Motor-like DNA motion due to an ATP-hydrolyzing protein under nanoconfinement

Sci Rep. 2018 Jul 3;8(1):10036. doi: 10.1038/s41598-018-28278-0.

Abstract

We report that long double-stranded DNA confined to quasi-1D nanochannels undergoes superdiffusive motion under the action of the enzyme T4 DNA ligase in the presence of necessary co-factors. Inside the confined environment of the nanochannel, double-stranded DNA molecules stretch out due to self-avoiding interactions. In absence of a catalytically active enzyme, we see classical diffusion of the center of mass. However, cooperative interactions of proteins with the DNA can lead to directed motion of DNA molecules inside the nanochannel. Here we show directed motion in this configuration for three different proteins (T4 DNA ligase, MutS, E. coli DNA ligase) in the presence of their energetic co-factors (ATP, NAD+).

Publication types

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

MeSH terms

  • Adenosine Triphosphate / metabolism
  • DNA / metabolism*
  • DNA Ligases / metabolism*
  • DNA Ligases / physiology
  • DNA-Binding Proteins / genetics
  • Diffusion
  • Escherichia coli / genetics
  • Escherichia coli / metabolism
  • Escherichia coli Proteins / metabolism*
  • Escherichia coli Proteins / physiology
  • Motion
  • MutS DNA Mismatch-Binding Protein / metabolism*
  • MutS DNA Mismatch-Binding Protein / physiology
  • NAD / metabolism

Substances

  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • NAD
  • Adenosine Triphosphate
  • DNA
  • MutS DNA Mismatch-Binding Protein
  • MutS protein, E coli
  • DNA Ligases