Bw. Zhou et al., RECOGNITION OF ALTERNATING OLIGOPURINE OLIGOPYRIMIDINE TRACTS OF DNA BY OLIGONUCLEOTIDES WITH BASE-TO-BASE LINKAGES, Bioconjugate chemistry, 6(5), 1995, pp. 516-523
A new concept is presented to design and synthesize modified oligonucl
eotides in order to extend the range of double-helical DNA sequences t
hat can be recognized by oligonucleotides via triple helix formation.
The DNA target is composed of adjacent oligopurine oligopyrimidine dom
ains where the oligopurine sequences alternate on the two DNA strands.
Canonical (C,T)-motif triple helices are formed with each oligopurine
. oligopyrimidine domain of the target sequence. The two third-strand
oligonucleotides were joined together via an appropriate linker betwe
en the two terminal bases with either a 3'-3' or a 5'-5' polarity. Mol
ecular modeling was used to predict the optimal length of the linker b
ridging two terminal bases. The interaction of DNA with such a modifie
d oligonucleotide containing a C-3-U-3 linkage was studied by thermal
dissociation, footprinting, and gel retardation experiments. They prov
ide experimental evidence that the oligonucleotide does form a switche
d triple helix on this extended DNA target sequence. The binding of th
e so-called ''switch oligonucleotide'' is enhanced as compared to the
two unlinked parental oligonucleotides which form triple helices with
each oligopurine oligopyrimidine domain of the target sequence.