title: C5-substituents of uridines and 2-thiouridines present at the wobble position of tRNA determine the formation of their keto-enol or zwitterionic forms - a factor important for accuracy of reading of guanosine at the 3΄-end of the mRNA codons.
abstract: Modified nucleosides present in the wobble position of the tRNA anticodons regulate protein translation through tuning the reading of mRNA codons. Among 40 of such nucleosides, there are modified uridines containing either a sulfur atom at the C2 position and/or a substituent at the C5 position of the nucleobase ring. It is already evidenced that tRNAs with 2-thiouridines at the wobble position preferentially read NNA codons, while the reading mode of the NNG codons by R5U/R5S2U-containing anticodons is still elusive. For a series of 18 modified uridines and 2-thiouridines, we determined the pKa values and demonstrated that both modifying elements alter the electron density of the uracil ring and modulate the acidity of their N3H proton. In aqueous solutions at physiological pH the 2-thiouridines containing aminoalkyl C5-substituents are ionized in ca. 50%. The results, confirmed also by theoretical calculations, indicate that the preferential binding of the modified units bearing non-ionizable 5-substituents to guanosine in the NNG codons may obey the alternative C-G-like (Watson-Crick) mode, while binding of those bearing aminoalkyl C5-substituents (protonated under physiological conditions) and especially those with a sulfur atom at the C2 position, adopt a zwitterionic form and interact with guanosine via a 'new wobble' pattern.
authors.affiliation: Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Sochacka
authors.affiliation: Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
authors.forename: Elzbieta
authors.initials: E
authors.lastname: Lodyga-Chruscinska
authors.affiliation: Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
authors.forename: Justyna
authors.initials: J
authors.lastname: Pawlak
authors.affiliation: Department of Bioorganic Chemistry, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
authors.forename: Marek
authors.initials: M
authors.lastname: Cypryk
authors.affiliation: Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
authors.forename: Paulina
authors.initials: P
authors.lastname: Bartos
authors.affiliation: Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.|Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Ebenryter-Olbinska
authors.affiliation: Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland.
authors.forename: Grazyna
authors.initials: G
authors.lastname: Leszczynska
authors.affiliation: Department of Computer Modeling, Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363 Lodz, Poland.
authors.forename: Barbara
authors.initials: B
authors.lastname: Nawrot
mesh_terms: D026921:Amino Acid Transport Systems, Neutral / Q000737:chemistry / Q000235:genetics; D003062:Codon / Q000235:genetics; D005815:Genetic Code; D006151:Guanosine / Q000235:genetics; D009690:Nucleic Acid Conformation; D014176:Protein Biosynthesis / Q000235:genetics*; D012333:RNA, Messenger / Q000737:chemistry / Q000235:genetics*; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics*; D013891:Thiouridine / Q000031:analogs & derivatives / Q000737:chemistry; D014529:Uridine / Q000737:chemistry / Q000235:genetics*
chemical_list: C105273:2-thiouridine; D026921:Amino Acid Transport Systems, Neutral; D003062:Codon; D012333:RNA, Messenger; D006151:Guanosine; D013891:Thiouridine; D012343:RNA, Transfer; D014529:Uridine