measurement (inductively coupled plasma mass spectrometry) of the Au signal intensities. The DNA-AuNPs can bind to GO in a concentration- and time-dependent manner. After optimizing the labeling conditions (DNA length, incubation pH, DNA-AuNP concentration, and incubation time) and the separation scheme (sample loading flow rate, rinsing volume, and eluent composition), we found that A₂₀R₂₀-AuNPs (R₂₀: random DNA sequence including A, T, C, and G) had the strongest binding affinity for labeling of the administered GO (dissociation constant: 36.0 fM) and that the method's detection limit reached 9.3 ag L^-1 with a calibration curve having a working range from 10^-1 to 10¹⁰ fg L^-1. Moreover, this approach revealed that the intravenously administered GO accumulated predominantly in the liver and spleen at 1 and 12 h post administration, with apparent discrepancies in the concentrations measured using pre- and postadministration labeling strategies.

Quenching of fluorescently labeled pyrrolidinyl peptide nucleic acid by oligodeoxyguanosine and its application in DNA sensing

Quenching by nucleobases can significantly affect the fluorescence properties of many fluorophores. The quenching efficiency depends on the electronic properties of the fluorophore and adjacent nucleobases. In this study, we present a hitherto unreported high-efficiency quenching (up to 90%) of various fluorescently labeled pyrrolidinyl peptide nucleic acid (acpcPNA) probes by oligodeoxyguanosine (dGX). The quenching principle relies on the electrostatic interaction between the positively charged lysine-modified acpcPNA probe and the negatively charged oligodeoxyguanosine. The addition of stoichiometric quantities of a DNA target with the sequence complementary to the PNA probe restored the fluorescence to the original level. This was explained by the binding of the DNA to the PNA via a specific base pairing, which resulted in the separation of the oligodeoxyguanosine quencher from the fluorophore. Much less fluorescence restoration was observed in the DNA containing one or more mismatched bases. Applications of the oligodeoxyguanosine-quenched PNA probes for DNA sequence determination, including in multiplex formats, are demonstrated. The performance in terms of sensitivity and mismatch discrimination is comparable to classical PNA-based molecular beacons but without the need for double-labeling, which is expensive and presents solubility issues, or a dedicated quencher probe. This exemplifies a novel use of the unique electrostatic properties of PNA to develop a DNA sensing platform for DNA sequence determination.

Hydrophobic Interaction: A Promising Driving Force for the Biomedical Applications of Nucleic Acids

The comprehensive understanding and proper use of supramolecular interactions have become critical for the development of functional materials, and so is the biomedical application of nucleic acids (NAs). Relatively rare attention has been paid to hydrophobic interaction compared with hydrogen bonding and electrostatic interaction of NAs. However, hydrophobic interaction shows some unique properties, such as high tunability for application interest, minimal effect on NA functionality, and sensitivity to external stimuli. Therefore, the widespread use of hydrophobic interaction has promoted the evolution of NA-based biomaterials in higher-order self-assembly, drug/gene-delivery systems, and stimuli-responsive systems. Herein, the recent progress of NA-based biomaterials whose fabrications or properties are highly determined by hydrophobic interactions is summarized. 1) The hydrophobic interaction of NA itself comes from the accumulation of base-stacking forces, by which the NAs with certain base compositions and chain lengths show properties similar to thermal-responsive polymers. 2) In conjugation with hydrophobic molecules, NA amphiphiles show interesting self-assembly structures with unique properties in many new biosensing and therapeutic strategies. 3) The working-mechanisms of some NA-based complex materials are also dependent on hydrophobic interactions. Moreover, in recent attempts, NA amphiphiles have been applied in organizing macroscopic self-assembly of DNA origami and controlling the cell-cell interactions.