One- and Two-Dimensional NMR Studies of the Structures of Simple Sequence DNAs

  • David R. Kearns
Part of the NATO ASI Series book series (volume 137)

Abstract

Progress towards understanding the biological functions of proteins and DNA at the molecular level is moving at a very rapid pace as a result of the development of DNA sequencing and footprinting methods, techniques for cloning and overproduction of proteins, and the crystallization of DNA, proteins and their complexes. Many of the original problems have been solved but important questions remain unanswered. Perhaps one of the most important questions still to be answered is, how do proteins recognize specific DNA sequences? Specific interactions (hydrogen bonding, electrostatic, hydrophobic) between the DNA bases and the amino acid residues will clearly play a major role (Seeman et al., 1976) but sequence dependent variations in conformation heterogeneity may be important. Several different DNA conformations have been identified including left-handed Z-DNA (see Fig. 1) and there is evidence that sequence can have a pronounced effect on the formation of certain conformations (Arnott, 1970; Arnott & Hukins, 1972; Pohl & Jovin, 1972; Wang et al., 1979, 1981; Dickerson, 1983).

Keywords

Sugar Crystallization Recombination Rubber Oligomer 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Abragam, A. (1978) in The Principles of Nuclear Magnetism (Marshall, W.C., & Wilkinson, D.H., Eds.), Ch. 8, Oxford University Press, Oxford, England.Google Scholar
  2. Altona, C. (1975) in Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid interactions (Sundaralingam, M., & Rao, S.T.), p 613–629, University Park Press, Baltimore.Google Scholar
  3. Altona, C., & Sundaralingam, M. (1973) J. Am. Chem. Soc. 95, 2333–2344.PubMedCrossRefGoogle Scholar
  4. Altona, C., van Boom, J.H., & Haasnoot, C.A.G. (1976) Eur. J. Biochem. 71, 557–562.PubMedCrossRefGoogle Scholar
  5. Anderson, W.F., Ohlendorf, D.H., Takeda, Y., & Matthews, B.W. (1981) Nature 290, 754–755.PubMedCrossRefGoogle Scholar
  6. Arnott, S. (1970) Prog. Biophys. Mol. Biol. 21, 267–319.CrossRefGoogle Scholar
  7. Arnott, S., & Hukins, D.W.L. (1972) Biochem. Biophys. Res. Commun. 47, 1506–1509.CrossRefGoogle Scholar
  8. Arnott, S., & Hukins, D.W.L. (1973) J. Mol. Biol. 81, 93–105.PubMedCrossRefGoogle Scholar
  9. Arnott, S., & Seising, E. (1974) J. Mol. Biol. 88, 509–521.PubMedCrossRefGoogle Scholar
  10. Arnott, S., Chandrasekaran, R., Hall, I.H., & Puigjaner, L.C. (1983) Nuc. Acids Res. 11, 4141–4155.CrossRefGoogle Scholar
  11. Assa-Munt, N., & Kearns, D.R. (1984) Biochemistry 23, 791–796.PubMedCrossRefGoogle Scholar
  12. Assa-Munt, N., Granot, J., & Kearns, D.R. (1981) presented at VII International Biophysics Congress, Aug. 23-28, Abstract Book p 96.Google Scholar
  13. Assa-Munt, N., Granot, J., Behling, R.W., & Kearns, D.R. (1984) Biochemistry 23, 944–955.PubMedCrossRefGoogle Scholar
  14. Behe, M., & Felsenfeld, G. (1981) Proc. Natl. Acad. Sci. USA 78, 1619–1623.PubMedCrossRefGoogle Scholar
  15. Behling, R.W., & Kearns, D.R. (1985) Biopolymers 24, 1157–1167.PubMedCrossRefGoogle Scholar
  16. Behling, R.W., & Kearns, D.R. (1986) Biochemistry 25, 3335–3346.PubMedCrossRefGoogle Scholar
  17. Behling, R.W., Rao, S.N., Kollman, P., & Kearns, D.R. (1986) Biochemistry, submitted.Google Scholar
  18. Bendel, P., Laub, O., & James, T.L. (1983) J. Am. Chem. Soc. 105, 6748.Google Scholar
  19. Benevides, J.M., Lemeur, D., & Thomas, G.J. (1984) Biopolymers 23, 1011–1024.PubMedCrossRefGoogle Scholar
  20. Bloomfield, V., Crothers, D.M., & Tinoco, I. (1974) in The Physical Chemistry of Nucleic Acids, Harper & Row, New York.Google Scholar
  21. Bolton, P.H., & James, T.L. (1979) J. Phys. Chem. 83, 3359–3366.CrossRefGoogle Scholar
  22. Bolton, P.H., & James, T.L. (1980) Biochemistry 19, 1388–1392.PubMedCrossRefGoogle Scholar
  23. Borah, B., Cohen, J.S., & Bax, A. (1985b) Biopolymers 24, 747–765.PubMedCrossRefGoogle Scholar
  24. Borah, B., Cohen, J.S., Howard, F.B., & Miles, H.T. (1985a) Biochemistry 24, 7456.PubMedCrossRefGoogle Scholar
  25. Bosch, C., Kumar, A., Baumànn, R., Ernst, R.R., & Wuthrich, K. (1981) J. Magn. Reson. 42, 159–163.Google Scholar
  26. Bothner-By, A.A., & Noggle, J.H. (1979) J. Am. Chem. Soc. 101, 5152–5155.CrossRefGoogle Scholar
  27. Brayer, G.D., & McPherson, A. (1983) J. Mol. Biol. 169, 565–596.PubMedCrossRefGoogle Scholar
  28. Broido, M.S., & Kearns, D.R. (1982) J. Am. Chem. Soc. 104, 5207–5216.CrossRefGoogle Scholar
  29. Chen, C-W., Cohen, J.S., & Behe, M. (1983) Biochemistry 22, 2136–2142.PubMedCrossRefGoogle Scholar
  30. Cheng, D.M., Kan, L.S., Leutzinger, E.E., Jayaraman, K., Miller, P.S., & Ts’o, P.O.P. (1982) Biochemistry 21, 621–630.PubMedCrossRefGoogle Scholar
  31. Clore, G.M., & Gronenborn, A.M. 1983 EMBO J. 2, 2109–2113.PubMedGoogle Scholar
  32. Clore, G.M., & Gronenborn, A.M. 1984 FEBS Lett. 172, 219–225.PubMedCrossRefGoogle Scholar
  33. Clore, G.M., & Gronenborn, A.M. 1985 EMBO J. 138, 447–472.Google Scholar
  34. Clore, G.M., Lauble, H., Frenkiel, T.A., & Gronenborn, A.M. (1984) Eur. J. Biochem. 145, 629–636.PubMedCrossRefGoogle Scholar
  35. Crawford, J., Kolpak, F., Wang, A., Quigley, G., van Boom, J., van der Marel, G., & Rich, A. (1980) Proc. Natl. Acad. Sci. USA 77, 4016–4020.PubMedCrossRefGoogle Scholar
  36. Davies, D.B. (1978) in Progress in NMR Spectroscopy, Vol. 12, p 135–186, Pergamon Press Ltd., Great Britain.Google Scholar
  37. Dickerson, R.E. (1983) in Nucleic Acids: The Vectors of Life (Pullman, B., & Jortner, J., Eds.), p 1–15, D. Reidel Pub. Co., Dordrecht, Holland.CrossRefGoogle Scholar
  38. Dickerson, R.E., & Drew, H.R. (1981) J. Mol. Biol. 149, 761–786.PubMedCrossRefGoogle Scholar
  39. Dickerson, R.E., & Kopka, M.L. (1983) in Nucleic Acids: The Vectors of Life (Pullman, B., & Jortner, J., Eds.), D. Reidel Pub. Co., Dordrecht, The Netherlands.Google Scholar
  40. Dickerson, R.E., Kopka, M.L., & Pjura, P. (1983) J. Biomol. Str. Dynam. 1, 755–771.CrossRefGoogle Scholar
  41. Drew, H.R., & Dickerson, R.E. (1982) EMBO J. 1, 663–667.PubMedGoogle Scholar
  42. Drew, H.R., Wing, R.M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R.E. (1981) Proc. Natl. Acad. Sci. USA 78, 2179–2183.PubMedCrossRefGoogle Scholar
  43. Early, T.A., Kearns, D.R., Hillen, W., & Wells, R.D. (1980) Nuc. Acids Res. 8, 5795–5812.CrossRefGoogle Scholar
  44. Feigon, J., & Kearns, D.R. (1979) Nuc. Acids Res. 6, 2327–2337.CrossRefGoogle Scholar
  45. Feigon, J., Denny, W.A., Leupin, W., & Kearns, D.R. (1983a) Biochemistry 22, 5930–5942.PubMedCrossRefGoogle Scholar
  46. Feigon, J., Leupin, W., Denny, W.A., & Kearns, D.R. (1983b) Biochemistry 22, 5943–5951.PubMedCrossRefGoogle Scholar
  47. Feigon, J., Wang, A.H.J., van der Marel, G.A., van Boom, J.H., & Rich, A. (1984) Nuc. Acids Res. 12, 1243–1263.CrossRefGoogle Scholar
  48. Feigon, J., Wang, A.H.J., van der Marel, G.A., van Boom, J.H., & Rich, A. (1985) Nuc. Acids Res., in press.Google Scholar
  49. Feigon, J., Wright, J.M., Denny, W.A., Leupin, W., & Kearns, D.R. (1983c) Cold Spring Harbor Symp. on Quant. Biol. 67, 207–217.CrossRefGoogle Scholar
  50. Feigon, J., Wright, J.M., Leupin, W., Denny, W.A., & Kearns, D.R. (1982) J. Am. Chem. Soc. 104, 5540–5541.CrossRefGoogle Scholar
  51. Frederick, C.A., Grable, J., Melia, M., Samudzi, C., Jen-Jacobson, L., Wang, B.C., Greene, P., Boyer, H.W., & Rosenberg, J.M. (1984) Nature 309, 327–331.PubMedCrossRefGoogle Scholar
  52. Freeman, R., & Morris, G.A. (1979) Bull. Magn. Reson. 1, 5.Google Scholar
  53. Fujii, S., Wang, A.H.J., van der Marel, G., van Boom, J.H., & Rich, A. (1982) Nuc. Acids Res. 10, 7879–7892.CrossRefGoogle Scholar
  54. Gaffney, B.L., Marky, L.A., & Jones, R.A. (1982) Nuc. Acids Res. 10, 4351–4361.CrossRefGoogle Scholar
  55. Grant, R., Kodama, M., & Wells, R. (1972) Biochemistry 11, 805–815.PubMedCrossRefGoogle Scholar
  56. Gupta, G., Sarma, M.H., & Sarma, R.H. (1985) J. Mol. Biol. 186, 463–469.PubMedCrossRefGoogle Scholar
  57. Gupta, G., Sarma, M.H., Dhingra, M.M., Sarma, R.H., Rajagopalan, M., & Sasisekharan, V. (1983) J. Biomol. Str. Dynam. 1, 395–416.CrossRefGoogle Scholar
  58. Haasnoot, C.A.G., de Leeuw, F.A.A.M., de Leeuw, H.P.M., & Altona, C. (1981) Org. Magn. Reson. 15, 43.CrossRefGoogle Scholar
  59. Hare, D.R., Wemmer, D.E., Chou, S.H., Drobny, G., & Reid, B.R. (1983) J. Mol. Biol. 171, 319–336.PubMedCrossRefGoogle Scholar
  60. Hogan, M.E., & Jardetzky, O. (1979) Proc. Natl. Acad. Sci. USA 76, 6341–6345.PubMedCrossRefGoogle Scholar
  61. Hogan, M.E., & Jardetzky, O. (1980a) Biochemistry 19, 2079–2085.PubMedCrossRefGoogle Scholar
  62. Hogan, M.E., & Jardetzky, O. (1980b) Biochemistry 19, 3460–3468.PubMedCrossRefGoogle Scholar
  63. Holbrook, S.R., & Kim, S.-H. (1984) J. Mol. Biol. 178, 361–388.CrossRefGoogle Scholar
  64. Hoogsteen, K. (1963) Acta Crystallogr. 16, 907–916.CrossRefGoogle Scholar
  65. Howard, F.B., & Miles, H.T. (1983) in Nucleic Acids: The Vectors of Life (Pullman, B., & Jortner, J., Eds.), p. 511–520, D. Reidel Pub. Co., Dordrecht, Holland.CrossRefGoogle Scholar
  66. James, T.L. (1984) in Phosphorus-31 NMR, Principles and Applications Ch. 12, p 349-400, Academic Press, Inc.Google Scholar
  67. Jeener, J., Meier, B.H., Bachman, P., & Ernst, R.R. (1979) J. Chem. Phys. 71, 4546–4553.CrossRefGoogle Scholar
  68. Kallenbach, N.R., Mandai, C., & Englander, S.W. (1981) in Biomolecular Stereodynamics (Sarma, R., Ed.), p 233, Adenine Press, New York.Google Scholar
  69. Kan, L.S., Cheng, D.M., Jayaraman, K., Leutzinger, E.E., Miller, P.S., & Ts’o, P.O.P. (1982) Biochemistry 21, 6723–6732.PubMedCrossRefGoogle Scholar
  70. Kearns, D.R. (1977) Ann. Rev. Biophys. Bioeng. 6, 477–523.CrossRefGoogle Scholar
  71. Kearns, D.R., Mirau, P.A., Assa-Munt, N., & Behling, R.W. (1983) in Nucleic Acids: The Vectors of Life (Pullman, B., & Jortner, J., Eds.), p 113–125, D. Reidel Pub. Co., Dordrecht, Holland.CrossRefGoogle Scholar
  72. Klug, A., Jack, A., Viswamitra, M.A., Kennard, O., Shakked, Z., & Steitz, T.A. (1979) J. Mol. Biol. 131, 669–680.PubMedCrossRefGoogle Scholar
  73. Kmiec, E.B., & Holloman, W.K. (1984) Cell 86, 593–598.CrossRefGoogle Scholar
  74. Lerner, D.B., Becktel, W.J., Everett, R., Goodman, M., & Kearns, D.R. (1984) Biopolymers 28, 2157–2172.CrossRefGoogle Scholar
  75. Mai, M.T., Wemmer, D.E., & Jardetzky, O. (1983) J. Am. Chem. Soc. 105, 7149–7152.CrossRefGoogle Scholar
  76. McClarin, J.A., Frederick, C.A., Wang, B.C., Greene, P., Boyer, H.W., Grable, J., & Rosenberg, J.M. (1986) Science, in press.Google Scholar
  77. McKay, D.B., & Steitz, T.A. (1981) Nature 290, 744–749.PubMedCrossRefGoogle Scholar
  78. Mirau, P.A., & Kearns, D.R. (1983) in Structure and Dynamics: Nucleic Acids and Proteins (Clementi, E., & Sarma, R.H., Eds.), p 227–239, Adenine Press, New York.Google Scholar
  79. Mirau, P.A., & Kearns, D.R. (1984) Biochemistry 28, 5439–5446.CrossRefGoogle Scholar
  80. Mirau, P.A., Behling, R.W., & Kearns, D.R. (1985) Biochemistry 24, 6200–6211.PubMedCrossRefGoogle Scholar
  81. Mitsui, Y., Langridge, R., Shortle, B., Cantor, C., Grant, R., Kodama, M., & Wells, R.D. (1970) Nature 228, 1166–1169.PubMedCrossRefGoogle Scholar
  82. Nagayama, K., Kumar, A., Wuthrich, K., & Ernst, R.R. (1980) J. Magn. Reson. 40, 321–334.Google Scholar
  83. Nagayama, K., Wuthrich, K., & Ernst, R.R. (1979) Biochem. Biophys. Res. Commun. 90, 305.PubMedCrossRefGoogle Scholar
  84. Nall, B.T., Rotwell, W.P., Waugh, J.S., & Rupprecht, A. (1981) Biochemistry 20, 1881–1887.PubMedCrossRefGoogle Scholar
  85. Nilsson, L., Clore, G.M., Gronenborn, A.M., Brunger, A.T., & Karplus, M. (1986) J. Mol. Biol. 188, 455–475.PubMedCrossRefGoogle Scholar
  86. Nordheim, A., Lafer, E.M., Peck, L.J., Wang, J.C., Stollar, D., & Rich, A. (1982) Cell 81, 309–318.CrossRefGoogle Scholar
  87. Opella, S.J., Wise, W.B., & DiVerdi, J.A. (1981) Biochemistry 20, 284–290.PubMedCrossRefGoogle Scholar
  88. Patel, D.J. (1978) J. Polymer Sci. 62, 117–141.Google Scholar
  89. Patel, D.J., Canuel, L., & Pohl, F. (1979) Proc. Natl. Acad. Sci. USA 76, 2508–2511.PubMedCrossRefGoogle Scholar
  90. Patel, D.J., Kozlowski, S.A., Nordheim, A., & Rich, A. (1982) Proc. Natl. Acad. Sci. USA 79, 1413–1417.PubMedCrossRefGoogle Scholar
  91. Pohl, F.M., & Jovin, T.M. (1972) J. Mol. Biol. 67, 375–396.PubMedCrossRefGoogle Scholar
  92. Ramaswamy, N., Bansal, M., Gupta, G., & Sasisekharan, V. (1982) Proc. Natl. Acad. Sci. USA 79, 6109–6113.PubMedCrossRefGoogle Scholar
  93. Rich, A., Nordheim, A., & Wang, H.-J. (1984) Ann. Rev. Biochem. 58, 791–846.CrossRefGoogle Scholar
  94. Rill, R.L., Hilliard, P.R., Bailey, J.T., & Levy, G.C. (1980) J. Am. Chem. Soc. 102, 418.CrossRefGoogle Scholar
  95. Rill, R.L., Hilliard, P.R., Levy, L.F., & Levy, G.C. (1981) in Biomolecular Stereodynamics Vol. I (Sarma, R.H., Ed.), p 383, Adenine Press, New York.Google Scholar
  96. Saenger, W. (1984) in Principles of Nucleic Acid Structure (Cantor, C.R., Ed.), Springer-Verlag, New York.CrossRefGoogle Scholar
  97. Scheek, R.M., Boelens, R., Russo, N., van Boom, J.H., & Kaptein, R. (1984) Biochemistry 23, 1371–1376.PubMedCrossRefGoogle Scholar
  98. Seeman, N.C., Rosenberg, J.M., & Rich, A. (1976) Proc. Natl. Acad. Sci. USA 73, 804–808.PubMedCrossRefGoogle Scholar
  99. Shindo, H. (1980) Biopolymers 19, 509–522.PubMedCrossRefGoogle Scholar
  100. Shindo, H., Wooten, J.B., Pheiffer, B.H., & Zimmerman, S.B. (1980) Biochemistry 19, 518–526.PubMedCrossRefGoogle Scholar
  101. Sober, H.A., & Harte, R.A. (1970) in CRC Handbook of Biochemistry, p H18, H19, The Chemical Rubber Co., Cleveland, Ohio.Google Scholar
  102. Steitz, T.A., Weber, I.T., & Matthew, J.B. (1983) Cold Spring Harbor Symp. Quant. Biol. 67, 419–426.CrossRefGoogle Scholar
  103. Stirdivant, S.M., Klysik, J., & Wells, R.D. (1982) J. Biol. Chem. 257, 10159–10165.PubMedGoogle Scholar
  104. Sutherland, J.C., & Griffin, K.P. (1983) Biopolymers 22, 1445–1448.CrossRefGoogle Scholar
  105. Tanaka, I., Appelt, K., Dijk, J., White, S.W., & Wilson, K.S. (1984) Nature 310, 376–381.PubMedCrossRefGoogle Scholar
  106. Viswamitra, M.A., Kennard, O., Jones, P.G., Sheldrick, G.M., Salisbury, S., Falvello, L., & Shakked, Z. (1978) Nature 273, 687–688.PubMedCrossRefGoogle Scholar
  107. Viswamitra, M.A., Shakked, Z., Jones, P.G., Sheldrick, G.M., Salisbury, S.A., & Kennard, O. (1982) Biopolymers 21, 513.PubMedCrossRefGoogle Scholar
  108. Vold, R.R., Brandes, R., Tsang, P., Kearns, D.R., Vold, R.L., & Rupprecht, A. (1986) J. Am. Chem. Soc. 108, 302–303.CrossRefGoogle Scholar
  109. Vorlickova, M., Kypr, J., & Sklenar, V. (1983) J. Mol. Biol. 166, 85–92.PubMedCrossRefGoogle Scholar
  110. Vorlickova, M., Kypr, J., Stokrova, S., & Sponar, J. (1982) Nuc. Acids Res. 10, 1071.CrossRefGoogle Scholar
  111. Wagner, G., & Wuthrich, K. (1979) J. Magn. Reson. 88, 675–680.Google Scholar
  112. Wang, A.H.J., Gessner, R., van der Mrel, G.A., van Boom, J.H., & Rich, A. (1985) Proc. Natl. Acad. Sci. USA 82, 3611.PubMedCrossRefGoogle Scholar
  113. Wang, A.H.J., Quigley, G., Kolpak, F., van der Marel, G., van Boom, J., & Rich, A. (1981) Science 211, 171–176.PubMedCrossRefGoogle Scholar
  114. Wang, A.H.J., Quigley, G.J., Kolpak, F.J., Crawford, J.L., van Boom, J.H., van der Marel, G., & Rich, A. (1979) Nature 282, 680–686.PubMedCrossRefGoogle Scholar
  115. Wartell, R.M., & Harrell, J.T. (1986) Biochemistry, in press.Google Scholar
  116. Weiner, S.J., Kollman, P.A., Case, D.A., Singh, U.C., Ghio, C., Alagona, G., Profeta, S., & Weiner, P. (1984) J. Am. Chem. Soc. 106, 765–784.CrossRefGoogle Scholar
  117. Weiss, M.A., Patel, D.J., Sauer, R.T., & Karplus, M. (1984) Proc. Natl. Acad. Sci. USA 81, 130–134.PubMedCrossRefGoogle Scholar
  118. 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, F.F., Nes, I.F., & Wartell, R.M. (1977) in CRC Critical Reviews in Biochemistry, p 305.Google Scholar
  119. Wells, R.D., Goodman, T.C., Hillen, W., Horn, G.T., Klein, R.D., Larson, J.E., Muller, U.R., Neuendorf, S.K., Panayotatos, N., & Stirdivant, S.M. (1980) Prog. Nuc. Acid Res. Mol. Biol. 24, 167–267.CrossRefGoogle Scholar
  120. Wemmer, D.E., Chou, S.H., Hare, D.R., & Reid, B.R. (1984) Biochemistry 23, 2262–2268.PubMedCrossRefGoogle Scholar
  121. Westerink, H.P., van der Marel, G.A., van Boom, J.H., & Haasnoot, C.A.G. (1984) Nuc. Acids Res. 12, 4323–4338.CrossRefGoogle Scholar
  122. Wing, R., Drew, H., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R.E. (1980) Nature 287, 755–758.PubMedCrossRefGoogle Scholar
  123. Zarling, D.A., Arndt-Jovin, D.J., Robert-Nicoud, M., McIntosh, L.P., Thomae, R., & Jovin, T.M. (1984) J. Mol. Biol. 176, 369–415.PubMedCrossRefGoogle Scholar
  124. Zimmerman, S.B., & Pheiffer, B.H. (1981) Proc. Natl. Acad. Sci. USA 78, 78–82.PubMedCrossRefGoogle Scholar

Copyright information

© Plenum Press, New York 1987

Authors and Affiliations

  • David R. Kearns
    • 1
  1. 1.Department of Chemistry, B-014University of CaliforniaSan Diego, La JollaUSA

Personalised recommendations