TY  - JOUR
AU  - Sabir, T.
AU  - Toulmin, A.
AU  - Ma, L.
AU  - Jones, A.C.
AU  - McGlynn, P.
AU  - Schröder, G.F.
AU  - Magennis, S.W.
TI  - Branchpoint expansion in a fully-complementary three-way DNA junction.
JO  - Journal of the American Chemical Society
VL  - 134
SN  - 0002-7863
CY  - Washington, DC
PB  - American Chemical Society
M1  - PreJuSER-111910
SP  - 6280 - 6285
PY  - 2012
N1  - We thank the BBSRC for support (BB/G00269X/1); Claus Seidel, Ralf Kuhnemuth, and Stefan Marawske for assistance in developing our MFD setup; Suren Felekyan for help with data analysis; and Jochen Ark for assistance with experiments. S.W.M. acknowledges the award of an EPSRC advanced research fellowship (EP/D073154), and L.M. acknowledges the award of a CSC scholarship.
AB  - 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.
KW  - Computer Simulation
KW  - DNA: chemistry
KW  - Fluorescence Resonance Energy Transfer: methods
KW  - Hydrogen Bonding
KW  - Ions
KW  - Kinetics
KW  - Molecular Dynamics Simulation
KW  - Nanotechnology: methods
KW  - Nucleic Acid Conformation
KW  - Nucleic Acids
KW  - Nucleotides: chemistry
KW  - RNA: chemistry
KW  - Reproducibility of Results
KW  - Spectrophotometry: methods
KW  - Ions (NLM Chemicals)
KW  - Nucleic Acids (NLM Chemicals)
KW  - Nucleotides (NLM Chemicals)
KW  - RNA (NLM Chemicals)
KW  - DNA (NLM Chemicals)
KW  - J (WoSType)
LB  - PUB:(DE-HGF)16
C6  - pmid:22329743
UR  - <Go to ISI:>//WOS:000302524800037
DO  - DOI:10.1021/ja211802z
UR  - https://juser.fz-juelich.de/record/111910
ER  -