Nucleic Acids Research, Vol 26, Issue 16 3677-3686, Copyright © 1998 by Oxford University Press
JL Asensio, T Brown and AN Lane
The solution conformations of the intramolecular triple helices
d(AGAAGA-X-TCTTCT-X-TC+TTC+T) and d(AAGGAA-X-TTCCTT-X-TTC+C+TT) (X =
non-nucleotide linker) have been determined by NMR.1H NMR spectra in H2O
showed that the third strand cytosine residues are fully paired with the
guanine residues, each using two Hoogsteen hydrogen bonds. Determination of
the13C chemical shifts of the cytosine C6 and C5 and their one-bond
coupling constants (1 J CH) conclusively showed that the Hoogsteen cytosine
residues are protonated at N3. The global conformations of the two
molecules determined with >19 restraints per residue are very similar
(RMSD = 0.96 A). However, some differences in local conformation and
dynamics were observed for the central two base triplets of the two
molecules. The C N3H were less labile in adjacent CG.C+triplets than in
non-adjacent ones, indicating that the adjacent charge does not kinetically
destabilize these triplets. The sugar conformations of the two adjacent
cytosine residues were different and the 5'-residue was atypical of
protonated cytosine. Hence, there are subtle effects of the interaction
between two adjacent cytosine residues. The central two purines in each
sequence showed non-standard backbone conformations, averaging between
gamma approximately 60 degrees and gamma approximately 180 degrees. This
may be related to the difference in the dependence of the thermodynamic
stability on pH observed for these two sequences.
ARTICLES
Comparison of the solution structures of intramolecular DNA triple helices containing adjacent and non-adjacent CG.C+ triplets
Division of Molecular Structure, National Institute for Medical Research, The Ridgeway, Mill Hill, London NW7 1AA, UK.
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