Structural Basis for Bifunctional
Zinc(II) Macrocyclic
Complex Recognition of Thymine Bulges in DNA
- Publication date
- Publisher
Abstract
The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane
(cy4q) binds selectively to thymine bulges in DNA and to a uracil
bulge in RNA. Binding constants are in the low-micromolar range for
thymine bulges in the stems of hairpins, for a thymine bulge in a
DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies
of Zn(cy4q) to a series of hairpins containing thymine bulges with
different flanking bases showed that the complex had a moderate selectivity
for thymine bulges with neighboring purines. The dissociation constants
of the most strongly bound Zn(cy4q)–DNA thymine bulge adducts
were 100-fold tighter than similar sequences with fully complementary
stems or than bulges containing cytosine, guanine, or adenine. In
order to probe the role of the pendent group, three additional zinc(II)
complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with
aromatic pendent groups were studied for binding to DNA including
1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane
(cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-<i>N</i>,<i>N</i>-dimethylnaphthalen-1-amine (dsc). The
Zn(cybp) complex binds with moderate affinity but little selectivity
to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly,
Zn(dsc) binds weakly both to thymine bulges and hairpins with fully
complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl
moiety bound to the Zn<sup>II</sup> center, as shown by <sup>1</sup>H NMR spectroscopy and pH–potentiometric titrations. As a
consequence, only weak (500 μM) binding is observed to DNA with
no appreciable selectivity. An NMR structure of a thymine-bulge-containing
hairpin shows that the thymine is extrahelical but rotated toward
the major groove. NMR data for Zn(cy4q) bound to DNA containing a
thymine bulge is consistent with binding of the zinc(II) complex to
the thymine N3<sup>–</sup> and stacking of the quinoline on
top of the thymine. The thymine-bulge bound zinc(II) complex is pointed
into the major groove, and there are interactions with the guanine
positioned 5′ to the thymine bulge