Skip to main content
PMC home page
RNA logoLink to RNA
. 2000 Nov;6(11):1516–1528. doi: 10.1017/s1355838200001114

Crystal structure of an RNA duplex containing phenyl-ribonucleotides, hydrophobic isosteres of the natural pyrimidines.

G Minasov 1, J Matulic-Adamic 1, C J Wilds 1, P Haeberli 1, N Usman 1, L Beigelman 1, M Egli 1
PMCID: PMC1370022  PMID: 11105752

Abstract

Chemically modified nucleotide analogs have gained widespread popularity for probing structure-function relationships. Among the modifications that were incorporated into RNAs for assessing the role of individual functional groups, the phenyl nucleotide has displayed surprising effects both in the contexts of the hammerhead ribozyme and pre-mRNA splicing. To examine the conformational properties of this hydrophobic base analog, we determined the crystal structure of an RNA double helix with incorporated phenyl ribonucleotides at 1.97 A resolution. In the structure, phenyl residues are engaged in self-pairing and their arrangements suggest energetically favorable stacking interactions with 3'-adjacent guanines. The presence of the phenyl rings in the center of the duplex results in only moderate changes of the helical geometry. This finding is in line with those of earlier experiments that showed the phenyl analog to be a remarkably good mimetic of natural base function. Because the stacking interactions displayed by phenyl residues appear to be similar to those for natural bases, reduced conformational restriction due to the lack of hydrogen bonds with phenyl as well as alterations in its solvent structure may be the main causes of the activity changes with phenyl-modified RNAs.

Full Text

The Full Text of this article is available as a PDF (3.9 MB).

Selected References

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

  1. Baidya N., Ammons G. E., Matulic-Adamic J., Karpeisky A. M., Beigelman L., Uhlenbeck O. C. Functional groups on the cleavage site pyrimidine nucleotide are required for stabilization of the hammerhead transition state. RNA. 1997 Oct;3(10):1135–1142. [PMC free article] [PubMed] [Google Scholar]
  2. Bennett C. F., Cowsert L. M. Antisense oligonucleotides as a tool for gene functionalization and target validation. Biochim Biophys Acta. 1999 Dec 10;1489(1):19–30. doi: 10.1016/s0167-4781(99)00144-x. [DOI] [PubMed] [Google Scholar]
  3. Burgin A. B., Jr, Gonzalez C., Matulic-Adamic J., Karpeisky A. M., Usman N., McSwiggen J. A., Beigelman L. Chemically modified hammerhead ribozymes with improved catalytic rates. Biochemistry. 1996 Nov 12;35(45):14090–14097. doi: 10.1021/bi961264u. [DOI] [PubMed] [Google Scholar]
  4. Burley S. K., Petsko G. A. Aromatic-aromatic interaction: a mechanism of protein structure stabilization. Science. 1985 Jul 5;229(4708):23–28. doi: 10.1126/science.3892686. [DOI] [PubMed] [Google Scholar]
  5. Cate J. H., Gooding A. R., Podell E., Zhou K., Golden B. L., Kundrot C. E., Cech T. R., Doudna J. A. Crystal structure of a group I ribozyme domain: principles of RNA packing. Science. 1996 Sep 20;273(5282):1678–1685. doi: 10.1126/science.273.5282.1678. [DOI] [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. Elghanian R., Storhoff J. J., Mucic R. C., Letsinger R. L., Mirkin C. A. Selective colorimetric detection of polynucleotides based on the distance-dependent optical properties of gold nanoparticles. Science. 1997 Aug 22;277(5329):1078–1081. doi: 10.1126/science.277.5329.1078. [DOI] [PubMed] [Google Scholar]
  8. Eschenmoser A. Chemical etiology of nucleic acid structure. Science. 1999 Jun 25;284(5423):2118–2124. doi: 10.1126/science.284.5423.2118. [DOI] [PubMed] [Google Scholar]
  9. Gaur R. K., Beigelman L., Haeberli P., Maniatis T. Role of adenine functional groups in the recognition of the 3'-splice-site AG during the second step of pre-mRNA splicing. Proc Natl Acad Sci U S A. 2000 Jan 4;97(1):115–120. doi: 10.1073/pnas.97.1.115. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Guckian K. M., Krugh T. R., Kool E. T. Solution structure of a DNA duplex containing a replicable difluorotoluene-adenine pair. Nat Struct Biol. 1998 Nov;5(11):954–959. doi: 10.1038/2930. [DOI] [PubMed] [Google Scholar]
  11. Hall J., Hüsken D., Häner R. Towards artificial ribonucleases: the sequence-specific cleavage of RNA in a duplex. Nucleic Acids Res. 1996 Sep 15;24(18):3522–3526. doi: 10.1093/nar/24.18.3522. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Lavery R., Sklenar H. Defining the structure of irregular nucleic acids: conventions and principles. J Biomol Struct Dyn. 1989 Feb;6(4):655–667. doi: 10.1080/07391102.1989.10507728. [DOI] [PubMed] [Google Scholar]
  13. Marky L. A., Breslauer K. J. Calculating thermodynamic data for transitions of any molecularity from equilibrium melting curves. Biopolymers. 1987 Sep;26(9):1601–1620. doi: 10.1002/bip.360260911. [DOI] [PubMed] [Google Scholar]
  14. Matray T. J., Kool E. T. A specific partner for abasic damage in DNA. Nature. 1999 Jun 17;399(6737):704–708. doi: 10.1038/21453. [DOI] [PubMed] [Google Scholar]
  15. Matulic-Adamic Jasenka, Beigelman Leonid, Portmann Stefan, Egli Martin, Usman Nassim. Synthesis and Structure of 1-Deoxy-1-phenyl-beta-D-ribofuranose and Its Incorporation into Oligonucleotides. J Org Chem. 1996 May 31;61(11):3909–3911. doi: 10.1021/jo960091b. [DOI] [PubMed] [Google Scholar]
  16. Morales J. C., Kool E. T. Efficient replication between non-hydrogen-bonded nucleoside shape analogs. Nat Struct Biol. 1998 Nov;5(11):950–954. doi: 10.1038/2925. [DOI] [PubMed] [Google Scholar]
  17. Murray J. B., Terwey D. P., Maloney L., Karpeisky A., Usman N., Beigelman L., Scott W. G. The structural basis of hammerhead ribozyme self-cleavage. Cell. 1998 Mar 6;92(5):665–673. doi: 10.1016/s0092-8674(00)81134-4. [DOI] [PubMed] [Google Scholar]
  18. Myers K. J., Dean N. M. Sensible use of antisense: how to use oligonucleotides as research tools. Trends Pharmacol Sci. 2000 Jan;21(1):19–23. doi: 10.1016/s0165-6147(99)01420-0. [DOI] [PubMed] [Google Scholar]
  19. Parkinson G., Vojtechovsky J., Clowney L., Brünger A. T., Berman H. M. New parameters for the refinement of nucleic acid-containing structures. Acta Crystallogr D Biol Crystallogr. 1996 Jan 1;52(Pt 1):57–64. doi: 10.1107/S0907444995011115. [DOI] [PubMed] [Google Scholar]
  20. Peracchi A., Matulic-Adamic J., Wang S., Beigelman L., Herschlag D. Structure-function relationships in the hammerhead ribozyme probed by base rescue. RNA. 1998 Nov;4(11):1332–1346. doi: 10.1017/s1355838298980979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Petersheim M., Turner D. H. Base-stacking and base-pairing contributions to helix stability: thermodynamics of double-helix formation with CCGG, CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):256–263. doi: 10.1021/bi00271a004. [DOI] [PubMed] [Google Scholar]
  22. Pley H. W., Flaherty K. M., McKay D. B. Three-dimensional structure of a hammerhead ribozyme. Nature. 1994 Nov 3;372(6501):68–74. doi: 10.1038/372068a0. [DOI] [PubMed] [Google Scholar]
  23. Portmann S., Usman N., Egli M. The crystal structure of r(CCCCGGGG) in two distinct lattices. Biochemistry. 1995 Jun 13;34(23):7569–7575. doi: 10.1021/bi00023a002. [DOI] [PubMed] [Google Scholar]
  24. Scott W. G., Finch J. T., Klug A. The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell. 1995 Jun 30;81(7):991–1002. doi: 10.1016/s0092-8674(05)80004-2. [DOI] [PubMed] [Google Scholar]
  25. Scott W. G., Murray J. B., Arnold J. R., Stoddard B. L., Klug A. Capturing the structure of a catalytic RNA intermediate: the hammerhead ribozyme. Science. 1996 Dec 20;274(5295):2065–2069. doi: 10.1126/science.274.5295.2065. [DOI] [PubMed] [Google Scholar]
  26. Strauss J. K., Prakash T. P., Roberts C., Switzer C., Maher L. J. DNA bending by a phantom protein. Chem Biol. 1996 Aug;3(8):671–678. doi: 10.1016/s1074-5521(96)90135-0. [DOI] [PubMed] [Google Scholar]
  27. Sugimoto N., Kierzek R., Turner D. H. Sequence dependence for the energetics of dangling ends and terminal base pairs in ribonucleic acid. Biochemistry. 1987 Jul 14;26(14):4554–4558. doi: 10.1021/bi00388a058. [DOI] [PubMed] [Google Scholar]
  28. Taylor MF, Wiederholt K, Sverdrup F. Antisense oligonucleotides: a systematic high-throughput approach to target validation and gene function determination. Drug Discov Today. 1999 Dec;4(12):562–567. doi: 10.1016/s1359-6446(99)01392-6. [DOI] [PubMed] [Google Scholar]
  29. Turner D. H. Thermodynamics of base pairing. Curr Opin Struct Biol. 1996 Jun;6(3):299–304. doi: 10.1016/s0959-440x(96)80047-9. [DOI] [PubMed] [Google Scholar]
  30. Wincott F., DiRenzo A., Shaffer C., Grimm S., Tracz D., Workman C., Sweedler D., Gonzalez C., Scaringe S., Usman N. Synthesis, deprotection, analysis and purification of RNA and ribozymes. Nucleic Acids Res. 1995 Jul 25;23(14):2677–2684. doi: 10.1093/nar/23.14.2677. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from RNA are provided here courtesy of The RNA Society

RESOURCES