ja211802z_si_001.pdf (2.4 MB)
Branchpoint Expansion in a Fully Complementary Three-Way DNA Junction
journal contribution
posted on 2012-04-11, 00:00 authored by Tara Sabir, Anita Toulmin, Long Ma, Anita C. Jones, Peter McGlynn, Gunnar F. Schröder, Steven W. MagennisBranched 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.