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. 1980 Nov 25;8(22):5519–5531. doi: 10.1093/nar/8.22.5519

Counterion dependent variation of DNA secondary structure in (A . T) clusters: evidence by use of netropsin as a structural probe.

K E Reinert, H Thrum, E Sarfert
PMCID: PMC324318  PMID: 6258145

Abstract

The interaction of the oligopeptide antibiotic netropsin (Nt) with (A . T) regions of DNA is characterized by a spectrum of discrete modes. This has been revealed by viscometric analysis, at 20 degrees C and 0.2 M "counterions", for NaDNA in a preceding and for NH4DNA in this paper. The increase of DNA contour length as induced by one Nt molecule was found to depend on the special mode only, while the respective stiffening is generally higher for NH4DNA. The latter property is interpreted in terms of an enhanced flexibility, relative to that of NaDNA, of the (A . T) cluster segments before complex formation. For some of the interaction modes of the DNA-Nt systems a difference in the number of corresponding binding sites has been observed. This phenomenon is understood by assuming an influence of the counterion species upon existing equilibria between different forms of the (A . T) cluster secondary structure. Not less than 5 to 10% of the total DNA are effected in this manner. Upper limits for the local differences in the axial rise per base pair are 0.04 nm and 0.02 nm.

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Selected References

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

  1. Anderson P., Bauer W. Supercoiling in closed circular DNA: dependence upon ion type and concentration. Biochemistry. 1978 Feb 21;17(4):594–601. doi: 10.1021/bi00597a006. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Chandrasekaran R., Birdsall D. L., Leslie A. G., Ratliff R. L. Left-handed DNA helices. Nature. 1980 Feb 21;283(5749):743–745. doi: 10.1038/283743a0. [DOI] [PubMed] [Google Scholar]
  3. Baase W. A., Johnson W. C., Jr Circular dichroism and DNA secondary structure. Nucleic Acids Res. 1979 Feb;6(2):797–814. doi: 10.1093/nar/6.2.797. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Berman H. M., Neidle S., Zimmer C., Thrum H. Netropsin, a DNA-binding oligopeptide structural and binding studies. Biochim Biophys Acta. 1979 Jan 26;561(1):124–131. doi: 10.1016/0005-2787(79)90496-9. [DOI] [PubMed] [Google Scholar]
  5. Brahms S., Brahms J., Van Holde K. E. Nature of conformational changes in poly[d(A-T)-d(A-T)] in the premelting region. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3453–3457. doi: 10.1073/pnas.73.10.3453. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Chan A., Kilkuskie R., Hanlon S. Correlations between the duplex winding angle and the circular dichroism spectrum of calf thymus DNA. Biochemistry. 1979 Jan 9;18(1):84–91. doi: 10.1021/bi00568a013. [DOI] [PubMed] [Google Scholar]
  7. Davies D. R., Zimmerman S. A new twist for DNA? Nature. 1980 Jan 3;283(5742):11–12. doi: 10.1038/283011a0. [DOI] [PubMed] [Google Scholar]
  8. Geller K., Reinert K. E. Evidence for an increase of DNA contour length at low ionic strength. Nucleic Acids Res. 1980 Jun 25;8(12):2807–2822. doi: 10.1093/nar/8.12.2807. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Gennis R. B., Cantor C. R. Optical studies of a conformational change in DNA before melting. J Mol Biol. 1972 Apr 14;65(3):381–399. doi: 10.1016/0022-2836(72)90196-9. [DOI] [PubMed] [Google Scholar]
  10. Greve J., Maestre M. F., Levin A. Circular dichroism of adenine and thymine containing synthetic polynucleotides. Biopolymers. 1977 Jul;16(7):1489–1504. doi: 10.1002/bip.1977.360160709. [DOI] [PubMed] [Google Scholar]
  11. Hanlon S., Brudno S., Wu T. T., Wolf B. Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. I. Reference spectra of conformational limits. Biochemistry. 1975 Apr 22;14(8):1648–1660. doi: 10.1021/bi00679a017. [DOI] [PubMed] [Google Scholar]
  12. Hanlon S., Chan A., Berman S. Specific cation effects on conformational transitions of DNA in aqueous solutions. Biochim Biophys Acta. 1978 Jul 24;519(2):526–536. doi: 10.1016/0005-2787(78)90105-3. [DOI] [PubMed] [Google Scholar]
  13. Hogan M., Dattagupta N., Crothers D. M. Transmission of allosteric effects in DNA. Nature. 1979 Apr 5;278(5704):521–524. doi: 10.1038/278521a0. [DOI] [PubMed] [Google Scholar]
  14. Ivanov V. I., Minchenkova L. E., Schyolkina A. K., Poletayev A. I. Different conformations of double-stranded nucleic acid in solution as revealed by circular dichroism. Biopolymers. 1973;12(1):89–110. doi: 10.1002/bip.1973.360120109. [DOI] [PubMed] [Google Scholar]
  15. Klug A., Jack A., Viswamitra M. A., Kennard O., Shakked Z., Steitz T. A. A hypothesis on a specific sequence-dependent conformation of DNA and its relation to the binding of the lac-repressor protein. J Mol Biol. 1979 Jul 15;131(4):669–680. doi: 10.1016/0022-2836(79)90196-7. [DOI] [PubMed] [Google Scholar]
  16. Luck G., Triebel H., Waring M., Zimmer C. Conformation dependent binding of netropsin and distamycin to DNA and DNA model polymers. Nucleic Acids Res. 1974 Mar;1(3):503–530. doi: 10.1093/nar/1.3.503. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Martin J. C., Wartell R. M., O'Shea D. C. Conformational features of distamycin-DNA and netropsin-DNA complexes by Raman spectroscopy. Proc Natl Acad Sci U S A. 1978 Nov;75(11):5483–5487. doi: 10.1073/pnas.75.11.5483. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Patel D. J., Canuel L. L. Netropsin-poly(dA-dT) complex in solution: structure and dynamics of antibiotic-free base pair regions and those centered on bound netropsin. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5207–5211. doi: 10.1073/pnas.74.12.5207. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Patel D. J., Canuel L. L., Pohl F. M. "Alternating B-DNA" conformation for the oligo(dG-dC) duplex in high-salt solution. Proc Natl Acad Sci U S A. 1979 Jun;76(6):2508–2511. doi: 10.1073/pnas.76.6.2508. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Reinert K. E. Adenosine-thymidine cluster-specific elongation and stiffening of DNA induced by the oligopeptide antibiotic netropsin. J Mol Biol. 1972 Dec 30;72(3):593–607. doi: 10.1016/0022-2836(72)90178-7. [DOI] [PubMed] [Google Scholar]
  21. Reinert K. E., Stutter E., Schweiss H. Aspects of specific protein-DNA interaction; multi-mode binding of the oligopeptide antibiotic netropsin to (A.T)-rich DNA segments. Nucleic Acids Res. 1979 Nov 10;7(5):1375–1392. doi: 10.1093/nar/7.5.1375. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Rinehart F. P., Hearst J. E. The ionic strength dependence of s o 20 w of phage DNA in NH 4 AC. Arch Biochem Biophys. 1972 Oct;152(2):712–722. doi: 10.1016/0003-9861(72)90267-6. [DOI] [PubMed] [Google Scholar]
  23. SARFERT E., VENNER H. UNTERSUCHUNGEN AN NUCLEINSAEUREN. XI. ISOLIERUNG VON DESOXYRIBONUCLEINSAEURE AUS MIKROORGANISMEN IN REINER, HOCHMOLEKULARER FORM. Hoppe Seylers Z Physiol Chem. 1965;340:157–173. doi: 10.1515/bchm2.1965.340.1-2.157. [DOI] [PubMed] [Google Scholar]
  24. Sarocchi M. T., Guschlbauer W. Protonated polynucleotide structures. Sequence-dependent and protonation-sensitive metastable states in DNA premelting. Eur J Biochem. 1973 Apr;34(2):232–240. doi: 10.1111/j.1432-1033.1973.tb02751.x. [DOI] [PubMed] [Google Scholar]
  25. Shindo H., Simpson R. T., Cohen J. S. An alternating conformation characterizes the phosphodiester backbone of poly(dA-dT) in solution. J Biol Chem. 1979 Sep 10;254(17):8125–8128. [PubMed] [Google Scholar]
  26. Shindo H., Zimmerman S. B. Sequence-dependent variations in the backbone geometry of a synthetic DNA fibre. Nature. 1980 Feb 14;283(5748):690–691. doi: 10.1038/283690a0. [DOI] [PubMed] [Google Scholar]
  27. Studdert D. S., Patroni M., Davis R. C. Circular dichroism of DNA: temperature and salt dependence. Biopolymers. 1972;11(4):761–779. doi: 10.1002/bip.1972.360110404. [DOI] [PubMed] [Google Scholar]
  28. Studdert D. S., Patroni M., Davis R. C. Circular dichroism of DNA: temperature and salt dependence. Biopolymers. 1972;11(4):761–779. doi: 10.1002/bip.1972.360110404. [DOI] [PubMed] [Google Scholar]
  29. Tunis-Schneider M. J., Maestre M. F. Circular dichroism spectra of oriented and unoriented deoxyribonucleic acid films--a preliminary study. J Mol Biol. 1970 Sep 28;52(3):521–541. doi: 10.1016/0022-2836(70)90417-1. [DOI] [PubMed] [Google Scholar]
  30. Tunis M. J., Hearst J. E. Optical rotatory dispersion of DNA in concentrated salt solutions. Biopolymers. 1968;6(8):1218–1223. doi: 10.1002/bip.1968.360060816. [DOI] [PubMed] [Google Scholar]
  31. Wang A. H., Quigley G. J., Kolpak F. J., Crawford J. L., van Boom J. H., van der Marel G., Rich A. Molecular structure of a left-handed double helical DNA fragment at atomic resolution. Nature. 1979 Dec 13;282(5740):680–686. doi: 10.1038/282680a0. [DOI] [PubMed] [Google Scholar]
  32. Wolf B., Hanlon S. Structural transitions of deoxyribonucleic acid in aqueous electrolyte solutions. II. The role of hydration. Biochemistry. 1975 Apr 22;14(8):1661–1670. doi: 10.1021/bi00679a018. [DOI] [PubMed] [Google Scholar]
  33. Zimmer C., Luck G. Conformation and reactivity of DNA. 3. Circular dichroism studies of the effects of aqueous concentrated univalent salt solutions upon helix conformation. Biochim Biophys Acta. 1973 Jun 23;312(2):215–227. [PubMed] [Google Scholar]
  34. Zimmer C., Luck G. Conformation and reactivity of DNA. VI. Circular dichroism studies of salt-induced conformational changes of DNAs of different base composition. Biochim Biophys Acta. 1974 Aug 15;361(1):11–32. [PubMed] [Google Scholar]

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