A Versatile Mismatch Recognition Agent:  Specific Cleavage of a Plasmid DNA at a Single Base Mispair

Abstract

[Rh(bpy)2(chrysi)]3+ is a novel, sterically bulky DNA intercalator that has been designed to bind specifically in the destabilized regions near DNA base mismatches and, upon photoactivation, to cleave the DNA backbone. Here the molecule is shown to be both a general and remarkably specific mismatch recognition agent. Specific DNA cleavage is observed at over 80% of mismatch sites in all the possible single base pair sequence contexts around the mispaired bases. Moreover, the complex is highly site-specific; it is shown to recognize and photocleave at a single base mismatch in a 2725 base pair linearized plasmid heteroduplex. Sterically demanding intercalators such as [Rh(bpy)2(chrysi)]3+ may have application both in mutation detection systems and as mismatch-specific chemotherapeutic agents.

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

“…This observation corroborates the direct correlation between the binding affinity of Δ-Rh(bpy-d 8 ) 2 chrysi 3+ for mismatches and the extent to which these mismatches destabilize DNA. [1][2][3] The C 2 symmetry of the palindromic oligonucleotide is broken upon insertion of the rhodium complex resulting in two distinct strands. Consequently, the two ejected bases are no longer equivalent: one of the two mismatched cytosines is significantly more flexible than the other.…”

“…[1][2][3] Rh(bpy) 2 chrysi 3+ (chrysi = 5,6-chrysenequinone diimine, Figure 1), is a sterically bulky DNA intercalator that binds specifically in the destabilized regions near DNA base mismatches and, upon photoactivation, cleaves the DNA backbone. The complex is both a general and remarkably specific mismatch recognition agent.…”

“…The complex is both a general and remarkably specific mismatch recognition agent. 3 Specific DNA cleavage is observed at over 80% of mismatch sites irrespective of the sequence context around the mispaired bases. Furthermore, the complex binds and with photoactivation cleaves at a single base mismatch in a 2725 base pair linearized plasmid heteroduplex.…”

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

“…In recent years, we have applied our understanding of molecular recognition elements to the development of complexes that selectively bind mispaired sites in DNA [3][4][5] . DNA mismatches occur in the cell as a result of polymerase errors or DNA damage 6,7 .…”

“…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 . As the complexes target only those sites that are thermodynamically destabilized in the base stack, however, more stable mismatches, for example those containing Gua, are not readily detected based upon photocleavage.…”