Phosphorothioate oligodeoxyribonucleotides were tested for their abili
ty to recognize double-helical DNA in two distinct triple helix motifs
. Purine-rich oligonucleotides containing a diastereomeric mixture of
phosphorothioate or stereoregular (all R(p)) phosphorothioate linkages
are shown to form triple-helical complexes with affinities similar to
those of the corresponding natural phosphodiester oligonucleotides. I
n contrast, pyrimidine-rich phosphorothioate oligonucleotides containi
ng a mixture of diastereomeric or stereoregular (all R(p)) linkages do
not bind to double-helical DNA with measurable affinity. These observ
ations have implications for triple helix structure and for biological
applications.