The Crystal Structure of Non‐Modified and Bipyridine‐Modified PNA Duplexes

Abstract

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o 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 nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while 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 are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, 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-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes.

The structural diversity of artificial genetic polymers

“…In contrast to natural helical conformations observed for DNA and RNA, XNAs adopt a variety of structural conformations. The 3D structures of XNA homoduplexes (Figure 1c ) range from those that are similar to the standard A-form RNA helix, like α-L-threofuranosyl-(3′ → 2′) nucleic acid (TNA) ( 51 ) and 2′,3′-dideoxy-1′,5′-anhydro-D-arabino-hexitol nucleic acid (HNA) ( 52 ) to more diverse structures, like the left-handed antiparallel, mirrored A-type helix of cyclohexene nucleic acid (CeNA) ( 53 ), the P-helix formed by peptide nucleic acid (PNA) ( 54 , 55 ), or the slowly writhing, more ladder-like (4′ → 6′) linked oligo-2′,3′-dideoxy-β-D-glucopyranose nucleic acid (homo-DNA or hDNA) ( 56 ). One interesting XNA structure is that of a self-complementary chimeric FANA-ANA-FNA strand that self-assembles into an antiparallel right-handed duplex in which the central and flanking regions undergo ANA:ANA and FANA:FANA self-pairing ( 57 ).…”

“…Crystal structures indicate that achiral PNA can form right-handed and left-handed P-type helices ( 54 ). In the P-type helix, an antiparallel double helix form uniquely attributed to PNA, the strands are held together by standard Watson–Crick base pairs and are wound more loosely relative to DNA.…”

The proto-Nucleic Acid Builder: a software tool for constructing nucleic acid analogs

“… XNA structures. Panels ( A ), ( C ), ( E ) and ( G ): Experimental structures for FRNA duplex (PDB: 3P4A) ( 75 ), LNA duplex (PDB: 2X2Q) ( 76 ), PNA duplex (PDB: 3MBS) ( 77 ) and RNA:CeNA duplex (PDB: 3KNC) ( 78 ), respectively, are superimposed with the structures generated by the program with the indicated RMSD values. The theoretical structure with the lowest total energy is used for comparison.…”

Therapeutic Genome Mutagenesis Using Synthetic Donor DNA and Triplex-Forming Molecules

“…( d ) For these exogenously introduced triplex-forming molecules, positive design is implemented based on major groove binding Hoogsteen oriented base pairing and strand-invading Watson-Crick oriented base pairing with genomic DNA, as well as negative design based on synthetic modifications to the linkages in the backbone to prevent endogenous nuclease and protease-mediated degradation and enhance electrostatic complementarity to negatively charged genomic DNA. Linkages for triplex-forming oligonucleotide and triplex-forming peptide nucleic acid molecular modeled from [98] and [99], respectively…”