Skip to main content
PMC home page
Biophysical Journal logoLink to Biophysical Journal
. 1997 Dec;73(6):3135–3141. doi: 10.1016/S0006-3495(97)78339-5

Sequence effects on the relative thermodynamic stabilities of B-Z junction-forming DNA oligomeric duplexes.

E O Otokiti 1, R D Sheardy 1
PMCID: PMC1181216  PMID: 9414225

Abstract

Circular dichroism (CD) and ultraviolet absorption techniques were employed in characterizing the sequence-dependent thermodynamic stabilities of B-Z junction-forming DNA duplexes. The Watson strand of the duplexes has the general sequence (5meC-G)4-NXYG-ACTG (where N = A or G and XY represents all permutations of pyrimidine bases). Duplexes were generated by mixing stoichiometric amounts of the complementary strands. Circular dichroism studies indicate that each duplex is fully right-handed at low salt (e.g., 115 mM Na+) but undergoes a salt-induced conformational transition to a structure that possesses both left- and right-handed conformations at high salt (4.5 M Na+), and hence a B-Z junction. Optical melting studies of the DNA duplexes at fixed DNA concentration with total Na+ concentration ranging from 15 mM to 5.0 M were determined. A nonlinear dependence of the melting temperature (Tm) on [Na+] was observed. Thermodynamic parameters at Na+ concentrations of 115 mM and 4.5 M with a wide range of DNA concentrations were determined from UV optical melting studies via construction of van't Hoff plots. A change of a single dinucleotide within these duplexes significantly affected the helix stabilities. The experimentally obtained free energies for the duplex to single-strand transitions were in close agreement with predicted values obtained from two different methods.

Full text

PDF
3135

Selected References

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

  1. Behe M., Felsenfeld G. Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A. 1981 Mar;78(3):1619–1623. doi: 10.1073/pnas.78.3.1619. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. 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]
  3. Buckin V. A., Kankiya B. I., Bulichov N. V., Lebedev A. V., Gukovsky IYa, Chuprina V. P., Sarvazyan A. P., Williams A. R. Measurement of anomalously high hydration of (dA)n.(dT)n double helices in dilute solution. Nature. 1989 Jul 27;340(6231):321–322. doi: 10.1038/340321a0. [DOI] [PubMed] [Google Scholar]
  4. Delcourt S. G., Blake R. D. Stacking energies in DNA. J Biol Chem. 1991 Aug 15;266(23):15160–15169. [PubMed] [Google Scholar]
  5. Doktycz M. J., Goldstein R. F., Paner T. M., Gallo F. J., Benight A. S. Studies of DNA dumbbells. I. Melting curves of 17 DNA dumbbells with different duplex stem sequences linked by T4 endloops: evaluation of the nearest-neighbor stacking interactions in DNA. Biopolymers. 1992 Jul;32(7):849–864. doi: 10.1002/bip.360320712. [DOI] [PubMed] [Google Scholar]
  6. Gaffney B. L., Jones R. A. Thermodynamic comparison of the base pairs formed by the carcinogenic lesion O6-methylguanine with reference both to Watson-Crick pairs and to mismatched pairs. Biochemistry. 1989 Jul 11;28(14):5881–5889. doi: 10.1021/bi00440a026. [DOI] [PubMed] [Google Scholar]
  7. Gruenwedel D. W., Hsu C. H., Lu D. S. The effects of aqueous neutral-salt solutions on the melting temperatures of deoxyribonucleic acids. Biopolymers. 1971;10(1):47–68. doi: 10.1002/bip.360100106. [DOI] [PubMed] [Google Scholar]
  8. Gruenwedel D. W. Salt effects on the denaturation of DNA. IV. A calorimetric study of the helix-coil conversion of the alternating copolymer poly[d(A-T)]. Biochim Biophys Acta. 1975 Jul 7;395(3):246–257. doi: 10.1016/0005-2787(75)90195-1. [DOI] [PubMed] [Google Scholar]
  9. Guo Q., Lu M., Shahrestanifar M., Sheardy R. D., Kallenbach N. R. Drug binding to a DNA BZ molecule: analysis by chemical footprinting. Biochemistry. 1991 Dec 24;30(51):11735–11741. doi: 10.1021/bi00115a001. [DOI] [PubMed] [Google Scholar]
  10. LeBlanc D. A., Morden K. M. Thermodynamic characterization of deoxyribooligonucleotide duplexes containing bulges. Biochemistry. 1991 Apr 23;30(16):4042–4047. doi: 10.1021/bi00230a031. [DOI] [PubMed] [Google Scholar]
  11. Li Y., Zon G., Wilson W. D. Thermodynamics of DNA duplexes with adjacent G.A mismatches. Biochemistry. 1991 Jul 30;30(30):7566–7572. doi: 10.1021/bi00244a028. [DOI] [PubMed] [Google Scholar]
  12. Lu M., Guo Q., Kallenbach N. R., Sheardy R. D. Conformational properties of B-Z junctions in DNA. Biochemistry. 1992 May 19;31(19):4712–4719. doi: 10.1021/bi00134a026. [DOI] [PubMed] [Google Scholar]
  13. Manning G. S. The molecular theory of polyelectrolyte solutions with applications to the electrostatic properties of polynucleotides. Q Rev Biophys. 1978 May;11(2):179–246. doi: 10.1017/s0033583500002031. [DOI] [PubMed] [Google Scholar]
  14. Manzini G., Xodo L. E., Quadrifoglio F., van Boom J. H., van der Marel G. A. dC-dG alternating oligonucleotides: thermodynamic and kinetic aspects of the B-Z transformation. J Biomol Struct Dyn. 1987 Feb;4(4):651–662. doi: 10.1080/07391102.1987.10507666. [DOI] [PubMed] [Google Scholar]
  15. 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]
  16. Olmsted M. C., Anderson C. F., Record M. T., Jr Importance of oligoelectrolyte end effects for the thermodynamics of conformational transitions of nucleic acid oligomers: a grand canonical Monte Carlo analysis. Biopolymers. 1991 Nov;31(13):1593–1604. doi: 10.1002/bip.360311314. [DOI] [PubMed] [Google Scholar]
  17. Paner T. M., Amaratunga M., Benight A. S. Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14). Biopolymers. 1992 Jul;32(7):881–892. doi: 10.1002/bip.360320714. [DOI] [PubMed] [Google Scholar]
  18. Paner T. M., Riccelli P. V., Owczarzy R., Benight A. S. Studies of DNA dumbbells. VI. Analysis of optical melting curves of dumbbells with a sixteen-base pair duplex stem and end-loops of variable size and sequence. Biopolymers. 1996 Dec;39(6):779–793. doi: 10.1002/(SICI)1097-0282(199612)39:6%3C779::AID-BIP5%3E3.0.CO;2-S. [DOI] [PubMed] [Google Scholar]
  19. Record M. T., Jr, Anderson C. F., Lohman T. M. Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity. Q Rev Biophys. 1978 May;11(2):103–178. doi: 10.1017/s003358350000202x. [DOI] [PubMed] [Google Scholar]
  20. Record M. T., Jr, Mazur S. J., Melançon P., Roe J. H., Shaner S. L., Unger L. Double helical DNA: conformations, physical properties, and interactions with ligands. Annu Rev Biochem. 1981;50:997–1024. doi: 10.1146/annurev.bi.50.070181.005025. [DOI] [PubMed] [Google Scholar]
  21. Rentzeperis D., Kupke D. W., Marky L. A. Differential hydration of dA.dT base pairs in parallel-stranded DNA relative to antiparallel DNA. Biochemistry. 1994 Aug 16;33(32):9588–9591. doi: 10.1021/bi00198a026. [DOI] [PubMed] [Google Scholar]
  22. Rentzeperis D., Kupke D. W., Marky L. A. Volume changes correlate with entropies and enthalpies in the formation of nucleic acid homoduplexes: differential hydration of A and B conformations. Biopolymers. 1993 Jan;33(1):117–125. doi: 10.1002/bip.360330111. [DOI] [PubMed] [Google Scholar]
  23. SantaLucia J., Jr, Allawi H. T., Seneviratne P. A. Improved nearest-neighbor parameters for predicting DNA duplex stability. Biochemistry. 1996 Mar 19;35(11):3555–3562. doi: 10.1021/bi951907q. [DOI] [PubMed] [Google Scholar]
  24. Senior M., Jones R. A., Breslauer K. J. Influence of dangling thymidine residues on the stability and structure of two DNA duplexes. Biochemistry. 1988 May 17;27(10):3879–3885. doi: 10.1021/bi00410a053. [DOI] [PubMed] [Google Scholar]
  25. Sheardy R. D., Levine N., Marotta S., Suh D., Chaires J. B. A thermodynamic investigation of the melting of B-Z junction forming DNA oligomers. Biochemistry. 1994 Feb 15;33(6):1385–1391. doi: 10.1021/bi00172a014. [DOI] [PubMed] [Google Scholar]
  26. Sheardy R. D. Preliminary spectroscopic characterization of a synthetic DNA oligomer containing a B-Z junction at high salt. Nucleic Acids Res. 1988 Feb 11;16(3):1153–1167. doi: 10.1093/nar/16.3.1153. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Sheardy R. D., Suh D., Kurzinsky R., Doktycz M. J., Benight A. S., Chaires J. B. Sequence dependence of the free energy of B-Z junction formation in deoxyoligonucleotides. J Mol Biol. 1993 May 20;231(2):475–488. doi: 10.1006/jmbi.1993.1295. [DOI] [PubMed] [Google Scholar]
  28. Sheardy R. D., Winkle S. A. Temperature-dependent CD and NMR studies on a synthetic oligonucleotide containing a B-Z junction at high salt. Biochemistry. 1989 Jan 24;28(2):720–725. doi: 10.1021/bi00428a046. [DOI] [PubMed] [Google Scholar]
  29. Singleton C. K., Klysik J., Wells R. D. Conformational flexibility of junctions between contiguous B- and Z-DNAs in supercoiled plasmids. Proc Natl Acad Sci U S A. 1983 May;80(9):2447–2451. doi: 10.1073/pnas.80.9.2447. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Suh D., Sheardy R. D., Chaires J. B. Unusual binding of ethidium to a deoxyoligonucleotide containing a B-Z junction. Biochemistry. 1991 Sep 10;30(36):8722–8726. doi: 10.1021/bi00100a002. [DOI] [PubMed] [Google Scholar]
  31. Tunis M. J., Hearst J. E. On the hydration of DNA. I. Preferential hydration and stability of DNA in concentrated trifluoroacetate solution. Biopolymers. 1968;6(9):1325–1344. doi: 10.1002/bip.1968.360060908. [DOI] [PubMed] [Google Scholar]
  32. Winkle S. A., Aloyo M. C., Morales N., Zambrano T. Y., Sheardy R. D. Enhanced reactivity of a B-Z junction for cleavage by the restriction enzyme MboI. Biochemistry. 1991 Nov 5;30(44):10601–10606. doi: 10.1021/bi00108a001. [DOI] [PubMed] [Google Scholar]

Articles from Biophysical Journal are provided here courtesy of The Biophysical Society

RESOURCES