Gemdimethyl Peptide Nucleic Acids (α/β/γ-gdm-PNA): E/Z-Rotamers Influence the Selectivity in the Formation of Parallel/Antiparallel gdm-PNA:DNA/RNA Duplexes

Abstract

Peptide nucleic acids (PNAs) consist of an aminoethylglycine (aeg) backbone to which the nucleobases are linked through a tertiary amide group and bind to complementary DNA/RNA in a sequence-specific manner. The flexible aeg backbone has been the target for several chemical modifications of the PNA to improve its properties such as specificity, solubility, etc. PNA monomers exhibit a mixture of two rotamers (Z/E) arising from the restricted rotation around the tertiary amide N−CO bond. We have recently demonstrated that achiral gemdimethyl substitution at the α, β, and γ sites on the aeg backbone induces exclusive Z (α-gdm)-or E-rotamer (β-gdm) selectivity at the monomer level. It is now shown that γ/β-gdm-PNA:DNA parallel duplexes are more stable than the analogous antiparallel duplexes, while γ/β-gdm-PNA:RNA antiparallel duplexes are more stable than parallel duplexes. Furthermore, the γ/β-gdm-PNA:RNA duplexes are more stable than the γ/β-gdm-PNA:DNA duplexes. These results with γ/β-gdm-PNA are the reverse of those previously seen with α-gdm-PNA oligomers that stabilized antiparallel α-gdm-PNA:DNA duplexes compared to α-gdm-PNA:RNA duplexes. The stability of antiparallel/parallel PNA:DNA/RNA duplexes is correlated with the preference for Z/E-rotamer selectivity in α/β-gdm-PNA monomers, with Z-rotamers (α-gdm) leading to antiparallel duplexes and E-rotamers (β/γ-gdm) leading to parallel duplexes. The results highlight the role and importance of Z-and E-rotamers in controlling the structural preferences of PNA:DNA/RNA duplexes.

Recent Advancements in Development and Therapeutic Applications of Genome-Targeting Triplex-Forming Oligonucleotides and Peptide Nucleic Acids

“…Recently, Ganesh's group reported that the introduction of the gem-dimethyl (gdm) group influenced the Z/E rotamer ratio of the tertiary amide. The α-gdm monomer exclusively exhibits the Z-rotamer, whereas the β-gdm monomer exhibits the E-rotamer (Figure 9, 35) [91,92]. Those E/Z-rotamers influenced the orientation preference of PNA in the formation of the complex.…”

Parameterization of the miniPEG-Modified γPNA Backbone: Toward Induced γPNA Duplex Dissociation

“…PNAs have been reported to be stronger in binding to a complementary DNA or RNA strand due to a lack of electron repulsion from the neutral backbone. − Moreover, PNAs are discriminatory in binding, allowing for high sequence specificity and affinity to a genetic target, and inherently capable of evading degradation by nucleases or proteases. , Unfortunately, the neutrality of the backbone of PNAs limits their incorporation into therapeutic design, as it has been reported that single-stranded PNAs suffer from aggregation in solution. , A way to prevent aggregation was to introduce chirality into the PNA backbone at positions α, β, or γ (Figure ). Modifications yielding αPNA − and γPNA ,, are the most common, greatly reducing its limitations (poor membrane permeability, low aqueous solubility, and ambiguity in RNA binding orientation), , while also exploring a new frontier of preferential preorganization . The αPNA modifications have been assessed, discovering a loss of binding affinity toward the intended genetic target relative to nonmodified PNAs. − On the other hand, γPNA modifications deliver improved binding affinity compared to nonmodified PNAs, ,, but the structure and dynamics of the promising miniature poly­(ethylene glycol) (miniPEG)-modified γPNAs have not been studied.…”

“… 10 , 11 A way to prevent aggregation was to introduce chirality into the PNA backbone at positions α, β, or γ ( Figure 1 ). Modifications yielding αPNA 12 − 16 and γPNA 7 , 17 , 18 are the most common, greatly reducing its limitations (poor membrane permeability, low aqueous solubility, and ambiguity in RNA binding orientation), 7 , 9 while also exploring a new frontier of preferential preorganization. 9 The αPNA modifications have been assessed, discovering a loss of binding affinity toward the intended genetic target relative to nonmodified PNAs.…”

The unusual structural properties and potential biological relevance of switchback DNA

“…22 Identical terminal polarities in a double helical context are typically achieved through the formation of parallel stranded DNA by specific sequence choices, DNA analogs, pH control or by the incorporation of 3¢-3¢ and 5¢-5¢ linkages that leaves two 5¢ ends or 3¢ ends on the DNA motifs, respectively. [23][24][25][26] To introduce left-handed helices, Z-DNA forming sequences 27 or L-DNA 28 are typically incorporated into component DNA strands. Detailed study of underlying DNA structures and new DNA motifs informs the rational design of functional characteristics in self-assembled nanostructures.The motifs used in the field of DNA nanotechnology were initially inspired by structures that exist in nature.…”

“…Chemical functionalization and design-based strategies yield nanostructures that are thermally stable 16 and nuclease-resistant. 17 Identical terminal polarities in a double helical context are typically achieved through specific sequence choices, DNA analogs or pH control to form parallel stranded DNA 18,19 and by the incorporation of 3′-3′ or 5′-5′ linkages that leaves two 5′ ends or 3′ ends on the DNA motifs respectively. 20 To introduce left-handed helices, Z-DNA forming sequences 21 or L-DNA component strands 22 are typically incorporated into component DNA strands.…”