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Proceedings of the National Academy of Sciences of the United States of America logoLink to Proceedings of the National Academy of Sciences of the United States of America
. 1991 Feb 15;88(4):1551–1555. doi: 10.1073/pnas.88.4.1551

A spectroscopic and calorimetric study of the melting behaviors of a "bent" and a "normal" DNA duplex: [d(GA4T4C)]2 versus [d(GT4A4C)]2.

Y W Park 1, K J Breslauer 1
PMCID: PMC51057  PMID: 1996356

Abstract

We have calorimetrically detected and energetically characterized a premelting event in the "bent" duplex [d(GA4T4C)]2 that is absent in the "normal" duplex [d(GT4A4C)]2. This premelting may correspond to the thermally induced "unbending" of the duplex. Specifically, we have used a combination of spectroscopic and calorimetric techniques to evaluate whether differences in the electrophoretic and hydrogen exchange properties of the bent duplex, [d(GA4T4C)]2, and the normal duplex, [d(GT4A4C)]2, are paralleled by differences in the equilibrium melting properties of these duplexes. Our results reveal that the bimolecular global meltings of both duplexes exhibit two-state behavior and are characterized by the expected thermodynamic changes, as well as the expected salt-dependencies. Significantly, however, at temperatures below duplex melting and over a similar temperature range in which the aberrant electrophoretic mobility is observed (approximately less than 35 degrees C), the bent duplex exhibits calorimetric premelting behavior absent in the normal duplex. Analysis of the calorimetric data in this preglobal melting domain (approximately less than 35 degrees C) allows us to estimate a lower-limit value of 1.6 kcal/(mol-base pair) for the thermally induced unbending of the decameric duplex.

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Selected References

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

  1. 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]
  2. Breslauer K. J., Sturtevant J. M., Tinoco I., Jr Calorimetric and spectroscopic investigation of the helix-to-coil transition of a ribo-oligonucleotide: rA7U7. J Mol Biol. 1975 Dec 25;99(4):549–565. doi: 10.1016/s0022-2836(75)80171-9. [DOI] [PubMed] [Google Scholar]
  3. Burkhoff A. M., Tullius T. D. Structural details of an adenine tract that does not cause DNA to bend. Nature. 1988 Feb 4;331(6155):455–457. doi: 10.1038/331455a0. [DOI] [PubMed] [Google Scholar]
  4. Cantor C. R., Warshaw M. M., Shapiro H. Oligonucleotide interactions. 3. Circular dichroism studies of the conformation of deoxyoligonucleotides. Biopolymers. 1970;9(9):1059–1077. doi: 10.1002/bip.1970.360090909. [DOI] [PubMed] [Google Scholar]
  5. Chan S. S., Breslauer K. J., Hogan M. E., Kessler D. J., Austin R. H., Ojemann J., Passner J. M., Wiles N. C. Physical studies of DNA premelting equilibria in duplexes with and without homo dA.dT tracts: correlations with DNA bending. Biochemistry. 1990 Jul 3;29(26):6161–6171. doi: 10.1021/bi00478a008. [DOI] [PubMed] [Google Scholar]
  6. Chen J. H., Seeman N. C., Kallenbach N. R. Tracts of A.T base pairs retard the electrophoretic mobility of short DNA duplexes. Nucleic Acids Res. 1988 Jul 25;16(14B):6803–6812. doi: 10.1093/nar/16.14.6803. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Dickerson R. E., Kopka M. L., Pjura P. A random-walk model for helix bending in B-DNA. Proc Natl Acad Sci U S A. 1983 Dec;80(23):7099–7103. doi: 10.1073/pnas.80.23.7099. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Diekmann S. Temperature and salt dependence of the gel migration anomaly of curved DNA fragments. Nucleic Acids Res. 1987 Jan 12;15(1):247–265. doi: 10.1093/nar/15.1.247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Ebralidse K. K., Grachev S. A., Mirzabekov A. D. A highly basic histone H4 domain bound to the sharply bent region of nucleosomal DNA. Nature. 1988 Jan 28;331(6154):365–367. doi: 10.1038/331365a0. [DOI] [PubMed] [Google Scholar]
  10. Froehler B. C., Matteucci M. D. Dialkylformamidines: depurination resistant N6-protecting group for deoxyadenosine. Nucleic Acids Res. 1983 Nov 25;11(22):8031–8036. doi: 10.1093/nar/11.22.8031. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Froehler B. C., Ng P. G., Matteucci M. D. Synthesis of DNA via deoxynucleoside H-phosphonate intermediates. Nucleic Acids Res. 1986 Jul 11;14(13):5399–5407. doi: 10.1093/nar/14.13.5399. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. 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]
  13. Gartenberg M. R., Crothers D. M. DNA sequence determinants of CAP-induced bending and protein binding affinity. Nature. 1988 Jun 30;333(6176):824–829. doi: 10.1038/333824a0. [DOI] [PubMed] [Google Scholar]
  14. Hagerman P. J. Evidence for the existence of stable curvature of DNA in solution. Proc Natl Acad Sci U S A. 1984 Aug;81(15):4632–4636. doi: 10.1073/pnas.81.15.4632. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Hagerman P. J. Sequence dependence of the curvature of DNA: a test of the phasing hypothesis. Biochemistry. 1985 Dec 3;24(25):7033–7037. doi: 10.1021/bi00346a001. [DOI] [PubMed] [Google Scholar]
  16. Hagerman P. J. Sequence-directed curvature of DNA. Nature. 1986 May 22;321(6068):449–450. doi: 10.1038/321449a0. [DOI] [PubMed] [Google Scholar]
  17. Hagerman P. J. Sequence-directed curvature of DNA. Annu Rev Biochem. 1990;59:755–781. doi: 10.1146/annurev.bi.59.070190.003543. [DOI] [PubMed] [Google Scholar]
  18. Herrera J. E., Chaires J. B. A premelting conformational transition in poly(dA)-Poly(dT) coupled to daunomycin binding. Biochemistry. 1989 Mar 7;28(5):1993–2000. doi: 10.1021/bi00431a006. [DOI] [PubMed] [Google Scholar]
  19. Koepsel R. R., Khan S. A. Static and initiator protein-enhanced bending of DNA at a replication origin. Science. 1986 Sep 19;233(4770):1316–1318. doi: 10.1126/science.3749879. [DOI] [PubMed] [Google Scholar]
  20. Koo H. S., Wu H. M., Crothers D. M. DNA bending at adenine . thymine tracts. Nature. 1986 Apr 10;320(6062):501–506. doi: 10.1038/320501a0. [DOI] [PubMed] [Google Scholar]
  21. Leroy J. L., Charretier E., Kochoyan M., Guéron M. Evidence from base-pair kinetics for two types of adenine tract structures in solution: their relation to DNA curvature. Biochemistry. 1988 Dec 13;27(25):8894–8898. doi: 10.1021/bi00425a004. [DOI] [PubMed] [Google Scholar]
  22. Linial M., Shlomai J. Sequence-directed bent DNA helix is the specific binding site for Crithidia fasciculata nicking enzyme. Proc Natl Acad Sci U S A. 1987 Dec;84(23):8205–8209. doi: 10.1073/pnas.84.23.8205. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. 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]
  24. Marini J. C., Effron P. N., Goodman T. C., Singleton C. K., Wells R. D., Wartell R. M., Englund P. T. Physical characterization of a kinetoplast DNA fragment with unusual properties. J Biol Chem. 1984 Jul 25;259(14):8974–8979. [PubMed] [Google Scholar]
  25. Marini J. C., Levene S. D., Crothers D. M., Englund P. T. Bent helical structure in kinetoplast DNA. Proc Natl Acad Sci U S A. 1982 Dec;79(24):7664–7668. doi: 10.1073/pnas.79.24.7664. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. 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]
  27. 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]
  28. Marky L. A., Canuel L., Jones R. A., Breslauer K. J. Calorimetric and spectroscopic investigation of the helix-to-coil transition of the self-complementary deoxyribonucleotide ATGCAT. Biophys Chem. 1981 Apr;13(2):141–149. doi: 10.1016/0301-4622(81)80013-0. [DOI] [PubMed] [Google Scholar]
  29. Moskaluk C., Bastia D. DNA bending is induced in an enhancer by the DNA-binding domain of the bovine papillomavirus E2 protein. Proc Natl Acad Sci U S A. 1988 Mar;85(6):1826–1830. doi: 10.1073/pnas.85.6.1826. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Nelson H. C., Finch J. T., Luisi B. F., Klug A. The structure of an oligo(dA).oligo(dT) tract and its biological implications. Nature. 1987 Nov 19;330(6145):221–226. doi: 10.1038/330221a0. [DOI] [PubMed] [Google Scholar]
  31. Privalov P. L., Potekhin S. A. Scanning microcalorimetry in studying temperature-induced changes in proteins. Methods Enzymol. 1986;131:4–51. doi: 10.1016/0076-6879(86)31033-4. [DOI] [PubMed] [Google Scholar]
  32. 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]
  33. Ryder K., Silver S., DeLucia A. L., Fanning E., Tegtmeyer P. An altered DNA conformation in origin region I is a determinant for the binding of SV40 large T antigen. Cell. 1986 Mar 14;44(5):719–725. doi: 10.1016/0092-8674(86)90838-x. [DOI] [PubMed] [Google Scholar]
  34. Travers A. A., Klug A. The bending of DNA in nucleosomes and its wider implications. Philos Trans R Soc Lond B Biol Sci. 1987 Dec 15;317(1187):537–561. doi: 10.1098/rstb.1987.0080. [DOI] [PubMed] [Google Scholar]
  35. Wu H. M., Crothers D. M. The locus of sequence-directed and protein-induced DNA bending. Nature. 1984 Apr 5;308(5959):509–513. doi: 10.1038/308509a0. [DOI] [PubMed] [Google Scholar]
  36. Zahn K., Blattner F. R. Direct evidence for DNA bending at the lambda replication origin. Science. 1987 Apr 24;236(4800):416–422. doi: 10.1126/science.2951850. [DOI] [PubMed] [Google Scholar]

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