title: Separation of preferential interaction and excluded volume effects on DNA duplex and hairpin stability.
abstract: Small solutes affect protein and nucleic acid processes because of favorable or unfavorable chemical interactions of the solute with the biopolymer surface exposed or buried in the process. Large solutes also exclude volume and affect processes where biopolymer molecularity and/or shape changes. Here, we develop an analysis to separate and interpret or predict excluded volume and chemical effects of a flexible coil polymer on a process. We report a study of the concentration-dependent effects of the full series from monomeric to polymeric PEG on intramolecular hairpin and intermolecular duplex formation by 12-nucleotide DNA strands. We find that chemical effects of PEG on these processes increase in proportion to the product of the amount of DNA surface exposed on melting and the amount of PEG surface that is accessible to this DNA, and these effects are completely described by two interaction terms that quantify the interactions between this DNA surface and PEG end and interior groups. We find that excluded volume effects, once separated from these chemical effects, are quantitatively described by the analytical theory of Hermans, which predicts the excluded volume between a flexible polymer and a rigid molecule. From this analysis, we show that at constant concentration of PEG monomer, increasing PEG size increases the excluded volume effect but decreases the chemical interaction effect, because in a large PEG coil a smaller fraction of the monomers are accessible to the DNA. Volume exclusion by PEG has a much larger effect on intermolecular duplex formation than on intramolecular hairpin formation.
authors: Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53705, USA.
authors: D B
authors: DB
authors: Knowles
authors: Andrew S
authors: AS
authors: LaCroix
authors: Nickolas F
authors: NF
authors: Deines
authors: Irina
authors: I
authors: Shkel
authors: M Thomas
authors: MT
authors: Record
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D004305:Dose-Response Relationship, Drug; D019855:Ethylene Glycol / Q000737:chemistry / Q000494:pharmacology; D005026:Ethylene Glycols / Q000737:chemistry / Q000494:pharmacology; D007700:Kinetics; D008956:Models, Chemical; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation / Q000187:drug effects; D011092:Polyethylene Glycols / Q000737:chemistry / Q000494:pharmacology; D011108:Polymers / Q000737:chemistry / Q000494:pharmacology; D011189:Potassium Chloride / Q000737:chemistry / Q000494:pharmacology; D013499:Surface Properties; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D005026:Ethylene Glycols; D011108:Polymers; D014867:Water; C028914:triethylene glycol; D011092:Polyethylene Glycols; C013484:diethylene glycol; D011189:Potassium Chloride; D004247:DNA; D019855:Ethylene Glycol