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. 1995 Nov 25;23(22):4576–4582. doi: 10.1093/nar/23.22.4576

A comparison of the hairpin stability of the palindromic d(CGCG(A/T)4CGCG) oligonucleotides.

M Hald 1, J B Pedersen 1, P C Stein 1, F Kirpekar 1, J P Jacobsen 1
PMCID: PMC307428  PMID: 8524645

Abstract

The palindromic deoxyribonucleotides 5'-CGCGA-TATCGCG-3' and 5'-CGCGTTAACGCG-3' have been characterized by 1H NMR spectroscopy. The NMR data identified both B-DNA duplex conformations and hairpin conformations, the latter with loop regions consisting of the four central nucleotides. The resonances of the various conformations were assigned by use of two-dimensional NMR methods. The relative stability of the various conformations was investigated as a function of temperature, ionic strength and nucleotide concentration. The duplexes were found to be stabilized at high ionic strength and at low temperature, while the hairpins were stabilized at low ionic strength and at medium temperature. The thermodynamics of the duplex-hairpin and the hairpin-random coil transitions were examined, and compared to the other two oligonucleotide in the palindromic d(CGCG(A/T)4CGCG) oligonucleotide family. The relative stabilities of the duplex conformations with respect to the random coil conformations are similar for the d(CGCGAATTCGCG), d(CGCGATATCGCG) and d(CGCGTATACGCG) oligonucleotides. The duplex conformation of d(CGCGTTAACGCG) is less stable. The hairpin of d(CGCGTTAACGCG) seems also to be less stable relative to the random coil conformation than in the case of the other oligonucleotides at an equal oligonucleotide concentration. A cruciform intermediate between the duplex and hairpin conformations is suggested to explain some discrepancies observed in this work in case of the d(CGCGTTAACGCG) oligonucleotide. This is similar to what has been reported for the d(CGCGTATACGCG) oligonucleotide.

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Selected References

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  1. Baxter S. M., Greizerstein M. B., Kushlan D. M., Ashley G. W. Conformational properties of DNA hairpins with TTT and TTTT loops. Biochemistry. 1993 Aug 24;32(33):8702–8711. doi: 10.1021/bi00084a042. [DOI] [PubMed] [Google Scholar]
  2. Blommers M. J., Walters J. A., Haasnoot C. A., Aelen J. M., van der Marel G. A., van Boom J. H., Hilbers C. W. Effects of base sequence on the loop folding in DNA hairpins. Biochemistry. 1989 Sep 5;28(18):7491–7498. doi: 10.1021/bi00444a049. [DOI] [PubMed] [Google Scholar]
  3. Blommers M. J., van de Ven F. J., van der Marel G. A., van Boom J. H., Hilbers C. W. The three-dimensional structure of a DNA hairpin in solution two-dimensional NMR studies and structural analysis of d(ATCCTATTTATAGGAT). Eur J Biochem. 1991 Oct 1;201(1):33–51. doi: 10.1111/j.1432-1033.1991.tb16253.x. [DOI] [PubMed] [Google Scholar]
  4. Drew H. R., Wing R. M., Takano T., Broka C., Tanaka S., Itakura K., Dickerson R. E. Structure of a B-DNA dodecamer: conformation and dynamics. Proc Natl Acad Sci U S A. 1981 Apr;78(4):2179–2183. doi: 10.1073/pnas.78.4.2179. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Feigon J., Leupin W., Denny W. A., Kearns D. R. Two-dimensional proton nuclear magnetic resonance investigation of the synthetic deoxyribonucleic acid decamer d(ATATCGATAT)2. Biochemistry. 1983 Dec 6;22(25):5943–5951. doi: 10.1021/bi00294a038. [DOI] [PubMed] [Google Scholar]
  6. Haasnoot C. A., Hilbers C. W., van der Marel G. A., van Boom J. H., Singh U. C., Pattabiraman N., Kollman P. A. On loop folding in nucleic acid hairpin-type structures. J Biomol Struct Dyn. 1986 Apr;3(5):843–857. doi: 10.1080/07391102.1986.10508468. [DOI] [PubMed] [Google Scholar]
  7. Haasnoot C. A., de Bruin S. H., Berendsen R. G., Janssen H. G., Binnendijk T. J., Hilbers C. W., van der Marel G. A., van Boom J. H. Structure, kinetics and thermodynamics of DNA hairpin fragments in solution. J Biomol Struct Dyn. 1983 Oct;1(1):115–129. doi: 10.1080/07391102.1983.10507429. [DOI] [PubMed] [Google Scholar]
  8. Hare D. R., Reid B. R. Three-dimensional structure of a DNA hairpin in solution: two-dimensional NMR studies and distance geometry calculations on d(CGCGTTTTCGCG). Biochemistry. 1986 Sep 9;25(18):5341–5350. doi: 10.1021/bi00366a053. [DOI] [PubMed] [Google Scholar]
  9. Hare D. R., Wemmer D. E., Chou S. H., Drobny G., Reid B. R. Assignment of the non-exchangeable proton resonances of d(C-G-C-G-A-A-T-T-C-G-C-G) using two-dimensional nuclear magnetic resonance methods. J Mol Biol. 1983 Dec 15;171(3):319–336. doi: 10.1016/0022-2836(83)90096-7. [DOI] [PubMed] [Google Scholar]
  10. Hilbers C. W., Haasnoot C. A., de Bruin S. H., Joordens J. J., van der Marel G. A., van Boom J. H. Hairpin formation in synthetic oligonucleotides. Biochimie. 1985 Jul-Aug;67(7-8):685–695. doi: 10.1016/s0300-9084(85)80156-5. [DOI] [PubMed] [Google Scholar]
  11. Ikuta S., Chattopadhyaya R., Ito H., Dickerson R. E., Kearns D. R. NMR study of a synthetic DNA hairpin. Biochemistry. 1986 Aug 26;25(17):4840–4849. doi: 10.1021/bi00365a018. [DOI] [PubMed] [Google Scholar]
  12. Kallick D. A., Wemmer D. E. 1H NMR of 5'CGCGTATATACGCG3', a duplex and a four-membered loop. Nucleic Acids Res. 1991 Nov 11;19(21):6041–6046. doi: 10.1093/nar/19.21.6041. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Marky L. A., Blumenfeld K. S., Kozlowski S., Breslauer K. J. Salt-dependent conformational transitions in the self-complementary deoxydodecanucleotide d(CGCAATTCGCG): evidence for hairpin formation. Biopolymers. 1983 Apr;22(4):1247–1257. doi: 10.1002/bip.360220416. [DOI] [PubMed] [Google Scholar]
  14. Marky L. A., Breslauer K. J. Calorimetric determination of base-stacking enthalpies in double-helical DNA molecules. Biopolymers. 1982 Nov;21(11):2185–2194. doi: 10.1002/bip.360211107. [DOI] [PubMed] [Google Scholar]
  15. Müller U. R., Fitch W. M. Evolutionary selection for perfect hairpin structures in viral DNAs. Nature. 1982 Aug 5;298(5874):582–585. doi: 10.1038/298582a0. [DOI] [PubMed] [Google Scholar]
  16. Patel D. J., Kozlowski S. A., Hare D. R., Reid B., Ikuta S., Lander N., Itakura K. Conformation, dynamics, and structural transitions of the TATA box region of self-complementary d[(C-G)n-T-A-T-A-(C-G)n] duplexes in solution. Biochemistry. 1985 Feb 12;24(4):926–935. doi: 10.1021/bi00325a018. [DOI] [PubMed] [Google Scholar]
  17. Patel D. J., Kozlowski S. A., Ikuta S., Itakura K., Bhatt R., Hare D. R. NMR studies of DNA conformation and dynamics in solution. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 1):197–206. doi: 10.1101/sqb.1983.047.01.025. [DOI] [PubMed] [Google Scholar]
  18. Patel D. J., Kozlowski S. A., Marky L. A., Broka C., Rice J. A., Itakura K., Breslauer K. J. Premelting and melting transitions in the d(CGCGAATTCGCG) self-complementary duplex in solution. Biochemistry. 1982 Feb 2;21(3):428–436. doi: 10.1021/bi00532a002. [DOI] [PubMed] [Google Scholar]
  19. Rinkel L. J., van der Marel G. A., van Boom J. H., Altona C. Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 1. The duplex form. Eur J Biochem. 1987 Mar 2;163(2):275–286. doi: 10.1111/j.1432-1033.1987.tb10798.x. [DOI] [PubMed] [Google Scholar]
  20. Rinkel L. J., van der Marel G. A., van Boom J. H., Altona C. Influence of N6-methylation of residue A(5) on the conformational behaviour of d(C-C-G-A-A-T-T-C-G-G) in solution studied by 1H-NMR spectroscopy. 2. The hairpin form. Eur J Biochem. 1987 Mar 2;163(2):287–296. doi: 10.1111/j.1432-1033.1987.tb10799.x. [DOI] [PubMed] [Google Scholar]
  21. Roy S., Weinstein S., Borah B., Nickol J., Appella E., Sussman J. L., Miller M., Shindo H., Cohen J. S. Mechanism of oligonucleotide loop formation in solution. Biochemistry. 1986 Nov 18;25(23):7417–7423. doi: 10.1021/bi00371a025. [DOI] [PubMed] [Google Scholar]
  22. Scheek R. M., Boelens R., Russo N., van Boom J. H., Kaptein R. Sequential resonance assignments in 1H NMR spectra of oligonucleotides by two-dimensional NMR spectroscopy. Biochemistry. 1984 Mar 27;23(7):1371–1376. doi: 10.1021/bi00302a006. [DOI] [PubMed] [Google Scholar]
  23. Van de Ven F. J., Hilbers C. W. Nucleic acids and nuclear magnetic resonance. Eur J Biochem. 1988 Dec 1;178(1):1–38. doi: 10.1111/j.1432-1033.1988.tb14425.x. [DOI] [PubMed] [Google Scholar]
  24. Wemmer D. E., Chou S. H., Hare D. R., Reid B. R. Duplex-hairpin transitions in DNA: NMR studies on CGCGTATACGCG. Nucleic Acids Res. 1985 May 24;13(10):3755–3772. doi: 10.1093/nar/13.10.3755. [DOI] [PMC free article] [PubMed] [Google Scholar]

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