DNA with branched internal side chains: synthesis of 5-tripropargylamine-dU and conjugation by an azide-alkyne double click reaction.
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.
Sirivolu
Venkata Ramana
VR
Laboratory for Bioorganic Chemistry and Chemical Biology, Center for Nanotechnology, Heisenbergstrasse 11, 48149 Münster, Germany.
Chittepu
Padmaja
P
Seela
Frank
F
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
C534522:5-tripropargylamine-2'-deoxyuridine; D000480:Alkynes; D001386:Azides; D009841:Oligonucleotides; D004247:DNA; D003857:Deoxyuridine