Protein-induced changes in DNA structure and dynamics observed with noncovalent site-directed spin-labeling and PELDOR

Gunnar Widtfeldt Reginsson, Sandip Shelke, Christophe Rouillon, Malcolm F White, Snorri T Sigurdsson, Olav Schiemann*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

19 Citations (Scopus)

Abstract

Site-directed spin labeling and pulsed electron–electron double resonance (PELDOR or DEER) have previously been applied successfully to study the structure and dynamics of nucleic acids. Spin labeling nucleic acids at specific sites requires the covalent attachment of spin labels, which involves rather complicated and laborious chemical synthesis. Here, we use a noncovalent label strategy that bypasses the covalent labeling chemistry and show that the binding specificity and efficiency are large enough to enable PELDOR or DEER measurements in DNA duplexes and a DNA duplex bound to the Lac repressor protein. In addition, the rigidity of the label not only allows resolution of the structure and dynamics of oligonucleotides but also the determination of label orientation and protein-induced conformational changes. The results prove that this labeling strategy in combination with PELDOR has a great potential for studying both structure and dynamics of oligonucleotides and their complexes with various ligands.
Original languageEnglish
Article numbere11
Number of pages10
JournalNucleic Acids Research
Volume41
Issue number1
Early online date31 Aug 2012
DOIs
Publication statusPublished - Jan 2013

Keywords

  • Binding
  • PULSED ELECTRON
  • Nucleic-acids
  • Conformation
  • Lactose operon
  • Distance measurements
  • Operator
  • EPR spectroscopy
  • Electron-paramagnetic-resonance
  • LAC repressor

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