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Recognition of DNA Three‐Way Junctions by Metallosupramolecular Cylinders: Gel Electrophoresis Studies
Author(s) -
Malina Jaroslav,
Han Michael J.,
Brabec Viktor
Publication year - 2007
Publication title -
chemistry – a european journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.687
H-Index - 242
eISSN - 1521-3765
pISSN - 0947-6539
DOI - 10.1002/chem.200700159
Subject(s) - palindrome , dna , crystallography , oligonucleotide , holliday junction , cylinder , nucleotide , electrophoresis , chemistry , chemical physics , biophysics , biology , crispr , gene , biochemistry , geometry , mathematics , homologous recombination
The interaction of metallosupramolecular cylinders with DNA three‐way junctions has been studied by gel electrophoresis. A recent X‐ray crystal structure of a palindromic oligonucleotide forming part of a complex with such a cylinder revealed binding at the heart of a three‐way junction structure. The studies reported herein confirm that this is not solely an artefact of crystallisation and reveal that this is a potentially very powerful new mode of DNA recognition with wide scope. The cylinders are much more effective at stabilizing three‐way junctions than simple magnesium dications or organic or metallo‐organic tetracations, with the M cylinder enantiomer being more effective than P . The recognition is not restricted to three‐way junctions formed from palindromic DNA with a central AT step at the junction; non‐palindromic three‐way junctions and those with GC steps are also stabilised. The cylinder is also revealed to stabilise other Y‐shaped junctions, such as that formed at a fraying point in duplex DNA (for example, a replication fork), and other DNA three‐way junction structures, such as those containing unpaired nucleotides, perhaps by opening up this structure to access the central cavity.