Improved Utility of Photolabile Solid Phase Synthesis Supports for the Synthesis of Oligonucleotides Containing 3‘-Hydroxyl Termini

Abstract

Oligonucleotides are synthesized on, and cleaved from, a solid phase support (6) using the o-nitrobenzyl intramolecular photochemical redox reaction. The yields of isolated oligonucleotides relative to yields obtained using conventional hydrolytic cleavage vary between 67% and 82.5%. Synthesis of oligonucleotides using phosphoramidites that do not contain N-benzoyl protecting groups enables one to photolytically cleave the biopolymers in good yields using a commonly available UV irradiation source. Tritium labeling indicates that less than 3% thymidine.thymidine photodimers are formed during photolytic cleavage of polythymidylates from 6 using a transilluminator. No UV-induced damage is detected via HPLC analysis of enzymatically digested oligonucleotides that were obtained following photolytic cleavage from 6.

Synthesis, Characterization, and Repair of a Flexible O6‐2′‐Deoxyguanosine‐alkylene‐O6‐2′‐deoxyguanosine Intrastrand Cross‐Link

“…The phenoxyacetyl, rather than an acetyl group, was selected for protection at the 3′‐OH position due to possible transamidation observed at the exocyclic N 2 during oligonucleotide assembly and for its facile removal under mild conditions which is ideal for the synthesis of O 6 ‐alkylated adducts 70. 72 Coupling of compound 2 at the O 6 ‐position with the appropriate tert ‐butyldiphenylsiloxy mono‐protected diol (1,4‐butanediol or 1,7‐heptanediol) was accomplished by the Mitsunobu reaction. This reaction is known for its selectivity at introducing alkyl groups at the O 6 ‐position of protected dG and has been utilized previously to generate O 6 ‐alkylene‐linked dimers containing dG for the preparation of ICL duplexes 61.…”

The breaking beads approach for photocleavage from solid support

“…[1][2][3] They are used as handles to connect a solid support to a synthesized molecule in solid phase synthesis (SPS). 4 These linkers are very attractive for SPS because they are stable to many reaction conditions and can be liberated under very mild conditions. [5][6][7][8][9][10][11][12][13][14][15][16] Photolabile linkers are especially valuable for oligosaccharides and glycoconjugates synthesis because they proved to be orthogonal and stable to the multiple synthetic manipulations required.…”

Solid-phase synthesis of base-sensitive oligonucleotides

“…unexpected long irradiation time or thymine-thymine photodimerization (cf, chapter 3.6) may sometimes be involved, a photolabile linker has most frequently been adopted for the synthesis of the base-sensitive oligonucleotides ( Figure 5). [21][22][23][24][25] As a contrast to 15-17, 18 (Dell'Aquila et al, 1997) is a universal linker and it may be used for the synthesis of 3'-phosphorylated oligonucleotides. Base stable disulfide linkers (Kumar et al, 1991) offer possibility to on-resin removal of Nacyl nucleobase protections, but the cleavage may be performed in mild conditions using reductive treatments with dithiotreitol (DTT) or tris-2-carboxyethyl phosphine (TCEP) ( Figure 6).…”