Skip to main content
NCBI home page
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
. 1981 Mar;78(3):1351–1355. doi: 10.1073/pnas.78.3.1351

Nitroaniline diamine.poly(dA-dT) complexes: 1H and 19F NMR parameters for full intercalation of aromatic rings into DNA.

D J Patel, E J Gabbay
PMCID: PMC319128  PMID: 6940162

Abstract

High-resolution proton, fluorine, and phosphorus NMR studies have been undertaken on complexes of methyl- and trifluoromethyl-substituted nitroaniline diamines with the synthetic DNA poly(dA-dT) in 10 mM buffer solution. We demonstrate full intercalation of the nitroaniline group of these reporter molecules between base pairs, based on large upfield proton shifts (1.3-1.7 ppm) at all four aromatic proton markers on complex formation. The temperature and pH dependences of the thymidine H-3 Watson-Crick proton chemical shift and line width require the formation of intact and stable base pairs in this intercalative complex in solution. The 19F chemical shift of the trifluoromethyl-labeled nitroaniline diamine shifts downfield by approximately 2 ppm on formation of the synthetic DNA complex and most likely reflects the nonpolar environment of the aromatic ring when sandwiched between base pairs. A sequence specificity in the binding of the nitroaniline dication to poly(dA-dT) is implied by the observation of two partially resolved 31P resonances with the phosphodiester at the intercalation site shifting downfield by approximately 0.4 ppm on complex formation.

Full text

PDF
1351

Selected References

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

  1. Adler K., Beyreuther K., Fanning E., Geisler N., Gronenborn B., Klemm A., Müller-Hill B., Pfahl M., Schmitz A. How lac repressor binds to DNA. Nature. 1972 Jun 9;237(5354):322–327. doi: 10.1038/237322a0. [DOI] [PubMed] [Google Scholar]
  2. Arter D. B., Schmidt P. G. Ring current shielding effects in nucleic acid double helices. Nucleic Acids Res. 1976 Jun;3(6):1437–1447. doi: 10.1093/nar/3.6.1437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Carter C. W., Jr, Kraut J. A proposed model for interaction of polypeptides with RNA. Proc Natl Acad Sci U S A. 1974 Feb;71(2):283–287. doi: 10.1073/pnas.71.2.283. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Chou P. Y., Adler A. J., Fasman G. D. Conformational prediction and circular dichroism studies on the lac repressor. J Mol Biol. 1975 Jul 25;96(1):29–45. doi: 10.1016/0022-2836(75)90180-1. [DOI] [PubMed] [Google Scholar]
  5. Church G. M., Sussman J. L., Kim S. H. Secondary structural complementarity between DNA and proteins. Proc Natl Acad Sci U S A. 1977 Apr;74(4):1458–1462. doi: 10.1073/pnas.74.4.1458. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Giessner-Prettre C., Pullman B., Borer P. N., Kan L. S., Ts'o P. O. Ring-current effects in the Nmr of nucleic acids: a graphical approach. Biopolymers. 1976 Nov;15(11):2277–2286. doi: 10.1002/bip.1976.360151114. [DOI] [PubMed] [Google Scholar]
  7. Giessner-Prettre C., Pullman B. On the conformational dependence of the proton chemical shifts in nucleosides and nucleotides. I. Proton shifts in the ribose ring of pyrimidine nucleosides as a function of the torsion angle about the glycosyl bond. J Theor Biol. 1977 Mar 7;65(1):171–188. doi: 10.1016/0022-5193(77)90082-0. [DOI] [PubMed] [Google Scholar]
  8. Hagen D. S., Weiner J. H., Sykes B. D. Investigation of solvent accessibility of the fluorotyrosyl residues of M13 coat protein in deoxycholate micelles and phospholipid vesicles. Biochemistry. 1979 May 15;18(10):2007–2012. doi: 10.1021/bi00577a026. [DOI] [PubMed] [Google Scholar]
  9. Helene C. Specific recognition of guanine bases in protein-nucleic acid complexes. FEBS Lett. 1977 Feb 15;74(1):10–13. doi: 10.1016/0014-5793(77)80740-0. [DOI] [PubMed] [Google Scholar]
  10. Hilbers C. W., Patel D. J. Proton nuclear magnetic resonance investigations of the nucleation and propagation reactions associated with the helix-coil transition of d-ApTpGpCpApT in H2O solution. Biochemistry. 1975 Jun 17;14(12):2656–2660. doi: 10.1021/bi00683a015. [DOI] [PubMed] [Google Scholar]
  11. Jovin T. M. Recognition mechanisms of DNA-specific enzymes. Annu Rev Biochem. 1976;45:889–920. doi: 10.1146/annurev.bi.45.070176.004325. [DOI] [PubMed] [Google Scholar]
  12. Kearns D. R., Patel D. J., Shulman R. G. High resolution nuclear magnetic resonance studies of hydrogen bonded protons of tRNA in water. Nature. 1971 Jan 29;229(5283):338–339. doi: 10.1038/229338a0. [DOI] [PubMed] [Google Scholar]
  13. Lu P., Jarema M., Mosser K., Daniel W. E. lac repressor: 3-fluorotyrosine substitution for nuclear magnetic resonance studies. Proc Natl Acad Sci U S A. 1976 Oct;73(10):3471–3475. doi: 10.1073/pnas.73.10.3471. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Mirzabekov A. D., Rich A. Asymmetric lateral distribution of unshielded phosphate groups in nucleosomal DNA and its role in DNA bending. Proc Natl Acad Sci U S A. 1979 Mar;76(3):1118–1121. doi: 10.1073/pnas.76.3.1118. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Patel D. J., Canuel L. L. Steroid diamine-nucleic acid interactions: partial insertion of dipyrandium between unstacked base pairs of the poly(dA-dT) duplex in solution. Proc Natl Acad Sci U S A. 1979 Jan;76(1):24–28. doi: 10.1073/pnas.76.1.24. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Patel D. J., Hilbers C. W. Proton nuclear magnetic resonance investigations of fraying in double-stranded d-ApTpGpCpApT in H2O solution. Biochemistry. 1975 Jun 17;14(12):2651–2656. doi: 10.1021/bi00683a014. [DOI] [PubMed] [Google Scholar]
  17. Patel D. J. The predicted secondary structure of the N-terminal sequence of the lac repressor and proposed models for its complexation to the lac operator. Biochemistry. 1975 Mar 11;14(5):1057–1059. doi: 10.1021/bi00676a027. [DOI] [PubMed] [Google Scholar]
  18. Seeman N. C., Rosenberg J. M., Rich A. Sequence-specific recognition of double helical nucleic acids by proteins. Proc Natl Acad Sci U S A. 1976 Mar;73(3):804–808. doi: 10.1073/pnas.73.3.804. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. 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]
  20. Von Hippel P. H., McGhee J. D. DNA-protein interactions. Annu Rev Biochem. 1972;41(10):231–300. doi: 10.1146/annurev.bi.41.070172.001311. [DOI] [PubMed] [Google Scholar]
  21. Warrant R. W., Kim S. H. alpha-Helix-double helix interaction shown in the structure of a protamine-transfer RNA complex and a nucleoprotamine model. Nature. 1978 Jan 12;271(5641):130–135. doi: 10.1038/271130a0. [DOI] [PubMed] [Google Scholar]
  22. 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]

Articles from Proceedings of the National Academy of Sciences of the United States of America are provided here courtesy of National Academy of Sciences

RESOURCES