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-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.

Figure 1

The four single strand PNAs in the asymmetric unit of Bipy PNA crystal structure.

Figure 2

Structural details of the hydrogen bonds that involve two of the four terminal lysines in the unit cell of Bipy PNA and atoms from the G1 nucleobase and the PNA backbone. Hydrogen bonds are identified by dotted lines.

Figure 3

Structural features of the Bipy PNA duplex. Note the out-of-duplex position of the central bipyridines. The figure identifies the N- and C-end of the two PNA strands at one of the ends of the PBA duplex and the central base pairs of the PNA duplex.

Figure 4

(a) Pair of π-stacked bipyridine ligands in the crystal structure of Bipy PNA. The view of the backbone of Bipy PNA shows the orientation of backbone carbonyl of T6 towards the N-end of the PNA and the minor groove of the duplex in contrast to that of the carbonyl groups in A4 and G7, which are oriented towards the C end and away from the duplex. (b) PNA backbone for the central base pairs in Bipy PNA and water molecules (red crosses) that are situated closest to the PNA backbone; (c) Relative orientation of bipyridines with respect to the Bipy PNA duplex from which they are extruded.

Scheme 1

Chemical structure of PNA and definitions of torsion angles: α = C6′-N1′-C2′-C3′ ; β = N1′-C2′-C3′-N4′ ; γ = C2′-C3′-N4′-C5′ ; δ= C3′-N4′-C5′-C6′; ε = N4′-C5′-C6′-O1′; ω= C5′-C6′-N1′-C2′; χ₁ = C3′-N4′-C7′-C8′; χ₂ = N4′-C7′-C8′-N1(py)/N9(pu); χ₃ = C7′-C8′-N1(py)/N9(pu)-C2(py)/C4(pu). The angle ε defines the orientation of the backbone carbonyl group. An alternative definition of ε as N4′-C5′-C6′-N1′ has been used in literature,^[4] which corresponds to the definition of the dihedral angle of ε in DNA.

Scheme 2

Sequences of non-modified and bipyridine-modified PNA duplexes