Journal Article

PreJuSER-111910

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png Branchpoint expansion in a fully-complementary three-way DNA junction.

Sabir, T. ; Toulmin, A. ; Ma, L. ; Jones, A. C. ; McGlynn, P. ; Schröder, G. F.FZJ* ; Magennis, S. W.

2012
American Chemical Society Washington, DC

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Please use a persistent id in citations: doi:10.1021/ja211802z

Abstract: 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.

Keyword(s): Computer Simulation (MeSH) ; DNA: chemistry (MeSH) ; Fluorescence Resonance Energy Transfer: methods (MeSH) ; Hydrogen Bonding (MeSH) ; Ions (MeSH) ; Kinetics (MeSH) ; Molecular Dynamics Simulation (MeSH) ; Nanotechnology: methods (MeSH) ; Nucleic Acid Conformation (MeSH) ; Nucleic Acids (MeSH) ; Nucleotides: chemistry (MeSH) ; RNA: chemistry (MeSH) ; Reproducibility of Results (MeSH) ; Spectrophotometry: methods (MeSH) ; Ions ; Nucleic Acids ; Nucleotides ; RNA ; DNA ; J

Note: 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.

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Contributing Institute(s):

1. Strukturbiochemie (ICS-6)

Research Program(s):

1. Funktion und Dysfunktion des Nervensystems (P33)
2. BioSoft: Makromolekulare Systeme und biologische Informationsverarbeitung (P45)

Appears in the scientific report 2012

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Database coverage:
; BIOSIS Previews ; Current Contents - Life Sciences ; Current Contents - Physical, Chemical and Earth Sciences ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Thomson Reuters Master Journal List ; Web of Science Core Collection

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