Nucleic Acids Research, Vol 26, Issue 11 2679-2685, Copyright © 1998 by Oxford University Press
M Vorlickova, M Zimulova, J Kovanda, P Fojtik and J Kypr
We studied DNA dodecamers (CAG)4, (CCG)4, (CGG)4 and (CTG)4by CD
spectroscopy and polyacrylamide gel electrophoresis. Each dodecamer adopted
several ordered conformers which denatured in a cooperative way. Stability
of the conformers depended on the dodecamer concentration, ionic strength,
temperature and pH. The dodecamers, having a pyrimidine base in the triplet
center, generated foldbacks at low ionic strength whose stem conformations
were governed by the GC pairs. At high salt, (CCG)4 isomerized into a
peculiar association of two strands. The association was also promoted by
high oligonucleotide concentrations. No similar behavior was exhibited by
(CTG)4. At low salt, (CGG)4 coexisted in two bimolecular conformers whose
populations were strongly dependent on the ionic strength. In addition,
(CGG)4 associated into a tetraplex at acidic pH. A tetraplex was even
observed at neutral pH if the (CGG)4 concentration was sufficiently high.
(CAG)4 was very stable in a monomolecular conformer similar to the known
extremely stable foldback of the (GCGAAGC) heptamer. Nevertheless, even
this very stable conformer disappeared if (CTG)4 was added to the solution
of (CAG)4. Association of the complementary strands was also strongly
preferred to the particular strand conformations by the other couple,
(CCG)4 and (CGG)4.
ARTICLES
Conformational properties of DNA dodecamers containing four tandem repeats of the CNG triplets
Institute of Biophysics, Academy of Sciences of the Czech Republic, Kralovopolska 135, CZ-612 65 Brno, Czech Republic. mifi@ibp.cz
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