Om. Ali et al., TARGETING OF NUCLEIC-ACID JUNCTIONS - ADDRESSING TO A BRANCH POINT ANOLIGODEOXYNUCLEOTIDE CONJUGATED WITH AN INTERCALATOR, Nucleic acids research, 26(21), 1998, pp. 4919-4924
It is possible to enhance targeting of a DNA stem flank domain with a
complementary DNA when it is conjugated with diphenyl ether at the bra
nch point, The nucleoside 2'-deoxy-5-methyl-N-4-(4-phenoxyphenyl)cytid
ine (5) was synthesized from thymidine by tritylation, acetylation, am
ination via 2,4,6-trimethylbenzenesulfonyl activation and subsequent d
e-protection. When a three-way junction is formed with a bulged nucleo
side 5 at the branch point, the thermal melting temperature was increa
sed by 9 degrees C when compared with wild-type DNA, When hybridizing
to one of the flanks at a stem allowing coaxial stacking to the stem,
modification at the branch point resulted in Delta T-m = 5,8 degrees C
, For targeting to RNA the results were more ambiguous. RNase H activi
ty was observed in some cases when an intercalating aromatic ring was
addressed at the branch point. RNase H activity was observed even for
a short 7mer ODN.