Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Jul 1;26(13):3104–3110. doi: 10.1093/nar/26.13.3104

The orientation and dynamics of the C2'-OH and hydration of RNA and DNA.RNA hybrids.

J I Gyi 1, A N Lane 1, G L Conn 1, T Brown 1
PMCID: PMC147665  PMID: 9628906

Abstract

The stereochemical and dynamic properties of the C2' hydroxyl group in several DNA.RNA hybrids have been measured by NMR and compared with the homologous RNA duplex. The C2'-OH NMR signals of the RNA strands were identified, and numerous specific assignments were made. The rate constants for exchange of the hydroxyl protons with water were determined at 5 degrees C, and were found to depend on both the position within a particular sequence and the nature of the duplex. On average, the exchange rate constants were slowest for the hybrids of composition rR.dY, and fastest for the RNA duplex, with an overall range of approximately 10-50/s. In the DNA.RNA hybrids, strong NOEs and ROEs were observed between the OH and the H1' of the same sugar, unambiguously showing that the OH proton points toward the H1' most of the time, and not toward the O3' of the same sugar. Evidence for significant hydration in both grooves of the DNA.RNA hybrids and the DNA duplex was found in ROESY and NOESY experiments. On average, the minor groove of the DNA.RNA hybrids showed more kinetically significant hydration than the DNA, which can be attributed to the hydrophilic lining of hydroxyl groups in RNA.

Full Text

The Full Text of this article is available as a PDF (908.7 KB).

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Auffinger P., Westhof E. RNA hydration: three nanoseconds of multiple molecular dynamics simulations of the solvated tRNA(Asp) anticodon hairpin. J Mol Biol. 1997 Jun 13;269(3):326–341. doi: 10.1006/jmbi.1997.1022. [DOI] [PubMed] [Google Scholar]
  2. Auffinger P., Westhof E. Rules governing the orientation of the 2'-hydroxyl group in RNA. J Mol Biol. 1997 Nov 21;274(1):54–63. doi: 10.1006/jmbi.1997.1370. [DOI] [PubMed] [Google Scholar]
  3. Chalikian T. V., Sarvazyan A. P., Plum G. E., Breslauer K. J. Influence of base composition, base sequence, and duplex structure on DNA hydration: apparent molar volumes and apparent molar adiabatic compressibilities of synthetic and natural DNA duplexes at 25 degrees C. Biochemistry. 1994 Mar 8;33(9):2394–2401. doi: 10.1021/bi00175a007. [DOI] [PubMed] [Google Scholar]
  4. Conte M. R., Conn G. L., Brown T., Lane A. N. Conformational properties and thermodynamics of the RNA duplex r(CGCAAAUUUGCG)2: comparison with the DNA analogue d(CGCAAATTTGCG)2. Nucleic Acids Res. 1997 Jul 1;25(13):2627–2634. doi: 10.1093/nar/25.13.2627. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Conte M. R., Conn G. L., Brown T., Lane A. N. Hydration of the RNA duplex r(CGCAAAUUUGCG)2 determined by NMR. Nucleic Acids Res. 1996 Oct 1;24(19):3693–3699. doi: 10.1093/nar/24.19.3693. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Egli M., Portmann S., Usman N. RNA hydration: a detailed look. Biochemistry. 1996 Jul 2;35(26):8489–8494. doi: 10.1021/bi9607214. [DOI] [PubMed] [Google Scholar]
  7. Fawthrop S. A., Yang J. C., Fisher J. Structural and dynamic studies of a non-self-complementary dodecamer DNA duplex. Nucleic Acids Res. 1993 Oct 25;21(21):4860–4866. doi: 10.1093/nar/21.21.4860. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Fedoroff OYu, Salazar M., Reid B. R. Structure of a DNA:RNA hybrid duplex. Why RNase H does not cleave pure RNA. J Mol Biol. 1993 Oct 5;233(3):509–523. doi: 10.1006/jmbi.1993.1528. [DOI] [PubMed] [Google Scholar]
  9. Fedoroff O. Y., Ge Y., Reid B. R. Solution structure of r(gaggacug):d(CAGTCCTC) hybrid: implications for the initiation of HIV-1 (+)-strand synthesis. J Mol Biol. 1997 Jun 6;269(2):225–239. doi: 10.1006/jmbi.1997.1024. [DOI] [PubMed] [Google Scholar]
  10. González C., Stec W., Kobylanska A., Hogrefe R. I., Reynolds M., James T. L. Structural study of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety by NMR: extraction of distance and torsion angle constraints and imino proton exchange rates. Biochemistry. 1994 Sep 20;33(37):11062–11072. doi: 10.1021/bi00203a002. [DOI] [PubMed] [Google Scholar]
  11. González C., Stec W., Reynolds M. A., James T. L. Structure and dynamics of a DNA.RNA hybrid duplex with a chiral phosphorothioate moiety: NMR and molecular dynamics with conventional and time-averaged restraints. Biochemistry. 1995 Apr 18;34(15):4969–4982. doi: 10.1021/bi00015a008. [DOI] [PubMed] [Google Scholar]
  12. Gyi J. I., Conn G. L., Lane A. N., Brown T. Comparison of the thermodynamic stabilities and solution conformations of DNA.RNA hybrids containing purine-rich and pyrimidine-rich strands with DNA and RNA duplexes. Biochemistry. 1996 Sep 24;35(38):12538–12548. doi: 10.1021/bi960948z. [DOI] [PubMed] [Google Scholar]
  13. Gyi J. I., Lane A. N., Conn G. L., Brown T. Solution structures of DNA.RNA hybrids with purine-rich and pyrimidine-rich strands: comparison with the homologous DNA and RNA duplexes. Biochemistry. 1998 Jan 6;37(1):73–80. doi: 10.1021/bi9719713. [DOI] [PubMed] [Google Scholar]
  14. Lane A. N., Ebel S., Brown T. NMR assignments and solution conformation of the DNA.RNA hybrid duplex d(GTGAACTT).r(AAGUUCAC). Eur J Biochem. 1993 Jul 15;215(2):297–306. doi: 10.1111/j.1432-1033.1993.tb18035.x. [DOI] [PubMed] [Google Scholar]
  15. Lane A. N., Jenkins T. C., Frenkiel T. A. Hydration and solution structure of d(CGCAAATTTGCG)2 and its complex with propamidine from NMR and molecular modelling. Biochim Biophys Acta. 1997 Feb 7;1350(2):205–220. doi: 10.1016/s0167-4781(96)00161-3. [DOI] [PubMed] [Google Scholar]
  16. Lane A. N. The determination of the conformational properties of nucleic acids in solution from NMR data. Biochim Biophys Acta. 1990 Jun 21;1049(2):189–204. doi: 10.1016/0167-4781(90)90040-9. [DOI] [PubMed] [Google Scholar]
  17. Leonard G. A., McAuley-Hecht K. E., Ebel S., Lough D. M., Brown T., Hunter W. N. Crystal and molecular structure of r(CGCGAAUUAGCG): an RNA duplex containing two G(anti).A(anti) base pairs. Structure. 1994 Jun 15;2(6):483–494. doi: 10.1016/S0969-2126(00)00049-6. [DOI] [PubMed] [Google Scholar]
  18. Lesnik E. A., Freier S. M. Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure. Biochemistry. 1995 Aug 29;34(34):10807–10815. doi: 10.1021/bi00034a013. [DOI] [PubMed] [Google Scholar]
  19. Liepinsh E., Leupin W., Otting G. Hydration of DNA in aqueous solution: NMR evidence for a kinetic destabilization of the minor groove hydration of d-(TTAA)2 versus d-(AATT)2 segments. Nucleic Acids Res. 1994 Jun 25;22(12):2249–2254. doi: 10.1093/nar/22.12.2249. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Liepinsh E., Otting G., Wüthrich K. NMR observation of individual molecules of hydration water bound to DNA duplexes: direct evidence for a spine of hydration water present in aqueous solution. Nucleic Acids Res. 1992 Dec 25;20(24):6549–6553. doi: 10.1093/nar/20.24.6549. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978 May;11(2):179–246. doi: 10.1017/s0033583500002031. [DOI] [PubMed] [Google Scholar]
  22. Piotto M., Saudek V., Sklenár V. Gradient-tailored excitation for single-quantum NMR spectroscopy of aqueous solutions. J Biomol NMR. 1992 Nov;2(6):661–665. doi: 10.1007/BF02192855. [DOI] [PubMed] [Google Scholar]
  23. Privé G. G., Heinemann U., Chandrasegaran S., Kan L. S., Kopka M. L., Dickerson R. E. Helix geometry, hydration, and G.A mismatch in a B-DNA decamer. Science. 1987 Oct 23;238(4826):498–504. doi: 10.1126/science.3310237. [DOI] [PubMed] [Google Scholar]
  24. Ratmeyer L., Vinayak R., Zhong Y. Y., Zon G., Wilson W. D. Sequence specific thermodynamic and structural properties for DNA.RNA duplexes. Biochemistry. 1994 May 3;33(17):5298–5304. doi: 10.1021/bi00183a037. [DOI] [PubMed] [Google Scholar]
  25. Record M. T., Jr, Anderson C. F., Lohman T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys. 1978 May;11(2):103–178. doi: 10.1017/s003358350000202x. [DOI] [PubMed] [Google Scholar]
  26. Salazar M., Champoux J. J., Reid B. R. Sugar conformations at hybrid duplex junctions in HIV-1 and Okazaki fragments. Biochemistry. 1993 Jan 26;32(3):739–744. doi: 10.1021/bi00054a002. [DOI] [PubMed] [Google Scholar]
  27. Salazar M., Fedoroff O. Y., Miller J. M., Ribeiro N. S., Reid B. R. The DNA strand in DNA.RNA hybrid duplexes is neither B-form nor A-form in solution. Biochemistry. 1993 Apr 27;32(16):4207–4215. doi: 10.1021/bi00067a007. [DOI] [PubMed] [Google Scholar]
  28. Searle M. S., Williams D. H. On the stability of nucleic acid structures in solution: enthalpy-entropy compensations, internal rotations and reversibility. Nucleic Acids Res. 1993 May 11;21(9):2051–2056. doi: 10.1093/nar/21.9.2051. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Wahl M. C., Ban C., Sekharudu C., Ramakrishnan B., Sundaralingam M. Structure of the purine-pyrimidine alternating RNA double helix, r(GUAUAUA)d(C), with a 3'-terminal deoxy residue. Acta Crystallogr D Biol Crystallogr. 1996 Jul 1;52(Pt 4):655–667. doi: 10.1107/S0907444996000248. [DOI] [PubMed] [Google Scholar]

Articles from Nucleic Acids Research are provided here courtesy of Oxford University Press

RESOURCES