Nucleic Acids Research, Vol 25, Issue 19 3787-3794, Copyright © 1997 by Oxford University Press
DM Gowers and KR Fox
We have used DNase I footprinting to assess the formation of triple helices
at 15mer oligopurine target sites which are interrupted by several (up to
four) adjacent central pyrimidine residues. Third strand oligonucleotides
were designed to generate complexes containing central (X.TA)nor (X.CG)n
triplets (X = each base in turn) surrounded by C+.GC and T.AT triplets. It
has previously been shown that G.TA and T.CG are the most stable triplets
for recognition of single TA and CG interruptions. We show that these
triplets are the most useful for recognizing consecutive pyrimidine
interruptions and find that addition of each pyrimidine residue leads to a
30-fold decrease in third strand affinity. The addition of 10 microM
naphthylquinoline triplex-binding ligand stabilizes each complex so that
all the oligonucleotides produce footprints at similar concentrations (0.3
microM). Targets containing two pyrimidines are only bound by
oligonucleotides generating (G.TA)2 and (T.CG)2 with a further 30-fold
decrease in affinity. (G.TA)2 is slightly more stable than (T.CG)2. In the
presence of the triplex- binding ligand the order of stability is (G.TA)2
> (C.TA)2 > (T.TA)2 > (A.TA)2 and (T.CG)2 > (C.CG)2 >
(G.CG)2 = (A.CG)2. No oligonucleotide footprints are generated at target
sites containing three consecutive pyrimidines, though addition of 10
microM triplex-binding ligand produces stable complexes with
oligonucleotides generating (G.TA)3, (T.CG)3 and (C.CG)3, with a further
30-fold reduction in affinity. No footprints are generated at targets
containing four Ts, though the ligand induces a weak interaction with the
oligonucleotide generating (T.CG)4.
ARTICLES
DNA triple helix formation at oligopurine sites containing multiple contiguous pyrimidines
Division of Biochemistry and Molecular Biology, School of Biological Sciences, University of Southampton, Bassett Crescent East, Southampton SO16 7PX, UK.
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  D. A. Rusling, V. E. C. Powers, R. T. Ranasinghe, Y. Wang, S. D. Osborne, T. Brown, and K. R. Fox Four base recognition by triplex-forming oligonucleotides at physiological pH Nucleic Acids Res., May 23, 2005; 33(9): 3025 - 3032. [Abstract] [Full Text] [PDF]
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