A new type of a bifunctional DNA architecture based on a three way junction is developed that combines the structural motif of sticky perylene bisimide caps with a tris-bipyridyl metal ion lock in the center part. A clear stabilizing effect was observed in the presence of Fe(3+), Ni(2+) and Zn(2+) by the formation of corresponding bipyridyl complexes in the branching part of the DNA three way junctions. The dimerization of the 5'-terminally attached perylene diimides (PDI) chromophores by hydrophobic interactions can be followed by significant changes in the UV/Vis absorption and steady-state fluorescence. The PDI-mediated DNA assembly occurs at temperatures below the melting temperature and is not influenced by the metal-ion bipyridyl locks in the central part. The corresponding AFM images revealed the formation of higher-ordered structures as the result of DNA assemblies mediated by the PDI interactions.
The carboxymethylmonobenzocyclooctyne group attached to the 5-position of a 2'-deoxyuridine in DNA allows rapid and efficient copper-free postsynthetic modification as demonstrated with a far-red emitting fluorescent azide probe. Upon labeling strong fluorescence intensity enhancement is observed.
Pyrrolidinyl PNA was immobilized on Fe(x)O(y) magnetic particles and was able to capture and thereby discriminate single base alterations in DNA counterstrands better than DNA. The selectivities of matched vs. mismatched oligonucleotides measured by the absorption differences were up to 10-12 which are remarkable values for linear probes.
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