title: The effect of molecular crowding on the stability of human c-MYC promoter sequence I-motif at neutral pH.
abstract: 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.
authors.affiliation: Department of Chemistry, Mississippi State University, Mississippi State, MS 39762, USA. Elewis@chemistry.msstate.edu.
authors.forename: Jingjing
authors.initials: J
authors.lastname: Cui
authors.forename: Phillip
authors.initials: P
authors.lastname: Waltman
authors.forename: Vu H
authors.initials: VH
authors.lastname: Le
authors.forename: Edwin A
authors.initials: EA
authors.lastname: Lewis
mesh_terms: D001483:Base Sequence; D002152:Calorimetry, Differential Scanning; D002942:Circular Dichroism; D004247:DNA / Q000737:chemistry / Q000235:genetics; D006801:Humans; D006863:Hydrogen-Ion Concentration; D009690:Nucleic Acid Conformation; D011092:Polyethylene Glycols / Q000737:chemistry; D011401:Promoter Regions, Genetic; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics*; D012996:Solutions; D044366:Transition Temperature
chemical_list: C489427:MYC protein, human; D016271:Proto-Oncogene Proteins c-myc; D012996:Solutions; D011092:Polyethylene Glycols; D004247:DNA