C. Escude et al., STABILITY OF TRIPLE HELICES CONTAINING RNA AND DNA STRANDS - EXPERIMENTAL AND MOLECULAR MODELING STUDIES, Nucleic acids research, 21(24), 1993, pp. 5547-5553
UV-absorption spectrophotometry and molecular modeling have been used
to study the influence of the chemical nature of sugars (ribose or deo
xyribose) on triple helix stability. For the Pyrimidine.Purine Pyrimi
dine motif, all eight combinations were tested with each of the three
strands composed of either DNA or RNA. The chemical nature of sugars h
as a dramatic influence on triple helix stability. For each double hel
ix composition, a more stable triple helix was formed when the third s
trand was RNA rather than DNA. No stable triple helix was detected whe
n the polypurine sequence was made of RNA with a third strand made of
DNA. Energy minimization studies using the JUMNA program suggested tha
t interactions between the 2'-hydroxyl group of the third strand and t
he phosphates of the polypurine strand play an important role in deter
mining the relative stabilities of triple-helical structures in which
the polypyrimidine third strand is oriented parallel to the polypurine
sequence. These interactions are not allowed when the third strand ad
opts an antiparallel orientation with respect to the target polypurine
sequence, as observed when the third strand contains G and A or G and
T/U. We show by footprinting and gel retardation experiments that an
oligoribonucleotide containing G and A or G and U fails to bind double
helical DNA, while the corresponding DNA oligomers form stable triple
-helical complexes.