title: Effect of molecular crowding and ionic strength on the isothermal hybridization of oligonucleotides.
abstract: The isothermal hybridization of complementary oligonucleotides, 15-mer, 25-mer, 35-mer, and a molecular beacon, was investigated under varying conditions of molecular crowding and ionic strength, using hypochromicity to follow strand pairing and polyethylene glycol as a crowding agent. Thermodynamic analysis of the results revealed the addition of counterions to the oligonucleotide backbones, DeltaPsi, to be dependent on the strand GC content and the molecular crowding. A decrease in DeltaPsi was observed, with both increasing GC% and solution PEG content. In contrast, the number of bound water molecules depended on the activity of Na(+), where two regimes were observed. At a(Na(+)) < 0.05 and increasing molecular crowding, water molecules were released into the DNA solutions, and oligonucleotide pairing was favored with both increasing hydrophobic forces, whereas at a(Na(+)) >or= 0.05, water molecules were bound to the strands, and the extent of double strand formation decreased with increasing PEG wt %.
authors.affiliation: Department of Chemistry and Biochemistry, The Florida State University, Tallahassee, Florida 32306, USA.
authors.forename: Marie Z
authors.initials: MZ
authors.lastname: Markarian
authors.forename: Joseph B
authors.initials: JB
authors.lastname: Schlenoff
mesh_terms: D004247:DNA / Q000737:chemistry*; D009841:Oligonucleotides / Q000737:chemistry*; D009994:Osmolar Concentration; D011092:Polyethylene Glycols / Q000737:chemistry; D012996:Solutions / Q000737:chemistry*; D012997:Solvents / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides; D012996:Solutions; D012997:Solvents; D011092:Polyethylene Glycols; D004247:DNA