Triplet Analysis That Identifies Unpaired Regions of Functional RNAs

We developed a novel method for analyzing RNA sequences, deemed triplet analysis, and applied the method in an in vitro RNA selection experiment in which HIV-1 Tat was the target. Aptamers are nucleic acids that bind a desired target (bait), and to date, many aptamers have been identified by in vitro selection from enough concentrated libraries in which many RNAs had an obvious consensus primary sequence after sufficient cycles of the selection. Therefore, the higher-order structural features of the aptamers that are indispensable for interaction with the bait must be determined by additional investigation of the aptamers. In contrast, our triplet analysis enabled us to extract important information on functional primary and secondary structure from minimally concentrated RNA libraries. As a result, by using our method, an important unpaired region that is similar to the bulge of TAR was readily predicted from a partially concentrated library in which no consensus sequence was revealed by a conventional sequence analysis. Moreover, our analysis method may be used to assess a variety of structural motifs with desired function

Building Movie Map -- A Tool for Exploring Areas in a City -- and its Evaluation

We propose a new Movie Map system, with an interface for exploring cities. The system consists of four stages; acquisition, analysis, management, and interaction. In the acquisition stage, omnidirectional videos are taken along streets in target areas. Frames of the video are localized on the map, intersections are detected, and videos are segmented. Turning views at intersections are subsequently generated. By connecting the video segments following the specified movement in an area, we can view the streets better. The interface allows for easy exploration of a target area, and it can show virtual billboards of stores in the view. We conducted user studies to compare our system to the GSV in a scenario where users could freely move and explore to find a landmark. The experiment showed that our system had a better user experience than GSV

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex

Growth of quantum three-dimensional structure of InGaAs emitting at ~1 µm applicable for a broadband near-infrared light source

We obtained a high-intensity and broadband emission centered at ~1 µm from InGaAs quantum three-dimensional (3D) structures grown on a GaAs substrate using molecular beam epitaxy. An InGaAs thin layer grown on GaAs with a thickness close to the critical layer thickness is normally affected by strain as a result of the lattice mismatch and introduced misfit dislocations. However, under certain growth conditions for the In concentration and growth temperature, the growth mode of the InGaAs layer can be transformed from two-dimensional to 3D growth. We found the optimal conditions to obtain a broadband emission from 3D structures with a high intensity and controlled center wavelength at ~1 µm. This method offers an alternative approach for fabricating a broadband near-infrared light source for telecommunication and medical imaging systems such as for optical coherence tomography

M-theory description of 1/4 BPS states in N=4 supersymmetric Yang-Mills theory

We discuss BPS states preserving 1/4 supersymmetries of N=4 supersymmetric Yang-Mills theory as M2-branes holomorphically embedded and ending on M5-branes. We use techniques in electrodynamics to find the M2-brane configurations, and give some explicit examples. In case the M2-brane worldsheet has handles, the worldsheet moduli of the M2-brane is constrained in a discrete manner. Several aspects of multi-pronged strings in type IIB string theory are beautifully reproduced in the M-theory description. We also discuss the relation between the above construction and the D2-brane dynamics in type IIA string theory.Comment: 16 pages, 4 Postscript figures, LaTe

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions