Recognition of a non-standard base pair by thermostable DNA polymerases

Bioorganic and Medicinal Chemistry Letters

Volumn 8, Issue 10, 1998, Pages 1149-1152

  Lutz, Michael J ^a,c   Horlacher, Jennifer ^a   Benner, Steven A ^b  

^a ETH ZURICH   (Switzerland)

^b University of Florida ^*  (United States)

^c NOVARTIS PHARMA AG   (Switzerland)

Author keywords

[No Author keywords available]

Indexed keywords

2,4 DIAMINOPYRIMIDINE DERIVATIVE; DNA POLYMERASE; NUCLEOSIDE TRIPHOSPHATE; XANTHOSINE;

ARTICLE; BASE PAIRING; DNA TEMPLATE; ENZYME STABILITY; HYDROGEN BOND; MOLECULAR RECOGNITION; PKA;

NON-PROGRAMMATIC;

BASE PAIRING; BASE SEQUENCE; DEOXYRIBONUCLEOTIDES; DNA PRIMERS; DNA-DIRECTED DNA POLYMERASE; ENZYME STABILITY; HYDROGEN BONDING; PYRIMIDINES; PYROCOCCUS; RIBONUCLEOSIDES; SUBSTRATE SPECIFICITY; TEMPLATES, GENETIC; THERMODYNAMICS; THERMUS;

EID: 0032546518     PISSN: 0960894X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0960-894X(98)00177-2     Document Type: Article

References (19)

1. 1. Gold, L. J. Biol. Chem. 1995, 270, 13581.
2. 2. Hager, A.J.; Pollard, J.D.; Szostak, J.W. Chem.& Biol. 1996, 3, 717; Breaker, R.R. Curr. Opin. Biotech. 1996, 7, 442-448.
3. 2. Hager, A.J.; Pollard, J.D.; Szostak, J.W. Chem.& Biol. 1996, 3, 717; Breaker, R.R. Curr. Opin. Biotech. 1996, 7, 442-448.
4. 3. Morris, K.N.; Tarasow, T.M.; Julin, C.M.; Simons, S.L.; Hilvert, D.; Gold, L. Proc. Natl. Acad. Sci. USA 1994, 91, 13028; Burgin, A.B.; Gonzalez, C.; Matulic-Adamic, J.; Karpeisky, A.M.; Usman, N.; McSwiggen, J.A.; Beigelman, L. Biochemistry 1996, 35, 14090.
5. 3. Morris, K.N.; Tarasow, T.M.; Julin, C.M.; Simons, S.L.; Hilvert, D.; Gold, L. Proc. Natl. Acad. Sci. USA 1994, 91, 13028; Burgin, A.B.; Gonzalez, C.; Matulic-Adamic, J.; Karpeisky, A.M.; Usman, N.; McSwiggen, J.A.; Beigelman, L. Biochemistry 1996, 35, 14090.
6. 4. Piccirilli, J.A.; Krauch, T.; Moroney, S.E.; Benner, S.A. Nature 1990, 343, 33.
7. 5. Roy, K.S.; Miles, H.T. Nucleosides Nucleotides 1983, 2, 231; Krauch, T. Dissertation 1990, ETH Zürich No. 8940.
8. 5. Roy, K.S.; Miles, H.T. Nucleosides Nucleotides 1983, 2, 231; Krauch, T. Dissertation 1990, ETH Zürich No. 8940.
9. 6. Horlacher, J.; Hottiger, M.; Podust, V.N.; Hübscher, U.; Benner, S.A. Proc. Natl. Acad. Sci. USA 1995, 92, 6329; Lutz, M.J.; Held, H.A.; Hottiger, M.; Hübscher, U.; Benner, S.A. Nucl. Acids. Res. 1996, 24, 1308.
10. 6. Horlacher, J.; Hottiger, M.; Podust, V.N.; Hübscher, U.; Benner, S.A. Proc. Natl. Acad. Sci. USA 1995, 92, 6329; Lutz, M.J.; Held, H.A.; Hottiger, M.; Hübscher, U.; Benner, S.A. Nucl. Acids. Res. 1996, 24, 1308.
11. 7. Lutz, M.J.; Benner, S.A.; Hein, S; Breipohl, G.; Uhlmann, E. J. Am. Chem. Soc. 1997, 119, 3177.
12. 8. Radioactivity was quantified using a Phosphor Imager (Molecular Dynamics), with 5 h exposures and the ImageQuant program from Molecular Dynamics. To determine the lower limit of specific formation of the non-standard base pair, the amount of products past the non-standard base in the template was quantified, divided by the total amount of radioactivity in the lane and expressed as a percentage. To correct for non-specific misincorporation of standard nucleobases opposite the non-standard nucleotides the amount of misincorporation of natural dNTPs, determined in a control experiment, was subtracted. This corrected percentage was then reported to the percentage of read-through past the non-standard bases when the cognate non-standard nucleoside triphosphate was present in solution to yield the lower limit of specific formation. Ideally, if no misincorporation of standard nucleosides opposite the non-standard bases occur the percentage specific non-standard base pair formation would be 100%.
13. 9. Eom, S.H.; Wang, J.; Steitz, T.A. Nature 1996, 382, 278.
14. 10. Southworth, M.W.; Kong, H.; Kuccera, R.B.; Ware, J.; Jannasch, H.W.; Perler, F.B. Proc. Natl. Acad. Sci. USA 1996, 93, 5281.
15. 11. Bernad, A.; Lázaro, J.M.; Salas, M.; Blanco, L. Proc. Natl. Acad. Sci. USA 1990, 87, 4610; Braithwaite, D.K.; Ito, J. Nucl. Acids Res. 1993, 21, 787.
16. 11. Bernad, A.; Lázaro, J.M.; Salas, M.; Blanco, L. Proc. Natl. Acad. Sci. USA 1990, 87, 4610; Braithwaite, D.K.; Ito, J. Nucl. Acids Res. 1993, 21, 787.
17. 12. Lutz, M.J. Dissertation 1997, ETH Zürich No. 12254.
18. 13. Sawaya, M.; Pelletier, H., Kumar, A.; Wilson, S.; Kraut, J. Science 1994, 264, 1930; Steitz, T.A.; Smerdon, S.J.; Jäger, J.; Joyce, C.M. Science 1994, 266, 2022.
19. 13. Sawaya, M.; Pelletier, H., Kumar, A.; Wilson, S.; Kraut, J. Science 1994, 264, 1930; Steitz, T.A.; Smerdon, S.J.; Jäger, J.; Joyce, C.M. Science 1994, 266, 2022.