Journal of Fluorescence

, Volume 11, Issue 1, pp 23–32 | Cite as

Temperature and Base Sequence Dependence of 2-Aminopurine Fluorescence Bands in Single- and Double-Stranded Oligodeoxynucleotides

  • Mikako Kawai
  • Michael J. Lee
  • Kervin O. Evans
  • Thomas M. Nordlund
Article

Abstract

Fluorescence excitation spectra of 2-aminopurine (2AP) incorporated into single-stranded DNA di- and trinucleotides, as well as into single- and double-stranded pentanucleotides, have been measured as a function of temperature from 5 to 65 °C. Spectral shifts have been precisely quantitated through difference spectroscopy and spectral fits. G(2AP)C and C(2AP)G oligonucleotides have relatively blue-shifted excitation spectra (especially the former) compared to the 2AP free base. The position of the excitation peak of 2AP free base is temperature independent, those of (2AP)T, G(2AP)C, C(2AP)G and TT(2AP)TT shift about 0.4 nm to the blue from 5 to 65 °C, though the spectra of the G-C-containing oligomers also change shape. The temperature dependence of the A(2AP)T spectral position is 2.5-times stronger, and just rises to that of the free base at high temperature. On the other hand, the decrease of yield with increasing temperature is smallest for A(2AP)T, even compared to the free base. The dominant effect when A neighbors 2AP appears to be temperature-dependent stacking with accompanying energy transfer, while in G- and C-containing trinucleotides a temperature-independent interaction keeps the 2AP excitation spectrum blue-shifted. The effect of double strand formation appears to be small compared to stacking interactions. These spectra can be useful in identifying base neighbors and structures of 2AP in unknown 2AP-labeled DNA.

Spectroscopy spectral shifts DNA nucleic acids base stacking adenine 

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REFERENCES

  1. 1.
    N. Hagag, E. R. Birnbaum, and D. W. Darnall (1983) Biochemistry 22, 2420-2427.Google Scholar
  2. 2.
    J. R. Lakowicz, I. Gryczynski, W. Wiczk, G. Laczko, F. C. Prendergast, and M. L. Johnson (1990) Biophys. Chem. 36, 99-115.Google Scholar
  3. 3.
    P. Wu and L. Brand (1994) Anal. Biochem. 218, 1-13.Google Scholar
  4. 4.
    P. R. Selvin (1995) Methods Enzymol. 246, 300-334.Google Scholar
  5. 5.
    M. P. Lillo, B. K. Szpikowska, M. T. Mas, J. D. Sutin, and J. M. Beechem (1997) Biochemistry 36(37), 11273-11281.Google Scholar
  6. 6.
    W. J. Dong, J. Xing, M. Villain, M. Hellinger, J. M. Robinson, M. Chandra, R. J. Solaro, P. K. Umeda, and H. C. Cheung (1999) J. Biol. Chem. 274(44), 31382-31390.Google Scholar
  7. 7.
    O. Tcherkasskaya and O. B. Ptitsyn (1999) Protein Eng. 12(6), 485-490.Google Scholar
  8. 8.
    M. Li, L. G. Reddy, R. Bennett, N. D. Silva, Jr., L. R. Jones, and D. D. Thomas (1999) Biophys. J. 76(5), 2587-2599.Google Scholar
  9. 9.
    W. J. Dong, J. M. Robinson, J. Xing, P. K. Umeda, and H. C. Cheung (2000) Protein Sci. 9(2), 280-289.Google Scholar
  10. 10.
    R. A. Keller, L. A. Bottomly, and N. J. Dovichi (eds.) (1992) in R. A. Keller, L. A. Bottomly, and N. J. Divichi (Eds.), Advances in DNA Sequencing Technology, SPIE, Los Angeles, Vol. 1891.Google Scholar
  11. 11.
    S. C. Hung, R. A. Mathies, and A. N. Glazer (1998) Anal. Biochem. 255(1), 32-38.Google Scholar
  12. 12.
    A. Van Orden, H. Cai, P. M. Goodwin, and R. A. Keller (1999) Anal. Chem. 71(11), 2108-2116.Google Scholar
  13. 13.
    M. Sauer, B. Angerer, K. T. Han, and C. Zander (1999) Phys. Chem. Chem. Phys. 1(10), 2471-2477.Google Scholar
  14. 14.
    S. McWhorter and S. A. Soper (2000) Electrophoresis 21(7), 1267-1280.Google Scholar
  15. 15.
    A. Ujvari and C. T. Martin (1996) Biochemistry 35(46), 14574-14582.Google Scholar
  16. 16.
    Y. Jia, A. Kumar, and S. S. Patel (1996) J. Biol. Chem. 271(48), 30451-30458.Google Scholar
  17. 17.
    B. W. Allan, N. O. Reich, and J. M. Beechem (1999) Biochemistry 38(17), 5308-5314.Google Scholar
  18. 18.
    L. B. Bloom, M. R. Otto, J. M. Beechem, and M. F. Goodman (1993) Biochemistry 32, 11247-11258.Google Scholar
  19. 19.
    L. B. Bloom, M. R. Otto, R. Eritja, L. J. Reha-Krantz, M. F. Goodman, and J. M. Beechem (1994) Biochemistry 33, 7576-7586.Google Scholar
  20. 20.
    K. D. Raney, L. C. Sowers, D. P. Millar, and S. J. Benkovic (1994) Proc. Natl. Acad. Sci. USA 91, 6644-6648.Google Scholar
  21. 21.
    B. W. Allan and N. O. Reich (1996) Biochemistry 35(47), 14757-14762.Google Scholar
  22. 22.
    J. M. Beechem, M. R. Otto, L. B. Bloom, R. Eritja, L. J. Reha-Krantz, and M. F. Goodman (1998) Biochemistry 37(28), 10144-10155.Google Scholar
  23. 23.
    M. R. Otto, L. B. Bloom, M. F. Goodman, and J. M. Beechem (1998) Biochemistry 37(28), 10156-10163.Google Scholar
  24. 24.
    L. J. Reha-Krantz, L. A. Marquez, E. Elisseeva, R. P. Baker, L. B. Bloom, H. B. Dunford, and M. F. Goodman (1998) J. Biol. Chem. 273(36), 22969-22976.Google Scholar
  25. 25.
    W. C. Lam, E. J. Van der Schans, L. C. Sowers, and D. P. Millar (1999) Biochemistry 38(9), 2661-2668.Google Scholar
  26. 26.
    M. Aida, K. Yamane, and C. Nagata (1986) Mutat. Res. 173(1), 49-54.Google Scholar
  27. 27.
    W. P. Diver and D. M. Woodcock (1989) Mutagenesis 4(4), 302-305.Google Scholar
  28. 28.
    G. Speit, S. Garkov, S. Haupter, and B. Koberle (1990) Mutagenesis 5(2), 185-190.Google Scholar
  29. 29.
    L. A. Marquez and L. J. Rehakrantz (1996) J. Biol. Chem. 271(46), 28903-28910.Google Scholar
  30. 30.
    M. F. Goodman and K. D. Fygenson (1998) Genetics 148(4), 1475-1482.Google Scholar
  31. 31.
    D. Xu (1996) University of Alabama at Birmingham.Google Scholar
  32. 32.
    T. M. Nordlund, D. Xu, and K. O. Evans (1993) Biochemistry 32, 12090-12095.Google Scholar
  33. 33.
    T. M. Nordlund, D. Xu, and K. Evans (1994) Proc. SPIE 2137, 634-643.Google Scholar
  34. 34.
    S. O. Kelley and J. K. Barton (1999) Science 283(5400), 375-381.Google Scholar
  35. 35.
    P. O. Lycksell, A. Gräslund, F. Claesens, L. W. McLaughlin, U. Larsson, and R. Rigler (1987) Nucleic Acids Res. 15(21), 9011-9025.Google Scholar
  36. 36.
    A. Gräslund, F. Claesens, L. W. McLaughlin, P.-O. Lycksell, U. Larsson, and R. Rigler (1987) In A. Ehrenberg, R. Rigler, A. Gräslund, and L. Nilsson (Eds.), Structure, Dynamics and Function of Biomolecules, Springer-Verlag, Berlin, pp. 201-207.Google Scholar
  37. 37.
    T. M. Nordlund, S. Andersson, L. Nilsson, R. Rigler, A. Gräslund, and L. W. McLaughlin (1989) Biochemistry 28(23), 9095-9103.Google Scholar
  38. 38.
    P. G. Wu, T. M. Nordlund, B. Gildea, and L. W. McLaughlin (1990) Biochemistry 29(27), 6508-14.Google Scholar
  39. 39.
    K. Evans, D.-G. Xu, Y.-S. Kim, and T. M. Nordlund (1992) J. Fluoresc. 2(4), 209-216.Google Scholar
  40. 40.
    D. Xu, K. O. Evans, and T. M. Nordlund (1994) Biochemistry 33, 9592-9599.Google Scholar
  41. 41.
    D. P. Millar and T. E. Carver (1994) Proc. SPIE 2137, 686-695.Google Scholar
  42. 42.
    D. P. Millar (1996) Curr. Opin. Struct. Biol. 6(3), 322-326.Google Scholar
  43. 43.
    D. C. Ward, E. Reich, and L. Stryer (1969) J. Biol. Chem. 244, 1228-1237.Google Scholar
  44. 44.
    A. Kawski, B. Bartoszewicz, I. Gryczynski, and M. Krajewski (1975) Bull. Acad. Polonaise Sci. (Ser. Sci. Math. Astr. Phys.) XXIII, 367-372.Google Scholar
  45. 45.
    A. Bierzynski, H. Kozlowska, and K. L. Wierzchowski (1977) Biophys. Chem. 6, 223-229.Google Scholar
  46. 46.
    J. D. Puglisi and I. J. Tinoco (1989) in J. E. Dahlberg and J. N. Abelson (Eds.), RNA Processing Part A. General Methods, Academic Press, San Diego, Vol. 180, pp. 304-325.Google Scholar
  47. 47.
    D. Xu and T. M. Nordlund (2000) Biophys. J. 78(2), 1042-1058.Google Scholar
  48. 48.
    W. Knox, T. M. Nordlund, and G. Mourou (1982) Appl. Phys. B 28, 174-175.Google Scholar
  49. 49.
    D. Xu, K. O. Evans, and T. M. Nordlund (1994) Biochemistry 33(32), 9592-9599.Google Scholar
  50. 50.
    J. Beechem and L. Brand (1985) Ann. Rev. Biochem. 54, 43-71.Google Scholar
  51. 51.
    J. H. Sommer, T. M. Nordlund, M. McGuire, and G. McLendon (1986) J. Phys. Chem. 90, 5173-5178.Google Scholar
  52. 52.
    E. R. Henry (1997) Biophys. J. 72(2), 652-673.Google Scholar
  53. 53.
    N. Le Novere (2000) http://bioweb.pasteur.fr/seqanal/interfaces/melting.html.Google Scholar
  54. 54.
    T. M. Nordlund, D. Xu, and K. O. Evans (1993) Biochemistry 32(45), 12090-12095.Google Scholar

Copyright information

© Plenum Publishing Corporation 2001

Authors and Affiliations

  • Mikako Kawai
    • 1
  • Michael J. Lee
    • 1
  • Kervin O. Evans
    • 1
  • Thomas M. Nordlund
    • 1
  1. 1.Department of PhysicsUniversity of Alabama at BirminghamBirmingham

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