X-ray crystallographic studies on PNA
B.B. Nielsen, B. Svendsen, H. Rasmussen, I.K Larsen and J.S. Kastrup
D e p a r t m e n t of Me d i c i n a l Ch e m i s t r y, Ro y a l Da n i sh Sch o o l of Ph a r m a c y, Un i ve r s i t e t sp a r k e n 2, DK-
2 1 0 0 Co p e n h a g e n , De n m a r k
PNA (peptide nucleic acid) is an oligonucleotide analog in which the entire backbone has been
replaced by a backbone composed of N-(2-aminoethyl)glycine units . PNA hybridizes with both
DNA and RNA and possesses many of the properties desired of an antisense/antigene drug
candidate, including stability towards nucleases, proteases, peptidases and human serum.
The structure of a hexameric PNA-PNA duplex has been determined to 1.7 resolution, revealing
a unique helix (P-form) among the known Watson-Crick base-paired helices . The structure was
solved using a bromouracil derivative and SR data to 1.9 resolution (X31). In addition, a PNA
analog with modifications in the backbone (N-methyl backbone) has been determined to 2.2
resolution , and a dataset to 1.8 resolution (X31) has been collected on a PNA analog with
modifications in one of the bases (thymine). As the MR method has has not given a clear solution,
the SIR/MIR method will be used to get initial phases. The aim of the structure determinations is to
investigate the dependence of the helical form on the backbone and the bases.
Figure 1: The structure of Lys-PNA showing the stacking of the left-and right-handed duplexes.
Furthermore, the structure of a PNA duplex with a chiral center introduced by the amino acid lysine
(Lys-PNA) has been solved to 2.4 resolution and refined. Structure determinations of a single
stranded PNA decamer and a PNA-PNA dodecamer are in progress based on SR data to 2.2
resolution (X11) and to 2.7 resolution (ESRF), respectively.
The work is performed in collaboration with professor Peter E. Nielsen, Panum Institute, University
of Copenhagen, Denmark.
 M. Egholm, O. Buchardt, L. Christensen, C. Behrens, S. M. Freier, D.A. Driver, R.H. Berg, S.K.
Kim, B. Norden, and P.E. Nielsen, Nature 365, 565 (1993)
 H. Rasmussen, J.S. Kastrup, J.N. Nielsen, J.M. Nielsen, and P.E. Nielsen, Nature Struct. Biology 4,
 G. Haaima, H. Rasmussen, G. Schmidt, D.K. Jensen, J.S. Kastrup, P.W. Stafshede, B. Norden, O.
Buchardt, and P.E. Nielsen, New J. Chem. 23, 833 (1999)