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Structural characterization of naturally occurring RNA single mismatches.

ABSTRACT: RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the most prevalent types of RNA secondary structure motifs are single mismatches, which occur when two canonical pairs are separated by a single non-canonical pair. To determine sequence-structure relationships and to identify structural patterns, we have systematically located, annotated and compared all available occurrences of the 30 most frequently occurring single mismatch-nearest neighbor sequence combinations found in experimentally determined 3D structures of RNA-containing molecules deposited into the Protein Data Bank. Hydrogen bonding, stacking and interaction of nucleotide edges for the mismatched and nearest neighbor base pairs are described and compared, allowing for the identification of several structural patterns. Such a database and comparison will allow researchers to gain insight into the structural features of unstudied sequences and to quickly look-up studied sequences.

SUBMITTER: Davis AR

PROVIDER: S-EPMC3035445 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature

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Structural characterization of naturally occurring RNA single mismatches.

Davis Amber R AR Kirkpatrick Charles C CC Znosko Brent M BM

Nucleic acids research 20100928 3

RNA is known to be involved in several cellular processes; however, it is only active when it is folded into its correct 3D conformation. The folding, bending and twisting of an RNA molecule is dependent upon the multitude of canonical and non-canonical secondary structure motifs. These motifs contribute to the structural complexity of RNA but also serve important integral biological functions, such as serving as recognition and binding sites for other biomolecules or small ligands. One of the m ...[more]

PMID: 20876693

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Project description:Collagen is the main structural element of connective tissues, and its favorable properties make it an ideal biomaterial for regenerative medicine. In dental medicine, collagen barrier membranes fabricated from naturally occurring tissues are used for guided bone regeneration. Since the morphological characteristics of collagen membranes play a crucial role in their mechanical properties and affect the cellular behavior at the defect site, in-depth knowledge of the structure is key. As a base for the development of novel collagen membranes, an extensive morphological analysis of four porcine membranes, including centrum tendineum, pericardium, plica venae cavae and small intestinal submucosa, was performed. Native membranes were analyzed in terms of their thickness. Second harmonic generation and two-photon excitation microscopy of the native membranes showed the 3D architecture of the collagen and elastic fibers, as well as a volumetric index of these two membrane components. The surface morphology, fiber arrangement, collagen fibril diameter and D-periodicity of decellularized membranes were investigated by scanning electron microscopy. All the membrane types showed significant differences in thickness. In general, undulating collagen fibers were arranged in stacked layers, which were parallel to the membrane surface. Multiphoton microscopy revealed a conspicuous superficial elastic fiber network, while the elastin content in deeper layers varied. The elastin/collagen volumetric index was very similar in the investigated membranes and indicated that the collagen content was clearly higher than the elastin content. The surface of both the pericardium and plica venae cavae and the cranial surface of the centrum tendineum revealed a smooth, tightly arranged and crumpled morphology. On the caudal face of the centrum tendineum, a compact collagen arrangement was interrupted by clusters of circular discontinuities. In contrast, both surfaces of the small intestinal submucosa were fibrous, fuzzy and irregular. All the membranes consisted of largely uniform fibrils displaying the characteristic D-banding. This study reveals similarities and relevant differences among the investigated porcine membranes, suggesting that each membrane represents a unique biomaterial suitable for specific applications.

Dataset Information

Structural characterization of naturally occurring RNA single mismatches.

Publications

Structural characterization of naturally occurring RNA single mismatches.

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