Solubilization of Single-walled Carbon Nanotubes with Single- stranded DNA Generated from Asymmetric PCR

Role of carbon nanotubes (CNTs) in transgenic plant development

Carbon nanotubes (CNTs) are nanostructures, allotropes of carbon which are made up of graphene sheets wrapped around it forming cylindrical structures. CNTs have been regarded to have interesting and attractive physical and chemical properties and have been tremendously used in genetic engineering. Understanding the role of CNTs in development of transgenic plants, review of research papers in the field was done. CNTs are classified into two categories: the single-walled and multiwalled (MWCNTs) structures. They are valuable vectors in various biomedicine fields such as Gene delivery, Drug delivery, Immunotherapy, Tissue engineering, and Biomedical imaging and also, they deliver the DNA without damaging the cells. Based on recent studies, the functionalization of CNTs when combined with some other suitable molecules can drastically subside their toxic effects. Having unique properties such as small size, larger surface area is useful in delivering DNA into mammalian cells as well. Modifications in CNTs can make nucleic acids adhere to them even more efficiently. Also, MWCNTs are crucial in delivery DNA into the cytoplasm. Based on other methods, the CNTs-DNA are a preferred choice and the inclination toward double-stranded DNA is used over single-stranded DNA in gene delivery shows effective results. The only downside of CNTs is that they are hydrophobic and are difficult to form an aqueous solution, thus limiting their applicability. This review will aid you in comprehending useful knowledge related to a general overview of topics related to CNTs.

Selection and colorimetric application of ssDNA aptamers against metamitron based on magnetic bead-SELEX

Metamitron (MTM) is a typical and widely used triazine herbicide in agricultural production. Its moderate toxicity and high residue in the environment have deleterious impacts on human health. The establishment of a rapid and efficient MTM detection method is of great significance. In this study, a magnetic-bead SELEX (systematic evolution of ligands by exponential enrichment) system was developed to select the MTM aptamers with high affinity and specificity. Through 10 rounds of screening, six candidate aptamers with the highest abundance were obtained by high-throughput sequencing. The homology, secondary structure, and affinity analyses were performed. The aptamer named MTM-6 was selected as the optimal aptamer with the dissociation constant (K_d) value of 16 nM. Then, a colorimetric detection method for MTM based on aptamer MTM-6 and the aggregation of gold nanoparticles (AuNPs) induced by NaCl was established with a linear range from 20 to 1000 nM (R = 0.9966) and a limit of detection (LOD) of 4.58 nM. The average recovery rate of MTM in the application of actual aqueous samples ranged from 95.40 to 107.83% with a relative standard deviation (RSD) from 1.11 to 3.48%. With considerable sensitivity and specificity, this colorimetric aptasensor is convenient and efficient, and shows bright application potential in MTM detection in aqueous samples.

Strategies for the preparation of non-amplified and amplified genomic dengue gene samples for electrochemical DNA biosensing applications

The application of electrochemical DNA biosensors in real genomic sample detection is challenging due to the existence of complex structures and low genomic concentrations, resulting in inconsistent and low current signals. This work highlights strategies for the treatment of non-amplified and amplified genomic dengue virus gene samples based on real samples before they can be used directly in our DNA electrochemical sensing system, using methylene blue (MB) as a redox indicator. The main steps in this study for preparing non-amplified cDNA were cDNA conversion, heat denaturation, and sonication. To prepare amplified cDNA dengue virus genomic samples using an RT-PCR approach, we optimized a few parameters, such as the annealing temperature, sonication time, and reverse to forward (R/F) primer concentration ratio. We discovered that the generated methylene blue (MB) signals during the electrochemical sensing of non-amplified and amplified samples differ due to the different MB binding affinities based on the sequence length and base composition. The findings show that our developed electrochemical DNA biosensor successfully discriminates MB current signals in the presence and absence of the target genomic dengue virus, indicating that both samples were successfully treated. This work also provides interesting information about the critical factors in the preparation of genomic gene samples for developing miniaturized PCR-based electrochemical sensing applications in the future. We also discuss the limitations and provide suggestions related to using redox-indicator-based electrochemical biosensors to detect real genomic nucleic acid genes.

Carbon Nanomaterials in Biological Studies and Biomedicine

The "carbon nano-world" has made over the past few decades huge contributions in diverse scientific disciplines and technological advances. While dramatic advances have been widely publicized in using carbon nanomaterials such as fullerenes, carbon nanotubes, and graphene in materials sciences, nano-electronics, and photonics, their contributions to biology and biomedicine have been noteworthy as well. This Review focuses on the use of carbon nanotubes (CNTs), graphene, and carbon quantum dots [encompassing graphene quantum dots (GQDs) and carbon dots (C-dots)] in biologically oriented materials and applications. Examples of these remarkable nanomaterials in bio-sensing, cell- and tissue-imaging, regenerative medicine, and other applications are presented and discussed, emphasizing the significance of their unique properties and their future potential.

The dispersion, solubilization and stabilization in “solution” of single-walled carbon nanotubes

Methods for the solubilization and dispersion of single-walled carbon nanotubes in water and organic solvents by physical and chemical methods have been reviewed.

Preparing long probes by an asymmetric polymerase chain reaction-based approach for multiplex ligation-dependent probe amplification

To clearly discriminate the results of simultaneous screening and quantification of up to 40 different targets-DNA sequences, long probes from 100 to 500 nt, rather than smaller or similar-sized synthetic ones, were adopted for multiplex ligation-dependent probe amplification (MLPA). To prepare the long probes, asymmetric polymerase chain reaction (PCR) was employed to introduce non-complementary stuffers in between the two parts of the MLPA probe with specially designed primers, then restriction enzymes were selected to digest the double-stranded DNAs, and finally polyacrylamide gel electrophoresis was used to purify the single-stranded DNAs (i.e., the long probes). By using this approach, 12 long probes were prepared and used to identify genetically modified (GM) maize. Our experimental results show that the prepared long probes were in full accordance with the designed ones and could be assembled in 4-, 7-, and 10-plex MLPA analysis without losing result specificity and accuracy, showing they were as effective and reliable in MLPA analysis as those prepared with M13-derived vectors. This novel asymmetric PCR-based approach does not need expensive equipment, special reagents, or complicated operations when compared with previous methods. Therefore, our new approach could make MLPA analysis more independent, efficient, and economical.

Optimisation of an asymmetric polymerase chain reaction assay for the amplification of single-stranded DNA from Wuchereria bancrofti for electrochemical detection

Single-stranded DNA (ssDNA) is a prerequisite for electrochemical sensor-based detection of parasite DNA and other diagnostic applications. To achieve this detection, an asymmetric polymerase chain reaction method was optimised. This method facilitates amplification of ssDNA from the human lymphatic filarial parasite Wuchereria bancrofti. This procedure produced ssDNA fragments of 188 bp in a single step when primer pairs (forward and reverse) were used at a 100:1 molar ratio in the presence of double-stranded template DNA. The ssDNA thus produced was suitable for immobilisation as probe onto the surface of an Indium tin oxide electrode and hybridisation in a system for sequence-specific electrochemical detection of W. bancrofti. The hybridisation of the ssDNA probe and target ssDNA led to considerable decreases in both the anodic and the cathodic currents of the system's redox couple compared with the unhybridised DNA and could be detected via cyclic voltammetry. This method is reproducible and avoids many of the difficulties encountered by conventional methods of filarial parasite DNA detection; thus, it has potential in xenomonitoring.

Selective binding of single-stranded DNA-binding proteins onto DNA molecules adsorbed on single-walled carbon nanotubes

Single-stranded DNA-binding (SSB) proteins were treated with hybrids of DNA and single-walled carbon nanotubes (SWNTs) to examine the biological function of the DNA molecules adsorbed on the SWNT surface. When single-stranded DNA (ssDNA) was used for the hybridization, significant binding of the SSB molecules to the ssDNA-SWNT hybrids was observed by using atomic force microscopy (AFM) and agarose gel electrophoresis. When double-stranded DNA (dsDNA) was used, the SSB molecules did not bind to the dsDNA-SWNT hybrids in most of the conditions that we evaluated. A specifically modified electrophoresis procedure was used to monitor the locations of the DNA, SSB, and SWNT molecules. Our results clearly showed that ssDNA/dsDNA molecules on the SWNT surfaces retained their single-stranded/double-stranded structures.

Recent development of nano-materials used in DNA biosensors

As knowledge of the structure and function of nucleic acid molecules has increased, sequence-specific DNA detection has gained increased importance. DNA biosensors based on nucleic acid hybridization have been actively developed because of their specificity, speed, portability, and low cost. Recently, there has been considerable interest in using nano-materials for DNA biosensors. Because of their high surface-to-volume ratios and excellent biological compatibilities, nano-materials could be used to increase the amount of DNA immobilization; moreover, DNA bound to nano-materials can maintain its biological activity. Alternatively, signal amplification by labeling a targeted analyte with nano-materials has also been reported for DNA biosensors in many papers. This review summarizes the applications of various nano-materials for DNA biosensors during past five years. We found that nano-materials of small sizes were advantageous as substrates for DNA attachment or as labels for signal amplification; and use of two or more types of nano-materials in the biosensors could improve their overall quality and to overcome the deficiencies of the individual nano-components. Most current DNA biosensors require the use of polymerase chain reaction (PCR) in their protocols. However, further development of nano-materials with smaller size and/or with improved biological and chemical properties would substantially enhance the accuracy, selectivity and sensitivity of DNA biosensors. Thus, DNA biosensors without PCR amplification may become a reality in the foreseeable future.

Recent Updates of DNA Incorporated in Carbon Nanotubes and Nanoparticles for Electrochemical Sensors and Biosensors

Innovations in the field of electrochemical sensors and biosensors are of much importance nowadays. These devices are designed with probes and micro electrodes. The miniaturized designs of these sensors allow analyses of materials without damaging the samples. Some of these sensors are also useful for real time analysis within the host system, so these sensors are considered to be more advantageous than other types of sensors. The active sensing materials used in these types of sensors can be any material that acts as a catalyst for the oxidation or reduction of particular analyte or set of analytes. Among various kinds of sensing materials, deoxyribonucleic acid (DNA), carbon nanotubes (CNTs) and nanoparticles have received considerable attraction in recent years. DNA is one of the classes of natural polymers, which can interact with CNTs and nanoparticles to form new types of composite materials. These composite materials have also been used as sensing materials for sensor applications. They have advantages in characteristics such as extraordinary low weight and multifunctional properties. In this article, advantages of DNA incorporated in CNT and nanoparticle hybrids for electrochemical sensors and biosensors are presented in detail, along with some key results noted from the literature.