Structural Basis for Bifunctional Zinc(II) Macrocyclic Complex Recognition of Thymine Bulges in DNA

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)-N,N-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(II) center, as shown by (1)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(-) 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.

Recognition of DNA/RNA bulges by antimicrobial and antitumor metallohelices

“…[6][7][8] In view of the importance of bulges in biological systems, compounds capable of targeting bulged sequences could be used as valuable probes for studying their role in nucleic acid function or could even have significant therapeutic potential. [10][11][12][13][14][15] Recently, we have demonstrated that DNA duplexes containing bulges are specifically recognized by [Fe 2 (I) 3 ]Cl 4 (I = C 25 H 20 N 4 ) metallosupramolecular helicates (Fig. The most promising bulge binding agents discovered to date are: those based on NCS-chrom, a wedge-shaped enediyne antitumor antibiotic neocarzinostatin chromophore, 2-acylamino-1,8-naphthyridine, rhodium intercalators or the zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane, and dinuclear ruthenium complexes.…”

Recognition of DNA bulges by dinuclear iron(II) metallosupramolecular helicates

“…Many attempts have been made to prepare such compounds. Examples of promising bulge-binding agents discovered to date are: those based on NCSchrom, a wedge-shaped enediyne antitumor antibiotic neocarzinostatin chromophore, 2-acylamino-1,8-naphthyridine, rhodium intercalators, the zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane, and dinuclear ruthenium complexes [8][9][10][11][12][13].…”

Combining a Ru(II) “Building Block” and Rapid Screening Approach to Identify DNA Structure-Selective “Light Switch” Compounds

“…In recent reports, the loop regions have been essential for the binding of certain metal complexes, specifically Zn 2+ , where they interact with the thymidines within the loop region rather than with the G-tetrad. 58–60 We hypothesize that the loop regions are also important for recognition by the Ru(II) dppz complexes by either preventing binding to the G-tetrad or by shielding the phenazine nitrogens. Seq27 lacks loops, whereas Seq28–Seq30 each have 3 loop regions (see Figure 7).…”