Native characterization of nucleic acid motif thermodynamics via non-covalent catalysis

Nature Communications
Chunyan WangDavid Yu Zhang

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.

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Citations

Oct 6, 2016·Journal of the American Chemical Society·Xiaolong YangFeng Li
Aug 2, 2019·Reports on Progress in Physics·Bortolo Matteo MognettiLorenzo Di Michele
Apr 28, 2020·Nucleic Acids Research·Yan Helen YanLucia R Wu
Jun 17, 2020·Nucleic Acids Research·Jin H BaeDavid Yu Zhang
Oct 11, 2016·Soft Matter·Stephan Jan BachmannBortolo Matteo Mognetti
Jul 27, 2021·Nucleic Acids Research·Jin H Bae, David Yu Zhang
Aug 19, 2021·Journal of the American Chemical Society·Guan Alex WangFeng Li
Oct 15, 2019·The Journal of Physical Chemistry Letters·Shiyan XiaoDavid J Wales

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fluorescence imaging

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