Escherichia coli single-stranded DNA-binding protein: nanoESI-MS studies of salt-modulated subunit exchange and DNA binding transactions

J Am Soc Mass Spectrom. 2013 Feb;24(2):274-85. doi: 10.1007/s13361-012-0552-2. Epub 2013 Jan 3.

Abstract

Single-stranded DNA-binding proteins (SSBs) are ubiquitous oligomeric proteins that bind with very high affinity to single-stranded DNA and have a variety of essential roles in DNA metabolism. Nanoelectrospray ionization mass spectrometry (nanoESI-MS) was used to monitor subunit exchange in full-length and truncated forms of the homotetrameric SSB from Escherichia coli. Subunit exchange in the native protein was found to occur slowly over a period of hours, but was significantly more rapid in a truncated variant of SSB from which the eight C-terminal residues were deleted. This effect is proposed to result from C-terminus mediated stabilization of the SSB tetramer, in which the C-termini interact with the DNA-binding cores of adjacent subunits. NanoESI-MS was also used to examine DNA binding to the SSB tetramer. Binding of single-stranded oligonucleotides [one molecule of (dT)(70), one molecule of (dT)(35), or two molecules of (dT)(35)] was found to prevent SSB subunit exchange. Transfer of SSB tetramers between discrete oligonucleotides was also observed and is consistent with predictions from solution-phase studies, suggesting that SSB-DNA complexes can be reliably analyzed by ESI mass spectrometry.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA, Single-Stranded / chemistry*
  • DNA, Single-Stranded / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Escherichia coli Proteins / chemistry*
  • Escherichia coli Proteins / metabolism
  • Models, Molecular
  • Nanotechnology
  • Oligonucleotides / chemistry
  • Oligonucleotides / metabolism
  • Protein Binding
  • Protein Subunits / chemistry
  • Protein Subunits / metabolism
  • Sodium Acetate / chemistry*
  • Spectrometry, Mass, Electrospray Ionization / methods*

Substances

  • DNA, Single-Stranded
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • Oligonucleotides
  • Protein Subunits
  • Sodium Acetate