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NMR Relaxation Footprinting: The [Cr(NH3)6]3+ Cation as a Probe for Drug Binding Sites on Oligonucleotides

  • Elwood V. Scott
  • Gerald Zon
  • Luigi G. Marzilli
Part of the Progress in Clinical Biochemistry and Medicine book series (PCBM, volume 10)

Abstract

[Cr(NH3)6] (N03)3 was used to probe structural features of the oligonucleotide, d(ATGCdCAT)2 (numbering of strand: 5′ A1T2G3C4G5C6A7T8 3′) and to footprint the binding site of actinomycin D(ActD) in the unique 2:1 ActD/d(ATGCGCAT)2 complex by proton longitudinal relaxation (T1) studies. Longitudinal relaxation rates (1/T1) of the 1H NMR signals were measured before and after the addition of the [Cr(NH3)6]3+ solution to determine the paramagnetic longitudinal relaxation rate (1/T1p = 1/T1(Cr) — l/T1(noCr)). The chromium complex seems to prefer the center of the duplex, since signals for protons on nucleotides in the center of the duplex have the largest 1/T1ps. Larger 1/T′1p values are observed for signals of major groove base protons on G3, C4, G5 and C6 ancfalso for signals of deoxyribose H1′ and H3′ protons which are close to the phosphate backbone (H3′ closer than H1′). We believe that electrostatic forces and hydrogen bonding are the main interactions between the chromium hexaammine cation and d(ATGCGCAT)2. To interpret our data we used distances from computer-generated models for five major binding modes. Four of these involved hydrogen bonding of the ammonia ligands to various sites on the oligonucleotide (phosphate oxygens, base oxygens and base nitrogens). One mode involved the approach of the [Cr(NH3)6]3+ cation into the minor groove of the duplex with no hydrogen bonding. Neither a single binding mode nor an equal weighting of all binding modes appeared to explain the results. Two modes appeared to have the greatest influence. One involved major groove interstrand binding at G3 and G5. The other involved interaction of the cation with a single phosphate group, with all phosphate groups exhibiting this binding mode. Other modes most likely do occur, but from modeling studies these modes appear to be less important.

Keywords

Cyclic Peptide Minor Groove Major Groove Chromium Complex Paramagnetic Effect 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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References

  1. 1.
    Chiao YC, Krugh TR (1977) Biochemistry 16: 747PubMedCrossRefGoogle Scholar
  2. 2.
    Tullius TD, Dombrowski BA (1985) Science 230: 679PubMedCrossRefGoogle Scholar
  3. 3.
    Fleisher MB, Waterman KC, Turro NJ, Barton JK (1986) Inorg. Chem. 25: 3549CrossRefGoogle Scholar
  4. 4.
    Kuwabara M, Yoon C, Goyne T, Thederahn T, Sigman DS (1986) Biochemistry 25: 7401PubMedCrossRefGoogle Scholar
  5. 5.
    Granot A, Kearns DR (1982) Biopolymers 21: 203PubMedCrossRefGoogle Scholar
  6. 6.
    Marzilli LG (1977) Prog. Inorg. Chem. 23: 255CrossRefGoogle Scholar
  7. 7.
    Derome AE In: Bardwin JE (ed) (1987) Modern NMR techniques for chemistry research. Pergamon, Oxford, p 89Google Scholar
  8. 8.
    Scott EV, Zon G, Marzilli LG, Wilson WD (1988) Biochemistry 27: 7490Google Scholar
  9. 9.
    Barton JK (1988) Chemical and Engineering News 66 (39): 30CrossRefGoogle Scholar
  10. 10.
    Braunlin WH, Anderson CF, Record MT (1987) Biochemistry 26: 7724PubMedCrossRefGoogle Scholar
  11. 11.
    Stec WJ, Zon G, Egan W, Byrd RA, Phillips LR, Gallo KA (1985) J. Org. Chem. 50: 3908CrossRefGoogle Scholar
  12. 12.
    Oppegard AL, Bailar JC (1950) Inorg Syntheses 3: 153CrossRefGoogle Scholar
  13. 13.
    Cutnell JD, Bleich HE, Glasel JA (1976) J. Magn. Reson. 21: 43CrossRefGoogle Scholar
  14. 14.
    Levy G, Peat I (1975) J. Magn. Reson. 18: 500CrossRefGoogle Scholar
  15. 15.
    Jones RL, Scott EV, Zon G, Marzilli LG, Wilson WD (1988) Biochemistry 27: 6021PubMedCrossRefGoogle Scholar
  16. 16.
    Arnott S, Campbell Smith PJ, Chandrasekaran R (1976) In: Fasman GD (ed) CRC Handbook of biochemistry and molecular biology. CRC, Ohio, p 411Google Scholar
  17. 17.
    Tran-Dinh S, Neumann J-M, Huynh-Dinh T, Igolen J, Kan SK (1982) Org. Magn. Reson. 18: 148CrossRefGoogle Scholar
  18. 18.
    Fouts CS (1987) Ph. D. Thesis, Emory University, Atlanta, GAGoogle Scholar
  19. 19.
    Wilson WD, Jones RL, Zon G, Scott EV, Banville DL, Marzilli LG (1986) J. Am. Chem. Soc. 108: 7113CrossRefGoogle Scholar
  20. 20.
    Raymond KN, Meek DW, Ibers JA (1968) Inorg. Chem. 7: 1111CrossRefGoogle Scholar
  21. 21.
    Gessner RV, Quigley GJ, Wang A, Van der Marel GA, van Boom JH, Rich A (1985) Biochemistry 24: 237PubMedCrossRefGoogle Scholar
  22. 22.
    Kopka ML, Yoon C, Goodsell D, Pjura P, Dickerson RE (1985) Proc. Natl. Acad. Sci. USA 82: 1376PubMedCrossRefGoogle Scholar
  23. 23.
    Coll M, Frederick CA, Wang A, Rich A (1987) Proc. Natl. Acad. Sci. USA 84: 8385CrossRefGoogle Scholar
  24. 24.
    Teng M, Usman N, Frederich CA, Wang A (1988) Nucleic Acids Res. 16: 2671PubMedCrossRefGoogle Scholar
  25. 25.
    Pjura P, Grzeskowiak K, Dickerson RE (197) J. Mol. Biol. 197: 257CrossRefGoogle Scholar
  26. 26.
    Bloembergen N (1957) J. Chem. Phys. 27: 572CrossRefGoogle Scholar
  27. 27.
    Solomon I (1955) Phys. Rev. 99: 559CrossRefGoogle Scholar
  28. 28.
    Values of 1/r6 for each site of modes 1-5 can be found in Scott EV (1988) Ph. D. Thesis, Emory University, Atalnta, GAGoogle Scholar
  29. 29.
    Fox KR, Waring MJ (1984) Nucl. Acids Res. 12: 9271PubMedCrossRefGoogle Scholar
  30. 30.
    Ascoli F, Branca M, Mancini C, Pispisa B (1972) J. Chem. Soc., Faraday Trans I 68: 1213CrossRefGoogle Scholar
  31. 31.
    Ascoli F, Branca M, Mancini C, Pispisa B (1973) Biopolymers 12: 2431CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1989

Authors and Affiliations

  • Elwood V. Scott
    • 1
  • Gerald Zon
    • 2
  • Luigi G. Marzilli
    • 1
  1. 1.Department of ChemistryEmory UniversityAtlantaUSA
  2. 2.Applied BiosystemsFoster CityUSA

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