Skip to main content
PMC home page
Nucleic Acids Research logoLink to Nucleic Acids Research
. 1997 Nov 15;25(22):4523–4531. doi: 10.1093/nar/25.22.4523

NMR determination of the conformational and drug binding properties of the DNA heptamer d(GpCpGpApApGpC) in aqueous solution.

D B Davies 1, V I Pahomov 1, A N Veselkov 1
PMCID: PMC147085  PMID: 9358161

Abstract

1D and 2D NMR spectroscopy (500/600 MHz) has been used to investigate the equilibrium conformational states of the deoxyheptanucleotide 5'-d(GpCpGpApApGpC), as well as its complexation with the phenanthridinium drug ethidium bromide (EB). Quantitative determination (reaction constants and thermodynamic parameters) of the conformational equilibrium of the heptamer in solution and its complexation with EB was based on analysis of the dependence of proton chemical shifts on concentration (at two temperatures, 298 and 308 K) and on temperature (in the range 278-353 K). The experimental results were analysed in terms of a model of the dynamic equilibrium between single-stranded, hairpin and bulged dimer forms of the deoxyheptanucleotide and its complexes with EB. Calculation of the relative amounts of the different complexes reveals important features of the dynamic equilibrium as a function of both temperature and the ratio of the drug and heptamer concentrations. The quantitative analysis also provides the limiting proton chemical shifts of EB in each complex which have been used to determine the most favourable structures of the intercalated complexes of EB with the (GC) sites of both the hairpin and dimer forms of the heptanucleotide.

Full Text

The Full Text of this article is available as a PDF (172.3 KB).

Selected References

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

  1. Arai K., Low R., Kobori J., Shlomai J., Kornberg A. Mechanism of dnaB protein action. V. Association of dnaB protein, protein n', and other repriming proteins in the primosome of DNA replication. J Biol Chem. 1981 May 25;256(10):5273–5280. [PubMed] [Google Scholar]
  2. Bianchi M. E., Beltrame M., Paonessa G. Specific recognition of cruciform DNA by nuclear protein HMG1. Science. 1989 Feb 24;243(4894 Pt 1):1056–1059. doi: 10.1126/science.2922595. [DOI] [PubMed] [Google Scholar]
  3. Breslauer K. J., Frank R., Blöcker H., Marky L. A. Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci U S A. 1986 Jun;83(11):3746–3750. doi: 10.1073/pnas.83.11.3746. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Bresloff J. L., Crothers D. M. Equilibrium studies of ethidium--polynucleotide interactions. Biochemistry. 1981 Jun 9;20(12):3547–3553. doi: 10.1021/bi00515a038. [DOI] [PubMed] [Google Scholar]
  5. Chastain M., Tinoco I., Jr Structural elements in RNA. Prog Nucleic Acid Res Mol Biol. 1991;41:131–177. doi: 10.1016/S0079-6603(08)60008-2. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chattopadhyaya R., Grzeskowiak K., Dickerson R. E. Structure of a T4 hairpin loop on a Z-DNA stem and comparison with A-RNA and B-DNA loops. J Mol Biol. 1990 Jan 5;211(1):189–210. doi: 10.1016/0022-2836(90)90020-M. [DOI] [PubMed] [Google Scholar]
  7. Cowing D. W., Bardwell J. C., Craig E. A., Woolford C., Hendrix R. W., Gross C. A. Consensus sequence for Escherichia coli heat shock gene promoters. Proc Natl Acad Sci U S A. 1985 May;82(9):2679–2683. doi: 10.1073/pnas.82.9.2679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Davies D. B., Karawajew L., Veselkov A. N. 1H-NMR structural analysis of ethidium bromide complexation with self-complementary deoxytetranucleotides 5'-d(ApCpGpT), 5'-d(ApGpCpT), and 5'-d(TpGpCpA) in aqueous solution. Biopolymers. 1996 Jun;38(6):745–757. doi: 10.1002/(sici)1097-0282(199602)38:6<745::aid-bip6>3.0.co;2-v. [DOI] [PubMed] [Google Scholar]
  9. Dickerson R. E. Definitions and nomenclature of nucleic acid structure parameters. J Biomol Struct Dyn. 1989 Feb;6(4):627–634. doi: 10.1080/07391102.1989.10507726. [DOI] [PubMed] [Google Scholar]
  10. Elias P., Lehman I. R. Interaction of origin binding protein with an origin of replication of herpes simplex virus 1. Proc Natl Acad Sci U S A. 1988 May;85(9):2959–2963. doi: 10.1073/pnas.85.9.2959. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Freier S. M., Albergo D. D., Turner D. H. Solvent effects on the dynamics of (dG-dC)3. Biopolymers. 1983 Apr;22(4):1107–1131. doi: 10.1002/bip.360220408. [DOI] [PubMed] [Google Scholar]
  12. Giessner-Prettre C., Pullman B. Quantum mechanical calculations of NMR chemical shifts in nucleic acids. Q Rev Biophys. 1987 Nov;20(3-4):113–172. doi: 10.1017/s0033583500004169. [DOI] [PubMed] [Google Scholar]
  13. Hirao I., Kawai G., Yoshizawa S., Nishimura Y., Ishido Y., Watanabe K., Miura K. Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat. Nucleic Acids Res. 1994 Feb 25;22(4):576–582. doi: 10.1093/nar/22.4.576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hirao I., Nishimura Y., Tagawa Y., Watanabe K., Miura K. Extraordinarily stable mini-hairpins: electrophoretical and thermal properties of the various sequence variants of d(GCGAAAGC) and their effect on DNA sequencing. Nucleic Acids Res. 1992 Aug 11;20(15):3891–3896. doi: 10.1093/nar/20.15.3891. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Jain S. C., Sobell H. M. Visualization of drug-nucleic acid interactions at atomic resolution. VII. Structure of an ethidium/dinucleoside monophosphate crystalline complex, ethidium: uridylyl(3'-5') adenosine. J Biomol Struct Dyn. 1984 Mar;1(5):1161–1177. doi: 10.1080/07391102.1984.10507510. [DOI] [PubMed] [Google Scholar]
  16. Lybrand T., Kollman P. Molecular mechanical calculations on the interaction of ethidium cation with double-helical DNA. Biopolymers. 1985 Oct;24(10):1863–1879. doi: 10.1002/bip.360241003. [DOI] [PubMed] [Google Scholar]
  17. McMurray C. T., Wilson W. D., Douglass J. O. Hairpin formation within the enhancer region of the human enkephalin gene. Proc Natl Acad Sci U S A. 1991 Jan 15;88(2):666–670. doi: 10.1073/pnas.88.2.666. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. 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]
  19. Poltev V. I., Teplukhin A. V. Vzaimodeistvie osnovanii i konformatsionnye proiavleniia posledovatel'nostei povtoriaiushchikhsia nukleotidov. Mol Biol (Mosk) 1987 Jan-Feb;21(1):102–115. [PubMed] [Google Scholar]
  20. Pramanik P., Kanhouwa N., Kan L. S. Hairpin and duplex formation in DNA fragments CCAATTTTGG, CCAATTTTTTGG, and CCATTTTTGG: a proton NMR study. Biochemistry. 1988 Apr 19;27(8):3024–3031. doi: 10.1021/bi00408a054. [DOI] [PubMed] [Google Scholar]
  21. Rentzeperis D., Alessi K., Marky L. A. Thermodynamics of DNA hairpins: contribution of loop size to hairpin stability and ethidium binding. Nucleic Acids Res. 1993 Jun 11;21(11):2683–2689. doi: 10.1093/nar/21.11.2683. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rentzeperis D., Medero M., Marky L. A. Thermodynamic investigation of the association of ethidium, propidium and bis-ethidium to DNA hairpins. Bioorg Med Chem. 1995 Jun;3(6):751–759. doi: 10.1016/0968-0896(95)00056-m. [DOI] [PubMed] [Google Scholar]
  23. Rosenberg M., Court D. Regulatory sequences involved in the promotion and termination of RNA transcription. Annu Rev Genet. 1979;13:319–353. doi: 10.1146/annurev.ge.13.120179.001535. [DOI] [PubMed] [Google Scholar]
  24. SantaLucia J., Jr, Kierzek R., Turner D. H. Context dependence of hydrogen bond free energy revealed by substitutions in an RNA hairpin. Science. 1992 Apr 10;256(5054):217–219. doi: 10.1126/science.1373521. [DOI] [PubMed] [Google Scholar]
  25. Searle M. S., Lane A. N. 31P NMR investigation of the backbone conformation and dynamics of the hexamer duplex d(5'-GCATGC)2 in its complex with the antibiotic nogalamycin. FEBS Lett. 1992 Feb 10;297(3):292–296. doi: 10.1016/0014-5793(92)80558-x. [DOI] [PubMed] [Google Scholar]
  26. Sobell H. M., Tsai C. C., Jain S. C., Gilbert S. G. Visualization of drug-nucleic acid interactions at atomic resolution. III. Unifying structural concepts in understanding drug-DNA interactions and their broader implications in understanding protein-DNA interactions. J Mol Biol. 1977 Aug 15;114(3):333–365. doi: 10.1016/0022-2836(77)90254-6. [DOI] [PubMed] [Google Scholar]
  27. Uhlenbeck O. C. Tetraloops and RNA folding. Nature. 1990 Aug 16;346(6285):613–614. doi: 10.1038/346613a0. [DOI] [PubMed] [Google Scholar]
  28. Veselkov A. N., Dymant L. N., Kodintsev V. V., Lisiutin V. A., Parkes H., Davies D. Issledovanie samoassotsiatsii molekul dezoksitetraribonukleozidtrifosfatov d(TpGpCpA) v vodnom rastvore metodom 1H IaMR spektroskopii. Biofizika. 1995 Mar-Apr;40(2):283–292. [PubMed] [Google Scholar]
  29. Wells R. D., Goodman T. C., Hillen W., Horn G. T., Klein R. D., Larson J. E., Müller U. R., Neuendorf S. K., Panayotatos N., Stirdivant S. M. DNA structure and gene regulation. Prog Nucleic Acid Res Mol Biol. 1980;24:167–267. doi: 10.1016/s0079-6603(08)60674-1. [DOI] [PubMed] [Google Scholar]
  30. Xodo L. E., Manzini G., Quadrifoglio F., van der Marel G., van Boom J. DNA hairpin loops in solution. Correlation between primary structure, thermostability and reactivity with single-strand-specific nuclease from mung bean. Nucleic Acids Res. 1991 Apr 11;19(7):1505–1511. doi: 10.1093/nar/19.7.1505. [DOI] [PMC free article] [PubMed] [Google Scholar]

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

RESOURCES