Characterization of the structural and protein recognition properties of hybrid PNA-DNA four-way junctions

Arch Biochem Biophys. 2015 Dec 1:587:1-11. doi: 10.1016/j.abb.2015.08.017. Epub 2015 Sep 5.

Abstract

The objective of this study is to evaluate the structure and protein recognition properties of hybrid four-way junctions (4WJs) composed of DNA and peptide nucleic acid (PNA) strands. We compare a classic immobile DNA junction, J1, vs. six PNA-DNA junctions, including a number with blunt DNA ends and multiple PNA strands. Circular dichroism (CD) analysis reveals that hybrid 4WJs are composed of helices that possess structures intermediate between A- and B-form DNA, the apparent level of A-form structure correlates with the PNA content. The structure of hybrids that contain one PNA strand is sensitive to Mg(+2). For these constructs, the apparent B-form structure and conformational stability (Tm) increase in high Mg(+2). The blunt-ended junction, b4WJ-PNA3, possesses the highest B-form CD signals and Tm (40.1 °C) values vs. all hybrids and J1. Protein recognition studies are carried out using the recombinant DNA-binding protein, HMGB1b. HMGB1b binds the blunt ended single-PNA hybrids, b4WJ-PNA1 and b4WJ-PNA3, with high affinity. HMGB1b binds the multi-PNA hybrids, 4WJ-PNA1,3 and b4WJ-PNA1,3, but does not form stable protein-nucleic acid complexes. Protein interactions with hybrid 4WJs are influenced by the ratio of A- to B-form helices: hybrids with helices composed of higher levels of B-form structure preferentially associate with HMGB1b.

Keywords: A-DNA helices; B-DNA helices; Four-way junctions; High mobility group proteins (HMG); Peptide nucleic acids (PNAs).

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • DNA, A-Form / chemistry*
  • DNA, A-Form / metabolism*
  • DNA, B-Form / chemistry*
  • DNA, B-Form / metabolism*
  • HMGB1 Protein / metabolism*
  • Magnesium / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Peptide Nucleic Acids / chemistry*
  • Peptide Nucleic Acids / metabolism*
  • Protein Binding
  • Rats

Substances

  • DNA, A-Form
  • DNA, B-Form
  • HMGB1 Protein
  • Peptide Nucleic Acids
  • Magnesium