Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1984 Oct 25;12(20):7793–7810. doi: 10.1093/nar/12.20.7793

Synthesis and conformational studies of ribooligonucleotides which contain an alternating C-G sequence and show unusual circular dichroism spectra.

S Uesugi, M Ohkubo, E Ohtsuka, M Ikehara, Y Kobayashi, Y Kyogoku
PMCID: PMC320201  PMID: 6493981

Abstract

The poly [r(C-G)] duplex shows an unusually large negative CD band in the long wavelength region. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized by a phosphotriester method and their properties were examined by UV, CD, 1H and 31P NMR spectroscopy. These ribooligomers form self-duplexes at low temperature, the CD spectra of which show negative bands at around 290 nm and positive bands at around 265 nm. The results of 1H nuclear Overhauser effect experiments, 1H chemical shift-temperature profiles of base protons, and the sharp singlet observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. The CD-temperature profiles and 31P NMR spectra support this conclusion. These results indicate that RNA duplexes with an alternating C-G sequence can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.

Full text

PDF
7793

Selected References

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

  1. Altona C., Sundaralingam M. Conformational analysis of the sugar ring in nucleosides and nucleotides. Improved method for the interpretation of proton magnetic resonance coupling constants. J Am Chem Soc. 1973 Apr 4;95(7):2333–2344. doi: 10.1021/ja00788a038. [DOI] [PubMed] [Google Scholar]
  2. Bubienko E., Uniack M. A., Borer P. N. Sequence and structure in double-stranded ribonucleic acid: (A-G-C-U)2 and (A-C-G-U)2. Biochemistry. 1981 Nov 24;20(24):6987–6994. doi: 10.1021/bi00527a032. [DOI] [PubMed] [Google Scholar]
  3. Frechet D., Cheng D. M., Kan L. S., Ts'o P. O. Nuclear Overhauser effect as a tool for the complete assignment of nonexchangeable proton resonances in short deoxyribonucleic acid helices. Biochemistry. 1983 Oct 25;22(22):5194–5200. doi: 10.1021/bi00291a020. [DOI] [PubMed] [Google Scholar]
  4. Gray D. M., Tinoco I., Jr, Chamberlin M. J. The circular dichroism of synthetic ribonucleic acids and the influence of uracil on conformation. Biopolymers. 1972;11(6):1235–1258. doi: 10.1002/bip.1972.360110609. [DOI] [PubMed] [Google Scholar]
  5. Ohtsuka E., Yamane A., Ikehara M. Studies on transfer ribonucleic acids and related compounds. XLV. Block condensation of ribooligonucleotides containing 2'-O-tetrahydrofuranyl-5'-O-dimethoxytritylnucleosides. Nucleic Acids Res. 1983 Mar 11;11(5):1325–1335. doi: 10.1093/nar/11.5.1325. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Patel D. J., Kozlowski S. A., Nordheim A., Rich A. Right-handed and left-handed DNA: studies of B- and Z-DNA by using proton nuclear Overhauser effect and P NMR. Proc Natl Acad Sci U S A. 1982 Mar;79(5):1413–1417. doi: 10.1073/pnas.79.5.1413. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Patel D. J. d-CpCpGpG and d-GpGpCpC self-complementary duplexes: Nmr studies of the helix-coil transition. Biopolymers. 1977 Aug;16(8):1635–1656. doi: 10.1002/bip.1977.360160804. [DOI] [PubMed] [Google Scholar]
  8. Petersheim M., Turner D. H. Proton magnetic resonance melting studies of CCGGp, CCGGAp, ACCGGp, CCGGUp, and ACCGGUp. Biochemistry. 1983 Jan 18;22(2):269–277. doi: 10.1021/bi00271a006. [DOI] [PubMed] [Google Scholar]
  9. Pohl F. M., Jovin T. M. Salt-induced co-operative conformational change of a synthetic DNA: equilibrium and kinetic studies with poly (dG-dC). J Mol Biol. 1972 Jun 28;67(3):375–396. doi: 10.1016/0022-2836(72)90457-3. [DOI] [PubMed] [Google Scholar]
  10. Sanger F., Donelson J. E., Coulson A. R., Kössel H., Fischer D. Use of DNA polymerase I primed by a synthetic oligonucleotide to determine a nucleotide sequence in phage fl DNA. Proc Natl Acad Sci U S A. 1973 Apr;70(4):1209–1213. doi: 10.1073/pnas.70.4.1209. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Silberklang M., Gillum A. M., RajBhandary U. L. The use of nuclease P1 in sequence analysis of end group labeled RNA. Nucleic Acids Res. 1977 Dec;4(12):4091–4108. doi: 10.1093/nar/4.12.4091. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Simpson R. T., Shindo H. Conformation of 145 base pair length poly (dG-dC) . poly (dG-dC) in solution and in association with histones. Nucleic Acids Res. 1980 May 10;8(9):2093–2103. doi: 10.1093/nar/8.9.2093. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. TOMLINSON R. V., TENER G. M. THE EFFECT OF UREA, FORMAMIDE, AND GLYCOLS ON THE SECONDARY BINDING FORCES IN THE ION-EXCHANGE CHROMATOGRAPHY OF POLYNUCLEOTIDES OF DEAE-CELLULOSE. Biochemistry. 1963 Jul-Aug;2:697–702. doi: 10.1021/bi00904a013. [DOI] [PubMed] [Google Scholar]
  14. Thamann T. J., Lord R. C., Wang A. H., Rich A. The high salt form of poly(dG-dC).poly(dG-dC) is left-handed Z-DNA: Raman spectra of crystals and solutions. Nucleic Acids Res. 1981 Oct 24;9(20):5443–5457. doi: 10.1093/nar/9.20.5443. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Uesugi S., Ohkubo M., Ohtsuka E., Ikehara M., Kobayashi Y., Kyogoku Y., Westerink H. P., van der Marel G. A., van Boom J. H., Haasnoot C. A. Conformation of ribooligonucleotide duplexes containing an alternating C-G sequence which show an unusual circular dichroism spectrum. J Biol Chem. 1984 Feb 10;259(3):1390–1393. [PubMed] [Google Scholar]
  16. Uesugi S., Shida T., Ikehara M. Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation. Biochemistry. 1982 Jul 6;21(14):3400–3408. doi: 10.1021/bi00257a024. [DOI] [PubMed] [Google Scholar]
  17. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
  18. Wang A. J., Quigley G. J., Kolpak F. J., van der Marel G., van Boom J. H., Rich A. Left-handed double helical DNA: variations in the backbone conformation. Science. 1981 Jan 9;211(4478):171–176. doi: 10.1126/science.7444458. [DOI] [PubMed] [Google Scholar]
  19. Westerink H. P., van der Marel G. A., van Boom J. H., Haasnoot C. A. Conformational analysis of r(CGCGCG) in aqueous solution: an A-type double helical conformation studied by two-dimensional nuclear Overhauser effect spectroscopy. Nucleic Acids Res. 1984 May 25;12(10):4323–4338. doi: 10.1093/nar/12.10.4323. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES