Trifluoroacetophenone-Linked Nucleotides and DNA for Studying of DNA-Protein Interactions by F-19 NMR Spectroscopy

Abstract

A series of 7-[4-(trifluoroacetyl)phenyl]-7-deazaadenine and -7-deazaguanine as well as 5-substituted uracil and cytosine 2'-deoxyribonudeosides and mono- and triphosphates were synthesized through aqueous Suzuki-Miyaura crosscoupling of halogenated nucleosides or nucleotides with 4-(trifluoroacetyl)phenylboronic acid. The modified nucleoside triphosphates were good substrates for DNA polymerases applicable in primer extension or PCR synthesis of modified oligonucleotides or DNA.

Attempted cross-linking with a serine-containing protein did not proceed, however the trifluoroacetophenone group was a sensitive probe for the study of DNA protein interactions by F-19 NMR.

Keywords

• RNA secondary structures
• cross-linking
• 2'-deoxyribonucleoside triphosphates
• nucleoside triphosphates
• unprotected nucleosides
• trifluoromethyl ketones
• enzymatic-synthesis
• primer extension
• high-density
• polymerase