Journal of Biosciences

, Volume 28, Issue 5, pp 547–555 | Cite as

Non-Watson Crick base pairs might stabilize RNA structural motifs in ribozymes — a comparative study of group-I intron structures

  • K. Chandrasekhar
  • R. Malathi


In recent decades studies on RNA structure and function have gained significance due to discoveries on diversified functions of RNA. A common element for RNA secondary structure formed by series of non-Watson/Watson Crick base pairs, internal loops and pseudoknots have been the highlighting feature of recent structural determination of RNAs. The recent crystal structure of group-I introns has demonstrated that these might constitute RNA structural motifs in ribozymes, playing a crucial role in their enzymatic activity. To understand the functional significance of these non-canonical base pairs in catalytic RNA, we analysed the sequences of group-I introns from nuclear genes. The results suggest that they might form the building blocks of folded RNA motifs which are crucial to the catalytic activity of the ribozyme. The conservation of these, as observed from divergent organisms, argues for the presence of non-canonical base pairs as an important requisite for the structure and enzymatic property of ribozymes by enabling them to carry out functions such as replication, polymerase activity etc. in primordial conditions in the absence of proteins.


Group-I intron non-canonical base pair ribozyme RNA structure Tetrahymena thermophila wobble base pair 

Abbreviations used








internal guide sequences










Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Alexander A, Szewczak L O D, Sean P R, Eileen M and Strobel S A 1998Nature Struct. Biol. 5 60–66CrossRefGoogle Scholar
  2. Baeyens K J and De BhHolbrook Sr 1995 Structure of an RNA double helix including uracil-uracil base pairs in a loop;Nature Struct. Biol. 2 56–62PubMedCrossRefGoogle Scholar
  3. Baeyens K J and De Bondt H L 1996 A curved RNA helix incorporating an internal loop with GA and AA;Proc. Natl. Acad. Sci. USA 93 12851–12855PubMedCrossRefGoogle Scholar
  4. Battisle J L, Mao H, Rao N S, Tan R, Muhandriam D R, Kay L E, Frankel A D and Williamson J R 1996 Alpha helix-RNA major groove recognition in an HIV-1 rev peptide-RRE-RNA complex;Science 273 1547–1551CrossRefGoogle Scholar
  5. Blanchard S C, Fourmy D, Eason R G and Puglisi D J 1998 rRNA chemical groups required for aminoglycoside binding;Biochemistry 37 7716–7724PubMedCrossRefGoogle Scholar
  6. Colmenarejo C and Tinoco I Jr 1999 Structure and thermodynamics of metal binding in the P5 helix of a group-I intron ribozyme;J. Mol. Biol. 290 119–135PubMedCrossRefGoogle Scholar
  7. Donnelly L O, Szewczak A A, Gutell R R and Strobel S A 1998 The chemical basis of adenosine conservation throughout theTetrahymena ribozyme;RNA 4 498–519CrossRefGoogle Scholar
  8. Francis R, Chen Mao and Uckun M F 2001 Binding interactions between the active center cleft of recombinant pokeweed antiviral protein and the α-sarcin/ricin stem loop of ribosomal RNA;J. Biol. Chem. 276 24075–24081CrossRefGoogle Scholar
  9. Gautheret D, Konings D and Gutell R R 1995 GU base pairing motifs in ribosomal RNA;RNA 8 807–814Google Scholar
  10. Golden B L, Gooding A R, Podell E R and Cech T R 1998 A preorganized active site in the crystal structure of theTetrahymena ribozyme;Science 282 251–252CrossRefGoogle Scholar
  11. Jeffrey B-H, Tok, Junhyeong Cho and Robert R R 1999 Aminoglycoside antibiotics are able to specifically bind the 5′ Untranslated region of Thymidylate synthase messenger RNA;Biochemistry 38 199–206CrossRefGoogle Scholar
  12. Michel F and Westhof E 1990 Modelling of the three-dimensional architecture of group-I catalytic introns based on comparative sequences analysis;J. Mol. Biol. 216 585–610PubMedCrossRefGoogle Scholar
  13. Michel F, Ellington D A, Couture S and Szostak W J 1990 Phylogenetic and genetic evidence for base-triples in the catalytic domain of group-I introns;Nature (London)47 578–580CrossRefGoogle Scholar
  14. Murphy L F and Cech T R 1994 GAAA Tetraloop and conserved bulge stabilize Tertiary structure of a group-I intron domain;J. Mol. Biol. 236 49–63PubMedCrossRefGoogle Scholar
  15. Pan B, Mitra N S and Sundaralingam M 1999 Crystal structure of an RNA 16-mer Duplex R(GCAGAGUUAAAUCUGC)2 with Nonadjacent G(Syn)* A+ (Anti Mispairs);Biochemistry 38 2826–2831PubMedCrossRefGoogle Scholar
  16. Pieczenik G 1994 The theory of genetypic selection; predicting the direction of evolution as a consequence of GU base pairing and the existence of non-pathogenic strains of HIV-1;Biochem. Mol. Biol. Int. 5 879–887Google Scholar
  17. Pley H W, Flaherty K M and McKay D B 1994 Three dimensional structure of a hammerhead ribozymes;Nature (London) 372 68–74CrossRefGoogle Scholar
  18. Ramos A and Varanu G 1997 Structure of the acceptor stem ofEscherichia coli tRNA Ala: role of the G3.U70 base pair in synthetase recognition;Nucleic Acid Res. 25 2083–2090PubMedCrossRefGoogle Scholar
  19. Walczak R, Carbon P and Krol A 1998 An essential non-Watson-Crick base pair motif in 3′ UTR to mediate seleno-protein translation;RNA 4 74–84PubMedGoogle Scholar

Copyright information

© Indian Academy of Sciences 2003

Authors and Affiliations

  1. 1.Department of Genetics Dr ALM PG Institute of Basic Medical SciencesUniversity of MadrasChennaiIndia

Personalised recommendations