title: Synthesis of oligonucleotides with 3'-terminal 5-(3-acylamidopropargyl)-3'-amino-2',3'-dideoxyuridine residues and their reactivity in single-nucleotide steps of chemical replication.
abstract: Oligonucleotides with a 3'-terminal 5-alkynyl-3'-amino-2',3'-dideoxyuridine residue were prepared, starting from 2'-deoxyuridine. The optimized route employs a 2',3'-dideoxy-3'-trifluoroacetamido-5-iodouridine 5'-phosphoramidite as building block for DNA synthesis and involves on-support Sonogashira coupling with N-tritylpropargylamine to generate oligonucleotides. The amino group of the propargylamine side chain was acylated to accelerate primer extension reactions involving the 3'-amino group. Three acyl groups were identified that decrease the half-life for DNA-templated extension steps with 7-azabenzotriazole esters of 2'-deoxynucleotides. The residue of 4-pyrenylbutyric acid was found to accelerate primer extension reactions and to render them more selective than those of the control primer. With this substituent, primer extension is also faster than previously measured for three-strand systems involving template, aminoprimer, and a downstream-binding helper oligonucleotide. Fast-reacting primers might become useful for genotyping single nucleotides.
authors.affiliation: Institute for Organic Chemistry, University of Karlsruhe (TH), D-76131 Karlsruhe, Germany.
authors.forename: Patrick
authors.initials: P
authors.lastname: Baumhof
authors.forename: Niels
authors.initials: N
authors.lastname: Griesang
authors.forename: Michael
authors.initials: M
authors.lastname: Bächle
authors.forename: Clemens
authors.initials: C
authors.lastname: Richert
mesh_terms: D001483:Base Sequence; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000737:chemistry; D008969:Molecular Sequence Data; D015394:Molecular Structure; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
chemical_list: C512021:3'-5-(3-acylamidopropargyl)-3'-amino-2',3'-dideoxyuridine; D009841:Oligonucleotides; D003857:Deoxyuridine