Branchpoint Expansion in a Fully Complementary Three-Way DNA Junction

Tara Sabir, Anita Toulmin, Long Ma, Anita C. Jones, Peter McGlynn, Gunnar F. Schroeder, Steven W. Magennis

Research output: Contribution to journalArticlepeer-review


Branched nucleic acid molecules serve as key intermediates in DNA replication, recombination, and repair; architectural elements in RNA; and building blocks and functional, components for nanoscience applications. Using a combination of high-resolution single-molecule FRET, time-resolved spectroscopy, and molecular modeling, we have probed the local and global structure of a DNA three-way junction (3WJ) in solution. We found that it adopts a Y-shaped, pyramidal structure, in which the bases adjacent to the branchpoint are unpaired, despite the full Watson-Crick complementarity of the molecule. The unpairing allows a nanoscale cavity to form at the junction center. Our structure accounts for earlier observations made of the structure, flexibility, and reactivity of 3WJs. We anticipate that these results will guide the development of new DNA-based supramolecular receptors and nanosystems.

Original languageEnglish
Pages (from-to)6280-6285
Number of pages6
JournalJournal of the American Chemical Society
Issue number14
Publication statusPublished - 11 Apr 2012


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