1. (a) Carroll, S. S.; Benkovic, S. J. Chem. Rev. 1990, 1291. (b) Benkovic, S. J.; Cameron, C. E. Methods Enzymol. 1995, 262, 257. (c) Kuchta, R. D.; Mizrahi, V.; Benkovic, P. A.; Johnson, K. A.; Benkovic, S. J. Biochemistry 1987, 26, 8410. (d) Eger, B. T.; Kuchta, R. D.; Carroll, S. S.; Benkovic, P. A.; Dahlberg, M. E.; Joyce, C. M.; Benkovic, S. J. Biochemistry 1991, 30, 1441. (e) Eger, B. T.; Benkovic, S. J. Biochemistry 1992, 31, 9227. (f) Polesky, A. H.; Dahlberg, M. E.; Benkovic, S. J.; Grindley, N. D. F.; Joyce, C. M. J. Biol. Chem. 1992, 267, 8417. (g) Dahlberg, M. E.; Benkovic, S. J. Biochemistry 1991, 30, 4835.
2. Hydrogen bonding revisited: Geometric selection as a principal determinant of DNA replication fidelity
3. A thymidine triphosphate shape analog lacking Watson-Crick pairing ability is replicated with high sequence selectivity
4. (a) 4-Thiothymidine was prepared as described in ref 4b except that the hydroxyl groups were protected as the tert-butyldimethylsilyl derivatives rather than the acetates. After deprotection with tert-butylammonium fluoride, 4-thiothymidine was converted to the 5′-O-triphosphate as described in ref 4c. The product was purified by HPLC on an ion-exchange column (SynchroPak AX100, 21.2×250 mm) eluted with a two step gradient at a flow rate of 8 mL/min. The first step is from 0 to 60% B in 15 min followed by increasing B to 100% in 5 min (solvent A, 0.025 M Et3N–H2CO3, pH 7.5; solvent B, 0.5 M Et3N–H2CO3, pH 7.5). The HPLC peak eluting at 25 min was collected, and the aqueous solution was concentrated at ambient temperature. Periodically, the solution pH was checked and maintained at 7.5. Methanol was added to the syrup and evaporation continued. The resulting syrup was dissolved in a minimum volume of 0.1 M Et3N–H2CO3, pH 7.5, and chromatographed on a reverse phase Hamilton PRP-1 column (7.0×305 mm) by ramping the gradient from 100% A to 100% B in 30 min (solvent A: 0.1 M Et3N–H2CO3; solvent B: 50:50 Et3N–H2CO3:CH3CN) in order to remove residual inorganic pyrophosphate. The peak eluting at 10 min was collected, and the solvent was carefully evaporated at ambient temperature. The triphosphate was characterized by 31P NMR (D2O, phosphoric acid external standard): δ −14.8, −2.95 and 2.2 ppm. Purity was confirmed by TLC as described in ref 4c. Concentrations of 4S–TTP were determined spectrophotometrically at 335 nm, ϵ=22 300 M−1 cm−1 (ref 4d). (b) Connolly, B. A.; Newman, P. C. Nucleic Acids Res. 1989, 17, 4957. (c) Kovacs, T.; Otvos, L. Tetrahedron Lett. 1988, 29, 4525. (d) Fox, J. J.; Von Praag, D.; Wempen, I.; Doerr, I .L.; Cheong, L.; Knoll, J. E.; Eidinoff, M. L.; Bendich, A.; Brown, G. B. J. Am. Chem. Soc. 1959, 81, 178.
5. (a) Hofer, B.; Koster, H. Nucleic Acids Res. 1981, 9, 753. (b) Lezius, A. G.; Scheit, K. H. Eur. J. Biochem. 1967, 3, 85.