Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology

Abstract

The structural reorganization of nanoscale DNA architectures is a fundamental aspect in dynamic DNA nanotechnology. Commonly, DNA nanoarchitectures are reorganized by means of toehold-expanded DNA sequences in a strand exchange process. Here we describe an unprecedented, toehold-free switching process that relies on pseudo-complementary peptide nucleic acid (pcPNA) by using a mechanism that involves double-strand invasion. The usefulness of this approach is demonstrated by application of these peptide nucleic acids (PNAs) as switches in a DNA rotaxane architecture. The monomers required for generating the pcPNA were obtained by an improved synthesis strategy and were incorporated into a PNA actuator sequence as well as into a short DNA strand that subsequently was integrated into the rotaxane architecture. Alternate addition of a DNA and PNA actuator sequence allowed the multiple reversible switching between a mobile rotaxane macrocycle and a stationary pseudorotaxane state. The switching occurs in an isothermal process at room temperature and is nearly quantitative in each switching step. pcPNAs can potentially be combined with light- and toehold-based switches, thus broadening the toolbox of orthogonal switching approaches for DNA architectures that open up new avenues in dynamic DNA nanotechnology.

Polarization Induced Electro-Functionalization of Pore Walls: A Contactless Technology

“…In order to be incorporated in the lipid bilayer, negative DNA origami should be engineered in order to carry a lipidic molecule capable of integrating it into the membrane [50]. An alternative method by engineering of non-negative DNA is applied to avoid lipid anchoring [51]. The limitation of these DNA nanopores comes from their complex anchoring to the biological lipid membrane with its inherent increased leakage and structural fluctuation of DNA nanopores compared to protein nanopores [52,53].…”

Versatility of peptide nucleic acids (PNAs): role in chemical biology, drug discovery, and origins of life

“…Pseudo‐complementary PNA actuators can be combined with both light and toehold‐based switches. Orthogonal switching approaches for DNA architectures may open up new avenues in dynamic DNA nanotechnology …”

“…Orthogonal switching approaches for DNA architectures may open up new avenues in dynamic DNA nanotechnology. [115] Notably, PNA-AuNP hybrids can be prepared without altering PNA functionality. The Au(111) surface has been widely used in biosensor applications due to strong gold-sulfur (thiol) interactions between the bifunctional linker molecules (cysteamine (thiol-amine terminated) or 1,4-benzenedithiol (thiol-thiol terminated)) and the substrate surface.…”

Incorporation of Pseudo‐complementary Bases 2,6‐Diaminopurine and 2‐Thiouracil into Serinol Nucleic Acid (SNA) to Promote SNA/RNA Hybridization

“…[26] We attempted to synthesize the SNA oligonucleotide containing a single MMPM-sU (SNA-1sU: (S)-TGCAGC MMPM sUA-(R)) using the standard phosphoramidite with the exception that the oxidation was performed using either (1S)-(+)-10-camphorsulfonyl)-oxaziridine (CSO) or t-BuOOH. [27][28] When CSO was used, analysis of the crude product obtained after incubation with 28 % aqueous ammonia by mass spectroscopy had many undesired peaks that were assignable to oxidized and desulfurized byproducts ( Figure S3a). Therefore, we changed the oxidizer to t-BuOOH for synthesis of SNA-1sU.…”

“…Therefore, we changed the oxidizer to t-BuOOH for synthesis of SNA-1sU. [27][28] After deprotection in 28 % aqueous ammonia the major peak in the mass spectrum corresponded to the sU-containing SNA oligonucleotide ( Figure S3b). Thus, t-BuOOH prevented unfavorable oxidization and desulfurization, and deprotection of the MMPM on sU was achieved during the standard aqueous ammonia treatment.…”