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Journal of Biochemistry 2006 139(3):431-438; doi:10.1093/jb/mvj045
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© 2006 The Japanese Biochemical Society.

Regular Paper

Evaluation of the Dynamic Structure of DsrA RNA from E. coli and Its Functional Consequences

Katarzyna Rolle*, Marek Zywicki*, Eliza Wyszko, Miroslawa Z. Barciszewska and Jan Barciszewski{dagger}

Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland

{dagger} To whom correspondence should be addressed. Tel: +48-61-8528 503 (Ext. 132), Fax: +48-61-8520 532, E-mail: Jan.Barciszewski{at}ibch.poznan.pl

DsrA RNA is an 87-nucleotide regulatory non-protein-coding RNA of Escherichia coli for which two secondary structure models (I and II) have been proposed. We have compared these models by the energy calculations, which revealed that the currently accepted model II should be rejected on the basis of thermodynamics. Here we provide new results of nuclease footprinting analysis and the application of RNA technologies that have not previously been used for DsrA RNA structural studies, such as hydrolysis with RNase H, DNAzyme, hydroxyl radicals and lead. These approaches together with bioinformatics calculations provided strong arguments for a new model III. This model clearly shows that the long U-rich region between hairpins 1 and 2 is double-stranded. These findings shed new light on DsrA RNA—Hfq interactions.

* Authors contributed equally to the work.


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