High-resolution NMR Structure of an RNA Model System: the 14-mer CUUCGg Tetraloop Hairpin RNA

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2009 Nov 13

PMID 19906714

Citations 95

Authors

Senada Nozinovic

Boris Furtig

Hendrik R A Jonker

Christian Richter

Harald Schwalbe

Affiliations

Soon will be listed here.

Abstract

We present a high-resolution nuclear magnetic resonance (NMR) solution structure of a 14-mer RNA hairpin capped by cUUCGg tetraloop. This short and very stable RNA presents an important model system for the study of RNA structure and dynamics using NMR spectroscopy, molecular dynamics (MD) simulations and RNA force-field development. The extraordinary high precision of the structure (root mean square deviation of 0.3 A) could be achieved by measuring and incorporating all currently accessible NMR parameters, including distances derived from nuclear Overhauser effect (NOE) intensities, torsion-angle dependent homonuclear and heteronuclear scalar coupling constants, projection-angle-dependent cross-correlated relaxation rates and residual dipolar couplings. The structure calculations were performed with the program CNS using the ARIA setup and protocols. The structure quality was further improved by a final refinement in explicit water using OPLS force field parameters for non-bonded interactions and charges. In addition, the 2'-hydroxyl groups have been assigned and their conformation has been analyzed based on NOE contacts. The structure currently defines a benchmark for the precision and accuracy amenable to RNA structure determination by NMR spectroscopy. Here, we discuss the impact of various NMR restraints on structure quality and discuss in detail the dynamics of this system as previously determined.

Citing Articles

Deciphering ligand and metal ion dependent intricate folding landscape of Vc2 c-di-GMP riboswitch aptamer.

Shin J, Choi S, An S, Bang K, Song H, Suh J Nucleic Acids Res. 2025; 53(1.

PMID: 39777471 PMC: 11705072. DOI: 10.1093/nar/gkae1296.

Dissecting the Conformational Heterogeneity of Stem-Loop Substructures of the Fifth Element in the 5'-Untranslated Region of SARS-CoV-2.

Mertinkus K, Oxenfarth A, Richter C, Wacker A, Mata C, Carazo J J Am Chem Soc. 2024; 146(44):30139-30154.

PMID: 39442924 PMC: 11544613. DOI: 10.1021/jacs.4c08406.

Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.

Linzer J, Aminov E, Abdullah A, Kirkup C, Diaz Ventura R, Bijoor V J Chem Inf Model. 2024; 64(15):6092-6104.

PMID: 39002142 PMC: 11584990. DOI: 10.1021/acs.jcim.4c00756.

RNA adapts its flexibility to efficiently fold and resist unfolding.

Jang S, Ray K, Lynall D, Shepard K, Nuckolls C, Gonzalez Jr R bioRxiv. 2024; .

PMID: 38853856 PMC: 11160689. DOI: 10.1101/2024.05.27.595525.

The 5'-terminal stem-loop RNA element of SARS-CoV-2 features highly dynamic structural elements that are sensitive to differences in cellular pH.

Toews S, Wacker A, Faison E, Duchardt-Ferner E, Richter C, Mathieu D Nucleic Acids Res. 2024; 52(13):7971-7986.

PMID: 38842942 PMC: 11260494. DOI: 10.1093/nar/gkae477.

References

Vallurupalli P, Kay L . A suite of 2H NMR spin relaxation experiments for the measurement of RNA dynamics. J Am Chem Soc. 2005; 127(18):6893-901. DOI: 10.1021/ja0427799. View

Brunger A, Adams P, Clore G, DeLano W, Gros P, Grosse-Kunstleve R . Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D Biol Crystallogr. 1998; 54(Pt 5):905-21. DOI: 10.1107/s0907444998003254. View

Lynch S, Puglisi J . Structure of a eukaryotic decoding region A-site RNA. J Mol Biol. 2001; 306(5):1023-35. DOI: 10.1006/jmbi.2000.4419. View

Richter C, Griesinger C, Felli I, Cole P, Varani G, Schwalbe H . Determination of sugar conformation in large RNA oligonucleotides from analysis of dipole-dipole cross correlated relaxation by solution NMR spectroscopy. J Biomol NMR. 2000; 15(3):241-50. DOI: 10.1023/a:1008319130714. View

Nikonowicz E, Sirr A, Legault P, Jucker F, Baer L, Pardi A . Preparation of 13C and 15N labelled RNAs for heteronuclear multi-dimensional NMR studies. Nucleic Acids Res. 1992; 20(17):4507-13. PMC: 334178. DOI: 10.1093/nar/20.17.4507. View

Walters K, Russu I . Sequence dependence of purine C8H exchange kinetics in the dodecamer 5'-d(CGCGAATTCGCG)-3'. Biopolymers. 1993; 33(6):943-51. DOI: 10.1002/bip.360330610. View

Tuerk C, Gauss P, Thermes C, Groebe D, Gayle M, Guild N . CUUCGG hairpins: extraordinarily stable RNA secondary structures associated with various biochemical processes. Proc Natl Acad Sci U S A. 1988; 85(5):1364-8. PMC: 279771. DOI: 10.1073/pnas.85.5.1364. View

Blose J, Proctor D, Veeraraghavan N, Misra V, Bevilacqua P . Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors. J Am Chem Soc. 2009; 131(24):8474-84. DOI: 10.1021/ja900065e. View

Yoshizawa S, Fourmy D, Puglisi J . Structural origins of gentamicin antibiotic action. EMBO J. 1998; 17(22):6437-48. PMC: 1170992. DOI: 10.1093/emboj/17.22.6437. View

10.

Nikulin A, Serganov A, Ennifar E, Tishchenko S, Nevskaya N, Shepard W . Crystal structure of the S15-rRNA complex. Nat Struct Biol. 2000; 7(4):273-7. DOI: 10.1038/74028. View

11.

Hennig M, Fohrer J, Carlomagno T . Assignment and NOE analysis of 2'-hydroxyl protons in RNA: implications for stabilization of RNA A-form duplexes. J Am Chem Soc. 2005; 127(7):2028-9. DOI: 10.1021/ja043390o. View

12.

Legault P, Jucker F, Pardi A . Improved measurement of 13C, 31P J coupling constants in isotopically labeled RNA. FEBS Lett. 1995; 362(2):156-60. DOI: 10.1016/0014-5793(95)00232-x. View

13.

Fohrer J, Hennig M, Carlomagno T . Influence of the 2'-hydroxyl group conformation on the stability of A-form helices in RNA. J Mol Biol. 2005; 356(2):280-7. DOI: 10.1016/j.jmb.2005.11.043. View

14.

Hansen M, Mueller L, Pardi A . Tunable alignment of macromolecules by filamentous phage yields dipolar coupling interactions. Nat Struct Biol. 1998; 5(12):1065-74. DOI: 10.1038/4176. View

15.

Schwalbe H, Marino J, King G, Wechselberger R, Bermel W, Griesinger C . Determination of a complete set of coupling constants in 13C-labeled oligonucleotides. J Biomol NMR. 1994; 4(5):631-44. DOI: 10.1007/BF00404274. View

16.

Linge J, ODonoghue S, Nilges M . Automated assignment of ambiguous nuclear overhauser effects with ARIA. Methods Enzymol. 2001; 339:71-90. DOI: 10.1016/s0076-6879(01)39310-2. View

17.

Furtig B, Richter C, Bermel W, Schwalbe H . New NMR experiments for RNA nucleobase resonance assignment and chemical shift analysis of an RNA UUCG tetraloop. J Biomol NMR. 2004; 28(1):69-79. DOI: 10.1023/B:JNMR.0000012863.63522.1f. View

18.

Duchardt E, Richter C, Ohlenschlager O, Gorlach M, Wohnert J, Schwalbe H . Determination of the glycosidic bond angle chi in RNA from cross-correlated relaxation of CH dipolar coupling and N chemical shift anisotropy. J Am Chem Soc. 2004; 126(7):1962-70. DOI: 10.1021/ja0367041. View

19.

Cheong C, Varani G, Tinoco Jr I . Solution structure of an unusually stable RNA hairpin, 5'GGAC(UUCG)GUCC. Nature. 1990; 346(6285):680-2. DOI: 10.1038/346680a0. View

20.

Lu X, Olson W . 3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures. Nat Protoc. 2008; 3(7):1213-27. PMC: 3065354. DOI: 10.1038/nprot.2008.104. View