Thermodynamic aspects of the self - assembly of DsrA, a small noncoding RNA from Escherichia coli

• Autorzy: Genguenaud F. , Gesson M. , Arluison V.
• Języki publikacji: EN

Abstrakty

EN

DsrA is an Escherichia coli small noncoding RNA that acts by base pairing to some mRNAs in order to control their translation and turnover. It was recently shown that DsrA is able to self-associate in a way similar to DNA and to build nanostructures. Although functional consequence of this RNA self-assembly in vivo is not yet understood, the formation of such an assemblage more than likely influences the noncoding RNA function. We report here for the first time the thermodynamic basis of this natural RNA self-assembly. In particular we show that assembling of the ribonucleic acid is enthalpy driven and that the versatility of the RNA molecule is important for the polymerisation; indeed, an equivalent DNA sequence is unable to make a nanoassembly. The origin of the difference is discussed herein.

• Wydawca: -
• Czasopismo: Acta Biochimica Polonica
• Rocznik: 2014
• Tom: 61
• Numer: 1
• Opis fizyczny: p.179-184,fig.,ref.

Twórcy

autor

Genguenaud F.

• UFR SMBH, Universite Paris 13, Sorbonne Paris Cite, 93017 Bobigny, France

autor

Gesson M.

• Laboratoire Leon Brillouin, Commissariat a l'Energie Atomique, CNRS-UMR 12, CEA-Saclay, Gif-sur-Yvette Cedex, 91191 France

autor

Arluison V.

• Laboratoire Leon Brillouin, Commissariat a l'Energie Atomique, CNRS-UMR 12, CEA-Saclay, Gif-sur-Yvette Cedex, 91191 France
• University Paris Diderot-Paris 7, Sorbonne Paris Cite, 75013 Paris, France

Bibliografia

• Afonin KA, Grabow WW, Walker FM, Bindewald E, Dobrovolskaia MA, Shapiro BA, Jaeger L (2011) Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine. Nat Protoc 6: 2022-2034. 
• Busi F, Cayrol B, Lavelle C, LeDerout J, Pietrement O, Le Cam E, Geinguenaud F, Lacoste J, Regnier P, Arluison V (2009) Auto-assembly as a new regulatory mechanism of noncoding RNA. Cell Cycle 8: 952-954. 
• Cantor CR, Warshaw MM, Shapiro H (1970) Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers 9: 1059-1077. 
• Cayrol B, Geinguenaud F, Lacoste J, Busi F, Le Derout J, Pietrement O, Le Cam E, Regnier P, Lavelle C, Arluison V (2009) Auto-assembly of E. coli DsrA small noncoding RNA: Molecular characteristics and functional consequences. RNA Biol 6: 434-445. 
• Demeshkina N, Jenner L, Westhof E, Yusupov M, Yusupova G (2013) New structural insights into the decoding mechanism: translation infidelity via a G.U pair with Watson-Crick geometry. FEBS Lett 587: 1848-1857. 
• Ebel S, Brown T, Lane AN (1994) Thermodynamic stability and solution conformation of tandem G.A mismatches in RNA and RNA.DNA hybrid duplexes. Eur J Biochem 220: 703-715. 
• Fontanille M, Gnanou Y (2010) In Chimie et physico-chimie des polymees. Dunod Ed, Paris.
• Gottesman S, Storz G (2011) Bacterial small RNA regulators: versatile roles and rapidly evolving variations. Cold Spring Harb Perspect Biol 3: (a003798). 
• Jaeger L, Chworos A (2006) The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol 16: 531-543. 
• Lease RA, Cusick ME, Belfort M (1998) Riboregulation in Escherichia coli: DsrA RNA acts by RNA:RNA interactions at multiple loci. Proc Natl Acad Sci USA 95: 12456-12461. 
• Lease RA, Belfort M (2000) Riboregulation by DsrA RNA: trans-actions for global economy. Mol Microbiol 38: 667-672. 
• Lease RA, Arluison V, Lavelle C (2012) Twins, quadruplexes, and more: functional aspects of native and engineered RNA self-assembly. Front Life Sci 6: 19-32. 
• Majdalani N, Cunning C, Sledjeski D, Elliott T, Gottesman S (1998) DsrA RNA regulates translation of RpoS message by an anti-antisense mechanism, independent of its action as an antisilencer of transcription. Proc Natl Acad Sci USA 95: 12462-12467. 
• Nakano S, Kirihata T, Fujii S, Sakai H, Kuwahara M, Sawai H, Sugimoto N (2007) Influence of cationic molecules on the hairpin to duplex equilibria of self-complementary DNA and RNA oligonucleotides. Nucleic Acids Res 35: 486-494. 
• Rolle K, Zywicki M, Wyszko E, Barciszewska MZ, Barciszewski J (2006) Evaluation of the dynamic structure of DsrA RNA from E. coli and its functional consequences. J Biochem 139: 431-438. 
• Storz G, Opdyke JA, Zhang A (2004) Controlling mRNA stability and translation with small, noncoding RNAs. Curr Opin Microbiol 7: 140-144. 
• Sun X, Li JM, Wartell RM (2007) Conversion of stable RNA hairpin to a metastable dimer in frozen solution. RNA 13: 2277-2286. 
• Varani G, McClain WH (2000) The G.U wobble base pair. A fundamental building block of RNA structure crucial to RNA function in diverse biological systems. EMBO Rep. 1: 18-23. 
• Wei B, Dai M, Yin P (2012) Complex shapes self-assembled from single-stranded DNA tiles. Nature 485: 623-626.