Cγ(S/R)-Bimodal Peptide Nucleic Acids (Cγ-bm-PNA) Form Coupled Double Duplexes by Synchronous Binding to Two Complementary DNA Strands

Abstract

Peptide nucleic acids (PNAs) are linear equivalents of DNA with a neutral acyclic polyamide backbone that has nucleobases attached via tert-amide link on repeating units of aminoethylglycine. They bind complementary DNA or RNA with sequence specificity to form hybrids that are more stable than the corresponding DNA/RNA self-duplexes. A new type of PNA termed bimodal PNA [Cγ­(S/R)-bm-PNA] is designed to have a second nucleobase attached via amide spacer to a side chain at Cγ on the repeating aeg units of PNA oligomer. Cγ-bimodal PNA oligomers that have two nucleobases per aeg unit are demonstrated to concurrently bind two different complementary DNAs, to form duplexes from both tert-amide side and Cγ side. In such PNA:DNA ternary complexes, the two duplexes share a common PNA backbone. The ternary DNA 1:Cγ­(S/R)-bm-PNA:DNA 2 complexes exhibit better thermal stability than the isolated duplexes, and the Cγ­(S)-bm-PNA duplexes are more stable than Cγ­(R)-bm-PNA duplexes. Bimodal PNAs are first examples of PNA analogues that can form DNA2:PNA:DNA1 double duplexes via recognition through natural bases. The conjoined duplexes of Cγ-bimodal PNAs can be used to generate novel higher-level assemblies.

Chemical approaches to discover the full potential of peptide nucleic acids in biomedical applications

“…Others have also investigated positively charged α-and γ-modifications of the PNA backbone, and most of them showed promising hybridization properties and improved cellular uptake [82][83][84][85][86]. Very recent work has used α-and γ-positions of the PNA backbone to attach additional nucleobases, which enable these "double face" PNAs to form higher order double and triple helical structures [87,88].…”

Peptide nucleic acids and their role in gene regulation and editing

“…A new class of PNA termed bimodal PNA [Cγ(S/R)‐bm‐PNA] (Figure 6) was designed by Ganesh et al ., where a second nucleobase was added, attached via an amide bond to a side chain at Cγ of the aeg PNA backbone. [ 60–61 ] The Cγ‐bimodal PNA oligomers that had two nucleobases per aeg unit, were able to simultaneously bind two different complementary DNAs, forming duplexes from both the Cγ side and the tert ‐amide side while sharing a common PNA backbone. In addition, the ternary DNA1/Cγ(S/R)‐bm‐PNA/DNA2 complexes exhibited higher thermal stability when compared to their respective isolated duplexes.…”

“…In addition, the ternary DNA1/Cγ(S/R)‐bm‐PNA/DNA2 complexes exhibited higher thermal stability when compared to their respective isolated duplexes. [ 60 ] Cγ bimodal PNAs are the first examples of PNA analogs that can form DNA1/PNA/DNA2 double duplexes via natural nucleobase recognition, and has the advantage of providing bifacial recognition without the need of preparing synthetically challenging bifacial nucleobases. Later, as a proof of concept, the same group went on to design a different bimodal PNA, bm‐Cα‐PNA (Figure 6), with very similar properties, yet restricted to homothymine and homocytosine sequences.…”

A simple fluorescent assay for the detection of peptide nucleic acid‐directed double strand duplex invasion

“…[ 9,10 ] However, general sequence recognition of the double‐stranded DNA via strand invasion by unmodified PNA (Figure 1) is limited. [ 11 ] Invasion of double‐stranded DNA can be achieved, for instance, by PNAs that contain modified nucleobases, [ 12–15 ] modification of the peptide backbone, [ 16–18 ] or by conjugation. [ 15,19 ] The most studied double strand invasion of duplex DNA involves pseudo‐complementary PNA (pcPNA), Figure 2, which remains of current interest.…”