Ribose 2‘-FLabeling:  A Simple Tool for the Characterization of RNA Secondary Structure Equilibria by19F NMR Spectroscopy

Abstract The RNA Characterization of Secondary Structure Motifs, RNA CoSSMos, database is a freely accessible online database that allows users to identify secondary structure motifs among RNA 3D structures and explore their structural features. RNA CoSSMos 2.0 now requires two closing base pairs for all RNA loop motifs to create a less redundant database of secondary structures. Furthermore, RNA CoSSMos 2.0 represents an upgraded database with new features that summarize search findings and aid in the search for 3D structural patterns among RNA secondary structure motifs. Previously, users were limited to viewing search results individually, with no built-in tools to compare search results. RNA CoSSMos 2.0 provides two new features, allowing users to summarize, analyze and compare their search result findings. A function has been added to the website that calculates the average and representative structures of the search results. Additionally, users can now view a summary page of their search results that reports percentages of each structural feature found, including sugar pucker, glycosidic linkage, hydrogen bonding patterns and stacking interactions. Other upgrades include a newly embedded NGL structural viewer, the option to download the clipped structure coordinates in *.pdb format and improved NMR structure results. RNA CoSSMos 2.0 is no longer simply a search engine for a structure database; it now has the capability of analyzing, comparing and summarizing search results. Database URL: http://rnacossmos.com

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Genetic characterization of the coxsackievirus B2 3′ untranslated region

Journal of General Virology ◽

10.1099/0022-1317-82-6-1339 ◽

2001 ◽

Vol 82 (6) ◽

pp. 1339-1348 ◽

Cited By ~ 2

Author(s):

Charlotta Polacek ◽

A. Michael Lindberg

Keyword(s):

Secondary Structure ◽

Rna Secondary Structure ◽

Untranslated Region ◽

Rna Synthesis ◽

Point Mutations ◽

Mutant Clone ◽

Wild Type ◽

Site Mutation ◽

Growth Properties

The secondary structure of the 3′ untranslated region (3′UTR) of picornaviruses is thought to be important for the initiation of negative-strand RNA synthesis. In this study, genetic and biological analyses of the 3′ terminus of coxsackievirus B2 (CVB2), which differs from other enteroviruses due to the presence of five additional nucleotides prior to the poly(A) tail, is reported. The importance of this extension was investigated using a 3′UTR mutant lacking the five nucleotides prior to the poly(A) tail and containing two point mutations. The predicted secondary structure within the 3′UTR of this mutant was less energetically favourable compared with that of the wild-type (wt) genotype. This mutant clone was transfected into green monkey kidney cells in four parallel experiments and propagated for multiple passages, enabling the virus to establish a stable revertant genotype. Genetic analysis of the virus progeny from these different passages revealed two major types of revertant. Both types showed wt-like growth properties and more stable and wt-like predicted secondary structures than the parent mutant clone. The first type of revertant neutralized the introduced point mutation with a compensatory second-site mutation, whereas the second type of revertant partly compensated for the deletion of the five proximal nucleotides by the insertion of nucleotides that matched the wt sequence. Therefore, the extended 3′ end of CVB2 may be considered to be a stabilizing sequence for RNA secondary structure and an important feature for the virus.

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19F NMR Spectroscopy for the Analysis of RNA Secondary Structure Populations

Journal of the American Chemical Society ◽

10.1021/ja806716s ◽

2008 ◽

Vol 130 (51) ◽

pp. 17230-17231 ◽

Cited By ~ 59

Author(s):

Dagmar Graber ◽

Holger Moroder ◽

Ronald Micura

Keyword(s):

Nmr Spectroscopy ◽

Secondary Structure ◽

Rna Secondary Structure ◽

19F Nmr ◽

19F Nmr Spectroscopy

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Characterization of Tamm-Horsfall Urinary Glycoprotein

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010007254x ◽

1973 ◽

Vol 31 ◽

pp. 420-421

Author(s):

John P. Robinson ◽

J. David Puett

Keyword(s):

Electron Microscopy ◽

Circular Dichroism ◽

Secondary Structure ◽

Quaternary Structure ◽

Normal Adult ◽

Morphological Properties ◽

Adult Males ◽

Circular Dichroïsm ◽

Urinary Glycoprotein

Much work has been reported on the chemical, physical and morphological properties of urinary Tamm-Horsfall glycoprotein (THG). Although it was once reported that cystic fibrotic (CF) individuals had a defective THG, more recent data indicate that THG and CF-THG are similar if not identical.No studies on the conformational aspects have been reported on this glycoprotein using circular dichroism (CD). We examined the secondary structure of THG and derivatives under various conditions and have correlated these results with quaternary structure using electron microscopy.THG was prepared from normal adult males and CF-THG from a 16-year old CF female by the method of Tamm and Horsfall. CF female by the method of Tamm and Horsfall.

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