title: Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes.
abstract: Information on the secondary structure and interactions of RNA is important to understand the biological function of RNA as well as in applying RNA as a tool for therapeutic purposes. Recently, the isoenergetic microarray mapping method was developed to improve the prediction of RNA secondary structure. Herein, for the first time, isoenergetic microarrays were used to study the binding of RNA to protein or other RNAs as well as the interactions of two different RNAs and protein in a three-component complex. The RNAs used as models were the regulatory DsrA and OxyS RNAs from Escherichia coli, the fragments of their target mRNAs (fhlA and rpoS), and their complexes with Hfq protein. The collected results showed the advantages and some limitations of microarray mapping.
authors.affiliation: Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland.
authors.forename: Agata
authors.initials: A
authors.lastname: Fratczak
authors.forename: Ryszard
authors.initials: R
authors.lastname: Kierzek
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Kierzek
mesh_terms: D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D001483:Base Sequence; D004734:Energy Metabolism / Q000235:genetics; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D008969:Molecular Sequence Data; D040081:Protein Array Analysis / Q000379:methods*; D011485:Protein Binding / Q000235:genetics; D025941:Protein Interaction Mapping / Q000379:methods / Q000639:trends; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D058727:RNA, Small Untranslated
chemical_list: D001425:Bacterial Outer Membrane Proteins; D029968:Escherichia coli Proteins; D012329:RNA, Bacterial; D012097:Repressor Proteins; C499660:DrsA protein, E coli; C499686:oxyS small RNA, E coli; D058727:RNA, Small Untranslated