Influence of C-5 halogenation of uridines on hairpin versus duplex RNA folding.
Halogenation of bases is a widespread method used for solving crystal structures of nucleic acids. However, this modification may have important consequences on RNA folding and thus on the success of crystallization. We have used a combination of UV thermal melting, steady-state fluorescence, X-ray crystallography, and gel electrophoresis techniques to study the influence of uridine halogenation (bromination or iodination) on the RNA folding. The HIV-1 Dimerization Initiation Site is an RNA hairpin that can adopt an alternative duplex conformation and was used as a model. We have shown that, unexpectedly, the RNA hairpin/duplex ratio is strongly dependent not only on the presence but also on the position of halogenation.
Ennifar
Eric
E
Architecture et Réactivité de l'ARN, Université Louis Pasteur, CNRS UPR 9002, Strasbourg, France. e.ennifar@ibmc.u-strasbg.fr
Bernacchi
Serena
S
Wolff
Philippe
P
Dumas
Philippe
P
D018360:Crystallography, X-Ray; D019281:Dimerization; D015497:HIV-1 / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006219:Halogens / Q000737:chemistry / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D014529:Uridine / Q000737:chemistry / Q000378:metabolism*
D006219:Halogens; D009692:Nucleic Acid Heteroduplexes; D012367:RNA, Viral; D014529:Uridine