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. 1981 May 25;9(10):2335–2349. doi: 10.1093/nar/9.10.2335

Temperature mediated variation of DNA secondary structure in (A.T) clusters; evidence by use of the oligopeptide netropsin as a structural probe.

K E Reinert, D Geller, E Stutter
PMCID: PMC326849  PMID: 6265870

Abstract

The titration viscometric investigation of the multi-mode interaction of netropsin (Nt) with (A.T) clusters of NaDNA12 and NH4DNA10 has been extended to different temperatures. The position of two boundaries on the r-scale (r= [Nt]bound/[DNA-P]) with increasing temperature steadily (rI/II) or more abruptly (rO/I) shifts to lower values. For the most (A.T) rich Nt-binding sites of modes (O), (I) and (II) this observation suggests the existence of an equilibrium between different DNA secondary structures with a different translation per base pair. The mode specific changes delta L1Nt of DNA contour length as induced by one Nt molecule proved to be almost independent of temperature. Concomitant stiffening effects increase with decreasing temperature, contrary to initial expectation. Conformational variability of (A.T) clusters may represent an essential feature in specific or selective DNA-protein interaction.

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Selected References

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

  1. 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]
  2. 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]
  3. Briscoe W. T., Griffin A. C., McBride C., Bowen J. M. The distribution and properties of aspartyl transfer RNA in human and animal tumors. Cancer Res. 1975 Sep;35(9):2586–2593. [PubMed] [Google Scholar]
  4. Burd J. F., Larson J. E., Wells R. D. Further studies on telestability in DNA. The synthesis and characterization of the duplex block polymers d(C20A10) - d(T10G20) and d(C20A15) - d(T15G20). J Biol Chem. 1975 Aug 10;250(15):6002–6007. [PubMed] [Google Scholar]
  5. Burd J. F., Wartell R. M., Dodgson J. B., Wells R. D. Transmission of stability (telestability) in deoxyribonucleic acid. Physical and enzymatic studies on the duplex block polymer d(C15A15) - d(T15G15). J Biol Chem. 1975 Jul 10;250(13):5109–5113. [PubMed] [Google Scholar]
  6. Burg A. W., Brown G. M. The biosynthesis of folic acid. 8. Purification and properties of the enzyme that catalyzes the production of formate from carbon atom 8 of guanosine triphosphate. J Biol Chem. 1968 May 10;243(9):2349–2358. [PubMed] [Google Scholar]
  7. Böttger M., Scherneck S., Fenske H. A sedimentation study of the interaction of superhelical SV40 DNA with H1 histone. Nucleic Acids Res. 1976 Feb;3(2):419–429. doi: 10.1093/nar/3.2.419. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. 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]
  9. Chan H. W., Wells R. D. Structural uniqueness of lactose operator. Nature. 1974 Nov 15;252(5480):205–209. doi: 10.1038/252205a0. [DOI] [PubMed] [Google Scholar]
  10. Cohen P., Kidson C. Conformational analysis of DNA-poly-L-lysine complexes by optical rotatory dispersion. J Mol Biol. 1968 Jul 14;35(1):241–245. doi: 10.1016/s0022-2836(68)80052-x. [DOI] [PubMed] [Google Scholar]
  11. Crain P. F., Sethi S. K., Katze J. R., McCloskey J. A. Structure of an amniotic fluid component, 7-(4,5-cis-dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanine (queuine), a substrate for tRNA: guanine transglycosylase. J Biol Chem. 1980 Sep 25;255(18):8405–8407. [PubMed] [Google Scholar]
  12. Dubrul E. F., Farkas W. R. Partial purification and properties of the reticulocyte guanylating enzyme. Biochim Biophys Acta. 1976 Sep 6;442(3):379–390. doi: 10.1016/0005-2787(76)90312-9. [DOI] [PubMed] [Google Scholar]
  13. Evans B. A., Howells A. J. Control of drosopterin synthesis in Drosophila melanogaster: mutants showing an altered pattern of GTP cyclohydrolase activity during development. Biochem Genet. 1978 Feb;16(1-2):13–26. doi: 10.1007/BF00484381. [DOI] [PubMed] [Google Scholar]
  14. Fan C. L., Hall L. M., Skrinska A. J., Brown G. M. Correlation of guanosine triphosphate cyclohydrolase activity and the synthesis of pterins in Drosophila melanogaster. Biochem Genet. 1976 Apr;14(3-4):271–280. doi: 10.1007/BF00484766. [DOI] [PubMed] [Google Scholar]
  15. Farkas W. R. Effect of diet on the queuosine family of tRNAs of germ-free mice. J Biol Chem. 1980 Jul 25;255(14):6832–6835. [PubMed] [Google Scholar]
  16. Farkas W. R., Singh R. D. Guanylation of transfer ribonucleic acid by a cell-free lysate of rabbit reticulocytes. J Biol Chem. 1973 Nov 25;248(22):7780–7785. [PubMed] [Google Scholar]
  17. Gregg T G, Smucker L A. Pteridines and Gene Homologies in the Eye Color Mutants of DROSOPHILA HYDEI and DROSOPHILA MELANOGASTER. Genetics. 1965 Nov;52(5):1023–1034. doi: 10.1093/genetics/52.5.1023. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Hankins W. D., Farkas W. R. Guanylation of transfer RNA by rabbit reticulocytes. Biochim Biophys Acta. 1970 Jul 16;213(1):77–89. doi: 10.1016/0005-2787(70)90009-2. [DOI] [PubMed] [Google Scholar]
  19. Hays J. B., Zimm B. H. Flexibility and stiffness in nicked DNA. J Mol Biol. 1970 Mar 14;48(2):297–317. doi: 10.1016/0022-2836(70)90162-2. [DOI] [PubMed] [Google Scholar]
  20. Hosbach H. A., Kubli E. Transfer RNA in aging Drosophila: II. Isoacceptor patterns. Mech Ageing Dev. 1979 Apr;10(1-2):141–149. doi: 10.1016/0047-6374(79)90077-0. [DOI] [PubMed] [Google Scholar]
  21. Howes N. K., Farkas W. R. Studies with a homogeneous enzyme from rabbit erythrocytes catalyzing the insertion of guanine into tRNA. J Biol Chem. 1978 Dec 25;253(24):9082–9087. [PubMed] [Google Scholar]
  22. 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]
  23. Jackson C. D., Irving C. C., Sells B. H. Changes in rat liver transfer RNA following growth hormone administration and in regenerating liver. Biochim Biophys Acta. 1970 Sep 17;217(1):64–71. doi: 10.1016/0005-2787(70)90123-1. [DOI] [PubMed] [Google Scholar]
  24. Jacobson K. B., Calviño J. F., Murphy J. B., Warner C. K. Mechanism of suppression in Drosophila. H. Enzymatic discrimination of wild-type and suppressor tyrosine transfer RNA. J Mol Biol. 1975 Mar 25;93(1):89–97. doi: 10.1016/0022-2836(75)90362-9. [DOI] [PubMed] [Google Scholar]
  25. Jacobson K. B. Mechanism of suppression in Drosophila. VII. Correlation between disappearance of an isoacceptor of tyrosine tRNA and activation of the vermilion locus. Nucleic Acids Res. 1978 Jul;5(7):2391–2404. doi: 10.1093/nar/5.7.2391. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Kasai H., Kuchino Y., Nihei K., Nishimura S. Distribution of the modified nucleoside Q and its derivatives in animal and plant transfer RNA's. Nucleic Acids Res. 1975 Oct;2(10):1931–1939. doi: 10.1093/nar/2.10.1931. [DOI] [PMC free article] [PubMed] [Google Scholar]
  27. Kasai H., Oashi Z., Harada F., Nishimura S., Oppenheimer N. J., Crain P. F., Liehr J. G., von Minden D. L., McCloskey J. A. Structure of the modified nucleoside Q isolated from Escherichia coli transfer ribonucleic acid. 7-(4,5-cis-Dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine. Biochemistry. 1975 Sep 23;14(19):4198–4208. doi: 10.1021/bi00690a008. [DOI] [PubMed] [Google Scholar]
  28. Katze J. R., Beck W. T. Administration of queuine to mice relieves modified nucleoside queuosine deficiency in Ehrlich ascites tumor tRNA. Biochem Biophys Res Commun. 1980 Sep 16;96(1):313–319. doi: 10.1016/0006-291x(80)91216-4. [DOI] [PubMed] [Google Scholar]
  29. Katze J. R., Farkas W. R. A factor in serum and amniotic fluid is a substrate for the tRNA-modifying enzyme tRNA-guanine transferase. Proc Natl Acad Sci U S A. 1979 Jul;76(7):3271–3275. doi: 10.1073/pnas.76.7.3271. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Katze J. R. Q-factor: a serum component required for the appearance of nucleoside Q in tRNA in tissue culture. Biochem Biophys Res Commun. 1978 Sep 29;84(2):527–535. doi: 10.1016/0006-291x(78)90201-2. [DOI] [PubMed] [Google Scholar]
  31. 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]
  32. Krivi G. G., Brown G. M. Purification and properties of the enzymes from Drosophila melanogaster that catalyze the synthesis of sepiapterin from dihydroneopterin triphosphate. Biochem Genet. 1979 Apr;17(3-4):371–390. doi: 10.1007/BF00498976. [DOI] [PubMed] [Google Scholar]
  33. Krylov A. S., Grokhovsky S. L., Zasedatelev A. S., Zhuze A. L., Gursky G. V., Gottikh B. P. Quantitative estimation of the contribution of pyrrolcarboxamide groups of the antibiotic distamycin A into specificity of its binding to DNA AT pairs. Nucleic Acids Res. 1979 Jan;6(1):289–304. doi: 10.1093/nar/6.1.289. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Kuchino Y., Kasai H., Nihei K., Nishimura S. Biosynthesis of the modified nucleoside Q in transfer RNA. Nucleic Acids Res. 1976 Feb;3(2):393–398. doi: 10.1093/nar/3.2.393. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Landin R. M., Boisnard M., Petrissant G. Correlation between the presence of tRNA His GUG and the erythropoietic function in foetal sheep liver. Nucleic Acids Res. 1979 Nov 24;7(6):1635–1648. doi: 10.1093/nar/7.6.1635. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Marini M., Mushinski J. F. Transfer ribonucleic acids from eleven immunoglobulin-secreting mouse plasmacytomas. Constant and variable chromatographic profiles compared with the myeloma protein sequences. Biochim Biophys Acta. 1979 Apr 26;562(2):252–270. doi: 10.1016/0005-2787(79)90171-0. [DOI] [PubMed] [Google Scholar]
  37. McKinnon R. D., Wosnick M. A., White B. N. The role of the guanine insertion enzyme in O-biosynthesis in Drosophila melanogaster. Nucleic Acids Res. 1978 Dec;5(12):4865–4876. doi: 10.1093/nar/5.12.4865. [DOI] [PMC free article] [PubMed] [Google Scholar]
  38. McNamara A. L., Smith D. W. The function of the histidine tRNA isoaccepting species in hemoglobin synthesis. J Biol Chem. 1978 Sep 10;253(17):5964–5970. [PubMed] [Google Scholar]
  39. Okada N., Shindo-Okada N., Sato S., Itoh Y. H., Oda K., Nishimura S. Detection of unique tRNA species in tumor tissues by Escherichia coli guanine insertion enzyme. Proc Natl Acad Sci U S A. 1978 Sep;75(9):4247–4251. doi: 10.1073/pnas.75.9.4247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  40. Olsen C. E., Penhoet E. E. Chromatographic and functional comparison of human placenta and HeLa cell tyrosine transfer ribonucleic acids. Biochemistry. 1976 Oct 19;15(21):4649–4654. doi: 10.1021/bi00666a016. [DOI] [PubMed] [Google Scholar]
  41. Owenby R. K., Stulberg M. P., Jacobson K. B. Alteration of the Q family of transfer RNAs in adult Drosophila melanogaster as a function of age, nutrition, and genotype. Mech Ageing Dev. 1979 Sep;11(2):91–103. doi: 10.1016/0047-6374(79)90027-7. [DOI] [PubMed] [Google Scholar]
  42. 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]
  43. 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]
  44. Reinert K. E. Aspects of specific DNA-protein interaction; local bending of DNA molecules by in-register binding of the oligopeptide antibiotic distamycin. Biophys Chem. 1981 Feb;13(1):1–14. doi: 10.1016/0301-4622(81)80019-1. [DOI] [PubMed] [Google Scholar]
  45. 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]
  46. Reinert K. E., Thrum H., Sarfert E. Counterion dependent variation of DNA secondary structure in (A . T) clusters: evidence by use of netropsin as a structural probe. Nucleic Acids Res. 1980 Nov 25;8(22):5519–5531. doi: 10.1093/nar/8.22.5519. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Renz M., Day L. A. Transition from noncooperative to cooperative and selective binding of histone H1 to DNA. Biochemistry. 1976 Jul 27;15(15):3220–3228. doi: 10.1021/bi00660a010. [DOI] [PubMed] [Google Scholar]
  48. Renz M. Preferential and cooperative binding of histone I to chromosomal mammalian DNA. Proc Natl Acad Sci U S A. 1975 Feb;72(2):733–736. doi: 10.1073/pnas.72.2.733. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Roe B. A., Stankiewicz A. F., Rizi H. L., Weisz C., DiLauro M. N., Pike D., Chen C. Y., Chen E. Y. Comparison of rat liver and Walker 256 carcinosarcoma tRNAs. Nucleic Acids Res. 1979 Feb;6(2):673–688. doi: 10.1093/nar/6.2.673. [DOI] [PMC free article] [PubMed] [Google Scholar]
  50. 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]
  51. Shindo H., Wooten J. B., Pheiffer B. H., Zimmerman S. B. Nonuniform backbone conformation of deoxyribonucleic acid indicated by phosphorus-31 nuclear magnetic resonance chemical shift anisotropy. Biochemistry. 1980 Feb 5;19(3):518–526. doi: 10.1021/bi00544a020. [DOI] [PubMed] [Google Scholar]
  52. 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]
  53. 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]
  54. Tobler J. E., Yim J. J., Grell E. H., Jacobson K. B. Developmental changes of sepiapterin synthase activity associated with a variegated purple gene in Drosophila melanogaster. Biochem Genet. 1979 Feb;17(1-2):197–206. doi: 10.1007/BF00484485. [DOI] [PubMed] [Google Scholar]
  55. Vogel T., Singer M. F. The effect of superhelicity on the interaction of histone f1 with closed circular duplex DNA. J Biol Chem. 1976 Apr 25;251(8):2334–2338. [PubMed] [Google Scholar]
  56. 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]
  57. Wasylyk B., Oudet P., Chambon P. Preferential in vitro assembly of nucleosome cores on some AT-rich regions of SV40 DNA. Nucleic Acids Res. 1979 Oct 10;7(3):705–713. doi: 10.1093/nar/7.3.705. [DOI] [PMC free article] [PubMed] [Google Scholar]
  58. Wells R. D., Blakesley R. W., Hardies S. C., Horn G. T., Larson J. E., Selsing E., Burd J. F., Chan H. W., Dodgson J. B., Jensen K. F. The role of DNA structure in genetic regulation. CRC Crit Rev Biochem. 1977;4(3):305–340. doi: 10.3109/10409237709102561. [DOI] [PubMed] [Google Scholar]
  59. White B. N., Tener G. M. Activity of a transfer RNA modifying enzyme during the development of Drosophila and its relationship to the su(s) locus. J Mol Biol. 1973 Mar 15;74(4):635–651. doi: 10.1016/0022-2836(73)90054-5. [DOI] [PubMed] [Google Scholar]
  60. Wilson T. G., Jacobson K. B. Isolation and characterization of pteridines from heads of Drosophila melanogaster by a modified thin-layer chromatography procedure. Biochem Genet. 1977 Apr;15(3-4):307–319. doi: 10.1007/BF00484462. [DOI] [PubMed] [Google Scholar]
  61. Wilson T. G., Jacobson K. B. Mechanism of suppression in Drosophila. V. Localization of the purple mutant of Drosophila melanogaster in the pteridine biosynthetic pathway. Biochem Genet. 1977 Apr;15(3-4):321–332. doi: 10.1007/BF00484463. [DOI] [PubMed] [Google Scholar]
  62. 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]
  63. Yim J. J., Brown G. M. Characteristics of guanosine triphosphate cyclohydrolase I purified from Escherichia coli. J Biol Chem. 1976 Aug 25;251(16):5087–5094. [PubMed] [Google Scholar]
  64. Yim J. J., Grell E. H., Jacobson K. B. Mechanism of suppression in Drosophila: control of sepiapterin synthase at the purple locus. Science. 1977 Dec 16;198(4322):1168–1170. doi: 10.1126/science.412253. [DOI] [PubMed] [Google Scholar]
  65. Yokoyama S., Miyazawa T., Iitaka Y., Yamaizumi Z., Kasai H., Nishimura S. Three-dimensional structure of hyper-modified nucleoside Q located in the wobbling position of tRNA. Nature. 1979 Nov 1;282(5734):107–109. doi: 10.1038/282107a0. [DOI] [PubMed] [Google Scholar]
  66. Zimmer C. Effects of the antibiotics netropsin and distamycin A on the structure and function of nucleic acids. Prog Nucleic Acid Res Mol Biol. 1975;15(0):285–318. doi: 10.1016/s0079-6603(08)60122-1. [DOI] [PubMed] [Google Scholar]

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