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

Nucleic Acids Res. 2013 Apr;41(8):4729-39. doi: 10.1093/nar/gkt121. Epub 2013 Feb 26.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA / chemical synthesis
  • DNA / chemistry*
  • Nanostructures / chemistry*
  • Peptide Nucleic Acids / chemical synthesis
  • Peptide Nucleic Acids / chemistry*
  • Rotaxanes / chemistry

Substances

  • Peptide Nucleic Acids
  • Rotaxanes
  • DNA