Abstract
N -Methylpyrrole carboxylic acids are building blocks for oligopyrroleamides that bind DNA duplexes via the minor groove. The reactivity of HBTU-based active esters of four methylpyrroles in amide-forming reactions was determined. When assayed against HBTU-activated N -acetylleucine, a 6-250-fold lower reactivity was found. When assayed against the NHS ester of Boc-valine, the reactivity was up to 4-fold lower. Despite large differences in reactivity, mixed couplings were successfully performed with all four pyrroles, generating small libraries of modified oligonucleotides suitable for spectrometrically monitored selection experiments. Microwave irradiation accelerated coupling of an Fmoc-protected pyrrole to an amine on solid support.
Key words
DNA - pyrroles - amides - combinatorial chemistry - solid-phase synthesis
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Reactivity Assay.
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Mixed Coupling.
Acids 1 -4 were activated individually with HBTU, HOBT, and DIEA, as described for the reactivity assay above. An aliquot of a stock solution of 13 (35 µL, 127 mM in DMF) was treated with DMF (18.4 µL) and DIEA (1.6 µL). Then, aliquots from solutions of activated acids corresponding to the amount of the building block given in Table
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23 A slurry of pyrrole 4 (19.3 mg, 53 µmol) in DMF (420 µL) was activated with HBTU, HOBT and DIEA in DMF for 1 h, as described for the reactivity assays above. The activation solution was added to a conical glass vial for small scale microwave-assisted reactions containing 19 (1.0 mg, approx. 33 nmol DNA), followed by irradiation in a CEM Discover chemical microwave apparatus using the settings for DMF at up to 200 W, a ceiling temperature of 80 °C, and a hold time of 10 min. After cooling, the support was washed with DMF, MeOH, and CH2 Cl2 , followed by air drying and deprotection with sat. aq NH3 .
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