Crystal structure of an 82-nucleotide RNA−DNA complex formed by
the 10-23 DNA enzyme
Jacek Nowakowski1, 2, Peter J. Shim2, G. Sridhar Prasad2, C. David Stout2
& Gerald F. Joyce1, 2
1
Department of Chemistry and The Skaggs Institute for
Chemical Biology, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California
92037, USA
2
Department of Molecular Biology, The Scripps Research
Institute 10550 North Torrey Pines Road, La Jolla,
California 92037, USA
The structure of a large nucleic acid complex formed by the 10−23
DNA enzyme bound to an RNA substrate was determined by X−ray diffraction
at 3.0 Å resolution. The 82−nucleotide complex contains two strands
of DNA and two strands of RNA that form five double−helical domains.
The spatial arrangement of these helices is maintained by two four−way
junctions that exhibit extensive base−stacking interactions and sharp
turns of the phosphodiester backbone stabilized by metal ions coordinated
to nucleotides at these junctions. Although it is unlikely that the structure
corresponds to the catalytically active conformation of the enzyme, it represents
a novel nucleic acid fold with implications for the Holliday junction structure.
