Abstract
In eukaryotes, a first step towards the nuclear DNA compaction process is the formation of a nucleosome, which is comprised of negatively charged DNA wrapped around a positively charged histone protein octamer. Often, it is assumed that the complexation of the DNA into the nucleosome completely attenuates the DNA charge and hence the electrostatic field generated by the molecule. In contrast, theoretical and computational studies suggest that the nucleosome retains a strong, negative electrostatic field. Despite their fundamental implications for chromatin organization and function, these opposing views of nucleosome electrostatics have not been experimentally tested. Herein, we directly measure nucleosome electrostatics and find that while nucleosome formation reduces the complex charge by half, the nucleosome nevertheless maintains a strong negative electrostatic field. Our studies highlight the importance of considering the polyelectrolyte nature of the nucleosome and its impact on processes ranging from factor binding to DNA compaction.
Highlights
The eukaryotic nuclear DNA forms a highly compact and organized structure referred to as chromatin
Polyelectrolytes are surrounded by ions that fully counterbalance their charge, but Poisson Boltzmann (PB) electrostatic theory predicts that this charge balance is achieved differently for molecules of low vs. high charge density, (Figure 1D and E) (Anderson and Record, 1980)
Ion counting reveals that nucleosomes generate a strong negative electrostatic field To determine the effect of nucleosome formation on DNA electrostatics, we experimentally measured the ions associated with free DNA and with nucleosomes by ion counting (Figure 2A) and from those values we calculated b+ and b– for Na+ and Br, respectively
Summary
The eukaryotic nuclear DNA forms a highly compact and organized structure referred to as chromatin. Molecules with high charge density and with strong electrostatic fields, like DNA, are predicted to achieve charge neutrality by preferentially attracting counterions (cations for DNA) and excluding fewer coions (anions for DNA; Figure 1D and E, right); the strong electrostatic field of high charge density molecules can counteract the thermal motions of cations and result in their condensation around the molecules and a larger number of cations than anions around the molecule (Muthukumar, 2004; Lyklema, 1995; Anderson and Record, 1980; Manning, 1977; Manning, 2002; Manning, 1969b). Because there is overall charge neutrality, the sum of the b values must be one (Equation 1c)
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