Papers by Keyword: DNA

Abstract: A SiCNWFET device serving as a biosensor was designed and simulated using Silvaco ATLAS device simulation software. The performance of the designed device in charges sensing was investigated. The device shows the ability to recognize different interface charge values ranging from-1.10E11 to-5.10E12 cm^-2 applied on the surface of the silicon carbide nanowire channel to simulate target charge biomolecules that bound to the biosensor. A significant change in the output current is observed due to the presence of different values of fixed interface charge densities. An optimum, according to the TCAD simulation, the 4H-SiC epitaxial structure has been grown. The designed device was fully fabricated on this structure and it exhibited acceptable electrical characteristics.

Abstract: This paper considers a novel approach for integration between molecular engineering of XNA-based structures and additive manufacturing of XNA-based devices based on multiparametric characterization of XNAs by different functional descriptors (such as physical properties of XNA-based materials and precursors of XNA-based molecular devices) and the possibility of thermal or electron-beam processing as a prerequisite of the industrial technical process development for such device implementation. This can be performed in the framework of additive manufacturing by connecting the output of the XNA synthesizer or nucleic acid synthesizer with 3D-printer nozzles in such a way that oligos / AGCTX products are supported into the nozzles separately.

Abstract: The Density Functional Theory method was employed to investigate the electronic structure and muonium hyperfine interaction of muonium trapped near carbon atom labelled as '5' in cytosine nucleobase. Eighteen different basis sets in combination with B3LYP functional were examined in geometry optimization calculations on the muoniated radical. There are significant quantitative differences in the calculated total energy. The employment of basis set that does not include polarization function produces an optimized structure with high total energy. The 6-311++G(d,p) basis set yielded the lowest total energy as compared to other basis sets. The bond order of muonium trapped at C5 atom is in the range of 0.841 to 0.862. The 6-31G basis set produced the muonium Fermi contact coupling constant that is the closest to the experimental value.

Abstract: In this study, measurement conditions of Capillary gel electrophoresis (CGE) were optimized in order to increase the separation accuracy for small DNA fragments. We adopted a 20-bp DNA Ladder including 13 small double-stranded fragments (20, 40, 60, 80, 100, 120, 140, 160, 180, 200, 300, 400, and 500-bp). The applied voltage and sieving polymer concentration were assessed because these two factors significantly affect the separation accuracy of DNA fragments. As a result, we succeeded in optimizing CGE separation conditions for small DNA fragments with a sufficient degree of accuracy.

Abstract: Abstract: In order to investigate the structure and electrical conductivity of (DNA), Scanning Tunnelling Microscopy (STM) studies were carried out on a model of DNA which was composed of a 12-mer single-stranded polyadenine connected via sugar-phosphate backbone. The 12-mer single-stranded polyadenine molecules were found to be aligned in parallel to each other at a separation 25±7.5 Å. This alignment formed a one-dimensional chain structure, which indicated that the side-by-side coupling among the molecules was strong. The STM measurements with constant current mode and fixed bias voltage, demonstrate that, the electrical conductivity of DNA bases could be deduced by monitoring the size of the structure of 12-mer single-stranded polyadenine.

Abstract: The DFT cluster method was employed to investigate the electronic structures and muonium hyperfine interactions in guanine nucleobase and nucleotide using three different basis sets. The total energy and Fermi contact values were calculated for muon trapped at carbon '8'. The three basis sets, 6-31G, 6-311G and 6-311G(d,p), were used in tandem with the B3LYP functional. There are significant quantitative differences in the calculated total energy. 6-311G(d,p) produced the lowest total energy as compared to the other basis sets. The lowering of the total energy is due to the increase in the number of basis functions to describe the atomic orbitals, which is consistent with the postulate on basis set completeness. The 6-31G basis set produced the muon Fermi contact value that is the closest to the experimental value. The calculated Fermi contact values for the nucleobase and nucleotide are significantly lowered in going from the double-zeta to the triple-zeta basis set by 5% and 4% respectively. The lowering of the Fermi contact value can be attributed to the extension of the triple-zeta basis set in describing the valence atomic orbitals. The presence of the sugar phosphate group in the nucleotide instead of the methyl group tends to lower the Fermi contact value. Thus, the sugar phosphate group should be taken into consideration when designing a calculation model.

Abstract: The reliability and specificity of the Pap smear rely on the eyewitness to perceive and an assortment of cell variations in clinically obtained cervical specimens. The improvement in early diagnosis to distinguish Human Papillomavirus (HPV) infection has been an issue. ELISA has been intended to analyze the immune response against HPV, and they can be utilized to distinguish the phase of the infection. The objective of this study to characterize the performance of In Vitro Nucleic Acid Hybridization with a correlation with Liquid-Based Cytology and HPV DNA Genotyping Test to assess its use as the potential for the identification of high-risk HPV in cervical clinical specimens. Hybridization utilizing an in vitro nucleic acid DNA-based ELISA method was performed with an improved chemiluminescent for the qualitative and semi-quantitative identification of high-risk HPV in cervical specimens. For analyzing the reliability to identify HPV DNA in cervical Pap smear, we studied the effectiveness of FDA-approved Hybrid Capture II (HCII) utilizing cervical swapping from 20 patient clinical specimens. Two scrapes-outs were positive for the occurrence of HPV. Only specimens displayed positive with HCII test were further confirmed by HPV Genotyping Test. Specimen 2 and 13 were positive for one of the 13 high-risk types in HCII test. Specimen 2 was confirmed by HPV genotyping test as a positive high-risk HPV type 58.

Abstract: The fast and direct detection of small quantities of biological and chemical species is of key importance for numerous biomedical applications. Extensive research has been conducted on nanoelectronic devices that can perform such detection with high sensitivity using silicon nanowires and nanostructures. However, it was recently demonstrated that Si material suffers a lack of long-term stability in physiological environments at nanometer scale [1,2], and is hence not suited for in situ sensing of biological molecules. The results presented here are two important steps toward the realization of core-shell Si-SiC NWFETs for the detection of biomolecules in liquid media. First, we show that SiC NWs exhibit higher chemical stability than Si NWs under physiological conditions. Second, we present the successful carburation of a thin film of Si resulting in a 3.6 nm thin SiC layer.

Abstract: Applications of computer and information technology are indispensable in various fields especially in the field of biology. The use of computer aided tools plays a key role in solving biological problems. The spontaneous process of molecular docking is important for finding potentially strong candidate of drug for various viruses. The binding of protein receptors with ligand molecules is essential in drug discovery process. The aim of molecular docking tools is to predict the interaction between protein and ligand. This review outlines the major tools for protein - ligand docking which in turn emphasize the importance of molecular docking in modern drug discovery process.

Abstract: Use of DNA molecules in molecular electronics is very promising. Close relationship between the charge transfer and conformational changes follows from experiment. For the theoretical descriptions of conformational transitions of DNA molecule the kink-like solutions of the modified sine-Gordon equation are mostly used. Our investigations show that the motion of the kink can be controlled by the external exposure.