Abstract
A water-soluble self-assembled supramolecular FeII4L4 tetrahedron binds to single stranded DNA, mismatched DNA base pairs, and three-way DNA junctions. Binding of the coordination cage quenches fluorescent labels on the DNA strand, which provides an optical means to detect the interaction and allows the position of the binding site to be gauged with respect to the fluorescent label. Utilizing the quenching and binding properties of the coordination cage, we developed a simple and rapid detection method based on fluorescence quenching to detect unpaired bases in double-stranded DNA.
Highlights
The three-way junction (3WJ) is an uncommon DNA structure, it is implicated in many DNA metabolic processes, such as replication, transcription, recombination, and repair.[5]
Errors in these processes can lead to DNA mutations, which may cause a cascade of problems in gene expression.[6]
Coll, and co-workers have employed metallosupramolecular cylinders to induce the formation of three-way DNA and RNA junctions.[11]
Summary
Communication to the recognition of 3WJ, as in the case of the 3-foldsymmetric cylinders reported by Hannon.[11]. Increasing the distance between the central cage binding site and the fluorescent label (FAM) is expected to reduce fluorescence quenching The results of this experiment were in agreement with our hypothesis (Figure 3a); an apparent linear relationship between the normalized fluorescence intensity and the distance was observed, agreeing with the presence of cage 1 at the branch point of the 3WJ. We hypothesized that cage 1 binds more readily to the unpaired bases present in the central cavity of the 3WJ To test this hypothesis, we introduced mismatched bases at the branch point of a 4WJ to destabilize the structure (Figure S7).[16] cage 1 minimally quenches the fluorescent dye on the 4WJ.
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