Crystal structure of the DNAzyme 9DB1

The first ever crystal structure of a deoxyribozyme has been solved at 2.8 Å resolution [1—3]. The work by researchers from Max Planck Institute for Biophysical Chemistry (Göttingen, Germany) also sheds light on a difference in catalytic mechanism of ribozymes and deoxyribozymes [4]:

Ribozymes use RNA’s 2´-hydroxyl groups, which are absent in DNA, for structural interactions or directly for catalysis. The new structure shows why the lack of these groups doesn’t diminish the catalytic activity of DNAzymes. The missing hydroxyls make DNA’s sugar-phosphate backbone more flexible, allowing acrobatic conformations that compensate for the absent hydroxyls in DNAzymes.

1. Ponce-Salvatierra, A., Wawrzyniak-Turek, K., Steuerwald, U., Höbartner, C. and Pena, V. (2016) Crystal structure of a DNA catalyst. Nature 529, 231—234.
2. PDB:5CKK
3. PDB:5CKI
4. Borman, S. (2016) After two decades of trying, scientists report first crystal structure of a DNAzyme. Chemical & Engineering News 94, issue 2, p. 3.