The effect of molecular crowding on the stability of human c-MYC promoter sequence I-motif at neutral pH

Molecules. 2013 Oct 15;18(10):12751-67. doi: 10.3390/molecules181012751.


We have previously shown that c-MYC promoter sequences can form stable i-motifs in acidic solution (pH 4.5-5.5). In terms of drug targeting, the question is whether c-MYC promoter sequence i-motifs will exist in the nucleus at neutral pH. In this work, we have investigated the stability of a mutant c-MYC i-motif in solutions containing a molecular crowding agent. The crowded nuclear environment was modeled by the addition of up to 40% w/w polyethylene glycols having molecular weights up to 12,000 g/mol. CD and DSC were used to establish the presence and stability of c-MYC i-motifs in buffer solutions over the pH range 4 to 7. We have shown that the c-MYC i-motif can exist as a stable structure at pH values as high as 6.7 in crowded solutions. Generic dielectric constant effects, e.g., a shift in the pKa of cytosine by more than 2 units (e.g., 4.8 to 7.0), or the formation of non-specific PEG/DNA complexes appear to contribute insignificantly to i-motif stabilization. Molecular crowding, largely an excluded volume effect of added PEG, having a molecular weight in excess of 1,000 g/mol, appears to be responsible for stabilizing the more compact i-motif over the random coil at higher pH values.

MeSH terms

  • Base Sequence
  • Calorimetry, Differential Scanning
  • Circular Dichroism
  • DNA / chemistry
  • DNA / genetics
  • Humans
  • Hydrogen-Ion Concentration
  • Nucleic Acid Conformation
  • Polyethylene Glycols / chemistry
  • Promoter Regions, Genetic*
  • Proto-Oncogene Proteins c-myc / genetics*
  • Solutions
  • Transition Temperature


  • MYC protein, human
  • Proto-Oncogene Proteins c-myc
  • Solutions
  • Polyethylene Glycols
  • DNA