title: DNA with branched internal side chains: synthesis of 5-tripropargylamine-dU and conjugation by an azide-alkyne double click reaction.
abstract: 5-Tripropargylamine-2'-deoxyuridine (1 a) containing two terminal triple bonds was synthesized by a Pd-assisted Sonogashira cross-coupling reaction and was subsequently converted into the corresponding phosphoramidite building block (9) and employed in solid-phase oligonucleotide synthesis. T(m) experiments demonstrate that the presence of covalently attached branched tripropargylamine residues has a positive effect on the base pair stability. The two terminal C[triple chemical bond]C bonds of modified DNA were functionalized by means of Cu(I)-mediated 1,3-dipolar cycloaddition reactions (click chemistry) with azides such as 3-azido-7-hydroxycoumarin or 3'-azido-3'-deoxythymidine (AZT) both in solution and on solid support. In particular, with the nonfluorescent 3-azido-7-hydroxycoumarin a strongly fluorescent oligonucleotide bis-dye conjugate was generated. For comparison, the N(3)-propargylated 2'-deoxyuridine 2 was prepared from 2'-deoxyuridine and propargyl bromide and incorporated into DNA. The two terminal triple bonds of 1 a allow the simultaneous post-modification of DNA by two reporter molecules and can be applied to almost any azido derivatives (oligonucleotides, proteins, polysaccharides etc.) including those forming dendrimeric side chains.
authors.affiliation: Laboratory for Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
authors.forename: Venkata Ramana
authors.initials: VR
authors.lastname: Sirivolu
authors.forename: Padmaja
authors.initials: P
authors.lastname: Chittepu
authors.forename: Frank
authors.initials: F
authors.lastname: Seela
mesh_terms: D000480:Alkynes / Q000737:chemistry*; D001386:Azides / Q000737:chemistry*; D004247:DNA / Q000737:chemistry*; D003857:Deoxyuridine / Q000031:analogs & derivatives* / Q000138:chemical synthesis* / Q000737:chemistry; D005453:Fluorescence; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D013056:Spectrophotometry, Ultraviolet
chemical_list: C534522:5-tripropargylamine-2'-deoxyuridine; D000480:Alkynes; D001386:Azides; D009841:Oligonucleotides; D004247:DNA; D003857:Deoxyuridine