Comparative Incorporation of PNA into DNA Nanostructures

Abstract

DNA has shown great promise as a building material for self-assembling nanoscale structures. To further develop the potential of this technology, more methods are needed for functionalizing DNA-based nanostructures to increase their chemical diversity. Peptide nucleic acid (PNA) holds great promise for realizing this goal, as it conveniently allows for inclusion of both amino acids and peptides in nucleic acid-based structures. In this work, we explored incorporation of a positively charged PNA within DNA nanostructures. We investigated the efficiency of annealing a lysine-containing PNA probe with complementary, single-stranded DNA sequences within nanostructures, as well as the efficiency of duplex invasion and its dependence on salt concentration. Our results show that PNA allows for toehold-free strand displacement and that incorporation yield depends critically on binding site geometry. These results provide guidance for the design of PNA binding sites on nucleic acid nanostructures with an eye towards optimizing fabrication yield.

Rationally Designed DNA Nanostructures for Drug Delivery

“…Chemical modification of the backbone can drastically enhance its biological stability by hindering the attack of nuclease. These backbone-modified nuclei acids containing unnatural components can be called synthetic nucleic acid polymers, which includes xeno-nucleic acids (XNA), peptide nucleic acids (PNA), locked nucleic acids (LNA), threose nucleic acids (TNA), and phosphorothioate DNA (Figure 2A) (Burns et al, 2013;Pedersen et al, 2015). These hybrid nanostructures function no less efficiently than their natural analog counterparts.…”

Nanostructures from Synthetic Genetic Polymers

“…[39] However, de novo design in the absence of detailed knowledge on XNA structural and conformational parameters is challenging. Hybrid nanostructures based on DNA designs have previously been demonstrated to retain overall architecture, despite invasion by strands composed of, inter alia, peptiden ucleic acids (PNA) [41][42][43] or phosphorothioate DNA (PS-DNA). [32] Furthermore, af unctional Phi29 DNA-packing motor can be assembled with partial substitution of RNA components with 2'-fluro-2'-deoxy-ribofuranose nucleic acid (2'F-RNA).…”

Chemistries for DNA Nanotechnology

“…229 The high stability of PNA−DNA complexes was shown to significantly improve incorporation of PNA compared to DNA into the center of rectangular DNA origami. 230 Besides improving incorporation and adding stability to structures, the stronger binding of PNA to DNA also allows for invasion of DNA−DNA duplexes without the need for toeholds. 220,231,232 This is mainly possible at low cation concentrations where the DNA−DNA duplex is less stabilized as demonstrated by a DNA−DNA duplex invasion using a DNA origami structure that switched from a closed to an open conformation upon sequence-specific PNA invasion.…”