title: Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis.
abstract: DNA hybridization thermodynamics is critical for accurate design of oligonucleotides for biotechnology and nanotechnology applications, but parameters currently in use are inaccurately extrapolated based on limited quantitative understanding of thermal behaviours. Here, we present a method to measure the ΔG° of DNA motifs at temperatures and buffer conditions of interest, with significantly better accuracy (6- to 14-fold lower s.e.) than prior methods. The equilibrium constant of a reaction with thermodynamics closely approximating that of a desired motif is numerically calculated from directly observed reactant and product equilibrium concentrations; a DNA catalyst is designed to accelerate equilibration. We measured the ΔG° of terminal fluorophores, single-nucleotide dangles and multinucleotide dangles, in temperatures ranging from 10 to 45 °C.
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas 77030, USA.
authors.forename: Chunyan
authors.initials: C
authors.lastname: Wang
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas 77030, USA.
authors.forename: Jin H
authors.initials: JH
authors.lastname: Bae
authors.affiliation: Department of Bioengineering, Rice University, Houston, Texas 77030, USA.|Systems, Synthetic, and Physical Biology, Rice University, Houston, Texas 77030, USA.
authors.forename: David Yu
authors.identifier: http://orcid.org/0000-0002-0213-7663
authors.initials: DY
authors.lastname: Zhang
mesh_terms: D002384:Catalysis; D009690:Nucleic Acid Conformation; D009841:Oligonucleotides / Q000737:chemistry*; D013696:Temperature; D013816:Thermodynamics
chemical_list: D009841:Oligonucleotides