The "ribose zipper", an important element of RNA tertiary structure, is characterized by consecutive hydrogen-bonding interactions between ribose 2 0 -hydroxyls from different regions of an RNA chain or between RNA chains. These tertiary contacts have previously been observed to also involve base -backbone and base -base interactions (A-minor type). We searched for ribose zipper tertiary interactions in the crystal structures of the large ribosomal subunit RNAs of Haloarcula marismortui and Deinococcus radiodurans, and the small ribosomal subunit RNA of Thermus thermophilus and identified a total of 97 ribose zippers. Of these, 20 were found in T. thermophilus 16 S rRNA, 44 in H. marismortui 23 S rRNA (plus 2 bridging 5 S and 23 S rRNAs) and 30 in D. radiodurans 23 S rRNA (plus 1 bridging 5 S and 23 S rRNAs). These were analyzed in terms of sequence conservation, structural conservation and stability, location in secondary structure, and phylogenetic conservation.Eleven types of ribose zippers were defined based on ribose -base interactions. Of these 11, seven were observed in the ribosomal RNAs. The most common of these is the canonical ribose zipper, originally observed in the P4 -P6 group I intron fragment. All ribose zippers were formed by antiparallel chain interactions and only a single example extended beyond two residues, forming an overlapping ribose zipper of three consecutive residues near the small subunit A-site. Almost all ribose zippers link stem (Watson-Crick duplex) or stem-like (base-paired), with loop (external, internal, or junction) chain segments. About two-thirds of the observed ribose zippers interact with ribosomal proteins. Most of these ribosomal proteins bridge the ribose zipper chain segments with basic amino acid residues hydrogen bonding to the RNA backbone. Proteins involved in crucial ribosome function and in early stages of ribosomal assembly also stabilize ribose zipper interactions.All ribose zippers show strong sequence conservation both within these three ribosomal RNA structures and in a large database of aligned prokaryotic sequences. The physical basis of the sequence conservation is stacked base triples formed between consecutive base-pairs on the stem or stem-like segment with bases (often adenines) from the loop-side segment. These triples have previously been characterized as Type I and Type II A-minor motifs and are stabilized by base -base and base -ribose hydrogen bonds.The sequence and structure conservation of ribose zippers can be directly used in tertiary structure prediction and may have applications in molecular modeling and design.

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SCOR, the Structural Classification of RNA (http://scor.lbl.gov), is a database designed to provide a comprehensive perspective and understanding of RNA motif three-dimensional structure, function, tertiary interactions and their relationships. SCOR 2.0 represents a major expansion and introduces a new classification organization. The new version represents the classification as a Directed Acyclic Graph (DAG), which allows a classification node to have multiple parents, in contrast to the strictly hierarchical classification used in SCOR 1.2. SCOR 2.0 supports three types of query terms in the updated search engine: PDB or NDB identifier, nucleotide sequence and keyword. We also provide parseable XML files for all information. This new release contains 511 RNA entries from the PDB as of 15 May 2003. A total of 5880 secondary structural elements are classified: 2104 hairpin loops and 3776 internal loops. RNA motifs reported in the literature, such as 'Kink turn' and 'GNRA loops', are now incorporated into the structural classification along with definitions and descriptions.

These data provide novel insights into the nature of dandruff and the therapeutic action of potentiated ZPT-containing shampoo, and provide a basis to explore many new mechanistic questions related to these topics.

Supramolecular light-harvesting antenna systems were constructed by using polyrotaxanes, in which cyclodextrin (CD) rings of alpha-CD and naphthalene (energy donor)-appended alpha-CD are threaded by a poly(ethylene glycol) chain with anthracene (energy acceptor) units at both ends (5-8). The effects of the component ratio of the polyrotaxanes on the efficiencies of energy migration and energy transfer were examined by fluorescence emission and excitation spectra and anisotropy and by fluorescence decay measurements. The observed results were explained by using the Forster mechanism.

Motivation: Microbial phenotypes are typically due to the concerted action of multiple gene functions, yet the presence of each gene may have only a weak correlation with the observed phenotype. Hence, it may be more appropriate to examine co-occurrence between sets of genes and a phenotype (multiple-to-one) instead of pairwise relations between a single gene and the phenotype. Here, we propose an efficient class association rule mining algorithm, netCAR, in order to extract sets of COGs (clusters of orthologous groups of proteins) associated with a phenotype from COG phylogenetic profiles and a phenotype profile. netCAR takes into account the phylogenetic co-occurrence graph between COGs to restrict hypothesis space, and uses mutual information to evaluate the biconditional relation.Results: We examined the mining capability of pairwise and multiple-to-one association by using netCAR to extract COGs relevant to six microbial phenotypes (aerobic, anaerobic, facultative, endospore, motility and Gram negative) from 11 969 unique COG profiles across 155 prokaryotic organisms. With the same level of false discovery rate, multiple-to-one association can extract about 10 times more relevant COGs than one-to-one association. We also reveal various topologies of association networks among COGs (modules) from extracted multiple-to-one correlation rules relevant with the six phenotypes; including a well-connected network for motility, a star-shaped network for aerobic and intermediate topologies for the other phenotypes. netCAR outperforms a standard CAR mining algorithm, CARapriori, while requiring several orders of magnitude less computational time for extracting 3-COG sets.Availability: Source code of the Java implementation is available as Supplementary Material at the Bioinformatics online website, or upon request to the author.Contact: makio323@gmail.comSupplementary information: Supplementary data are available at Bioinformatics online.

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A rotaxane with a naphthalene-modified α-cyclodextrin penetrated by a dansyl-terminal poly(ethylene glycol) was prepared. In the rotaxane, singlet energy transfer occurs from the naphthalene moiety to the terminal dansyl units.