title: Conserved unpaired adenine residues are important for ordered structures of 5S ribosomal RNA. An infrared study of the secondary and tertiary structure of Thermus thermophilus 5S rRNA.
abstract: An improved set of infrared calibration spectra for the determination of G X C and A X U base pairs leads to 32 +/- 3 G X C (+ G X U) and 4 +/- 1 A X U base pairs for Thermus thermophilus 5S RNA in the presence and absence of Mg2+. These results give further support for the consensus secondary structure of 5S RNA recently proposed by several groups. T. thermophilus 5S RNA shows, in the presence of Mg2+, a distinct two-step thermal melting of its ordered structure. Based on new data about the stacking dependence of infrared intensities of unpaired ribonucleotides the spectral changes of the low-temperature transition should be explained by melting of stacked arrangements of unpaired bases and/or non-standard base pairs. Striking is the reduction in A stacking, which is not related to the melting of A X U base pairs, indicating the importance of the mostly conserved unpaired adenines for the Mg2+ stabilized higher-order structures especially within internal loops of 5S RNA.
authors.forename: S
authors.initials: S
authors.lastname: Böhm
authors.lastname: Venyaminov SYu
authors.forename: H
authors.initials: H
authors.lastname: Fabian
authors.forename: V V
authors.initials: VV
authors.lastname: Filimonov
authors.forename: H
authors.initials: H
authors.lastname: Welfle
mesh_terms: D000225:Adenine; D001482:Base Composition; D055598:Chemical Phenomena; D002621:Chemistry; D009690:Nucleic Acid Conformation; D012329:RNA, Bacterial / Q000302:isolation & purification; D012335:RNA, Ribosomal / Q000302:isolation & purification; D012015:Reference Standards; D013055:Spectrophotometry, Infrared; D013816:Thermodynamics; D013824:Thermus / Q000235:genetics*
chemical_list: D012329:RNA, Bacterial; D012335:RNA, Ribosomal; D000225:Adenine