Skip to main content
NCBI home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1998 Aug 15;26(16):3677–3686. doi: 10.1093/nar/26.16.3677

Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets.

J L Asensio 1, T Brown 1, A N Lane 1
PMCID: PMC147772  PMID: 9685482

Abstract

The solution conformations of the intramolecular triple helices d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X = non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O showed that the third strand cytosine residues are fully paired with the guanine residues, each using two Hoogsteen hydrogen bonds. Determination of the13C chemical shifts of the cytosine C6 and C5 and their one-bond coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine residues are protonated at N3. The global conformations of the two molecules determined with >19 restraints per residue are very similar (RMSD = 0.96 A). However, some differences in local conformation and dynamics were observed for the central two base triplets of the two molecules. The C N3H were less labile in adjacent CG.C+triplets than in non-adjacent ones, indicating that the adjacent charge does not kinetically destabilize these triplets. The sugar conformations of the two adjacent cytosine residues were different and the 5'-residue was atypical of protonated cytosine. Hence, there are subtle effects of the interaction between two adjacent cytosine residues. The central two purines in each sequence showed non-standard backbone conformations, averaging between gamma approximately 60 degrees and gamma approximately 180 degrees. This may be related to the difference in the dependence of the thermodynamic stability on pH observed for these two sequences.

Full Text

The Full Text of this article is available as a PDF (1.1 MB).

Selected References

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

  1. Asensio J. L., Lane A. N., Dhesi J., Bergqvist S., Brown T. The contribution of cytosine protonation to the stability of parallel DNA triple helices. J Mol Biol. 1998 Feb 6;275(5):811–822. doi: 10.1006/jmbi.1997.1520. [DOI] [PubMed] [Google Scholar]
  2. Bartley J. P., Brown T., Lane A. N. Solution conformation of an intramolecular DNA triplex containing a nonnucleotide linker: comparison with the DNA duplex. Biochemistry. 1997 Nov 25;36(47):14502–14511. doi: 10.1021/bi970710q. [DOI] [PubMed] [Google Scholar]
  3. Conte M. R., Bauer C. J., Lane A. N. Determination of sugar conformations by NMR in larger DNA duplexes using both dipolar and scalar data: application to d(CATGTGACGTCACATG)2. J Biomol NMR. 1996 May;7(3):190–206. doi: 10.1007/BF00202036. [DOI] [PubMed] [Google Scholar]
  4. Durand M., Peloille S., Thuong N. T., Maurizot J. C. Triple-helix formation by an oligonucleotide containing one (dA)12 and two (dT)12 sequences bridged by two hexaethylene glycol chains. Biochemistry. 1992 Sep 29;31(38):9197–9204. doi: 10.1021/bi00153a012. [DOI] [PubMed] [Google Scholar]
  5. Feigon J., Koshlap K. M., Smith F. W. 1H NMR spectroscopy of DNA triplexes and quadruplexes. Methods Enzymol. 1995;261:225–255. doi: 10.1016/s0076-6879(95)61012-x. [DOI] [PubMed] [Google Scholar]
  6. Guéron M., Leroy J. L. Studies of base pair kinetics by NMR measurement of proton exchange. Methods Enzymol. 1995;261:383–413. doi: 10.1016/s0076-6879(95)61018-9. [DOI] [PubMed] [Google Scholar]
  7. 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]
  8. Ji J., Hogan M. E., Gao X. Solution structure of an antiparallel purine motif triplex containing a T.CG pyrimidine base triple. Structure. 1996 Apr 15;4(4):425–435. doi: 10.1016/s0969-2126(96)00048-2. [DOI] [PubMed] [Google Scholar]
  9. Kiessling L. L., Griffin L. C., Dervan P. B. Flanking sequence effects within the pyrimidine triple-helix motif characterized by affinity cleaving. Biochemistry. 1992 Mar 17;31(10):2829–2834. doi: 10.1021/bi00125a026. [DOI] [PubMed] [Google Scholar]
  10. Kim S. G., Reid B. R. Solution structure of the TnAn DNA duplex GCCGTTAACGCG containing the HpaI restriction site. Biochemistry. 1992 Dec 8;31(48):12103–12116. doi: 10.1021/bi00163a020. [DOI] [PubMed] [Google Scholar]
  11. Koshlap K. M., Schultze P., Brunar H., Dervan P. B., Feigon J. Solution structure of an intramolecular DNA triplex containing an N7-glycosylated guanine which mimics a protonated cytosine. Biochemistry. 1997 Mar 4;36(9):2659–2668. doi: 10.1021/bi962438a. [DOI] [PubMed] [Google Scholar]
  12. Nunn C. M., Trent J. O., Neidle S. A model for the [C+-GxC]n triple helix derived from observation of the C+-GxC base triplet in a crystal structure. FEBS Lett. 1997 Oct 13;416(1):86–89. doi: 10.1016/s0014-5793(97)01130-7. [DOI] [PubMed] [Google Scholar]
  13. Pilch D. S., Levenson C., Shafer R. H. Structural analysis of the (dA)10.2(dT)10 triple helix. Proc Natl Acad Sci U S A. 1990 Mar;87(5):1942–1946. doi: 10.1073/pnas.87.5.1942. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. 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]
  15. Plum G. E., Breslauer K. J. Thermodynamics of an intramolecular DNA triple helix: a calorimetric and spectroscopic study of the pH and salt dependence of thermally induced structural transitions. J Mol Biol. 1995 May 5;248(3):679–695. doi: 10.1006/jmbi.1995.0251. [DOI] [PubMed] [Google Scholar]
  16. Radhakrishnan I., Patel D. J. Solution structure of a purine.purine.pyrimidine DNA triplex containing G.GC and T.AT triples. Structure. 1993 Oct 15;1(2):135–152. doi: 10.1016/0969-2126(93)90028-f. [DOI] [PubMed] [Google Scholar]
  17. Radhakrishnan I., Patel D. J. Solution structure of a pyrimidine.purine.pyrimidine DNA triplex containing T.AT, C+.GC and G.TA triples. Structure. 1994 Jan 15;2(1):17–32. doi: 10.1016/s0969-2126(00)00005-8. [DOI] [PubMed] [Google Scholar]
  18. Roberts R. W., Crothers D. M. Prediction of the stability of DNA triplexes. Proc Natl Acad Sci U S A. 1996 Apr 30;93(9):4320–4325. doi: 10.1073/pnas.93.9.4320. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Schmitz U., James T. L. How to generate accurate solution structures of double-helical nucleic acid fragments using nuclear magnetic resonance and restrained molecular dynamics. Methods Enzymol. 1995;261:3–44. doi: 10.1016/s0076-6879(95)61003-0. [DOI] [PubMed] [Google Scholar]
  20. van Wijk J., Huckriede B. D., Ippel J. H., Altona C. Furanose sugar conformations in DNA from NMR coupling constants. Methods Enzymol. 1992;211:286–306. doi: 10.1016/0076-6879(92)11017-d. [DOI] [PubMed] [Google Scholar]

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

RESOURCES