Macrocyclic DNA‐Mismatch‐Binding Ligands: Structural Determinants of Selectivity

Abstract

A collection of 15 homodimeric and 5 heterodimeric macrocyclic bisintercalators was prepared by one- or two-step condensation of aromatic dialdehydes with aliphatic diamines; notably, the heterodimeric scaffolds were synthesized for the first time. The binding of these macrocycles to DNA duplexes containing a mispaired thymine residue (TX), as well as to the fully paired control (TA), was investigated by thermal denaturation and fluorescent-intercalator-displacement experiments. The bisnaphthalene derivatives, in particular, the 2,7-disubstituted ones, have the highest selectivity for the TX mismatches, as these macrocycles show no apparent binding to the fully paired DNA. By contrast, other macrocyclic ligands, as well as seven conventional DNA binders, show lesser or no selectivity for the mismatch sites. The study demonstrates that the topology of the ligands plays a crucial role in determining the mismatch-binding affinity and selectivity of the macrocyclic bisintercalators.

Double threading through DNA: NMR structural study of a bis-naphthalene macrocycle bound to a thymine–thymine mismatch

“…The synthesis and characterization data of 2,7-BisNP × 4 HCl were reported previously (48). Crystals suitable for X-ray diffraction analysis were obtained by vapor diffusion of Et 2 O or t -BuOMe into solutions of 2,7-BisNP × 4 HCl in MeOH.…”

“…Thermal denaturation studies were performed in triplicate according to the previously publishing protocol in 10 mM sodium cacodylate buffer containing 50 mM NaCl, pH 6 (48). The concentration of duplex TT-DNA or TA-DNA (5′-CGT CGT AGT GC-3′/5-GCA CTA CGA CG-3′) was 2 µM, and the concentration of ligand was varied from 0 to 8 µM.…”

“…The initial studies were performed with the 2,7–substituted bis-acridine (BisA) and 2,6-substitued bis-naphthalene (2,6-BisNP) macrocycles. Later, however, screening of a panel of 20 homo- and heterodimeric macrocyclic ligands led to the identification of the 2,7–substituted bis-naphthalene isomer (2,7-BisNP, Scheme 1) as the ligand with the highest binding selectivity for mismatched versus fully matched DNA duplexes (48). The selective binding of this family of ligands to DNA lesion sites is, presumably, due to their peculiar constrained conformation and the short distance between the two aromatic planes, which does not allow their simultaneous intercalation into regular DNA, as it would violate the neighbor-exclusion principle (49).…”

Detection of single nucleotide polymorphisms by the specific interaction between transition metal ions and mismatched base pairs in duplex DNA

“…Previously reported methods to detect the newly produced mismatched base pairs in the heteroduplex DNAs were not always convenient and accurate [19][20][21]24]. For example, the preparations of small molecules to recognize the mismatched base pairs in the heteroduplex DNA were timeconsuming for the organic synthesis of the molecules, and the small molecules did not always accurately discriminate between the target mismatched base pair and the other base pairs [19][20][21]24]. In contrast, the UV melting and the FRET analyses proposed in this study by only adding the Hg 2?…”

“…Additionally, some groups prepared novel small molecules to recognize mismatched base pairs in the heteroduplex DNA [19][20][21][22][23][24]. However, such preparations by organic synthesis were time-consuming, and the small molecules did not always accurately discriminate between the target mismatched base pair and the other base pairs [19][20][21]24]. More convenient and accurate methods therefore need to be established.…”