Cooperative strand invasion of supercoiled plasmid DNA by mixed linear PNA and PNA-peptide chimeras

Karin E. Lundin, Rongbin Ge, Mathias G. Svahn, Elisabeth Törnquist, Mikael Leijon, Lars J. Brandén, C. I.Edvard Smith

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

Abstract

Peptide nucleic acid (PNA) is a DNA analog with broad biotechnical applications, and possibly also treatment applications. Its suggested uses include that of a specific anchor sequence for biologically active peptides to plasmids in a sequence-specific manner. Such complexes, referred to as Bioplex, have already been used to enhance non-viral gene transfer in vitro. To investigate how hybridization of PNAs to supercoiled plasmids would be affected by the binding of multiple PNA-peptides to the same strand of DNA, we have developed a method of quantifying the specific binding of PNA using a PNA labeled with a derivative of the fluorophore thiazole orange (TO). Cooperative effects were found at a distance of up to three bases. With a peptide present at the end of one of the PNAs, steric hindrance occurred, reducing the increase in binding rate when the distance between the two sites was less than two bases. In addition, we found increased binding kinetics when two PNAs binding to overlapping sites on opposite DNA strands were used, without the use of chemically modified bases in the PNAs.

Original languageEnglish
Pages (from-to)51-59
Number of pages9
JournalBiomolecular Engineering
Volume21
Issue number2
DOIs
StatePublished - Apr 2004

Keywords

  • Asymmetric cyanine dye
  • Mixed-base PNA
  • Peptide nucleic acids (PNA)
  • Supercoiled DNA

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