title: The role of 2'-hydroxyl groups in an RNA-protein interaction.
abstract: The role of the 2'-hydroxyl group in RNA--protein interaction has been investigated using MS2 coat protein and its hairpin RNA operator as a model system. Derivatives of the MS2 translational operator were prepared where individual riboses were replaced by deoxyribose and their binding affinities to MS2 coat protein were determined. Only 1 (U-5) out of 15 positions tested reduced protein affinity by 1.6 kcal/mol. A variety of other 2'-modifications were tested at this position to understand the role of this particular 2'-hydroxyl group. Normal binding of the U-NH2 variant and weaker binding of the U-O-methyl variant are consistent with the ability of these functional groups to provide a hydrogen bond donor. This is also supported by recent crystallographic data which indicate a possible interaction between the 2'-hydroxyl of U-5 and the carboxylate group of glutamate 63 [Valegård et al. (1994) Nature 371, 623-626]. Complementary experiments introducing riboses into a DNA hairpin confirm the putative protein contact, and also identify a requirement for riboses in the two upper base pairs of the hairpin. Several arguments suggest these riboses are required to maintain an A-form helix in this region of the binding site. A minimum requirement of four 2'-hydroxyl groups for wild-type coat protein binding has been determined, one of which is at the -5 position and other three in the upper stem in any combination.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Chemistry and Biochemistry, University of Colorado, Boulder 80309-0215, USA.
authors.forename: N
authors.initials: N
authors.lastname: Baidya
authors.forename: O C
authors.initials: OC
authors.lastname: Uhlenbeck
mesh_terms: D001483:Base Sequence; D002213:Capsid / Q000378:metabolism*; D036022:Capsid Proteins; D004247:DNA / Q000378:metabolism; D003854:Deoxyribonucleotides / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011485:Protein Binding; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism*; D016601:RNA-Binding Proteins; D012266:Ribose / Q000031:analogs & derivatives; D013329:Structure-Activity Relationship
chemical_list: D036022:Capsid Proteins; D003854:Deoxyribonucleotides; D012367:RNA, Viral; D016601:RNA-Binding Proteins; D012266:Ribose; D004247:DNA