AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices - PubMed (original) (raw)
Comparative Study
. 2001 Jul 20;310(4):735-53.
doi: 10.1006/jmbi.2001.4807.
Affiliations
- PMID: 11453684
- DOI: 10.1006/jmbi.2001.4807
Comparative Study
AA.AG@helix.ends: A:A and A:G base-pairs at the ends of 16 S and 23 S rRNA helices
T Elgavish et al. J Mol Biol. 2001.
Abstract
This study reveals that AA and AG oppositions occur frequently at the ends of helices in RNA crystal and NMR structures in the PDB database and in the 16 S and 23 S rRNA comparative structure models, with the G usually 3' to the helix for the AG oppositions. In addition, these oppositions are frequently base-paired and usually in the sheared conformation, although other conformations are present in NMR and crystal structures. These A:A and A:G base-pairs are present in a variety of structural environments, including GNRA tetraloops, E and E-like loops, interfaced between two helices that are coaxially stacked, tandem G:A base-pairs, U-turns, and adenosine platforms. Finally, given structural studies that reveal conformational rearrangements occurring in regions of the RNA with AA and AG oppositions at the ends of helices, we suggest that these conformationally unique helix extensions might be associated with functionally important structural rearrangements.
Copyright 2001 Academic Press.
Similar articles
- A story: unpaired adenosine bases in ribosomal RNAs.
Gutell RR, Cannone JJ, Shang Z, Du Y, Serra MJ. Gutell RR, et al. J Mol Biol. 2000 Dec 1;304(3):335-54. doi: 10.1006/jmbi.2000.4172. J Mol Biol. 2000. PMID: 11090278 - The 3D arrangement of the 23 S and 5 S rRNA in the Escherichia coli 50 S ribosomal subunit based on a cryo-electron microscopic reconstruction at 7.5 A resolution.
Mueller F, Sommer I, Baranov P, Matadeen R, Stoldt M, Wöhnert J, Görlach M, van Heel M, Brimacombe R. Mueller F, et al. J Mol Biol. 2000 Apr 21;298(1):35-59. doi: 10.1006/jmbi.2000.3635. J Mol Biol. 2000. PMID: 10756104 - Predicting U-turns in ribosomal RNA with comparative sequence analysis.
Gutell RR, Cannone JJ, Konings D, Gautheret D. Gutell RR, et al. J Mol Biol. 2000 Jul 21;300(4):791-803. doi: 10.1006/jmbi.2000.3900. J Mol Biol. 2000. PMID: 10891269 - Lessons from an evolving rRNA: 16S and 23S rRNA structures from a comparative perspective.
Gutell RR, Larsen N, Woese CR. Gutell RR, et al. Microbiol Rev. 1994 Mar;58(1):10-26. doi: 10.1128/mr.58.1.10-26.1994. Microbiol Rev. 1994. PMID: 8177168 Free PMC article. Review. - An introduction to recurrent nucleotide interactions in RNA.
Sweeney BA, Roy P, Leontis NB. Sweeney BA, et al. Wiley Interdiscip Rev RNA. 2015 Jan-Feb;6(1):17-45. doi: 10.1002/wrna.1258. Wiley Interdiscip Rev RNA. 2015. PMID: 25664365 Review.
Cited by
- Nuclear magnetic resonance reveals a two hairpin equilibrium near the 3'-splice site of influenza A segment 7 mRNA that can be shifted by oligonucleotides.
Kauffmann AD, Kennedy SD, Moss WN, Kierzek E, Kierzek R, Turner DH. Kauffmann AD, et al. RNA. 2022 Apr;28(4):508-522. doi: 10.1261/rna.078951.121. Epub 2022 Jan 4. RNA. 2022. PMID: 34983822 Free PMC article. - Effects of Noncanonical Base Pairing on RNA Folding: Structural Context and Spatial Arrangements of G·A Pairs.
Olson WK, Li S, Kaukonen T, Colasanti AV, Xin Y, Lu XJ. Olson WK, et al. Biochemistry. 2019 May 21;58(20):2474-2487. doi: 10.1021/acs.biochem.9b00122. Epub 2019 May 8. Biochemistry. 2019. PMID: 31008589 Free PMC article. - Structural Basis for Regulation of METTL16, an S-Adenosylmethionine Homeostasis Factor.
Doxtader KA, Wang P, Scarborough AM, Seo D, Conrad NK, Nam Y. Doxtader KA, et al. Mol Cell. 2018 Sep 20;71(6):1001-1011.e4. doi: 10.1016/j.molcel.2018.07.025. Epub 2018 Sep 6. Mol Cell. 2018. PMID: 30197297 Free PMC article. - ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding.
Zhang W, Yuan Y, Yang S, Huang J, Huang L. Zhang W, et al. PLoS One. 2015 Jul 1;10(7):e0131185. doi: 10.1371/journal.pone.0131185. eCollection 2015. PLoS One. 2015. PMID: 26132382 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Molecular Biology Databases