Noncoding RNAs database (ncRNAdb)

The noncoding RNA database (ncRNAdb) was created as a source of information on RNA molecules, which do not possess protein-coding capacity. It is now widely accepted that, in addition to constitutively expressed, housekeeping or infrastructural RNAs, there is a wide variety of RNAs participating in mechanisms involved in regulation of gene expression at all levels of transmission of genetic information from DNA to proteins. Noncoding RNAs' activities include chromatin structure remodeling, transcriptional and translational regulation of gene expression, modulation of protein function and regulation of subcellular distribution of RNAs as well as proteins. Noncoding transcripts have been identified in organisms belonging to all domains of life. Currently, the ncRNAdb contains >30 000 ncRNA sequences from Eukaryotes, Eubacteria and Archaea, but does not include housekeeping transcripts or microRNAs and snoRNAs for which more specialized databases are available. The contents of the database can be accessed via the WWW at

5SRNAdb: an information resource for 5S ribosomal RNAs

Ribosomal 5S RNA (5S rRNA) is the ubiquitous RNA component found in the large subunit of ribosomes in all known organisms. Due to its small size, abundance and evolutionary conservation 5S rRNA for many years now is used as a model molecule in studies on RNA structure, RNA–protein interactions and molecular phylogeny. 5SRNAdb (http://combio.pl/5srnadb/) is the first database that provides a high quality reference set of ribosomal 5S RNAs (5S rRNA) across three domains of life. Here, we give an overview of new developments in the database and associated web tools since 2002, including updates to database content, curation processes and user web interfaces

Crystallization and preliminary X-ray diffraction studies of intact EF-Tu from Thermus aquaticus YT-1

AbstractMany attempts have been made to elucidate the three-dimensional structure from elongation factor Tu, but so far the only crystals suitable for X-ray crystallography contained a partially degraded protein. Here, we report the crystallization of a fully active, intact EF-Tu from Thermus aquaticus. The crystals belong to hexagonal space group P6322 and diffract up to 2.6 Å. The cell dimensions are a = b = 178 Å, c = 238 Å and 6 molecules are contained per asymmetric unit

A calibrated diversity assay for nucleic acid libraries using DiStRO—a Diversity Standard of Random Oligonucleotides

We have determined diversities exceeding 1012 different sequences in an annealing and melting assay using synthetic randomized oligonucleotides as a standard. For such high diversities, the annealing kinetics differ from those observed for low diversities, favouring the remelting curve after annealing as the best indicator of complexity. Direct comparisons of nucleic acid pools obtained from an aptamer selection demonstrate that even highly complex populations can be evaluated by using DiStRO, without the need of complicated calculations

Probing the SELEX Process with Next-Generation Sequencing

Background SELEX is an iterative process in which highly diverse synthetic nucleic acid libraries are selected over many rounds to finally identify aptamers with desired properties. However, little is understood as how binders are enriched during the selection course. Next-generation sequencing offers the opportunity to open the black box and observe a large part of the population dynamics during the selection process. Methodology We have performed a semi-automated SELEX procedure on the model target streptavidin starting with a synthetic DNA oligonucleotide library and compared results obtained by the conventional analysis via cloning and Sanger sequencing with next-generation sequencing. In order to follow the population dynamics during the selection, pools from all selection rounds were barcoded and sequenced in parallel. Conclusions High affinity aptamers can be readily identified simply by copy number enrichment in the first selection rounds. Based on our results, we suggest a new selection scheme that avoids a high number of iterative selection rounds while reducing time, PCR bias, and artifacts

The crystal structure of an ‘All Locked’ nucleic acid duplex

‘Locked nucleic acids’ (LNAs) are known to introduce enhanced bio- and thermostability into natural nucleic acids rendering them powerful tools for diagnostic and therapeutic applications. We present the 1.9 Å X-ray structure of an ‘all LNA’ duplex containing exclusively modified β-d-2′-O-4′C-methylene ribofuranose nucleotides. The helix illustrates a new type of nucleic acid geometry that contributes to the understanding of the enhanced thermostability of LNA duplexes. A notable decrease of several local and overall helical parameters like twist, roll and propeller twist influence the structure of the LNA helix and result in a widening of the major groove, a decrease in helical winding and an enlarged helical pitch. A detailed structural comparison to the previously solved RNA crystal structure with the corresponding base pair sequence underlines the differences in conformation. The surrounding water network of the RNA and the LNA helix shows a similar hydration pattern

Search for pair-produced resonances decaying to jet pairs in proton-proton collisions at √s=8 TeV

Results are reported of a general search for pair production of heavy resonances decaying to pairs of hadronic jets in events with at least four jets. The study is based on up to 19.4 fb(-1) of integrated luminosity from proton-proton collisions at a center-of-mass energy of 8 TeV, recorded with the CMS detector at the LHC. Limits are determined on the production of scalar top quarks (top squarks) in the framework of R-parity violating supersymmetry and on the production of color-octet vector bosons (colorons). First limits at the LHC are placed on top squark production for two scenarios. The first assumes decay to a bottom quark and a light-flavor quark and is excluded for masses between 200 and 385 GeV, and the second assumes decay to a pair of light-flavor quarks and is excluded for masses between 200 and 350 GeV at 95% confidence level. Previous limits on colorons decaying to light-flavor quarks are extended to exclude masses from 200 to 835 GeV