Xford, UK. Email: [email protected] reports (2013) 14, 581?82; published online 14 June 2013; doi:ten.1038/embor.2013.?013 EUROPEAN MOLECULAR BIOLOGY ORGANIZATION
NIH Public AccessAuthor ManuscriptJ Am Chem Soc. Author manuscript; out there in PMC 2014 April 17.Published in final edited type as: J Am Chem Soc. 2013 April 17; 135(15): . doi:10.1021/ja400965n.NIH-PA Author Manuscript NIH-PA Author Manuscript NIH-PA Author ManuscriptQuantifying Functional Group Interactions that Decide Urea Effects on Nucleic Acid Helix FormationEmily J. Guinn,*, Jeffrey J. Schwinefus#,*, Hyo Keun Cha?*, Joseph L. McDevitt#, Wolf E. Merker#, Ryan Ritzer#, Gregory W. Muth#, Samuel W. Engelsgjerd#, Kathryn E. Mangold#, Perry J. Thompson#, Michael J. Kerins? and Thomas Record Jr,?Department of Chemistry, University of Wisconsin-Madison, Madison, WIepartment #Departmentof Biochemistry, University of Wisconsin-Madison, Madison, WI 53706 of Chemistry, St. Olaf College, Northfield, MNJeffrey J. Schwinefus: [email protected]; Thomas Record: [email protected] destabilizes helical and folded conformations of nucleic acids and proteins, too as protein-nucleic acid complexes.1S,2S-DHAC-Phenyl Trost Ligand web To know these effects, extend preceding characterizations of interactions of urea with protein functional groups, and thereby develop urea as a probe of conformational modifications in protein and nucleic acid processes, we get chemical potential derivatives (23 = d2/dm3) quantifying interactions of urea (element 3) with nucleic acid bases, base analogs, nucleosides and nucleotide monophosphates (element two) applying osmometry and hexanol-water distribution assays. Dissection of those 23 yields interaction potentials quantifying interactions of urea with unit surface places of nucleic acid functional groups (heterocyclic aromatic ring, ring methyl, carbonyl and phosphate O, amino N, sugar (C,O)); urea interacts favorably with all these groups, relative to interactions with water.3-Bromo-6-fluoropicolinic acid In stock 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.PMID:33724908 Urea m-values determined for double helix formation by DNA dodecamers close to 25 are within the variety 0.72 to 0.85 kcal mol-1 m-1 and exhibit small systematic dependence on nucleobase composition (17?2 GC). Interpretation of those final results working with the urea interaction potentials indicates that comprehensive (60?0 ) stacking of nucleobases in the separated strands within the transition region is necessary to explain the m-value. Results for RNA and DNA dodecamers obtained at greater temperatures, and literature information, are constant with this conclusion. This demonstrates the utility of urea as a quantitative probe of adjustments in surface region (ASA) in nucleic acid processes.*Co-first authors Supporting Facts Accessible Information of materials utilised, 5′-NMP VPO sample preparation, assumptions in determining 23/RT from KDWH values, determining molal scale KDWH values, distribution assay information evaluation, figuring out urea in the hexanol phase, controls for the distribution assay, DNA and RNA dodecamer sample preparation, reanalysis of Guinn et al4 information, urea-aliphatic C interactions, determining interactions of urea with triton micelles, molecular dynamics simulations of 5′-NMPs, figuring out the impact of urea around the salt dependence of melting, the temperature dependence of m-values vs m-values/RT. Tables containin.
