Challenging artificial genetic systems: thymidine analogs with 5‐position sulfur functionality

• Published in: Nucleic acids research 2002-09, Vol.30 (17), p.3857-3869
• Main Authors: Held, Heike A., Benner, Steven A.
• Format: Article
• Language: English
• Subjects: Deoxyuracil Nucleotides - chemistry; Deoxyuracil Nucleotides - metabolism; DNA Primers - genetics; DNA-Directed DNA Polymerase - metabolism; Oligonucleotides - chemistry; Oligonucleotides - genetics; Oligonucleotides - metabolism; Polymerase Chain Reaction - methods; Sulfur - chemistry; Templates, Genetic; Thymidine - chemistry; Thymidine - metabolism
• ISSN: 0305-1048; 1362-4962; 1362-4962
• DOI: 10.1093/nar/gkf500

Eight different polymerases, chosen from evolutionary families A (Taq, Tfl, HotTub and Tth) and B (Pfu, Pwo, Vent and Deep Vent), were examined for their ability to incorporate 5‐position modified 2′‐deoxyuridine derivatives that carry a protected thiol group appended via different linkers containing either three or four carbon atoms. This represents the first attempt to incorporate the thiol functionality into DNA via enzymatic synthesis. Each polymerase–substrate combination was evaluated using a hierarchy of increasingly more difficult challenges, starting with incorporation of a single derivative, proceeding to incorporation of two derivatives at adjacent sites and non‐adjacent sites, then examining the ability of the polymerase to accept the derivative within the template, and concluding with a challenge involving PCR. The evaluation of thiol‐bearing 2′‐deoxyuridine derivatives was then extended to consider their chemical stabilities. Stability was found to be less than satisfactory when the thiol functionality has a ‘propargylic’ relationship to the unsaturation in the linker. The best polymerase–appendage combination used the polymerase from Pyrococcus woesei (Pwo) and the 5′‐tBu‐SS‐CH2‐CH2‐C≡C‐ linker. This pair supported PCR amplification and therefore should have value in artificial in vitro selection experiments. Indeed, we discovered that Pwo and Pfu preferred the derivative triphosphate over TTP, the natural substrate, in competition studies. These studies confirm an earlier suggestion that membership of an evolutionary family of polymerases is a partial predictor of the ability of the polymerase to accept 5‐modified 2′‐deoxyuridines. Considerable differences are displayed by different members within a polymerase family, however. This remains curious, as the ability of the polymerase to replicate natural DNA with high fidelity and its propensity to exclude unnatural analogs are presumed to be correlated.