Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity v1

protocols.io ◽  
2020 ◽  
Author(s):  
Pilar Menendez-Gil ◽  
Carlos J. Caballero ◽  
Cristina Solano ◽  
Alejandro Toledo-Arana
Keyword(s):  
Secondary Structures ◽  
Chaperone Activity ◽  
Molecular Beacons ◽  
Rna Chaperone ◽  
Rna Secondary Structures

scholarly journals Fluorescent Molecular Beacons Mimicking RNA Secondary Structures to Study RNA Chaperone Activity

2019 ◽  
pp. 41-58
Author(s):  
Pilar Menendez-Gil ◽  
Carlos J. Caballero ◽  
Cristina Solano ◽  
Alejandro Toledo-Arana
Keyword(s):  
Secondary Structures ◽  
Chaperone Activity ◽  
Molecular Beacons ◽  
Rna Chaperone ◽  
Rna Secondary Structures

scholarly journals Transcription Antitermination by Translation Initiation Factor IF1

2007 ◽  
Vol 189 (11) ◽  
pp. 4087-4093 ◽  
Author(s):  
Sangita Phadtare ◽  
Teymur Kazakov ◽  
Mikhail Bubunenko ◽  
Donald L. Court ◽  
Tatyana Pestova ◽  
...  
Keyword(s):  
Transcription Regulation ◽  
Translation Initiation ◽  
Cold Shock ◽  
Secondary Structures ◽  
Chaperone Activity ◽  
Translation Initiation Factor ◽  
Initiation Factor ◽  
Rna Chaperone ◽  
Transcription Antitermination ◽  
Ob Fold

ABSTRACT Bacterial translation initiation factor IF1 is an S1 domain protein that belongs to the oligomer binding (OB) fold proteins. Cold shock domain (CSD)-containing proteins such as CspA (the major cold shock protein of Escherichia coli) and its homologues also belong to the OB fold protein family. The striking structural similarity between IF1 and CspA homologues suggests a functional overlap between these proteins. Certain members of the CspA family of cold shock proteins act as nucleic acid chaperones: they melt secondary structures in nucleic acids and act as transcription antiterminators. This activity may help the cell to acclimatize to low temperatures, since cold-induced stabilization of secondary structures in nascent RNA can impede transcription elongation. Here we show that the E. coli translation initiation factor, IF1, also has RNA chaperone activity and acts as a transcription antiterminator in vivo and in vitro. We further show that the RNA chaperone activity of IF1, although critical for transcription antitermination, is not essential for its role in supporting cell growth, which presumably functions in translation. The results thus indicate that IF1 may participate in transcription regulation and that cross talk and/or functional overlap may exist between the Csp family proteins, known to be involved in transcription regulation at cold shock, and S1 domain proteins, known to function in translation.

scholarly journals Arginine methylation enhances the RNA chaperone activity of the West Nile virus host factor AUF1 p45

RNA ◽  
2016 ◽  
Vol 22 (10) ◽  
pp. 1574-1591 ◽  
Author(s):  
Susann Friedrich ◽  
Tobias Schmidt ◽  
Angelika Schierhorn ◽  
Hauke Lilie ◽  
Grit Szczepankiewicz ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Arginine Methylation ◽  
Host Factor ◽  
Chaperone Activity ◽  
The West ◽  
West Nile ◽  
Rna Chaperone

scholarly journals Mutually exclusive RNA secondary structures regulate translation initiation of DinQ in Escherichia coli

RNA ◽  
2016 ◽  
Vol 22 (11) ◽  
pp. 1739-1749 ◽  
Author(s):  
Knut I. Kristiansen ◽  
Ragnhild Weel-Sneve ◽  
James A. Booth ◽  
Magnar Bjørås
Keyword(s):  
Escherichia Coli ◽  
Translation Initiation ◽  
Secondary Structures ◽  
Rna Secondary Structures

Interval-Based Similarity for Classifying Conserved RNA Secondary Structures

2016 ◽  
Vol 31 (3) ◽  
pp. 78-85 ◽  
Author(s):  
Qingfeng Chen ◽  
Yi-Ping Phoebe Chen ◽  
Chengqi Zhang
Keyword(s):  
Secondary Structures ◽  
Rna Secondary Structures

scholarly journals Integration of Expressed Sequence Tag Data Flanking Predicted RNA Secondary Structures Facilitates Novel Non-Coding RNA Discovery

PLoS ONE ◽  
2011 ◽  
Vol 6 (6) ◽  
pp. e20561 ◽  
Author(s):  
Paul M. Krzyzanowski ◽  
Feodor D. Price ◽  
Enrique M. Muro ◽  
Michael A. Rudnicki ◽  
Miguel A. Andrade-Navarro
Keyword(s):  
Expressed Sequence Tag ◽  
Secondary Structures ◽  
Rna Secondary Structures ◽  
Non Coding Rna ◽  
Expressed Sequence

scholarly journals Memory efficient folding algorithms for circular RNA secondary structures

2006 ◽  
Vol 22 (10) ◽  
pp. 1172-1176 ◽  
Author(s):  
I. L. Hofacker ◽  
P. F. Stadler
Keyword(s):  
Secondary Structures ◽  
Circular Rna ◽  
Rna Secondary Structures ◽  
Memory Efficient

scholarly journals Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids

Biochimie ◽  
2011 ◽  
Vol 93 (11) ◽  
pp. 2019-2023 ◽  
Author(s):  
Sven Findeiß ◽  
Jan Engelhardt ◽  
Sonja J. Prohaska ◽  
Peter F. Stadler
Keyword(s):  
Secondary Structures ◽  
Protein Coding ◽  
Rna Secondary Structures ◽  
Coding Regions
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