Single-stranded Deoxyribonucleic Acid Research Articles

In vitro selection of human cerebrospinal fluid-specific aptamers using clinical samples.

Cerebrospinal fluid (CSF) leaks may occur due to numerous etiologies and are associated with severe morbidity. Currently in the U.S., confirming the presence of a CSF leak requires protein electrophoresis testing, oftentimes involving specialized processing, and there exists no point-of-care (POC) device for CSF detection. We aimed to discover a single-stranded deoxyribonucleic acid (ssDNA) aptamer capable of selectively binding to CSF-specific biomarkers, with the future goal of developing an aptamer-based POC CSF detection device. To identify a candidate aptamer, we performed Systematic Evolution of Ligands by EXponential enrichment (SELEX) using a DNA library containing a randomized 63-nucleotide (nt) stretch flanked by 2 primer-binding sites. Quantitative polymerase chain reaction (qPCR) and fluorescence anisotropy (FA) assessed aptamer binding affinity and kinetics. Following 14 SELEX cycles, 2 dominant and functionally viable 98-nt ssDNA sequences (C2 and C3) were found. C2 and C3 demonstrated ~586x and ~82x higher affinity for CSF compared to serum, respectively. Increases in FA upon aptamer exposure to higher CSF concentrations demonstrated a K1⁄2 of 5.0% and 14.1% for C2 and C3, respectively. In vitro selection of a diverse pool of ssDNA sequences yielded 2 aptamers with high selectivity for CSF-specific biomarkers, with potential for integration into a rapid POC electrochemical diagnostic system.

Chaos-driven seven-core optical transmission scheme based on DNA full information chained analog-transcription

This paper proposes a chaos-driven seven-core optical transmission scheme based on DNA full information chained analog-transcription. Unlike traditional deoxyribonucleic acid (DNA) coded encryption schemes in the bit dimension, this scheme uses chaotic sequences to generate perturbed bit streams corresponding to the initial bit stream. These two sets of bit streams are encoded from a set of DNA double-stranded sequences, which are then intertwined into a single-stranded DNA containing all the information through the full-information class transcription algorithm proposed in this paper. Finally, the DNA decoding process is driven by a set of sequences derived from another chaotic model to transform the DNA sequence containing all information back into a bit sequence for subsequent transmission. Additional chaotic sequences interfere with the subcarriers, symbols, and constellation angles. Moreover, to maintain spectral efficiency, hiding the key in the frame header allows for the dynamic simultaneous transmission of signal and key. The transmission of encrypted 16 quadrature amplitude modulation-orthogonal chirp division multiplexing (16QAM-OCDM) signals is experimentally demonstrated at a net bit rate of 51.72 Gb/s over 2 km weakly coupled seven-core fiber. At the receiving end, the correct key decoder is able to accurately recover the data, while the bit error ratio (BER) at the illegal receiving end is 0.5. Finally, quantitative experiments validate the receiver-side decryption algorithm, showing that the proposed encryption scheme achieves a large key space of 10397. The key can be fully decoded when the optical power is above -20dBm. This scheme significantly enhances the security and flexibility of the communication system, making it a promising candidate for future optical communication physical layer encryption.

Nature of TiO2–oligonucleotides interactions by atomistic molecular dynamics simulations

We used molecular dynamics simulations to investigate the adsorption behavior of single-stranded deoxyribonucleic acid (ssDNA) segments on the anatase (101) surface. Four different ssDNA oligonucleotides, each consisting of six/twelve adenine (A6 and A12), six guanine (G6), six cytosine (C6) or six/twelve thymine (T6 and T12) nucleobases, were considered. We observed that the initial interaction between the ssDNA and the surface occurs primarily through hydrogen bonding between the nucleobases and the surface, followed by strong chemical bonding between the terminal phosphate group and the anatase surface. The interactions between the nucleobases and the surface varied between the different ssDNA segments. Adenine showed the highest affinity for the surface, whereas thymine showed the lowest affinity. In addition, the purine bases interact more strongly when the surface is negatively charged (as it would be at physiological pH) than in neutral surface (slightly acidic conditions), in agreement with experimental data from fluorescence experiments and ATR-FTIR spectroscopy. Moreover, our study provides mechanistic insights into the dynamic behavior of ssDNA on the anatase surface and comparative analyses on how different conditions (pH, fragment length, composition, etc.) affect DNA/TiO2 interactions. Therefore, we expect that experimental scientists will benefit from our work in the design of optimal nanoconjugates for their specific final goals and applications.

Monolithic DNApatite: An Elastic Apatite with Sub-Nanometer Scale Organo-Inorganic Structures.

Hydroxyapatite (HA) exhibits outstanding biocompatibility, bioactivity, osteoconductivity, and natural anti-inflammatory properties. Pure HA, ion-doped HA, and HA-polymer composites are investigated, butcritical limitations such as brittleness remain; numerous efforts are being made to address them. Herein, the novel self-crystallization of a polymeric single-stranded deoxyribonucleic acid (ssDNA) without additional phosphate ions for synthesizing deoxyribonucleic apatite (DNApatite) is presented. The synthesized DNApatite, DNA1Ca2.2(PO4)1.3OH2.1, has a repetitive dual phase of inorganic HA crystals and amorphous organic ssDNA at the sub-nm scale, forming nanorods. Its mechanical properties, including toughness and elasticity, are significantly enhanced compared with those of HA nanorod, with a Young's modulus similar to that of natural bone.

Manganese carbonate superparticles as DNA- and pH-responsive magnetic resonance imaging contrast agents

Manganese carbonate nanoparticles (NPs) have been developed as pH-triggered responsive magnetic resonance imaging (MRI) contrast agents for tumor diagnosis, but the signal amplification of MRI is still limited due to the lack of response to other pathological parameters of tumors. Here, random single-stranded deoxyribonucleic acid (ssDNA) was explored as a biomimetic template to prepare manganese carbonate superparticles (MnCO3 SPs) assembled from ultrasmall particles. We focused on the degradation ability of DNA-MnCO3 SPs triggered by DNA and its trigger mechanism. The results show that different sequences of DNA could trigger the disassembly of these DNA-MnCO3 SPs and result in MR signal amplification. Further investigations show the DNA-MnCO3 SPs possess good physiological stability, but increased degradation sensitivity under dual triggering of DNA and low pH. In vivo MR and FL dual-modal imaging for tumor region display T1-signal rapid amplification, suggesting rapid responsiveness of DNA-MnCO3 SPs to DNA. Therefore, the design of DNA- and pH-triggered DNA-MnCO3 SPs may provide a new idea for the construction of next-generation activatable contrast agents with high specificity and high sensitivity.

18F]F-Poly(ADP-Ribose) Polymerase Inhibitor Radiotracers for Imaging PARP Expression and Their Potential Clinical Applications in Oncology.

Including poly(ADP-ribose) polymerase (PARP) inhibitors in managing patients with inoperable tumors has significantly improved outcomes. The PARP inhibitors hamper single-strand deoxyribonucleic acid (DNA) repair by trapping poly(ADP-ribose)polymerase (PARP) at sites of DNA damage, forming a non-functional "PARP enzyme-inhibitor complex" leading to cell cytotoxicity. The effect is more pronounced in the presence of PARP upregulation and homologous recombination (HR) deficiencies such as breast cancer-associated gene (BRCA1/2). Hence, identifying HR-deficiencies by genomic analysis-for instance, BRCA1/2 used in triple-negative breast cancer-should be a part of the selection process for PARP inhibitor therapy. Published data suggest BRCA1/2 germline mutations do not consistently predict favorable responses to PARP inhibitors, suggesting that other factors beyond tumor mutation status may be at play. A variety of factors, including tumor heterogeneity in PARP expression and intrinsic and/or acquired resistance to PARP inhibitors, may be contributing factors. This justifies the use of an additional tool for appropriate patient selection, which is noninvasive, and capable of assessing whole-body in vivo PARP expression and evaluating PARP inhibitor pharmacokinetics as complementary to the currently available BRCA1/2 analysis. In this review, we discuss [18F]Fluorine PARP inhibitor radiotracers and their potential in the imaging of PARP expression and PARP inhibitor pharmacokinetics. To provide context we also briefly discuss possible causes of PARP inhibitor resistance or ineffectiveness. The discussion focuses on TNBC, which is a tumor type where PARP inhibitors are used as part of the standard-of-care treatment strategy.

Purification of DNA Nanoparticles Using Photocleavable Biotin Tethers.

The number of applications of self-assembled deoxyribonucleic acid (DNA) origami nanoparticles (DNA NPs) has increased drastically, following the development of a variety of single-stranded template DNA (ssDNA) that can serve as the scaffold strand. In addition to viral genomes, such as M13 bacteriophage and lambda DNAs, enzymatically produced ssDNA from various template sources is rapidly gaining traction and being applied as the scaffold for DNA NP preparation. However, separating fully formed DNA NPs that have custom scaffolds from crude assembly mixes is often a multistep process of first separating the ssDNA scaffold from its enzymatic amplification process and then isolating the assembled DNA NPs from excess precursor strands. Only then is the DNA NP sample ready for downstream characterization and application. In this work, we highlight a single-step purification of custom sequence- or M13-derived scaffold-based DNA NPs using photocleavable biotin tethers. The process only requires an inexpensive ultraviolet (UV) lamp, and DNA NPs with up to 90% yield and high purity are obtained. We show the versatility of the process in separating two multihelix bundle structures and a wireframe polyhedral architecture.

Detection of intracellular microRNA-21 for cancer diagnosis by a nanosystem containing a ZnO@polydopamine and DNAzyme probe.

MicroRNAs (miRNAs) are a series of single-stranded non-coding ribonucleic acid (RNA) molecules which associated closely with various human diseases. Efficient strategies for detecting miRNAs are of great significance to cancer diagnosis and prognosis. Here we provide a novel nanosystem that can be applied for the detection of miRNAs. The nanosystem consists of a single-stranded deoxyribonucleic acid (DNA) probe and a probe carrier. The DNA probe was designed based on a deoxyribozyme (DNAzyme) with several necessary functional sequences and two fluorescent dyes labeled at proper sites. The ZnO@polydopamine (ZnO@PDA) nanomaterial serves not only as a probe carrier, but also as a supplier of Zn2+ that can activate the DNAzyme. The DNA probe will undergo a conformation alteration induced by miRNA-21, which then trigger the DNAzyme catalyzed self-cleavage reaction with the assist of Zn2+ provided by ZnO decomposition under weak acid environment. A change of fluorescent color will occur due to the interruption of fluorescence resonance energy transfer between the two fluorescent dyes, and the dissociated miRNA-21 can repeatedly induce the above responses to amplify the fluorescence signal. The feasibility of the whole procedure was demonstrated by various experiments. This nanosystem showed a good selectivity towards miRNA-21, and under the optimal incubation time of 2 hours, a good linear relationship was obtained in a concentration range of 0.01-2.0 nM with a detection limit of 3.8 pM. In in vivo detection, an obvious fluorescence color change from red to green can be observed in the presence of miRNA-21. The results proved that this miRNA detection strategy has a broad application prospect in tumor diagnosis and miRNA related biological studies.

Recent advances in DNA nanomaterials for cancer diagnosis and treatment

Abstract The elucidation of the structural characteristics of deoxyribonucleic acid (DNA) by Watson and Crick, the advent of polymerase chain reaction technology, and the development of primer-synthesis methods, enable DNA to be replicated and transformed in an increasingly easy manner, such that it is among the most directed and evolving nanomaterials in molecular biology. Traditional cancer diagnosis methods are somewhat limited and are unable to meet existing needs; consequently, DNA nanostructures with wide ranging properties are receiving increasingly more attention because a number of DNA materials have been shown to exhibit diagnostic properties. Some DNA materials can functionally alter the biological behavior of cells, such as cell migration, cell proliferation, cell differentiation, autophagy, and anti-inflammatory effects. Some single-stranded DNA or ribonucleic acid with secondary structure through self-pairing, called aptamer, systematic evolution of ligands by exponential enrichment (SELEX), have targeting capabilities and can be applied to tumor targeted diagnosis and therapy. Several DNA nanomaterials with three-dimensional nanostructures and stable structures are being investigated as drug carrier systems to act on a variety of antitumor drugs or gene therapy agents. This article reviews the use of functionalized DNA nanostructures in cancer diagnosis and treatment applications. Various biosensors and carriers based on DNA nanostructures are introduced and chemical reactions related to the preparation of the carrier and the signal transduction mechanism of the sensor are discussed. Efficient carrier/biosensor platforms based on various structural developments and current DNA nanomaterial developments are also presented.

Fabrication of Ag nanoparticles coated leonardite basalt ceramic membrane with improved antimicrobial properties for DNA cleavage, E. coli removal and antibiofilm effects

This study aimed to fabricate a novel, low-cost, and environmental-friendly ceramic membrane based on basalt and leonardite powders via press and sintering methods. The fabricated leonardite basalt ceramic membrane (LBCM) was coated with silver nanoparticles (AgNPs); to create an antibacterial surface. The capabilities of the bare and coated membranes were examined. In this context, water permeability reached 554 ± 2.61 and 447 ± 1.21 L/m2hbar for bare LBCM and AgNPs-coated LBCM, respectively. The fabricated membranes indicated 100% Escherichia coli (E. coli) removal efficiency at a transmembrane pressure of 0.5 bar. The solid surface antimicrobial activity of the LBCM and AgNPs-coated LBCM reached 26.38% and 100%, respectively. The LBCM and AgNPs-coated LBCM were analyzed for the in-vitro 2,2- diphenyl-1-picrylhydrazyl (DPPH) antioxidant. Accordingly, AgNPs-coated LBCM exhibited higher antioxidant activities than raw LBCM. The scavenging capacity reached 83.91% with AgNPs-coated LBCM, while only 58.95% was achieved with raw LBCM, indicating that AgNPs-coated LBCM was better than bare LBCM from an antioxidant activities perspective. AgNPs-coated LBCM had a deoxyribonucleic acid (DNA) cleavage activity (single-strand DNA cleavage activity at 50 mg/L and double-strand DNA cleavage activity at 100 and 200 mg/L). In contrast, the raw LBCM did not exhibit DNA cleavage activity at any concentration. AgNPs-coated LBCM showed higher antimicrobial activities (minimum inhibition concentrations (MICs) were 32 mg/L against Enterococcus faecalis (E. faecalis) and 64 mg/L against Staphylococcus aureus (S. aureus), Candida tropicalis (C. tropicalis), and Enterococcus hirae (E. hirae)). The biofilm inhibition of LBCM and AgNPs-coated LBCM powders was tested against S. aureus and Pseudomonas aeruginosa (P. aeruginosa). The maximum S. aureus inhabitations by LBCM and AgNP-coated LBCM were 60.34% and 99.12%, respectively. The inhabitation of P. aeruginosa increased from 52.38% before coating to 96.37% at the end of the coating process. Regarding E.coli microbial cell viability inhibition, LBCM powders and AgNPs-coated LBCM powders were found to inhibit E. coli growth by 68.35% and 100%, respectively.

Evolutionary mechanisms of virus variability

ABSTRACT. The evolutionary changes of viruses are primarily associated with the replication processes of viruses containing deoxyribonucleic and ribonucleic acids, which differ significantly. The genomes of most viruses containing ribonucleic acid are replicated with much less accuracy compared to the genomes of viruses containing deoxyribonucleic acid. Comparing the number of mutations in an infected cell reflects an inverse relationship between genome size and the frequency of mutations carried out by these two categories of viruses. Viruses with double-stranded deoxyribonucleic acid genomes have a low mutation rate compared to single-stranded genomes. The genome of viruses is not a stable unique structure, but rather an average, variable number of different amino acid sequences. It is in the virus population that a high mutation rate is maintained, and low variability is not beneficial for the preservation of viruses in nature. Some animal species may be intermediate hosts when new epidemic viruses appear. The introduction of non-viral nucleic acid into the viral genome can also contribute to the evolutionary changes of the virus, lead to the formation of defective genomes or to the emergence of hypervirulent strains. Viral genomes encode numerous molecules that modulate a wide range of protective immune mechanisms. The variability of viruses is also facilitated by the simultaneous integration of several proviral genomes into one cell, which activates the processes of recombination and genetic shift. An important evolutionary point may be the conversion of ribonucleic acid ribose into deoxyribose of deoxyribonucleic acid, which increases the stability of nucleic acids by more than 100 times. Horizontal gene transfer between viruses that infect different hosts is a central feature of the evolution of viruses containing ribonucleic acid. Eukaryote viruses with single-stranded deoxyribonucleic acid probably evolved from bacterial plasmids after they acquired capsid protein genes from the (+) ribonucleic acid chain of viruses. In addition to megaviruses and adenoviruses, polintons are likely precursors to bidnaviruses and virophages.

Efficient Electrocatalytic Nitrate Reduction to Ammonia Based on DNA-Templated Copper Nanoclusters

In alkaline solutions, the electrocatalytic conversion of nitrates to ammonia (NH3) (NO3RR) is hindered by the sluggish hydrogenation step due to the lack of protons on the electrode surface, making it a grand challenge to synthesize NH3 at a high rate and selectivity. Herein, single-stranded deoxyribonucleic acid (ssDNA)-templated copper nanoclusters (CuNCs) were synthesized for the electrocatalytic production of NH3. Because ssDNA was involved in the optimization of the interfacial water distribution and H-bond network connectivity, the water-electrolysis-induced proton generation was enhanced on the electrode surface, which facilitated the NO3RR kinetics. The activation energy (Ea) and in situ spectroscopy studies adequately demonstrated that the NO3RR was exothermic until NH3 desorption, indicating that, in alkaline media, the NO3RR catalyzed by ssDNA-templated CuNCs followed the same reaction path as the NO3RR in acidic media. Electrocatalytic tests further verified the efficiency of ssDNA-templated CuNCs, which achieved a high NH3 yield rate of 2.62 mg h-1 cm-2 and a Faraday efficiency of 96.8% at -0.6 V vs reversible hydrogen electrode. The results of this study lay the foundation for engineering catalyst surface ligands for the electrocatalytic NO3RR.

Study of reaction-diffusion controlled mass transport in stopped-flow fluidics for spatiotemporal multiplexing

Integration of biochemical reaction networks (BRNs) with biosensor platforms has emerged as a technological niche overcoming challenges related to the loss of sensitivity and selectivity in biological media. Optimal operation of BRNs in microfluidics requires control over reaction-diffusion dominated mass transport, heavily influenced by fluidic parameters. In this work, we study and design an on-chip platform combining a programable unique molecular amplification as BRNs with nanoscale biologically sensitive field-effect transistor (BioFET) arrays, which employs a physical diffusion barrier to gain spatial and temporal control over mass transport. Computational and numerical approaches, such as finite element and finite volume methods, were implemented to solve partial differential equations numerically after domain approximation by numerous finite elements. The focus on geometrical optimizations of fluidics is aimed at mass transport to occur with precise spatial and temporal control toward BioFET-arrays. Adopting a 0.5 pM limit-of-detection (LoD) for biochemical monitoring of BRNs via a single-stranded deoxyribonucleic acid (ssDNA) output, we show that it was possible to compartmentalize the mass transport spatiotemporally without crosstalk, which can be of critical advantage for using biosensor arrays in order to realize simplified multiplexed point-of-care biosensors.

Lateral flow biosensor based on LAMP-CRISPR/Cas12a for sensitive and visualized detection of Salmonella spp.

Salmonella is a major pathogen that causes serious foodborne diseases in humans and poses a serious threat to food safety and public health worldwide. Its rapid and accurate diagnosis is essential to prevent bacterial contamination of food. This study aimed to develop a lateral flow biosensor (LFB) based on loop-mediated isothermal amplification (LAMP)-clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 12a (Cas12a) that is affordable and can aid in visually detecting Salmonella in a food sample. False positives were prevented by synthesizing CRISPR ribonucleic acid (crRNA) with a selected 21-base pair protospacer that did not overlap with the used LAMP primers. A single-stranded deoxyribonucleic acid (DNA) probe labeled with biotin and 6-Carboxyfluorescein (6-FAM) was used for designing the LFB. The duration of these processes was as follows: DNA extraction (20 min), LAMP (60 min), Cas12a cleavage (5 min), and LFB (5 min). The detection limit was 1.22 × 10° CFU/mL in pure culture. The validity of the LAMP-CRISPR/Cas12a based LFB was verified by detecting Salmonella in onions, melon, and salami. Consequently, the developed LAMP-CRISPR/Cas12a based LFB assay show the potential for rapid on-site detection of Salmonella with high specificity, sensitivity, convenience, mobility, low cost, and affordability. • LFB based on LAMP-CRISPR/Cas12a was developed for detection of Salmonella. • The developed method demonstrated suitability for naked-eye detection of Salmonella. • The detection can be completed within 100 min for on-site detection.

The Role of TRL7/8 Agonists in Cancer Therapy, with Special Emphasis on Hematologic Malignancies.

Toll-like receptors (TLR) belong to the pattern recognition receptors (PRR). TLR7 and the closely correlated TLR8 affiliate with toll-like receptors family, are located in endosomes. They recognize single-stranded ribonucleic acid (RNA) molecules and synthetic deoxyribonucleic acid (DNA)/RNA analogs-oligoribonucleotides. TLRs are primarily expressed in hematopoietic cells. There is compiling evidence implying that TLRs also direct the formation of blood cellular components and make a contribution to the pathogenesis of certain hematopoietic malignancies. The latest research shows a positive effect of therapy with TRL agonists on the course of hemato-oncological diseases. Ligands impact activation of antigen-presenting cells which results in production of cytokines, transfer of mentioned cells to the lymphoid tissue and co-stimulatory surface molecules expression required for T-cell activation. Toll-like receptor agonists have already been used in oncology especially in the treatment of dermatological neoplastic lesions. The usage of these substances in the treatment of solid tumors is being investigated. The present review discusses the direct and indirect influence that TLR7/8 agonists, such as imiquimod, imidazoquinolines and resiquimod have on neoplastic cells and their promising role as adjuvants in anticancer vaccines.

Studies on the application of single-stranded DNA and PNA probes for electrochemical detection of miRNA 141

The abnormal concentration of microRNAs (miRNAs) can be associated with occurrence of various diseases including cancer, cardiovascular and neurodegenerative, hence they can be considered as potential biomarkers. An attractive approach could be the application of electrochemical methods, particularly where hybridization event between single-stranded deoxyribonucleic acid (ssDNA) or peptide-nucleic acid (PNA) with miRNA strand happens. Recently, the use of various nanomaterials such as gold nanoparticles, graphene oxide, quantum dots as well as catalyzed hairpin assembly or hybridization chain reaction were proposed to further enhance the performance of elaborated sensors.Herein, we present the studies on selection of receptor layer composition for detection of miRNA 141. The possibility of formation of receptor layer and further duplex monolayer between ssDNA or PNA with miRNA was analyzed by atomic force microscopy (AFM) technique. The interaction of ssDNA and PNA probes with miRNA was further verified using surface plasmon resonance (SPR) and quartz – crystal microbalance (QCM) techniques. On the basis of impedance spectroscopy it was shown that the use of unlabelled ssDNA as receptor layer provided 0.1 pM detection limit. This shows that proposed biosensor that is simple in preparation and use is an attractive alternative to other recently presented approaches.

Review on the Selection of Aptamers and Application in Paper-Based Sensors.

An aptamer is a synthetic oligonucleotide, referring to a single-stranded deoxyribonucleic acid or ribonucleic acid ligand produced by synthesis from outside the body using systematic evolution of ligands by exponential enrichment (SELEX) technology. Owing to their special screening process and adjustable tertiary structures, aptamers can bind to multiple targets (small molecules, proteins, and even whole cells) with high specificity and affinity. Moreover, due to their simple preparation and stable modification, they have been widely used to construct biosensors for target detection. The paper-based sensor is a product with a low price, short detection time, simple operation, and other superior characteristics, and is widely used as a rapid detection method. This review mainly focuses on the screening methods of aptamers, paper-based devices, and applicable sensing strategies. Furthermore, the design of the aptamer-based lateral flow assay (LFA), which underlies the most promising devices for commercialization, is emphasized. In addition, the development prospects and potential applications of paper-based biosensors using aptamers as recognition molecules are also discussed.

An ultra-sensitive electrochemical aptasensor based on Co-MOF/ZIF-8 nano-thin-film by the in-situ electrochemical synthesis for simultaneous detection of multiple biomarkers of breast cancer

This work developed a new electrochemical aptasensor based on the functional hybrid film for simultaneous single step detection of human epidermal growth factor receptor-2 (HER2) and estrogen receptor (ER) biomarkers. The platform is achieved by in-situ electrochemical synthesis of Zn-MOF (ZIF-8) thin film with the conductivity, the specific surface area, and the easy assembly of 2D Co-MOF nanosheets which can adsorbed the amount of aptamer chains on indium tin oxide (ITO) slices. The aptamers were labeled by adsorption of two organic dyes – neutral red (NB) and methylene blue (MB) through electrostatic action, respectively. In the presence of HER2/ER biomarkers, the aptamers of ER/HER2 will combine with ER/HER2 biomarkers to generate new complexes which will far away from the ITO surface due to the specific coupling between MB/NB-labeled single-stranded deoxyribonucleic acid (ssDNA) aptamer and HER2/ER biomarkers is stronger than the aptamer adhered to the Co-MOF/ZIF-8 film on ITO through intermolecular interaction, electrostatic interaction, and π-π stacking. Therefore, it can sensitive single step detection of HER2-ER biomarkers in only 60 min with the detection range are 0 to 15 pg/mL and detection limits as low as 3.8 fg/mL and 6.8 fg/mL, respectively.

In vitro and in silico binding studies of phytochemical isochroman with calf thymus DNA using multi-spectroscopic and computational modelling techniques

A wide range of therapeutic molecules uses deoxyribonucleic acid (DNA) as an intracellular target. The interaction of small molecules to DNA is a key feature in pharmacology and plays a vital role in the development of novel and more efficient drugs with increased selective activity and enhanced therapeutic effectiveness. Isochroman (IC) is a constituent of Olea europea plant, which has been shown to exhibit several beneficial pharmacological activities. At present, its interaction studies using calf thymus DNA (ct-DNA) have not been explained. A set of multi-spectroscopic techniques has been performed to determine the interaction mechanism of isochroman with ct-DNA. Absorption spectra and quenching in fluorescence studies show that isochroman and ct-DNA form a complex. The static mode of quenching was determined by the Stern-Volmer plot. The value of binding constant, Kb = 4.0 × 103 M−1 revealed moderate type of binding. Effects of single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) and ionic strength were studied to examine the isochroman binding to ct-DNA. Potassium iodide (KI) quenching effects and competitive binding studies clearly showed that isochroman binds in the minor groove of ct-DNA. Circular dichroic and DNA melting experiments also confirmed these results. The experimental outputs were further corroborated via in silico computational modelling studies. Lipinski’s rule of 5 and SwissADME showed drug-likeness and oral bioavailability scores. Protox ІІ online software predicts oral and organ toxicity. Communicated by Ramaswamy H. Sarma

Nanopore Probes Using Hydrogel-Filled Nanopipettes as Sensors for Chemical Imaging

Scanning ion conductance microscopy (SICM) using biological nanopores is a powerful analytical tool that can provide spatially resolved topography and chemical information. However, the low spatial resolution caused by the large tip diameter of the probe has limited the practical application of the SICM system. Although the tip-dip method has conventionally been used to form a lipid bilayer at the tip of pipettes, an alternative method to form the lipid bilayer is required because the lifetime of lipid bilayers formed by the tip-dip method is too short to map chemical information by stochastic nanopore sensing. Here, we propose a method to prepare lipid bilayers using a hydrogel-filled nanopipette. The lipid bilayer is formed at the tip of the pipette by inserting the pipette into a layered solution of an oil/lipid mixture and an aqueous electrolyte. Since the hydrogel supports the lipid bilayer, the lifetime of the lipid bilayers prepared by this method is improved over that formed by the tip-dip method. Furthermore, the hydrogel at the pore aperture reduces the translocation speed of analytes through nanopores, indicating that the hydrogel-filled nanopipette system can offer highly sensitive chemical sensing. Finally, we measure local single-strand deoxyribonucleic acid concentrations in the concentration gradient generated by a microhole using the biological nanopore probe. We believe that the SICM system using the hydrogel-filled nanopipette-based biological nanopore probe will offer a powerful analytical system for biological phenomena, including cell communication and signal transduction.