title: Quantifying functional group interactions that determine urea effects on nucleic acid helix formation.
abstract: Urea destabilizes helical and folded conformations of nucleic acids and proteins, as well as protein-nucleic acid complexes. To understand these effects, extend previous characterizations of interactions of urea with protein functional groups, and thereby develop urea as a probe of conformational changes in protein and nucleic acid processes, we obtain chemical potential derivatives (μ23 = dμ2/dm3) quantifying interactions of urea (component 3) with nucleic acid bases, base analogues, nucleosides, and nucleotide monophosphates (component 2) using osmometry and hexanol-water distribution assays. Dissection of these μ23 values yields interaction potentials quantifying interactions of urea with unit surface areas of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C and O); urea interacts favorably with all these groups, relative to interactions with water. Interactions of urea with heterocyclic aromatic rings and attached methyl groups (as on thymine) are particularly favorable, as previously observed for urea-homocyclic aromatic ring interactions. Urea m-values determined for double helix formation by DNA dodecamers near 25 °C are in the range of 0.72-0.85 kcal mol(-1)m(-1) and exhibit little systematic dependence on nucleobase composition (17-42% GC). Interpretation of these results using the urea interaction potentials indicates that extensive (60-90%) stacking of nucleobases in the separated strands in the transition region is required to explain the m-value. Results for RNA and DNA dodecamers obtained at higher temperatures, and literature data, are consistent with this conclusion. This demonstrates the utility of urea as a quantitative probe of changes in surface area (ΔASA) in nucleic acid processes.
authors.affiliation: Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.
authors.forename: Emily J
authors.initials: EJ
authors.lastname: Guinn
authors.forename: Jeffrey J
authors.initials: JJ
authors.lastname: Schwinefus
authors.forename: Hyo Keun
authors.initials: HK
authors.lastname: Cha
authors.forename: Joseph L
authors.initials: JL
authors.lastname: McDevitt
authors.forename: Wolf E
authors.initials: WE
authors.lastname: Merker
authors.forename: Ryan
authors.initials: R
authors.lastname: Ritzer
authors.forename: Gregory W
authors.initials: GW
authors.lastname: Muth
authors.forename: Samuel W
authors.initials: SW
authors.lastname: Engelsgjerd
authors.forename: Kathryn E
authors.initials: KE
authors.lastname: Mangold
authors.forename: Perry J
authors.initials: PJ
authors.lastname: Thompson
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Kerins
authors.forename: M Thomas
authors.initials: MT
authors.lastname: Record
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation / Q000187:drug effects*; D009691:Nucleic Acid Denaturation; D012313:RNA / Q000737:chemistry* / Q000235:genetics; D013816:Thermodynamics; D044366:Transition Temperature; D014508:Urea / Q000494:pharmacology*; D014835:Volatilization
chemical_list: D012313:RNA; D014508:Urea; D004247:DNA