title: Ribosome binding of DNA analogs of tRNA requires base modifications and supports the "extended anticodon".
abstract: The efficiency of translation depends on correct tRNA-ribosome interactions. The ability of chemically synthesized yeast tRNA(Phe) anticodon domains to effectively inhibit the binding of native yeast tRNA(Phe) to poly(U)-programmed Escherichia coli 30S ribosomal subunits was dependent on a Mg(2+)-stabilized stem and an open anticodon loop, both facilitated by base modifications. Analysis of tRNA sequences has revealed that base modifications which negate canonical hydrogen bonding are found in 95% of those tRNA anticodon loop sequences with the potential to form two Watson-Crick base pairs across the loop. Therefore, we postulated that a stable anticodon stem and an open loop are prerequisites for ribosome binding. To test this hypothesis, DNA analogs of the yeast tRNA(Phe) anticodon domain were designed to have modification-induced, Mg(2+)-stabilized stems and open loops. The unmodified DNA analog neither bound to poly(U)-programmed 30S ribosomal subunits nor inhibited the binding of native tRNA(Phe). However, specifically modified DNA analogs did bind to ribosomal subunits and effectively inhibited tRNA(Phe) from binding. Thus, modification-dependent Mg(2+)-stabilized anticodon domain structures with open loops have evolved as the preferred anticodon conformations for ribosome binding.
authors.affiliation: Department of Biochemistry, North Carolina State University, Raleigh 27695-7622.
authors.forename: V
authors.initials: V
authors.lastname: Dao
authors.forename: R
authors.initials: R
authors.lastname: Guenther
authors.forename: A
authors.initials: A
authors.lastname: Malkiewicz
authors.forename: B
authors.initials: B
authors.lastname: Nawrot
authors.forename: E
authors.initials: E
authors.lastname: Sochacka
authors.forename: A
authors.initials: A
authors.lastname: Kraszewski
authors.forename: J
authors.initials: J
authors.lastname: Jankowska
authors.forename: K
authors.initials: K
authors.lastname: Everett
authors.forename: P F
authors.initials: PF
authors.lastname: Agris
mesh_terms: D000926:Anticodon; D001482:Base Composition; D001483:Base Sequence; D004269:DNA, Bacterial / Q000378:metabolism*; D006860:Hydrogen Bonding; D008274:Magnesium / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009705:Nucleosides / Q000378:metabolism; D011072:Poly U / Q000378:metabolism; D014176:Protein Biosynthesis; D012329:RNA, Bacterial; D012360:RNA, Transfer, Phe / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D000926:Anticodon; D004269:DNA, Bacterial; D009705:Nucleosides; D012329:RNA, Bacterial; D012360:RNA, Transfer, Phe; D011072:Poly U; D008274:Magnesium