Formation of 4,4'-dimethoxytrityl-C-phosphonate oligonucleotides.
Incomplete sulfurization during solid-phase synthesis of phosphorothioate oligonucleotides using phosphoramidite chemistry was identified as the cause of formation of two new classes of process-related oligonucleotide impurities containing a DMTr-C-phosphonate (DMTr=4,4'-dimethoxytrityl) moiety. Phosphite triester intermediates that failed to oxidize (sulfurize) to the corresponding phosphorothioate triester react during the subsequent acid-induced (dichloroacetic acid) detritylation with the DMTr cation or its equivalent in an Arbuzov-type reaction. This leads to formation of DMTr-C-phosphonate mono- and diesters resulting in oligonucleotides modified with a DMTr-C-phosphonate moiety located internally or at the 5'terminal hydroxy group. DMTr-C-phosphonate derivatives are not detected when optimized sulfurization conditions are employed.
Capaldi
Daniel C
DC
Isis Pharmaceuticals, Inc., 2292 Faraday Avenue, Carlsbad, CA 92008, USA.
Gaus
Hans J
HJ
Carty
Recaldo L
RL
Moore
Max N
MN
Turney
Brett J
BJ
Decottignies
Stella D
SD
McArdle
James V
JV
Scozzari
Anthony N
AN
Ravikumar
Vasulinga T
VT
Krotz
Achim H
AH
D002851:Chromatography, High Pressure Liquid; D009841:Oligonucleotides / Q000138:chemical synthesis* / Q000737:chemistry; D063065:Organophosphonates / Q000138:chemical synthesis* / Q000737:chemistry; D017905:Phosphites / Q000737:chemistry; D013329:Structure-Activity Relationship; D014320:Triphenylmethyl Compounds / Q000138:chemical synthesis* / Q000737:chemistry / Q000494:pharmacology
D009841:Oligonucleotides; D063065:Organophosphonates; D017905:Phosphites; D014320:Triphenylmethyl Compounds