Difluoroacetic acid: an alternative acid in the detritylation reaction for the solid-phase synthesis of oligonucleotides.

Dichloroacetic acid or trichloroacetic acid are commonly used in the detritylation reaction of the automated solid-phase synthesis of oligonucleotides. Dichloroacetic acid, however, is often contaminated with trichloroacetaldehyde (chloral), leading to the formation of inseparable impurities in the final oligonucleotide product. In this work, three different sequences, namely T, d(TAA), and an 18-mer mixed sequence, were used as models to compare the deprotection efficiency of three acids: trichloroacetic acid, dichloroacetic acid, and difluoroacetic acid.

Anion exchange chromatography of oligonucleotides under denaturing conditions.

Denaturing anion exchange HPLC simplifies the chromatographic profiles of self-complementary sequences such as d(CG), d(CG) with locked nucleic acid modifications, d(AT), and polymerase chain reaction mixtures. These chromatographic conditions use eluents containing up to 4  urea at pH 12.4, and lead to the abolishment of secondary structures and meaningful chromatographic patterns of self-complementary sequences.

Further investigation on the nitration of BODIPY with cupric nitrate: crystal structures of 4,4-di-fluoro-1,3,5,7,8-penta-methyl-2-nitro-4-bora-3a,4a-di-aza--indacene, 4,4-di-fluoro-3-nitro-8-phenyl-4-bora-3a,4a-di-aza--indacene, and 3-chloro-6-ethyl-5,7,8-trimethyl-2-nitro-4,4-diphenyl-4-bora-3a,4a-di-aza--indacene.

The treatment of non-fully substituted 4,4-di-fluoro-4-bora-3a,4a-di-aza--indacene (BODIPY) with cupric nitrate leads to the introduction of a nitro group at different positions of the BODIPY core, depending on the substitution pattern. This methodology complements the treatment of fully substituted BODIPY with cupric nitrate that was previously reported. The crystal structures of 4,4-di-fluoro-1,3,5,7,8-penta-methyl-2-nitro-4-bora-3a,4a-di-aza--indacene, CHBFNO () 4,4-di-fluoro-3-nitro-8-phenyl-4-bora-3a,4a-di-aza--indacene, CHBFNO) and 3-chloro-6-ethyl-5,7,8-trimethyl-2-nitro-4,4-diphenyl-4-bora-3a,4a-di-aza--indacene, CHBClNO () are presented.

Incorporation of cyclic azobenzene into oligodeoxynucleotides for the photo-regulation of DNA hybridization.

Cyclic azobenzene carboxylic acid was synthesized using a shortened route. After reaction with D-threolinol, the resulting cyclic azobenzene-D-threolinol (cAB-Thr) building block was transformed into the corresponding DMTr-protected phosphoramidite, and incorporated into oligodeoxynucleotides at various positions and frequencies by solid phase synthesis. The melting temperatures of these modified oligonucleotides were determined by UV spectrometry.