271 research outputs found
Prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations
Ab initio RNA secondary structure predictions have long dismissed helices
interior to loops, so-called pseudoknots, despite their structural importance.
Here, we report that many pseudoknots can be predicted through long time scales
RNA folding simulations, which follow the stochastic closing and opening of
individual RNA helices. The numerical efficacy of these stochastic simulations
relies on an O(n^2) clustering algorithm which computes time averages over a
continously updated set of n reference structures. Applying this exact
stochastic clustering approach, we typically obtain a 5- to 100-fold simulation
speed-up for RNA sequences up to 400 bases, while the effective acceleration
can be as high as 100,000-fold for short multistable molecules (<150 bases). We
performed extensive folding statistics on random and natural RNA sequences, and
found that pseudoknots are unevenly distributed amongst RNAstructures and
account for up to 30% of base pairs in G+C rich RNA sequences (Online RNA
folding kinetics server including pseudoknots : http://kinefold.u-strasbg.fr/
).Comment: 6 pages, 5 figure
Stem-loop structures can effectively substitute for an RNA pseudoknot in-1 ribosomal frameshifting
Biophysical Structural ChemistrySupramolecular & Biomaterials Chemistr
Structural parameters affecting the kinetics of RNA hairpin formation
There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program ‘Kinfold’. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem–loop structures
Protonation of non-Watson-Crick base pairs and encapsidation of turnip yellow mosaic virus RNA
Border skirmishes and the question of belonging: An authoethnographic account of everyday exclusion in multicultural society
Transnational migration has transformed most European countries, making the problem of how to 'integrate' an increasingly popular topic in public debates and social policy. It is assumed that as long as the newcomer learns the language, adapts to the local customs and finds work, s/he will be integrated and welcomed with open arms as a full-fledged member of society. Based on an autoethnography of our experiences as US-born, long-term and fully 'integrated' residents of the Netherlands, one of Europe's most multicultural societies, we have explored some of the subtle, well-intentioned practices of distancing and exclusion that are part of the fabric of everyday life. We will show how, contrary to the official discourse of integration, 'Dutch-ness' as a white/ethnic national identity is continuously constructed as a 'we', which excludes all 'others'. And, indeed, we have discovered that, paradoxically, the closer the 'other' comes to being completely assimilated into Dutch society, the more the symbolic borders of national belonging may need to be policed and tightened. © The Author(s) 2011
Functional analysis of the SRV-1 RNA frameshifting pseudoknot
Simian retrovirus type-1 uses programmed ribosomal frameshifting to control expression of the Gag-Pol polyprotein from overlapping gag and pol open-reading frames. The frameshifting signal consists of a heptanucleotide slippery sequence and a downstream-located 12-base pair pseudoknot. The solution structure of this pseudoknot, previously solved by NMR [Michiels,P.J., Versleijen,A.A., Verlaan,P.W., Pleij,C.W., Hilbers,C.W. and Heus,H.A. (2001) Solution structure of the pseudoknot of SRV-1 RNA, involved in ribosomal frameshifting. J. Mol. Biol., 310, 1109–1123] has a classical H-type fold and forms an extended triple helix by interactions between loop 2 and the minor groove of stem 1 involving base–base and base–sugar contacts. A mutational analysis was performed to test the functional importance of the triple helix for −1 frameshifting in vitro. Changing bases in L2 or base pairs in S1 involved in a base triple resulted in a 2- to 5-fold decrease in frameshifting efficiency. Alterations in the length of L2 had adverse effects on frameshifting. The in vitro effects were well reproduced in vivo, although the effect of enlarging L2 was more dramatic in vivo. The putative role of refolding kinetics of frameshifter pseudoknots is discussed. Overall, the data emphasize the role of the triple helix in −1 frameshifting
Abstracts of presentations on plant protection issues at the xth international congress of virology: August 11-16,1996 Binyanei haOoma, Jerusalem, Israel Part 2 Plenary Lectures
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