A rhodium(III) complex for high-affinity DNA base-pair mismatch recognition

Abstract

A rhodium(III) complex, rac-[Rh(bpy)2phzi] 3؉ (bpy, 2,2-bipyridine; phzi, benzo[a]phenazine-5,6-quinone diimine) has been designed as a sterically demanding intercalator targeted to destabilized mismatched sites in double-helical DNA. The complex is readily synthesized by condensation of the phenazine quinone with the corresponding diammine complex. Upon photoactivation, the complex promotes direct strand scission at singlebase mismatch sites within the DNA duplex. As with the parent mismatch-specific reagent, [Rh(bpy)2(chrysi)] 3؉ [chrysene-5,6-quinone diimine (chrysi)], mismatch selectivity depends on the helix destabilization associated with mispairing. Unlike the parent chrysi complex, the phzi analogue binds and cleaves with high affinity and efficiency. The specific binding constants for CA, CC, and CT mismatches within a 31-mer oligonucleotide duplex are 0.3, 1, and 6 ؋ 10 7 M ؊1 , respectively; site-specific photocleavage is evident at nanomolar concentrations. Moreover, the specificity, defined as the ratio in binding affinities for mispaired vs. well paired sites, is maintained. The increase in affinity is attributed to greater stability in the mismatched site associated with stacking by the heterocyclic aromatic ligand. The high-affinity complex is also applied in the differential cleavage of DNA obtained from cell lines deficient in mismatch repair vs. those proficient in mismatch repair. Agreement is found between photocleavage by the mismatch-specific probes and deficiency in mismatch repair. This mismatch-specific targeting, therefore, offers a potential strategy for new chemotherapeutic design.T he targeting of single-base mismatches in DNA represents a challenging problem in molecular recognition. The mismatched site may be of variable sequence and within a variable sequence context. What distinguishes such a site, instead, is the local destabilization in opposing bases because of the absence of Watson-Crick hydrogen bonding (1). Although challenging, however, the development of small molecules targeted to mismatches offers many applications. Site-specific mismatch probes could be used in discovery efforts to identify single-nucleotide polymorphisms. Moreover, such molecules could provide the basis for the development of novel chemotherapeutics. Many cancers are associated with a deficiency in mismatch repair (2, 3). Hence, by directing small molecules to the accumulated mismatches, a cancer-specific targeting strategy could be envisioned.In our laboratory, we have exploited the local helix destabilization associated with mispairing in the design of a metal complex targeted to mismatches (4, 5). Shown in Fig. 1 is a rhodium complex containing the benzo[a]phenazine-5,6-quinone diimine (phzi) ligand, as well as chrysene-5,6-quinone diimine (chrysi) and phenanthrene quinone diimine (phi) ligands (4). Octahedral rhodium(III) complexes containing the phi ligand bind avidly to double-helical DNA by intercalation (6); on photoactivation, direct DNA strand cleavage is also promoted at the bound site (7)...

Insertion of a Bulky Rhodium Complex into a DNA Cytosine−Cytosine Mismatch: An NMR Solution Study

“…Measurements of the abundance of mismatches provides an early report on deficiencies in mismatch repair. 9 Towards that end, we have developed luminescent analogues as probes for mismatches. 10,11 Bifunctional complexes have also been designed to target alkylators and platinating agents to mismatched sites.…”

DNA base mismatch detection with bulky rhodium intercalators: synthesis and applications

“…Indeed, mutations in MMR genes have been identified in 80% of hereditary non-polyposis colon cancers, and 15-20% of biopsied solid tumors have shown evidence of somatic mutations associated with MMR [10][11][12] . Mismatch detection may provide an early indicator of these cancerous transformations 13 .…”

“…2) 3,13 . The preparation of the simplest complexes in each family, Rh(bpy) 2 (chrysi) 3+ and Rh(bpy) 2 (phzi) 3+ , is described here.…”

“…Site selectivity in solution can be readily discerned through DNA photocleavage experiments. In addition to binding mismatches tightly and selectively, the complexes promote direct strand scission adjacent to the mismatch site with photoactivation 3,13 . The selectivity of the complexes is a tremendous asset; Rh(bpy) 2 (chrysi) 3+ , for example, is capable of binding and cleaving a single CC mismatch in a 2,725 bp plasmid 4 .…”

Karyotypic “state” as a potential determinant for anticancer drug discovery

“…Any characteristic or state that distinguishes the neoplastic cell may represent a potential target, especially if it is not easily modifiable by the tumor cell during the process of growth and evolution either in the absence or presence of therapy. We and others have previously suggested that defective nucleotide mismatch recognition and repair (MMR) could be one such state (3,4). Another targetable and relatively irreversible cellular state might be the complexity and instability of the chromosomal complement of cancer cells.…”