Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine

Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology

Synthesis of 2′-O-methyl-RNAs incorporating a 3-deazaguanine, and UV melting and computational studies on its hybridization properties

2′-O-Methyl-RNAs incorporating 3-deazaguanine (c(3)G) were synthesized by use of N,N-diphenylcarbamoyl and N,N-dimethylaminomethylene as its base protecting groups to suppress sheared-type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairing which requires the N(3) atom. These modified RNAs hybridized more weakly with the complementary and single mismatch-containing RNAs than the unmodified RNAs. The T(m) experiments were performed to clarify the effects of replacement of the fifth G with c(3)G on stabilization of 2′-O-methyl-(5′-CGGCGAGGAG-3′)/5′-CUCCGAGCCG-3′ and 2′-O-methyl-(5′-CGGGGACGAG-3′)/5′-CUCGGACCCG-3′duplexes, which form sheared-type and face-to-face type 5′-GA-3′/5′-GA-3′ tandem mismatched base pairs, respectively. Consequently, this replacement led to more pronounced destabilization of the former duplex that needs the N(3) atom for the sheared-type base pair than the latter that does not need it for the face-to-face type base pair. A similar tendency was observed for 2′-O-methyl-RNA/DNA duplexes. These results suggest that the N(3) atom of G plays an important role in stabilization of the canonical G/C base pair as well as the base discrimination and its loss suppressed formation of the undesired sheared-type mismatched base pair. Computational studies based on ab initio calculations suggest that the weaker hydrogen bonding ability and larger dipole moment of c(3)G can be the origin of the lower T(m)

A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2′-O-methyl RNA/RNA heteroduplexes

Modified nucleotides are useful tools to study the structures, biological functions and chemical and thermodynamic stabilities of nucleic acids. Derivatives of 2,6-diaminopurine riboside (D) are one type of modified nucleotide. The presence of an additional amino group at position 2 relative to adenine results in formation of a third hydrogen bond when interacting with uridine. New method for chemical synthesis of protected 3′-O-phosphoramidite of LNA-2,6-diaminopurine riboside is described. The derivatives of 2′-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides were used to prepare complete 2′-O-methyl RNA and LNA-2′-O-methyl RNA chimeric oligonucleotides to pair with RNA oligonucleotides. Thermodynamic stabilities of these duplexes demonstrated that replacement of a single internal 2′-O-methyladenosine with 2′-O-methyl-2,6-diaminopurine riboside (DM) or LNA-2,6-diaminopurine riboside (DL) increases the thermodynamic stability (ΔΔG°37) on average by 0.9 and 2.3 kcal/mol, respectively. Moreover, the results fit a nearest neighbor model for predicting duplex stability at 37°C. D-A and D-G but not D-C mismatches formed by DM or DL generally destabilize 2′-O-methyl RNA/RNA and LNA-2′-O-methyl RNA/RNA duplexes relative to the same type of mismatches formed by 2′-O-methyladenosine and LNA-adenosine, respectively. The enhanced thermodynamic stability of fully complementary duplexes and decreased thermodynamic stability of some mismatched duplexes are useful for many RNA studies, including those involving microarrays

tRNA structural and functional changes induced by oxidative stress

Oxidatively damaged biomolecules impair cellular functions and contribute to the pathology of a variety of diseases. RNA is also attacked by reactive oxygen species, and oxidized RNA is increasingly recognized as an important contributor to neurodegenerative complications in humans. Recently, evidence has accumulated supporting the notion that tRNA is involved in cellular responses to various stress conditions. This review focuses on the intriguing consequences of oxidative modification of tRNA at the structural and functional level

Application of Cascade Forward Backpropagation Neural Networks for Selecting Mining Methods

Decision-making is very important in many fields, such as mining engineering. In addition, there has been a growth of computer applications in all fields, especially mining operations. One of these application fields is mine design and the selection of suitable mining methods, and computer applications can help mine engineers to decide upon and choose more satisfactory methods. The selection of mining methods depends on the rock-layer specification. All rock characteristics should be classified in terms of technical and economic concerns related to mining rock specifications, such as mechanical and physical properties, and evaluated according to their weights and ratings. Methodologically, in this study, the criteria considered in the University of British Columbia (UBC) method were used as references to establish general criteria. These criteria consist of general shape, ore thickness, ore plunge, and grade distribution, in addition to the rock quality designation (ore zone, hanging wall, and foot wall) and rock substance strength (ore zone, hanging wall, and foot wall). The technique for order of preference by similarity to ideal solution (TOPSIS) was adopted, and an improved TOPSIS method was developed based on experimental testing and checked by means of the application of cascade forward backpropagation neural networks in mining method selection. The results provide indicators that decision makers can use to choose between different mining methods based on the total points given to all ore properties. The best mining method is cut and fill stopping, with a rank of 0.70, and the second is top slicing, with a rank of 0.67

Evaluation of autogenous tooth transplantation for replacement of the missing or unrestorable mandibular molar tooth

This study was undertaken to evaluate the functional and occlusal stability of autogenous tooth transplantation. A total of 30 patients were included. Among them, 21 participants received transplanted first molar and the remaining 9 received transplanted second molar. In all the cases, donor tooth were third molar. In each participant, extraction of un-restorable first or second molar tooth was performed which was then replaced by atrumatic extracted third molar tooth. Each third molar tooth was placed in the recipient extracted socket, followed by the evaluation of the occlusion and then stabilized with arch bar and ligature wire. Clinical follow-up evaluation was performed at 15 days, 3 and 12 months in respect to occlusal stability, tooth mobility and periodontal status. It was found that 23 transplanted tooth were successful and the remaining 7 tooth need long-term observation for the final outcome, which was statistically significant. It can be concluded that the autogenous tooth transplantation can replace missing tooth to ensure the preservation of function, aesthetic and to prevent bone resorption of the missing area of the jaw, which can lead to exceptional esthetic and functional outcome