REGIOSPECIFIC SOLID-PHASE SYNTHESIS OF BRANCHED OLIGONUCLEOTIDES - EFFECT OF VICINAL 2',5'-PHOSPHODIESTER (OR 2',3'-PHOSPHODIESTER) AND 3',5'-PHOSPHODIESTER LINKAGES ON THE FORMATION OF HAIRPIN DNA
Rs. Braich et Mj. Damha, REGIOSPECIFIC SOLID-PHASE SYNTHESIS OF BRANCHED OLIGONUCLEOTIDES - EFFECT OF VICINAL 2',5'-PHOSPHODIESTER (OR 2',3'-PHOSPHODIESTER) AND 3',5'-PHOSPHODIESTER LINKAGES ON THE FORMATION OF HAIRPIN DNA, Bioconjugate chemistry, 8(3), 1997, pp. 370-377
A general procedure for the solid-phase regiospecific synthesis of bra
nched oligonucleotides (bNA) analogues using readily available phospho
ramidite reagents has been developed. The key feature of this method i
s use of the solid-phase phosphoramidite procedure to assemble linear
oligonucleotide sequences and sequential removal of the phosphate (bet
a-cyanoethyl or methyl) and silyl protecting groups without detaching
the nascent oligonucleotide from the solid support. Conversion of the
phosphate backbone into the more stable phosphodiester linkages allows
for removal of the 2'-O-tert-butyldimethylsilyl protecting group with
out cleavage or isomerization at the branch point. This method allows
for the formation of branched oligonucleotides with sequences of arbit
rary base composition, length, and orientation around the branch point
junction, including a ''Y''-shaped octadecamer d(TACTA)-rA[(2',5')d(G
TATGT)](3',5')d(CAAGTT). Studies to explore structural effects in the
use of a branched adenosine as replacement for nucleotide loops in dup
lex and tripler DNA are also described. Branched oligonucleotides of t
he type rA[(2',5')dC(n)dA(10)-5'](3',5')dC(n)dT(10)-3' and rA[(2',5')d
C(n)3',3'dA(10)-5'](3',5')dC(n)T(10)-3' form hairpin duplexes with the
rmal stability comparable to or better than that of one with a natural
deoxynucleotide loop.