Analogs with Modified Sugar Moieties

Most functional studies have focused on nucleobase-recognition processes. Little is known about the impact of DNA polymerase interactions with the 2 '-deoxyribose moiety and their participation in processes which contribute to fidelity. Crystal structures of DNA polymerases together with enzyme mutation studies suggest that the sugar moiety of the incoming triphosphate is fully embedded in the nu-cleotide binding pocket and undergoes essential interactions with the enzyme [3, 6]. This issue has been addressed and a functional strategy was developed to monitor steric constraints in DNA polymerases within the nucleotide binding pocket acting on the sugar moiety of an incoming nucleoside triphosphate [14, 15]. To sense interactions of DNA polymerases with the sugar moiety of incoming triphosphates alkyl labels at the 4'-position of the 2 '-deoxyribose were introduced in such a way that they did not interfere with hydrogen bonding, nucleobase pairing, and stacking. The steric probes TRTP were designed by substituting the 4' -hydrogen atom of thymidine triphosphate (TTP) with alkyl groups of continually increasing steric bulk (Figure 4.1.5).

If sugar recognition processes are involved in DNA polymerase fidelity mecha-



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