Skip to main content

Advertisement

SpringerLink
Log in

Hydration dependent dynamics in RNA

  • Article
  • Published:
Journal of Biomolecular NMR Aims and scope Submit manuscript

Abstract

The essential role played by local and collective motions in RNA function has led to a growing interest in the characterization of RNA dynamics. Recent investigations have revealed that even relatively simple RNAs experience complex motions over multiple time scales covering the entire ms–ps motional range. In this work, we use deuterium solid-state NMR to systematically investigate motions in HIV-1 TAR RNA as a function of hydration. We probe dynamics at three uridine residues in different structural environments ranging from helical to completely unrestrained. We observe distinct and substantial changes in 2H solid-state relaxation times and lineshapes at each site as hydration levels increase. By comparing solid-state and solution state 13C relaxation measurements, we establish that ns–μs motions that may be indicative of collective dynamics suddenly arise in the RNA as hydration reaches a critical point coincident with the onset of bulk hydration. Beyond that point, we observe smaller changes in relaxation rates and lineshapes in these highly hydrated solid samples, compared to the dramatic activation of motion occurring at moderate hydration.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5
Fig. 6

Similar content being viewed by others

References

  • Aboul-ela F, Varani G (1998) Recognition of HIV-1 TAR RNA by tat protein and tat-derived peptides. J Mol Struct 423:29–39

    Google Scholar 

  • Aboul-ela F, Karn J, Varani G (1995) The structure of the human immunodeficiency virus type-1 TAR RNA reveals principles of RNA recognition by Tat protein. J Mol Biol 253(2):313–332

    Article  Google Scholar 

  • Aboul-ela F, Karn J, Varani G (1996) Structure of HIV-1 TAR RNA in the absence of ligands reveals a novel conformation of the trinucleotide bulge. Nucleic Acids Res 24(20):3974–3981

    Article  Google Scholar 

  • Alam TM, Drobny GP (1991) Solid-state NMR studies of DNA structure and dynamics. Chem Rev 91:1545–1590

    Article  Google Scholar 

  • Al-Hashimi HM, Gosser Y, Gorin A, Hu W, Majumdar A, Patel DJ (2002) Concerted motions in HIV-1 TAR RNA may allow access to bound state conformations: RNA dynamics from NMR residual dipolar couplings. J Mol Biol 315:95–102

    Article  Google Scholar 

  • Bardaro MF Jr, Shajani Z, Patora-Komisarska K, Robinson JA, Varani G (2009) How binding of small molecule and peptide ligands to HIV-1 TAR alters the RNA motional landscape. Nucleic Acids Res 37:1529–1540

    Article  Google Scholar 

  • Barnes RG (ed) (1974) In advances in nuclear quadrupole resonance. New York

  • Brandes R, Vold RR, Vold RL, Kearns DR (1986) Effects of hydration on purine motion in solid DNA. Biochemistry 25:7744–7751

    Article  Google Scholar 

  • Brandes R, Vold RR, Kearns DR, Rupprecht A (1988) A 2H-NMR study of the A-DNA conformation in films of oriented Na-DNA: evidence of a disordered B-DNA contribution. Biopolymers 27:1159–1170

    Article  Google Scholar 

  • Casiano-Negroni A, Sun X, Al-Hashimi HM (2007) Probing Na(+)-induced changes in the HIV-1 TAR conformational dynamics using NMR residual dipolar couplings: new insights into the role of counterions and electrostatic interactions in adaptive recognition. Biochemistry 46:6525–6535

    Article  Google Scholar 

  • Cruse WBT, Salisbury SA, Brown T, Cosstick R, Eckstein F, Kennard O (1986) Chiral phosphorothioate analogues of B-DNA. The crystal structure of Rp-dGp(S)CpGp(S)CpGp(S)C. J Mol Biol 192:891–905

    Article  Google Scholar 

  • Davis JH, Jeffrey KR, Bloom M, Valic MI, Higgs TP (1976) Quadrupolar echo deuteron magnetic resonance spectroscopy in ordered hydrocarbon chains. Chem Phys Lett 42:390–394

    Article  ADS  Google Scholar 

  • Dayie KT, Brodsky AS, Williamson JR (2002) Base flexibility in HIV-2 TAR RNA mapped by solution 15N, 13C NMR relaxation. J Mol Biol 317:263–278

    Article  Google Scholar 

  • Falk M, Hartman KA, Lord RC (1962a) Hydration of deoxyribonucleic acid. I. a gravimetric study. J Am Chem Soc 84:3843–3846

    Article  Google Scholar 

  • Falk M, Hartman KA, Lord RC (1962b) Hydration of deoxyribonucleic acid. II. An infrared study. J Am Chem Soc 85:387–391

    Article  Google Scholar 

  • Falk M, Hartman KA, Lord RC (1962c) Hydration of deoxyribonucleic acid. III. A spectroscopic study of the effect of hydration on the structure of deoxyribonucleic acid. J Am Chem Soc 85:391–394

    Article  Google Scholar 

  • Farrow NA, Muhandiram DR, Singer AU, Pascal SM, Kay CM, Gish G, Shoelson SE, Pawson T, Forman-Kay JD, Kay LE (1994) Backbone dynamics of a free and a phosphopeptide-complexed Src homology 2 domain studied by 15N NMR relaxation. Biochemistry 33:5984–6003

    Article  Google Scholar 

  • Farrow AN, Zhang O, Szabo A, Torchia DA, Kay LE (1995) Spectral density function mapping using 15N relaxation data exclusively. J Biomol NMR 6:153–162

    Article  Google Scholar 

  • Hansen AL, Al-Hashimi HM (2007) RNA dynamics by carbon relaxation and domain elongation. J Am Chem Soc 129:16072–16082

    Article  Google Scholar 

  • Hoatson GL (1990) Broadband composite excitation sequences for creating quadrupolar order in 2H NMR. J Magn Reson 94:152–159

    Google Scholar 

  • Huang X, Yu P, LeProust E, Gao X (1997) An effficient and economic site-specific deuteration strategy for NMR studies of homologous oligonucleotide repeat sequences. Nucleic Acids Res 25:4758–4763

    Article  Google Scholar 

  • Jaeger JA, Tinoco I Jr (1993) An NMR study of the HIV-1 TAR element hairpin. Biochemistry 32:12522–12530

    Article  Google Scholar 

  • Karn J (1999) Tackling tat. J Mol Biol 293:235–254

    Article  Google Scholar 

  • Kempf GJ, Loria JP (2003) Protein dynamics from solution NMR. Cell Biochem Biophys 37:187–211

    Article  Google Scholar 

  • Kintanar A, Alam TM, Huang W, Schindele DC, Wemmer DE, Drobny GP (1988) Solid-state 2H NMR investigation of internal motion. J Am Chem Soc 110:6367–6372

    Article  Google Scholar 

  • Kintanar A, Huang WC, Schindele DC, Wemmer DE, Drobny GP (1989) Dynamics of bases in hydrated [d(CGCGAATTCGCG)]2. Biochemistry 28:282–293

    Article  Google Scholar 

  • Korzhnev DM, Skrynnikov NR, Millet O, Torchia DA, Kay LE (2002) An NMR experiment for the accurate measurement of heteronuclear spin-lock relaxation rates. J Am Chem Soc 124:10743–10753

    Article  Google Scholar 

  • Leulliot N, Varani G (2001) Current topics in RNA-protein recognition: control of specificity and biological function through induced fit and conformational capture. Biochemistry 40(27):7947–7956

    Article  Google Scholar 

  • Merritt ME, Sigurdsson ST, Drobny GP (1999) Long-range measurements to the phosphodiester backbone of solid nucleic acids using 31P–19F REDOR NMR. J Am Chem Soc 121:6070–6071

    Article  Google Scholar 

  • Milligan JF, Uhlenbeck OC (1989) Synthesis of small RNAs using T7 RNA polymerase and synthetic DNA templates. Methods Enzymol 180:51–62

    Article  Google Scholar 

  • Milligan JF, Groebe DR, Witherell WG, Uhlenbeck OC (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783–8798

    Article  Google Scholar 

  • Noeske J, Buck J, Furtig B, Nasiri HR, Schwalbe H, Wohnert J (2007) Interplay of ‘Induced Fit’ and preorganization in the ligand induced folding of the aptamer domain of the guanine binding riboswitch. Nucleic Acids Res 35:572–583

    Article  Google Scholar 

  • Olsen GL, Edwards TE, Deka P, Varani G, Sigurdsson ST, Drobny GP (2005) Monitoring tat peptide binding to TAR RNA by solid-state 31P–19F REDOR NMR. Nucleic Acids Res 33(11):3447–3454

    Article  Google Scholar 

  • Olsen GL, Echodu DC, Shajani Z, Bardaro MF Jr, Varani G, Drobny GP (2008) Solid-state deuterium NMR studies reveal micros-ns motions in the HIV-1 transactivation response RNA recognition site. J Am Chem Soc 10:2896–2897

    Article  Google Scholar 

  • Palmer AGIII (2001) NMR probes of molecular dynamics: overview and comparison with other techniques. Annu Rev Biophys Biomol Struct 30:129–155

    Article  Google Scholar 

  • Palmer AGIII (2004) NMR characterization of the dynamics of biomacromolecules. Chem Rev 104:3623–3640

    Article  Google Scholar 

  • Palmer AGIII, Wagner G (1992) Mapping of spectral density functions using heteronuclear NMR relaxation experiments. J Magn Res 98:308–332

    Google Scholar 

  • Palmer AGIII, Williams J, McDermott A (1996) Nuclear magnetic resonance studies of biopolymer dynamics. J Phys Chem 100:13293–13310

    Article  Google Scholar 

  • Pitt SW, Majumdar A, Serganov A, Patel DJ, Al-Hashimi HM (2004) Argininamide binding arrests global motions in HIV-1 TAR RNA: comparison with Mg+2-induced conformational stabilization. J Mol Biol 338:7–16

    Article  Google Scholar 

  • Puglisi JD, Tan R, Calnan BJ, Frankel AD, Williamson JR (1992) Conformation of the TAR RNA-arginine complex by NMR spectroscopy. Science 257:76–80

    Article  ADS  Google Scholar 

  • Puglisi JD, Chen L, Frankel AD, Williamson JR (1993) Role of RNA structure in arginine recognition of TAR RNA. PNAS 90(8):3680–3684

    Article  ADS  Google Scholar 

  • Saenger W (1984) Principles of nucleic acid structure. Springer, New York

    Google Scholar 

  • Shajani Z, Varani G (2005) 13C NMR relaxation studies of RNA base and ribose nuclei reveal a complex pattern of motions in the RNA binding site for human U1A protein. J Mol Biol 349(4):699–715

    Article  Google Scholar 

  • Shajani Z, Varani G (2007) NMR studies of dynamics in RNA and DNA by 13C relaxation. Biopolymers 86:348–359

    Article  Google Scholar 

  • Tsang P, Kearns KR, Vold RR (1992) Deuterium quadrupole echo NMR spectra and spin-lattice relaxation of synthetic polyribonucleotides. J Am Chem Soc 114:6585–6587

    Article  Google Scholar 

  • Vold RR, Vold RL (1991) Deuterium relaxation in molecular solids. Adv Magn Opt Reson 16:85–171

    Google Scholar 

  • Wang AC, Kennedy MA, Reid BR, Drobny GP (1992) A solid-state 2H NMR relaxation study of a 12 base pair RNA duplex. J Am Chem Soc 114:6583–6585

    Article  Google Scholar 

  • Wang AC, Kennedy MA, Reid DR, Drobny GP (1994) A solid-state 2H NMR investigation of purine motion in a 12-base-pair RNA duplex. Journal of Magnetic Resonance B 105:1–10

    Article  Google Scholar 

  • Weast RC (1979) Handbook of chemistry and physics. CRC Press, Boca Raton

  • Williamson JR (2000) Induced-fit in RNA-protein recognition. Nature Struct Biol 7:834–837

    Article  Google Scholar 

  • Wimperis S, Bodenhausen G (1986) Broadband excitation of quadrupolar order by modified Jeener-Broekaert sequences. Chem Phys Lett 132:194–199

    Article  ADS  Google Scholar 

  • Zhang Q, Sun X, Watt ED, Al-Hashimi HM (2006) Resolving the motional modes that code for RNA adaption. Science 311:653–656

    Article  ADS  Google Scholar 

  • Zhang Q, Stelzer AC, Fisher CK, Al-Hashimi HM (2007) Visualizing spatially correlated dynamics that directs RNA conformational transitions. Nature 450:1263–1268

    Article  ADS  Google Scholar 

Download references

Acknowledgements

We thank professors J Michael Schurr and Bruce Robinson for helpful discussions of hydration and interpretation of relaxation data. This work was supported by a grant from the NSF MCB 0642253.

Author information

Authors and Affiliations

  1. Department of Chemistry, University of Washington, Box 351700, Seattle, WA, 98195, USA

    Greg L. Olsen, Michael F. Bardaro Jr., Dorothy C. Echodu, Gary P. Drobny & Gabriele Varani

  2. Department of Biochemistry, University of Washington, Box 357350, Seattle, WA, 98195, USA

    Gabriele Varani

Authors
  1. Greg L. Olsen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Michael F. Bardaro Jr.
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Dorothy C. Echodu
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Gary P. Drobny
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gabriele Varani
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Gary P. Drobny or Gabriele Varani.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Olsen, G.L., Bardaro, M.F., Echodu, D.C. et al. Hydration dependent dynamics in RNA. J Biomol NMR 45, 133–142 (2009). https://doi.org/10.1007/s10858-009-9355-6

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s10858-009-9355-6

Keywords

Search

Navigation