Peptide nucleic acid-dependent artifact can lead to false-positive triplex gene editing signals

Proc Natl Acad Sci U S A. 2021 Nov 9;118(45):e2109175118. doi: 10.1073/pnas.2109175118.


Triplex gene editing relies on binding a stable peptide nucleic acid (PNA) sequence to a chromosomal target, which alters the helical structure of DNA to stimulate site-specific recombination with a single-strand DNA (ssDNA) donor template and elicits gene correction. Here, we assessed whether the codelivery of PNA and donor template encapsulated in Poly Lactic-co-Glycolic Acid (PLGA)-based nanoparticles can correct sickle cell disease and x-linked severe combined immunodeficiency. However, through this process we have identified a false-positive PCR artifact due to the intrinsic capability of PNAs to aggregate with ssDNA donor templates. Here, we show that the combination of PNA and donor templates but not either agent alone results in different degrees of aggregation that result in varying but highly reproducible levels of false-positive signal. We have identified this phenomenon in vitro and confirmed that the PNA sequences producing the highest supposed correction in vitro are not active in vivo in both disease models, which highlights the importance of interrogating and eliminating carryover of ssDNA donor templates in assessing various gene editing technologies such as PNA-mediated gene editing.

Keywords: DNA repair; gene editing; hematopoietic stem cell; peptide nucleic acid.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural

MeSH terms

  • Anemia, Sickle Cell / genetics
  • Animals
  • False Positive Reactions
  • Gene Editing / methods*
  • Interleukin Receptor Common gamma Subunit / genetics
  • Mice
  • Mice, SCID
  • Molecular Probe Techniques
  • Peptide Nucleic Acids
  • Polylactic Acid-Polyglycolic Acid Copolymer


  • IL2RG protein, human
  • Interleukin Receptor Common gamma Subunit
  • Peptide Nucleic Acids
  • Polylactic Acid-Polyglycolic Acid Copolymer