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We reported previously on NMR studies of (Y+)n.(R+)n(Y-)n DNA triple helices
containing one oligopurine strand (R)n and two oligopyrimidine strands (Y)n
stabilized by T.AT and C+.GC base triples [de los Santos, C., Rosen, M., &
Patel, D. J. (1989) Biochemistry 28, 7282-7289]. Recently, it has been
established that guanosine can recognize a thymidine.adenosine base pair to form
a G.TA triple in an otherwise (Y+)n.(R+)n(Y-)n triple-helix motif. [Griffin, L.
C., & Dervan, P. B. (1989) Science 245, 967-971]. The present study extends
the NMR research to the characterization of structural features of a 31-mer
deoxyoligonucleotide that folds intramolecularly into a 7-mer (Y+)n.(R+)n(Y-)n
triplex with the strands linked through two T5 loops and that contains a central
G.TA triple flanked by T.AT triples. The G.TA triplex exhibits an unusually well
resolved and narrow imino and amino exchangeable proton and nonexchangeable
proton spectrum in H2O solution, pH 4.85, at 5 degrees C. We have assigned the
imino protons of thymidine and amino protons of adenosine involved in
Watson-Crick and Hoogsteen pairing in T.AT triples, as well as the guanosine
imino and cytidine amino protons involved in Watson-Crick pairing and the
protonated cytidine imino and amino protons involved in Hoogsteen pairing in
C+.GC triples in the NOESY spectrum of the G.TA triplex. The NMR data are
consistent with the proposed pairing alignment for the G.TA triple where the
guanosine in an anti orientation pairs through a single hydrogen bond from one
of its 2-amino protons to the 4-carbonyl group of thymidine in the Watson-Crick
TA pair.(ABSTRACT TRUNCATED AT 250 WORDS)
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