Nucleic Acids Research, Vol 26, Issue 16 3845-3853, Copyright © 1998 by Oxford University Press
Y Jing, JF Kao and JS Taylor
Cis-syn dimers, (6-4) products and their Dewar valence isomers are the
major photoproducts of DNA and have different mutagenic properties and
rates of repair. To begin to understand the physical basis for these
differences, the thermal stability and base pairing properties of the
corresponding photoproducts of the TT site in d(GAGTATTATGAG) were
investigated. The (6-4) and Dewar products destabilize the duplex form by
approximately 6 kcal/mol of free energy at 37 degreesC relative to the
parent, whereas a cis-syn dimer only destabilizes the duplex form by 1.5
kcal/mol. Duplexes with G opposite the 3'-T of the (6-4) and Dewar products
are more stable than those with A by approximately 0.4 kcal/mol, whereas
the cis-syn dimer prefers A over G by 0.7 kcal/mol. Proton NMR suggests
that wobble base pairing takes place between the 3'- T of the cis-syn dimer
and an opposed G, whereas there is no evidence of significant H-bonding
between these two bases in the (6-4) product. The thermodynamic and
H-bonding data for the (6-4) product are consistent with a 4 nt interior
loop structure which may facilitate flipping of the photoproduct in and out
of the helix.
ARTICLES
Thermodynamic and base-pairing studies of matched and mismatched DNA dodecamer duplexes containing cis-syn, (6-4) and Dewar photoproducts of TT
Department of Chemistry and Chemistry Department High Resolution NMR Facility, Washington University, St Louis, MO 63130, USA.
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