Solid-phase synthesis of positively charged deoxynucleic guanidine (DNG) oligonucleotide incorporating 7-deazaguanine bases

Abstract

DNG nucleotides represent a positively charged DNA analog in which the negatively charged phosphodiester linkages of DNA are replaced by positively charged guanidinium linkages. We report herein the synthesis of 3′-end, middle, and 5′-end monomers required for the synthesis of a DNG sequence in which the natural guanine base is replaced by 7-deazaguanine (c 7G). 7-Deazaguanine nucleobase was chosen because of their unique glycoside bond stability and their ability to prevent G-quartet formation. A facile and high yield two-step synthesis of xylo-7-deazaguanine 7, a key intermediate for introducing 3′-amino functionality, is carried out under Mitsunobu conditions. Subsequently, the 3′-Fmoc-protected thiourea monomers 13 and 19 were prepared from 7 via their corresponding 3′-amino-7-deazaguanines 11 and 18, respectively. The smooth coupling of these thiourea monomers with monomethoxytrityl (MMTr)-protected 3′-end monomer 25, prepared from 5, occurred on solid phase in 3′ → 5′ direction. The resultant trimeric HO-c 7Ggc 7Ggc 7G-OH ( 1) has been designed to be included into DNA using standard DNA synthesis technology. The combination of C-c 7G base pairing and electrostatic association of phosphodiester and guanidinium backbone allows the small synthesized DNG trimer 1 to form 1:1 complex with DNA-C pentamer.