RNA Structure: Tetraloops


RNA hairpins are among the most common RNA secondary structural elements and are frequently capped by RNA tetraloops. RNA tetraloops are composed of characteristic four‐loop nucleotides that form a compact and stable structure. While they can be formed by many different nucleotide sequences, UNCG (N = A, C, G, or U), GNRA (R = A or G), and CUUG tetraloops are found most often. Tetraloops usually help initiate RNA‐folding processes and provide sites for tertiary contacts within or between RNAs and for protein binding, thereby facilitating the assembly of ribonucleoprotein particles. Tetraloop interactions can be either sequence‐ or structure‐specific. Herein, we discuss the structures of RNA tetraloops and their interactions with other RNA structural motifs and with RNA‐binding proteins.

Key Concepts

  • RNA hairpins play important structural and functional roles in RNA.
  • RNA tetraloops are composed of four‐loop nucleotides that form a compact and stable structure.
  • Tetraloops assist RNA folding and provide sites for RNA–RNA and RNA–protein interactions.
  • Tetraloop interactions can be either sequence‐ or structure‐specific.
  • We discuss the structures of RNA tetraloops and their interactions with other RNAs and proteins.

Keywords: tetraloop; hairpin; RNA structure; RNA–RNA interaction; RNA–protein interaction

Figure 1. UUCG (PDB ID: 2KOC) (a) and GCAA (PDB ID: 1ZIH) (b) tetraloop structures. Hydrogen bonds are shown as dotted black lines. Carbon atoms are shown in green, phosphorus in purple, nitrogen in blue, oxygen in red, and hydrogen in white.
Figure 2. (a, b) Close stereo‐view of the NMR structure of GAAA tetraloop/11‐nt receptor (PDB ID: 2I7Z). A, U, G, and C are shown in yellow, green, blue, and red, respectively.
Figure 3. The tertiary interactions between tetraloop and its receptor identified in large RNA molecules. (a) a GAAA–11 nt interaction in the P4–P6 domain of Tetrahymena Group I intron (PDB ID: 1GID), (b) a GCGA from stem IC docks to UU‐AG base pair in DII (left‐bottom), and a GAAC tetraloop from DV interacts with the UGA bulge in ID1 (middle), of Group II intron from Oceanobacillus iheyensis (PDB ID: 3BWP), (c) a GAAA tetraloop from P2 interacts with 10‐nt receptor from P3 shown in class I c‐di‐GMP riboswitch from Vibrio Cholerae (PDB ID: 3IRW). The tetraloop and receptor are indicated in blue and red, respectively.


Akopian D, Shen K, Zhang X and Shan SO (2013) Signal recognition particle: an essential protein‐targeting machine. Annual Review of Biochemistry 82: 693–721.

Allain FH and Varani G (1995) Structure of the P1 helix from group I self‐splicing introns. Journal of Molecular Biology 250: 333–353.

Antao VP and Tinoco I Jr (1992) Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops. Nucleic Acids Research 20: 819–824.

Ataide SF, Schmitz N, Shen K, et al. (2011) The crystal structure of the signal recognition particle in complex with its receptor. Science 331: 881–886.

Borer PN, Lin Y, Wang S, et al. (1995) Proton NMR and structural features of a 24‐nucleotide RNA hairpin. Biochemistry 34: 6488–6503.

Butcher SE and Pyle AM (2011) The molecular interactions that stabilize RNA tertiary structure: RNA motifs, patterns, and networks. Accounts of Chemical Research 44: 1302–1311.

Butcher SE, Dieckmann T and Feigon J (1997) Solution structure of a GAAA tetraloop receptor RNA. EMBO Journal 16: 7490–7499.

Cai Z, Gorin A, Frederick R, et al. (1998) Solution structure of P22 transcriptional antitermination N peptide‐boxB RNA complex. Natural Structural Biology 5: 203–212.

Cate JH, Gooding AR, Podell E, et al. (1996) Crystal structure of a group I ribozyme domain: principles of RNA packing. Science 273: 1678–1685.

Chanfreau G, Rotondo G, Legrain P and Jacquier A (1998) Processing of a dicistronic small nucleolar RNA precursor by the RNA endonuclease Rnt1. EMBO Journal 17: 3726–3737.

Chanfreau G, Buckle M and Jacquier A (2000) Recognition of a conserved class of RNA tetraloops by Saccharomyces cerevisiae RNase III. Proceedings of the National Academy of Sciences of the United States of America 97: 3142–3147.

Cheong C, Varani G and Tinoco I Jr (1990) Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC. Nature 346: 680–682.

Correll CC, Munishkin A, Chan YL, et al. (1998) Crystal structure of the ribosomal RNA domain essential for binding elongation factors. Proceedings of the National Academy of Sciences of the United States of America 95: 13436–13441.

Costa M and Michel F (1995) Frequent use of the same tertiary motif by self‐folding RNAs. EMBO Journal 14: 1276–1285.

Dieckmann T, Suzuki E, Nakamura GK and Feigon J (1996) Solution structure of an ATP‐binding RNA aptamer reveals a novel fold. RNA 2: 628–640.

Elela SA, Igel H and Ares M Jr (1996) RNase III cleaves eukaryotic preribosomal RNA at a U3 snoRNP‐dependent site. Cell 85: 115–124.

Fedoruk‐Wyszomirska A, Szymanski M, Wyszko E, Barciszewska MZ and Barciszewski J (2009) Highly active low magnesium hammerhead ribozyme. Journal of Biochemistry 145: 451–459.

Ferre‐D'Amare AR, Zhou K and Doudna JA (1998) A general module for RNA crystallization. Journal of Molecular Biology 279: 621–631.

Fiore JL and Nesbitt DJ (2013) An RNA folding motif: GNRA tetraloop‐receptor interactions. Quarterly Reviews of Biophysics 46: 223–264.

Geary C, Baudrey S and Jaeger L (2008) Comprehensive features of natural and in vitro selected GNRA tetraloop‐binding receptors. Nucleic Acids Research 36: 1138–1152.

Hendrix DK, Brenner SE and Holbrook SR (2005) RNA structural motifs: building blocks of a modular biomolecule. Quarterly Reviews of Biophysics 38: 221–243.

Huppler A, Nikstad LJ, Allmann AM, Brow DA and Butcher SE (2002) Metal binding and base ionization in the U6 RNA intramolecular stem‐loop structure. Nature Structural Biology 9: 431–435.

Ikawa Y, Naito D, Aono N, Shiraishi H and Inoue T (1999) A conserved motif in group IC3 introns is a new class of GNRA receptor. Nucleic Acids Research 27: 1859–1865.

Jaeger L and Chworos A (2006) The architectonics of programmable RNA and DNA nanostructures. Current Opinion in Structural Biology 16: 531–543.

Jagath JR, Matassova NB, de Leeuw E, et al. (2001) Important role of the tetraloop region of 4.5S RNA in SRP binding to its receptor FtsY. RNA 7: 293–301.

Jucker FM and Pardi A (1995) Solution structure of the CUUG hairpin loop: a novel RNA tetraloop motif. Biochemistry 34: 14416–14427.

Jucker FM, Heus HA, Yip PF, Moors EH and Pardi A (1996) A network of heterogeneous hydrogen bonds in GNRA tetraloops. Journal of Molecular Biology 264: 968–980.

Klosterman PS, Hendrix DK, Tamura M, Holbrook SR and Brenner SE (2004) Three‐dimensional motifs from the SCOR, structural classification of RNA database: extruded strands, base triples, tetraloops and U‐turns. Nucleic Acids Research 32: 2342–2352.

Krasilnikov AS, Yang X, Pan T and Mondragon A (2003) Crystal structure of the specificity domain of ribonuclease P. Nature 421: 760–764.

Legault P, Li J, Mogridge J, Kay LE and Greenblatt J (1998) NMR structure of the bacteriophage lambda N peptide/boxB RNA complex: recognition of a GNRA fold by an arginine‐rich motif. Cell 93: 289–299.

Masliah G, Barraud P and Allain FH (2013) RNA recognition by double‐stranded RNA binding domains: a matter of shape and sequence. Cellular and Molecular Life Sciences 70: 1875–1895.

Michel F and Westhof E (1990) Modelling of the three‐dimensional architecture of group I catalytic introns based on comparative sequence analysis. Journal of Molecular Biology 216: 585–610.

Murphy FL, Wang YH, Griffith JD and Cech TR (1994) Coaxially stacked RNA helices in the catalytic center of the Tetrahymena ribozyme. Science 265: 1709–1712.

Nissen P, Ippolito JA, Ban N, Moore PB and Steitz TA (2001) RNA tertiary interactions in the large ribosomal subunit: the A‐minor motif. Proceedings of the National Academy of Sciences of the United States of America 98: 4899–4903.

Nozinovic S, Furtig B, Jonker HR, Richter C and Schwalbe H (2010) High‐resolution NMR structure of an RNA model system: the 14‐mer cUUCGg tetraloop hairpin RNA. Nucleic Acids Research 38: 683–694.

Pley HW, Flaherty KM and McKay DB (1994) Three‐dimensional structure of a hammerhead ribozyme. Nature 372: 68–74.

Ramos A, Grunert S, Adams J, et al. (2000) RNA recognition by a Staufen double‐stranded RNA‐binding domain. EMBO Journal 19: 997–1009.

Regulski EE, Moy RH, Weinberg Z, et al. (2008) A widespread riboswitch candidate that controls bacterial genes involved in molybdenum cofactor and tungsten cofactor metabolism. Molecular Microbiology 68: 918–932.

Smith JS and Nikonowicz EP (1998) NMR structure and dynamics of an RNA motif common to the spliceosome branch‐point helix and the RNA‐binding site for phage GA coat protein. Biochemistry 37: 13486–13498.

Smith KD, Lipchock SV, Ames TD, et al. (2009) Structural basis of ligand binding by a c‐di‐GMP riboswitch. Nature Structural and Molecular Biology 16: 1218–1223.

Tanner MA and Cech TR (1995) An important RNA tertiary interaction of group I and group II introns is implicated in gram‐positive RNase P RNAs. RNA 1: 349–350.

Toor N, Keating KS, Taylor SD and Pyle AM (2008) Crystal structure of a self‐spliced group II intron. Science 320: 77–82.

Valegard K, Murray JB, Stonehouse NJ, et al. (1997) The three‐dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence‐specific protein‐RNA interactions. Journal of Molecular Biology 270: 724–738.

Varani G, Cheong C and Tinoco I Jr (1991) Structure of an unusually stable RNA hairpin. Biochemistry 30: 3280–3289.

Voigts‐Hoffmann F, Schmitz N, Shen K, et al. (2013) The structural basis of FtsY recruitment and GTPase activation by SRP RNA. Molecular Cell 52: 643–654.

Wang Z, Hartman E, Roy K, Chanfreau G and Feigon J (2011) Structure of a yeast RNase III dsRBD complex with a noncanonical RNA substrate provides new insights into binding specificity of dsRBDs. Structure 19: 999–1010.

Wu H, Yang PK, Butcher SE, et al. (2001) A novel family of RNA tetraloop structure forms the recognition site for Saccharomyces cerevisiae RNase III. EMBO Journal 20: 7240–7249.

Wu H, Henras A, Chanfreau G and Feigon J (2004) Structural basis for recognition of the AGNN tetraloop RNA fold by the double‐stranded RNA‐binding domain of Rnt1p RNase III. Proceedings of the National Academy of Sciences of the United States of America 101: 8307–8312.

Yang X, Gerczei T, Glover LT and Correll CC (2001) Crystal structures of restrictocin‐inhibitor complexes with implications for RNA recognition and base flipping. Natural Structural Biology 8: 968–973.

Zhou J, Bean RL, Vogt VM and Summers M (2007) Solution structure of the Rous sarcoma virus nucleocapsid protein: muPsi RNA packaging signal complex. Journal of Molecular Biology 365: 453–467.

Further Reading

Ishikawa J, Fujita Y, Maeda Y, Furuta H and Ikawa Y (2011) GNRA/receptor interacting modules: versatile modular units for natural and artificial RNA architectures. Methods 54: 226–38. 10.1016/j.ymeth.2010.12.011. Review. PMID:21163353

Reiter NJ, Chan CW and Mondragón A (2011) Emerging structural themes in large RNA molecules. Current Opinion in Structural Biology 21: 319–26. 10.1016/j.sbi.2011.03.003. Review. PMID:21474301

Thapar R, Denmon AP and Nikonowicz EP (2014) Recognition modes of RNA tetraloops and tetraloop‐like motifs by RNA‐binding proteins. Wiley Interdisciplinary Reviews. RNA 5: 49–67. 10.1002/wrna.1196. Review. PMID:24124096

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Cheong, Hae‐Kap, Kim, Nak‐Kyoon, and Cheong, Chaejoon(Feb 2015) RNA Structure: Tetraloops. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0003135.pub3]