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.

Four‐Color, Enzyme‐Free Interrogation of DNA Sequences with Chemically Activated, 3′‐Fluorophore‐Labeled Nucleotides

“…The more‐sophisticated form involving microarrays and a chip scanner might prove an inexpensive alternative to current genotyping systems. Modifications in the helper22 and primer,23 as well as adjustments in the nucleotide concentration and activation chemistry might eventually lead to assays that go to completion in minutes, rather than in hours. Though far from competitive at the moment, assay formats involving removable fluorophores might thus become suitable for reading short stretches of DNA.…”

“Double‐Click” Protocol for Synthesis of Heterobifunctional Multivalent Ligands: Toward a Focused Library of Specific Norovirus Inhibitors

“…To further investigate this phenomenon, we hypothesized that the basicity of the adjacent triazole ring is responsible for intramolecular acceleration of carbamate hydrolysis. As a model, compound 28 was synthesized from 2-azidoethyl lactoside 26 and alkyne 27 [20] by using a cycloaddition reaction (Scheme 6). To study the stability of this compound, it was incubated at 37 8C in D 2 O/phosphate buffer at pH 6, 7, or 8 and the decomposition behavior was periodically monitored by NMR spectroscopy.…”

5‐Substituted Nucleosides in Biochemistry and Biotechnology

“…The oligonucleotide is then deprotected by conventional means following the organopalladium coupling reaction. In a more recent variation on this approach, Richert and coworkers have described a 5-iodo-3 0 -amino-3 0 -deoxyuridine derivative that can be incorporated into oligonucleotides at the 5 0 -terminus and then coupled to alkynes by the Sonogashira reaction and acylated at the 3 0 -amino group [12]. The modified oligonucleotides constructed by this strategy were designed to explore chemical ligation.…”