Detecting Counterion Dynamics in DNA–Protein Association

Channing C. Pletka, Ridvan Nepravishta, Junji Iwahara

Research output: Contribution to journalArticle

Abstract

Due to a high density of negative charges on its surface, DNA condenses cations as counterions, forming the so-called “ion atmosphere”. Although the release of counterions upon DNA–protein association has been postulated to have a major contribution to the binding thermodynamics, this release remains to be confirmed through a direct observation of the ions. Herein, we report the characterization of the ion atmosphere around DNA using NMR spectroscopy and directly detect the release of counterions upon DNA–protein association. NMR-based diffusion data reveal the highly dynamic nature of counterions within the ion atmosphere around DNA. Counterion release is observed as an increase in the apparent ionic diffusion coefficient, which directly provides the number of counterions released upon DNA–protein association.

Original languageEnglish (US)
JournalAngewandte Chemie - International Edition
DOIs
StateAccepted/In press - Jan 1 2019

Keywords

  • DNA recognition
  • dynamics
  • ion pairs
  • NMR spectroscopy
  • protein–DNA interactions

ASJC Scopus subject areas

  • Catalysis
  • Chemistry(all)

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