3MBU
Structure of a bipyridine-modified PNA duplex
Summary for 3MBU
| Entry DOI | 10.2210/pdb3mbu/pdb |
| Related | 3MBS |
| Descriptor | Bipyridine-PNA, 1,2-ETHANEDIOL, R-1,2-PROPANEDIOL, ... (7 entities in total) |
| Functional Keywords | bipyridine, peptide nucleic acid, pna |
| Total number of polymer chains | 4 |
| Total formula weight | 11229.24 |
| Authors | |
| Primary citation | Yeh, J.I.,Pohl, E.,Truan, D.,He, W.,Sheldrick, G.M.,Du, S.,Achim, C. The crystal structure of non-modified and bipyridine-modified PNA duplexes. Chemistry, 16:11867-11875, 2010 Cited by PubMed Abstract: Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethyl glycine backbone. The crystal structures of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATGCC)(2), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands, have been solved with a resolution of 1.22 and 1.10 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure similar to that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and the nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. Our results support the notion that whereas PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base-pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines bulge out of the duplex and are aligned parallel to the major groove of the PNA. In addition, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π stacked with adjacent nucleobase pairs and adopt an intrahelical geometry. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PubMed: 20859960DOI: 10.1002/chem.201000392 PDB entries with the same primary citation |
| Experimental method | X-RAY DIFFRACTION (1.05 Å) |
Structure validation
Download full validation report
