title: Synthesis and enzymatic incorporation of modified deoxyuridine triphosphates.
abstract: We describe the synthesis of 2'-deoxyuridine-5'-triphosphate derivatives bearing linkers of varying length, bulk and flexibility, at position 5 of the pyrimidine base. Nucleotide analogues with terminal functional groups are of interest due to their application potential for the functional labelling of DNA strands. In the course of the synthesis of the nucleotide analogues, the methodology for the Yoshikawa phosphorylation procedure was optimised, resulting in an approach which reduces the amount of side-products and is compatible with labile functional groups attached to the base. The effect of linker composition on the enzymatic incorporation into DNA was systematically investigated using two different DNA polymerases. Deep Vent(R) exo(-) from the B-polymerase family accepted most nucleotide analogues as substrates, while Taq from the A-family was slightly less proficient. Both polymerases had difficulties incorporating 5-(3-amino-prop-1-ynyl)-2'-deoxyuridine triphosphate. A molecular model of the active site of the polymerase was used to rationalise why this nucleotide was not accepted as a substrate.
authors.affiliation: University College London, Department of Chemistry, 20 Gordon Street, London, UKWC1H OAJ.
authors.forename: Vinciane
authors.initials: V
authors.lastname: Borsenberger
authors.forename: Mikiembo
authors.initials: M
authors.lastname: Kukwikila
authors.forename: Stefan
authors.initials: S
authors.lastname: Howorka
mesh_terms: D000114:Acetylene / Q000737:chemistry; D000588:Amines / Q000737:chemistry; D000595:Amino Acid Sequence; D001483:Base Sequence; D055162:Biocatalysis; D020134:Catalytic Domain; D004259:DNA-Directed DNA Polymerase / Q000378:metabolism*; D003856:Deoxyuracil Nucleotides / Q000138:chemical synthesis* / Q000737:chemistry / Q000378:metabolism*; D007065:Idoxuridine / Q000737:chemistry; D008958:Models, Molecular; D010455:Peptides / Q000737:chemistry / Q000378:metabolism; D010766:Phosphorylation; D019914:Taq Polymerase / Q000378:metabolism*
chemical_list: D000588:Amines; D003856:Deoxyuracil Nucleotides; D010455:Peptides; C027078:deoxyuridine triphosphate; C088944:Deep Vent DNA polymerase; D019914:Taq Polymerase; D004259:DNA-Directed DNA Polymerase; D007065:Idoxuridine; D000114:Acetylene