Skip to main content

Hybrid Enzymes and the Sequence-Specific Cleavage of Nucleic Acids

  • Conference paper
  • 88 Accesses

Part of the book series: Bioorganic Chemistry Frontiers ((BIOORGANIC,volume 2))

Abstract

Catalysts have been generated that sequence-specifically hydrolyze RNA and DNA at predefined sites, i.e., a new class of restriction enzymes. New binding domains (oligonucleotides or peptides of defined sequence) were introduced site-selectively into the relatively nonselective phosphodiesterases, staphylococcal nuclease and ribonuclease S, to generate hybrid enzymes that site-specifically cleave nucleic acids. Subsequent mutagenesis of the hybrid enzymes has generated enzymes that siteselectively hydrolyze one bond in large RNAs and DNAs in a catalytic fashion. We have been able to use these hybrid enzymes to selectively cleave duplex plasmid DNAs via D-loop formation. This work has not only resulted in powerful tools for studying RNA and DNA structure but also may provide a general strategy for designing other selective hybrid enzymes for important biological transformations, such as the selective cleavage of genomic DNA, or selective cleavage of peptide amide bonds.

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   84.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   109.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Sharpless KB, Woodward SS, Finn MG (1984) In: Bartmann W, Trost BM (eds) Selectivity-A goal for synthetic efficiency, Verlag Chemie, Weinheim, Federal Republic of Germany, 377

    Google Scholar 

  2. Noyori R, Ohkuna T, Kitamura M, Takaya H, Sayo N, Kumobayshi H, Akutagawa S (1987) J Am Chem Soc, 109: 5856

    Article  CAS  Google Scholar 

  3. Rebek J (1987) Science 235: 78

    Article  Google Scholar 

  4. Lehn J (1988) Angew Chem Int Ed, 27: 90

    Google Scholar 

  5. Breslow R, (1986) Adv Enzymol, 58: 1

    CAS  Google Scholar 

  6. Knowles JR (1987) Science 236: 1252

    Article  CAS  Google Scholar 

  7. Wells JA, Cunningham BC, Graycar TP, Estell DA (1987) Proc Natl Acad Sci, 84: 5167

    Article  CAS  Google Scholar 

  8. Cronin CN, Malcolm BA, Kirsch JF (1987) J Am Chem Soc, 109: 2222

    Article  CAS  Google Scholar 

  9. Noren CJ, Anthony-Cahill SJ, Griffith MC, Schultz PG (1989) Science, 244: 182

    Article  CAS  Google Scholar 

  10. Youderian P, Vershon A, Bouvier S, Sauer RT, Susskind MM (1983) Cell, 35: 111

    Article  Google Scholar 

  11. Masazumi M, Aiba S (1985) J Biol Chem, 260: 15298

    Google Scholar 

  12. Das G, Hickey DR, McLendon D, McLendon G, Sherman F (1989) Proc Natl Acad Sci USA, 86: 496

    Article  CAS  Google Scholar 

  13. Liao H, Mckenzie T, Hageman R (1986) Proc Natl Acad Sci USA, 83: 576

    Article  CAS  Google Scholar 

  14. Regan L, DeGrado WF (1988) Science, 241: 976

    Article  CAS  Google Scholar 

  15. Kim PS (1988) Protein Engineering 2: 249

    Article  CAS  Google Scholar 

  16. DeGrado WF, Wasserman ZR, Lear JD (1989) Science, 243: 622

    Article  CAS  Google Scholar 

  17. Richardson JS, Richardson DC (1989) Trends Biochem Sci, 14: 304

    Article  CAS  Google Scholar 

  18. Pollack SJ, Jacobs JW, Schultz PG (1986) Science, 234: 1570

    Article  CAS  Google Scholar 

  19. Tramontano A, Janda KD, Lerner RA (1986) Science, 234: 1566

    Article  CAS  Google Scholar 

  20. Iverson BL, Lerner RA (1989) Science, 243: 1184

    Article  CAS  Google Scholar 

  21. Cochran AG, Sugasawara R, Schultz PG (1988) J Am Chem Soc, 110: 7888

    Article  CAS  Google Scholar 

  22. Shokat KM, Leumann CJ, Sugasawara R, Schultz PG (1989) Nature, 338: 269

    Article  CAS  Google Scholar 

  23. Jackson DY, Jacobs JW, Sugasawara R, Reich SH, Bartlett PA, Schultz PG (1988) J Am Chem Soc, 110: 4841

    Article  CAS  Google Scholar 

  24. Hilvert D, Carpenter SH, Nared KD, Auditor M-T.M (1988) Proc Natl Acad Sci USA, 85: 4953

    Article  CAS  Google Scholar 

  25. Neet KE, Koshland DE (1966) Proc Natl Acad USA, 56: 1606

    Article  CAS  Google Scholar 

  26. Polgar L, Bender ML (1966) J Am Chem Soc, 88: 3153

    Article  CAS  Google Scholar 

  27. Neet KE, Nanci A, Koshland DE (1968) J Biol Chem, 243: 6392

    CAS  Google Scholar 

  28. Polgar L, Bender ML (1970) Adv Enzymol, 33: 381

    CAS  Google Scholar 

  29. Yokosawa H, Ojima S, Ishii J (1977) J Biochem (Tokyo), 82: 869

    CAS  Google Scholar 

  30. Clark PI, Lowe G (1978) Eur J Biochem, 84: 293

    Article  CAS  Google Scholar 

  31. Nakatsuka T, Sasaki T, Kaiser ET (1987) J Am Chem Soc, 109: 3808

    Article  CAS  Google Scholar 

  32. Wong C.-H (1989) Science, 244: 1145

    Article  CAS  Google Scholar 

  33. a) Kaiser ET, Lawrence DS (1984) Science, 226: 505 (b) Radziejewski C, Hilvert D, Kaiser ET ( 1985 ) Biocatalysts in organic syntheses, Amsterdam, p 81

    Google Scholar 

  34. Pollack SJ, Nakayama GR, Schultz PG (1988) Science, 242: 1038

    Article  CAS  Google Scholar 

  35. Pollack SJ, Schultz PG (1989) J Am Chem Soc, 111: 1929

    Article  CAS  Google Scholar 

  36. Vitetta ES, Krolick KA, Miyama-Inaba M, Cushley W, Uhr JW (1983) Science, 219: 644

    Article  CAS  Google Scholar 

  37. Bode C, Matsueda GR, Hui HY, Haber E (1985) Science, 229: 765

    Article  CAS  Google Scholar 

  38. Haber E, Quartermous T, Matsueda GR, Runge MS (1989) Science, 243: 51

    Article  CAS  Google Scholar 

  39. Westerberg DA, Carney PL, Rogers PE, Kline SJ, Johnson DK (1989) J Med Chem 32: 236

    Article  CAS  Google Scholar 

  40. Ji TH (1983) Methods in Enzymol, 91: 580

    Article  CAS  Google Scholar 

  41. Brennan M, Davidson PF, Paulus H (1985) Science, 229: 81

    Article  CAS  Google Scholar 

  42. McClellend M, Jones R, Patel Y, Nelson M (1987) Nucleic Acids Res, 15: 5985

    Article  Google Scholar 

  43. Kim SC, Podhajska AJ, Syzblski W (1988) Science, 240: 504

    Article  CAS  Google Scholar 

  44. Crouch RJ, Dirksen ML (1982) In: Linn SN, Roberts RJ (eds) Nucleases Vol 14, Cold Spring Harbor Press, p 211

    Google Scholar 

  45. Shibahara S, Mukai S, Nishihara T, Inoue H, Ohtsuka E, Morisawa H (1987) Nucl Acids Res 15: 4403

    Article  CAS  Google Scholar 

  46. Cech TR, Bass BL (1986) Ann Rev Biochem 55: 599

    Article  CAS  Google Scholar 

  47. Noller H (1984) Ann Rev Biochem 53: 119

    Article  CAS  Google Scholar 

  48. Cimino GD, Gamper HB, Issacs ST, Hearst JE (1985) Ann Rev Biochem 54: 1151

    Article  CAS  Google Scholar 

  49. Dervan PB (1986) Science, 232: 464

    Article  CAS  Google Scholar 

  50. a) Dreyer GB, Dervan PB (1985) Proc Natl Acad Sci USA, 82: 968

    Google Scholar 

  51. (b) Chu BCF, Orgel LE, Proc Natl Acad Sci USA, 82: 963

    Google Scholar 

  52. (c) Chen CB, Sigman DS (1988) J Am Chem Soc, 110: 6570

    Google Scholar 

  53. Moser HE, Dervan PB (1987) Science, 238: 645

    Article  CAS  Google Scholar 

  54. Stroebel SA, Moser HE, Dervan PB (1988) J Am Chem Soc, 110: 7927

    Article  Google Scholar 

  55. Mack DP, Iverson BL, Dervan PB (1988) J Am Chem Soc, 110: 7572

    Article  CAS  Google Scholar 

  56. Chen BC, Sigman DS (1987) Science, 237: 1197

    Article  CAS  Google Scholar 

  57. Wallace RB, Shaffer J, Murphy RF, Bonner J, Hirose T, Itakura K (1979) Nucleic Acids Res, 6: 3543

    Article  CAS  Google Scholar 

  58. Li P, Medon PP, Skingle DC, Lanser J A, Symons RH (1987) Nucleic Acids Res, 15: 5275

    Article  CAS  Google Scholar 

  59. Sanger F, Nicklen S, Coulson AR (1977) Proc Natl Acad Sci USA, 24: 5463

    Article  Google Scholar 

  60. Zoller M, Smith M (1983) Methods Enzymol, 100: 468

    Article  CAS  Google Scholar 

  61. Green PJ, Pines O, Inouye M (1986) Ann Rev Biochem, 55: 569

    Article  CAS  Google Scholar 

  62. Zuckermann R, Corey DR, Schultz PG (1987) Nucleic Acid Res, 15: 5305

    Article  CAS  Google Scholar 

  63. Corey DR, Schultz PG, unpublished results

    Google Scholar 

  64. Tucker PW, Hazen EE, Cotton FA (1978) Mol Cell Biochem, 22: 67

    Article  CAS  Google Scholar 

  65. Tucker PW, Cotton FA, Hazen EE (1979) Mol Cell Biochem, 23: 3

    CAS  Google Scholar 

  66. Tucker PW, Cotdon FA, Hazen EE (1979) Mol Cell Biochem, 23:

    Google Scholar 

  67. Tucker PW, Hazen EE, Cotton FA (1979) Mol Cell Biochem, 23: 131

    CAS  Google Scholar 

  68. a) Serpersu EH, Shortle D, Mildvan AS (1987) Biochemistry, 26: 1289

    Google Scholar 

  69. (b)Serpersu EH, Shortle D, Mildvan AS(1986) Biochemistry 25: 68

    Google Scholar 

  70. Cuatrecasas P, Fuchs S, Anfinsen C (1967) J Biol Chem, 242: 1541

    CAS  Google Scholar 

  71. Cotton FA, Hazen EE, Legg MJ (1979) Proc Natl Acad Sci USA 76: 2551

    Article  CAS  Google Scholar 

  72. Takahara M, Hibler DW, Barr PJ, Gerlt JA, Inouye M (1985) J Biol Chem 260: 2670

    CAS  Google Scholar 

  73. Shortle D (1986) J Cell Biochem, 30: 281

    Article  CAS  Google Scholar 

  74. Alber T, Sun DB, Wilson K, Woznial JA, Cook SP, Matthews BW (1987) Nature, 330: 41

    Article  CAS  Google Scholar 

  75. Perry LJ, Wetzel R (1986) Biochemistry, 25: 733

    Article  CAS  Google Scholar 

  76. Falke JJ, Koshland DE (1987) Science, 237: 1596

    Article  CAS  Google Scholar 

  77. Matsumura M, Matthews BW (1989) Science, 243: 792

    Article  CAS  Google Scholar 

  78. Corey DR, Schultz PG (1989) J Biol Chem, 264: 3666

    CAS  Google Scholar 

  79. Kunkel TA (1985) Proc Natl Acad Sci, 82: 488

    Article  CAS  Google Scholar 

  80. Corey DR, Schultz PG (1987) Science, 238: 1401

    Article  CAS  Google Scholar 

  81. Wang D (1979) Biochemistry, 18: 4449

    Article  CAS  Google Scholar 

  82. Glazer AN, DeLang RJ, Sigman DS Chemical Modification of Proteins, North Holland/ Elsevier, Amsterdam, 1975

    Google Scholar 

  83. Corey DR, Pei D, Schultz PG (1989) Biochemistry, in Press

    Google Scholar 

  84. Messing J (1983) Methods in Enzymol, 101: 20

    Article  CAS  Google Scholar 

  85. Zuckermann RN, Schultz PG (1989) Proc Natl Acad Sci USA, 86: 1766

    Article  CAS  Google Scholar 

  86. Wiegand RC, Beattie KL, Holloman WK, Radding CM (1977) J Mol Biol, 116: 805

    Article  CAS  Google Scholar 

  87. Landgren U, Kaiser R, Sanders J, Hood L (1988) Science, 241: 1077

    Article  Google Scholar 

  88. Wang Y (1988) Biotechniques, 6: 843

    CAS  Google Scholar 

  89. Cheng S, Van Houten B, Gamper HB, Sancar A, Hearst JE (1988) J Biol Chem 263: 15110

    CAS  Google Scholar 

  90. Pugh BF, Cox MM (1988) J Mol Biol 203: 479

    Article  CAS  Google Scholar 

  91. Corey DR, Pei D, Schultz PG (1989) J Am Chem Soc, in Press

    Google Scholar 

  92. Yanisch-Perron C, Viere J, Messing J (1985) Gene, 33: 103

    Article  CAS  Google Scholar 

  93. Milligan JF, Groebe DR, Witherell GW, Uhlenbeck OC (1987) Nucleic Acids Res, 15: 8783

    Article  CAS  Google Scholar 

  94. Sampson JR, Uhlenbeck OC (1988) Proc Natl Acad Sci USA, 85: 1033

    Article  CAS  Google Scholar 

  95. Zuckermann RN, Corey DR, Schultz PG (1988) J Am Chem Soc, 110: 1614

    Article  CAS  Google Scholar 

  96. James BD, Olsen GJ, Lieu J, Pace NR (1988) Cell, 52: 19

    Article  CAS  Google Scholar 

  97. Stern S, Weiser B, Noller HE (1988) J Mol Biol, 204: 447

    Article  CAS  Google Scholar 

  98. Blackburn P, Moore S (1982) The Enzymes, 3rd edition, 15: 317

    Google Scholar 

  99. Erman JE, Hammes GGJ (1966) Am Chem Soc, 88: 5614

    Article  CAS  Google Scholar 

  100. Wlodawer A, Bott R, Sjolin L (1982) J Biol Chem, 257: 1325

    CAS  Google Scholar 

  101. 98.-Witzel H, Barnard EA (1962) Biochem Biophys Res Comm, 7: 289

    Google Scholar 

  102. Brocklehurst K, Crook EM, Wharton CW (1967) Chem Comm, 63: 66

    Google Scholar 

  103. Richards FM, Vithayathil PJ (1959) J Biol Chem, 234: 1459

    CAS  Google Scholar 

  104. Finn FM (1972) Biochemistry, 11: 1474

    Article  CAS  Google Scholar 

  105. Walder RY, Walder JA (1988) Proc Natl Acad Sci USA, 85: 5011

    Article  CAS  Google Scholar 

  106. Chaikin IM (1981) CRC Crit Rev Biochem, 11: 255

    Article  Google Scholar 

  107. Zuckermann RN, Schultz PG (1988) J Am Chem Soc, 110: 6592

    Article  CAS  Google Scholar 

  108. Raines RT, Rutter WJ, Manuscript in preparation

    Google Scholar 

  109. Zuckermann R, Schultz PG, Raines RT, Rutter WJ. Manuscript in preparation

    Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 1991 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Corey, D.R., Zuckermann, R.N., Schultz, P.G. (1991). Hybrid Enzymes and the Sequence-Specific Cleavage of Nucleic Acids. In: Dugas, H. (eds) Bioorganic Chemistry Frontiers. Bioorganic Chemistry Frontiers, vol 2. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-76241-3_1

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-76241-3_1

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-76243-7

  • Online ISBN: 978-3-642-76241-3

  • eBook Packages: Springer Book Archive

Publish with us

Policies and ethics