Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes

scientific article published on 15 August 2011

Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes is …
instance of (P31):
scholarly articleQ13442814

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P356DOI10.1021/BI200463P
P932PMC publication ID3312101
P698PubMed publication ID21793590
P5875ResearchGate publication ID51525271

P50authorElzbieta KierzekQ89947142
Ryszard KierzekQ58902417
P2093author name stringAgata Fratczak
P2860cites workThe Escherichia coli OxyS regulatory RNA represses fhlA translation by blocking ribosome bindingQ24533360
Identification of the Hfq-binding site on DsrA RNA: Hfq binds without altering DsrA secondary structureQ24540168
Hfq is necessary for regulation by the untranslated RNA DsrAQ24548921
The small RNA, DsrA, is essential for the low temperature expression of RpoS during exponential growth in Escherichia coliQ24562141
Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structureQ24562398
A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coliQ24563821
Regulatory RNAs in bacteriaQ24595082
Accurate SHAPE-directed RNA structure determinationQ24646758
A trans-acting RNA as a control switch in Escherichia coli: DsrA modulates function by forming alternative structuresQ24652762
The influence of locked nucleic acid residues on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexesQ24812616
Structure of the 70S ribosome complexed with mRNA and tRNAQ27860602
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structureQ27860806
The Sm-like Hfq protein increases OxyS RNA interaction with target mRNAsQ28216159
Enzymatic approaches to probing of RNA secondary and tertiary structureQ69127615
fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complexQ74027600
The rpoS mRNA leader recruits Hfq to facilitate annealing with DsrA sRNAQ28288672
Escherichia coli Hfq has distinct interaction surfaces for DsrA, rpoS and poly(A) RNAsQ28292183
Cycling of the Sm-like protein Hfq on the DsrA small regulatory RNAQ28294752
Evaluation of the dynamic structure of DsrA RNA from E. coli and its functional consequencesQ28304057
Escherichia coli Hfq binds A18 and DsrA domain II with similar 2:1 Hfq6/RNA stoichiometry using different surface sitesQ28306489
On finding all suboptimal foldings of an RNA moleculeQ29547627
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE): quantitative RNA structure analysis at single nucleotide resolutionQ29617336
The small RNA regulators of Escherichia coli: roles and mechanisms*Q29618536
Hfq: a bacterial Sm-like protein that mediates RNA-RNA interactionQ29619904
Preparation of DNA and protein micro arrays on glass slides coated with an agarose filmQ30882912
An upstream Hfq binding site in the fhlA mRNA leader region facilitates the OxyS-fhlA interactionQ33712153
The OxyS regulatory RNA represses rpoS translation and binds the Hfq (HF-I) proteinQ33889724
Positive regulation by small RNAs and the role of HfqQ34006620
Hfq, a new chaperoning role: binding to messenger RNA determines access for small RNA regulatorQ34107548
An expanding universe of noncoding RNAsQ34129019
How to find small non-coding RNAs in bacteriaQ34473835
Isoenergetic penta- and hexanucleotide microarray probing and chemical mapping provide a secondary structure model for an RNA element orchestrating R2 retrotransposon protein functionQ34588002
Identification of small RNAs in diverse bacterial speciesQ34611996
Antisense technologies. Improvement through novel chemical modificationsQ35106663
RNA structure: experimental analysisQ36833147
High-throughput SHAPE and hydroxyl radical analysis of RNA structure and ribonucleoprotein assemblyQ36960961
Probing the structure of RNAs in solutionQ38181797
Isoenergetic microarray mapping--the advantages of this method in studying the structure of Saccharomyces cerevisiae tRNAPheQ38287625
Isoenergetic microarray mapping reveals differences in structure between tRNAiMet and tRNAmMet from Lupinus luteusQ38287629
Facilitating RNA structure prediction with microarraysQ38316976
Binding of short oligonucleotides to RNA: studies of the binding of common RNA structural motifs to isoenergetic microarraysQ38349573
Secondary structures for 5' regions of R2 retrotransposon RNAs reveal a novel conserved pseudoknot and regions that evolve under different constraintsQ38354666
Probing RNA structure with chemical reagents and enzymesQ42007408
A chemical synthesis of LNA-2,6-diaminopurine riboside, and the influence of 2'-O-methyl-2,6-diaminopurine and LNA-2,6-diaminopurine ribosides on the thermodynamic properties of 2'-O-methyl RNA/RNA heteroduplexesQ42547349
Nearest neighbor parameters for Watson-Crick complementary heteroduplexes formed between 2'-O-methyl RNA and RNA oligonucleotidesQ42589910
Bacterial proteins required for replication of phage Q ribonucleic acid. Pruification and properties of host factor I, a ribonucleic acid-binding proteinQ44199523
The thermodynamics of 3'-terminal pyrene and guanosine for the design of isoenergetic 2'-O-methyl-RNA-LNA chimeric oligonucleotide probes of RNA structureQ46821903
A small, stable RNA induced by oxidative stress: role as a pleiotropic regulator and antimutatorQ48047346
A periodic table of symmetric tandem mismatches in RNA.Q52347120
LNA-modified primers drastically improve hybridization to target RNA and reverse transcription.Q54411555
P4510describes a project that usesImageQuantQ112270642
P433issue35
P407language of work or nameEnglishQ1860
P1104number of pages19
P304page(s)7647-7665
P577publication date2011-08-15
P1433published inBiochemistryQ764876
P1476titleIsoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes
P478volume50

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cites work (P2860)
Q35815859A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation
Q37346798C-terminal domain of the RNA chaperone Hfq drives sRNA competition and release of target RNA.
Q34740470Identifying and characterizing Hfq-RNA interactions
Q34883490Microarrays for identifying binding sites and probing structure of RNAs
Q34070147Secondary structure of a conserved domain in an intron of influenza A M1 mRNA
Q28536401Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA
Q64123599Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides
Q28553150Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus
Q47767055The important conformational plasticity of DsrA sRNA for adapting multiple target regulation

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