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. 1976 Mar;3(3):561–580. doi: 10.1093/nar/3.3.561

Conformation and reactivity of DNA in the complex with protein. IV. Circular dichroism of poly-L-histidine model complexes with DNA polymers and specificity of the interaction.

G Burchkardt, G Zimmer, G Luck
PMCID: PMC342925  PMID: 5706

Abstract

The CD study of the DNA-poly-L-histidine complex at high degree of protonation revealed that complex formation is already observable at 2 M NaCl. The influence of salt together with 5 M urea suggests that in addition to electrostatic interactions probably hydrogen bonding may favour specific complexes. Affinity of protonated histidines to AT-rich regions is strongly supported by the complexes formed with (dA.dT)-containing polymers. The psi-type structure occurs with poly(dA-dT)-poly(dA-dT) while poly(dA)-poly(dT) is restricted to form a similar psi-state on interaction with highly protonated poly-L-histidine. Differences in the helix winding properties due to variation in the sequence is suggested as a possible factor in the formation of the psi-type complexes. The mechanism of interaction including hydrogen bonding of histidine side-chains with an AT pair at high degree of protonation and with GC-regions at lower degree of protonation in the polypeptide structure is discussed.

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Selected References

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

  1. Adler A. J., Schaffhausen B., Langan T. A., Fasman G. D. Altered conformational effects of phosphorylated lysine-rich histone (f-1) in f-1--deoxyribonucleic acid complexes. Circular dichroism and immunological studies. Biochemistry. 1971 Mar 2;10(5):909–913. doi: 10.1021/bi00781a028. [DOI] [PubMed] [Google Scholar]
  2. Arnott S., Hukins D. W., Dover S. D., Fuller W., Hodgson A. R. Structures of synthetic polynucleotides in the A-RNA and A'-RNA conformations: x-ray diffraction analyses of the molecular conformations of polyadenylic acid--polyuridylic acid and polyinosinic acid--polycytidylic acid. J Mol Biol. 1973 Dec 5;81(2):107–122. doi: 10.1016/0022-2836(73)90183-6. [DOI] [PubMed] [Google Scholar]
  3. Arnott S., Selsing E. Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). J Mol Biol. 1974 Sep 15;88(2):509–521. doi: 10.1016/0022-2836(74)90498-7. [DOI] [PubMed] [Google Scholar]
  4. Beychok S., Pflumm M. N., Lehmann J. E. Sense of helix of poly-L-histidine. J Am Chem Soc. 1965 Sep 5;87(17):3990–3991. doi: 10.1021/ja01095a042. [DOI] [PubMed] [Google Scholar]
  5. Bram S. The secondary structure of DNA in solution and in nucleohistone. J Mol Biol. 1971 May 28;58(1):277–288. doi: 10.1016/0022-2836(71)90246-4. [DOI] [PubMed] [Google Scholar]
  6. Brunner W. C., Maestre M. F. Circular dichroism of films of polynucleotides. Biopolymers. 1974;13(2):345–357. doi: 10.1002/bip.1974.360130210. [DOI] [PubMed] [Google Scholar]
  7. Burckhardt G., Zimmer Ch, Luck G. Conformation and reactivity of DNA V. pH-dependent conformational changes of DNA in complexes with poly-L-histidine: Transitions from B- to A-form and to a condensed state. FEBS Lett. 1973 Feb 15;30(1):35–39. doi: 10.1016/0014-5793(73)80613-1. [DOI] [PubMed] [Google Scholar]
  8. Cantor K. P., Hearst J. E. The structure of metaphase chromosomes. I. Electrometric titration, magnesium ion binding and circular dichroism. J Mol Biol. 1970 Apr 14;49(1):213–229. doi: 10.1016/0022-2836(70)90387-6. [DOI] [PubMed] [Google Scholar]
  9. Carroll D. Optical properties of deoxyribonucleic acid--polylysine complexes. Biochemistry. 1972 Feb 1;11(3):421–426. doi: 10.1021/bi00753a019. [DOI] [PubMed] [Google Scholar]
  10. Chang C., Weiskopf M., Li H. J. Conformational studies of nucleoprotein. Circular dichroism of deoxyribonucleic acid base pairs bound by polylysine. Biochemistry. 1973 Jul 31;12(16):3028–3032. doi: 10.1021/bi00740a013. [DOI] [PubMed] [Google Scholar]
  11. Cheng S. M., Mohr S. C. The thermal transition of 'psi' DNA monitored by circular dichroism. FEBS Lett. 1974 Dec 1;49(1):37–42. doi: 10.1016/0014-5793(74)80626-5. [DOI] [PubMed] [Google Scholar]
  12. Chung S. Y., Holzwarth G. Circular dichroism of flow-oriented nucleic acids. I. Experimental results. J Mol Biol. 1975 Mar 5;92(3):449–466. doi: 10.1016/0022-2836(75)90291-0. [DOI] [PubMed] [Google Scholar]
  13. Courtois Y., Fromageot P., Guschlbauer W. Protonated polynucleotide structures. 3. An optical rotatory dispersion study of the protonation of DNA. Eur J Biochem. 1968 Dec 5;6(4):493–501. doi: 10.1111/j.1432-1033.1968.tb00472.x. [DOI] [PubMed] [Google Scholar]
  14. DAVIES D. R., BALDWIN R. L. X-ray studies on two synthetic DNA copolymers. J Mol Biol. 1963 Apr;6:251–255. doi: 10.1016/s0022-2836(63)80086-8. [DOI] [PubMed] [Google Scholar]
  15. Dorman B. P., Maestre M. F. Experimental differential light-scattering correction to the circular dichroism of bacteriophage T2. Proc Natl Acad Sci U S A. 1973 Jan;70(1):255–259. doi: 10.1073/pnas.70.1.255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Evdokimov YuM, Akimenko N. M., Glukhova N. E., Varshavskii YaM Compact form of DNA in solution. I. Features of the absorption spectra of polyribonucleotides and DNA in aqueous salt solutions containing polyethyleneglycol. Mol Biol. 1974 Nov;8(3):317–325. [PubMed] [Google Scholar]
  17. Evdokimov Y. M., Platonov A. L., Tikhonenko A. S., Varshavsky Y. M. A compact form of double-stranded DNA in solution. FEBS Lett. 1972 Jun 15;23(2):180–184. doi: 10.1016/0014-5793(72)80335-1. [DOI] [PubMed] [Google Scholar]
  18. Fasman G. D., Schaffhausen B., Goldsmith L., Adler A. Conformational changes associated with f-1 histone-deoxyribonucleic acid complexes. Circular dichroism studies. Biochemistry. 1970 Jul 7;9(14):2814–2822. doi: 10.1021/bi00816a010. [DOI] [PubMed] [Google Scholar]
  19. 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]
  20. Gourévitch M., Puigdoménech P., Cavé A., Etienne G., Méry J., Parello J. Model studies in relation to the molecular structure of chromatin. Biochimie. 1974;56(6-7):967–985. doi: 10.1016/s0300-9084(74)80518-3. [DOI] [PubMed] [Google Scholar]
  21. Haynes M., Garrett R. A., Gratzer W. B. Structure of nucleic acid-poly base complexes. Biochemistry. 1970 Oct 27;9(22):4410–4416. doi: 10.1021/bi00824a600. [DOI] [PubMed] [Google Scholar]
  22. Holzwarth G., Gordon D. G., McGinness J. E., Dorman B. P., Maestre M. F. Mie scattering contributions to the optical density and circular dichroism of T2 bacteriophage. Biochemistry. 1974 Jan 1;13(1):126–132. doi: 10.1021/bi00698a020. [DOI] [PubMed] [Google Scholar]
  23. Ivanov V. I., Minchenkova L. E., Minyat E. E., Frank-Kamenetskii M. D., Schyolkina A. K. The B to A transition of DNA in solution. J Mol Biol. 1974 Aug 25;87(4):817–833. doi: 10.1016/0022-2836(74)90086-2. [DOI] [PubMed] [Google Scholar]
  24. 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]
  25. Jordan C. F., Lerman L. S., Venable J. H. Structure and circular dichroism of DNA in concentrated polymer solutions. Nat New Biol. 1972 Mar 22;236(64):67–70. doi: 10.1038/newbio236067a0. [DOI] [PubMed] [Google Scholar]
  26. Li H. J., Epstein P., Yu S. S., Brand B. Investigation of huge negative circular dichroism spectra of some nucleoproteins. Nucleic Acids Res. 1974 Nov;1(11):1371–1383. doi: 10.1093/nar/1.11.1371. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Luck G., Zimmer C., Snatzke G. Circular dichroism of protonated DNA. Biochim Biophys Acta. 1968 Dec 17;169(2):548–549. doi: 10.1016/0005-2787(68)90066-x. [DOI] [PubMed] [Google Scholar]
  28. Maestre M. F., Wang J. C. Circular dichroism of superhelical DNA. Biopolymers. 1971 Jun;10(6):1021–1030. doi: 10.1002/bip.360100608. [DOI] [PubMed] [Google Scholar]
  29. Maniatis T., Venable J. H., Jr, Lerman L. S. The structure of psi DNA. J Mol Biol. 1974 Mar 25;84(1):37–64. doi: 10.1016/0022-2836(74)90211-3. [DOI] [PubMed] [Google Scholar]
  30. Muehlinghaus J., Zundel G. Infrared investigation of poly-L-histidine structure dependent on protonation. Biopolymers. 1971;10(4):711–719. doi: 10.1002/bip.360100409. [DOI] [PubMed] [Google Scholar]
  31. Muehlinghaus J., Zundel G. Infrared investigation of poly-L-histidine structure dependent on protonation. Biopolymers. 1971;10(4):711–719. doi: 10.1002/bip.360100409. [DOI] [PubMed] [Google Scholar]
  32. Myer Y. P., Barnard E. A. Structure-reactivity relations of imidazole in polypeptides. II. Structural transitions and a -structure in poly-L-histidine solutions. Arch Biochem Biophys. 1971 Mar;143(1):116–122. doi: 10.1016/0003-9861(71)90190-1. [DOI] [PubMed] [Google Scholar]
  33. Palumbo M., Peggion E. Letter: Optical activity of the charge-transfer complex between poly-L-histidine hydrochloride and indole. Biopolymers. 1975 Feb;14(2):431–432. doi: 10.1002/bip.1975.360140215. [DOI] [PubMed] [Google Scholar]
  34. Pardon J. F., Wilkins M. H., Richards B. M. Super-helical model for nucleohistone. Nature. 1967 Jul 29;215(5100):508–509. doi: 10.1038/215508a0. [DOI] [PubMed] [Google Scholar]
  35. Santella R. M., Li H. J. Studies on poly(L-lysine50, L-tyrosine50)-DNA interaction. Biopolymers. 1974;13(9):1909–1926. doi: 10.1002/bip.1974.360130919. [DOI] [PubMed] [Google Scholar]
  36. Sponar J., Fric I., Bláha K. Basic polypeptides as histone models: circular dichroism of complexes of model polypeptides with DNA. Biophys Chem. 1975 Jul;3(3):255–262. doi: 10.1016/0301-4622(75)80018-4. [DOI] [PubMed] [Google Scholar]
  37. Wells R. D., Larson J. E., Grant R. C., Shortle B. E., Cantor C. R. Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. J Mol Biol. 1970 Dec 28;54(3):465–497. doi: 10.1016/0022-2836(70)90121-x. [DOI] [PubMed] [Google Scholar]
  38. Yu S. S., Epstein P., Li H. J. Helix-coil transition and conformational studies of nucleoprotein: poly(L-arginine)- and poly(L-arginine87, L-ornithine13)-DNA complexes. II. Circular dichroism. Biochemistry. 1974 Aug 27;13(18):3713–3717. doi: 10.1021/bi00715a015. [DOI] [PubMed] [Google Scholar]
  39. Zama M., Ichimura S. Difference between polylysine and polyarginine in changing DNA structure upon complex formation. Biochem Biophys Res Commun. 1971 Aug 20;44(4):936–942. doi: 10.1016/0006-291x(71)90802-3. [DOI] [PubMed] [Google Scholar]
  40. 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]
  41. Zimmer C., Luck G., Triebel H. Conformation and reactivity of DNA. IV. Base binding ability of transition metal ions to native DNA and effect on helix conformation with special reference to DNA-Zn(II) complex. Biopolymers. 1974;13(3):425–453. doi: 10.1002/bip.1974.360130302. [DOI] [PubMed] [Google Scholar]
  42. Zimmer C., Triebel H. Studies on conformational changes in the DNA structure induced by protonation: reversible and irreversible acid titrations and sedimentation measurments. Biopolymers. 1969;8(5):573–593. doi: 10.1002/bip.1969.360080503. [DOI] [PubMed] [Google Scholar]
  43. Zimmer C., Venner H. Protonation of cytosine in DNA. Biopolymers. 1966 Dec;4(10):1073–1079. doi: 10.1002/bip.1966.360041004. [DOI] [PubMed] [Google Scholar]

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