Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes

Yuhang Dong; Chi Yao; Zhi Wang; Dan Luo; Dayong Yang

doi:10.1016/j.isci.2019.10.029

Target-Triggered Polymerization of Branched DNA Enables Enzyme-free and Fast Discrimination of Single-Base Changes

iScience. 2019 Nov 22:21:228-240. doi: 10.1016/j.isci.2019.10.029. Epub 2019 Oct 18.

Authors

Yuhang Dong¹, Chi Yao¹, Zhi Wang¹, Dan Luo², Dayong Yang³

Affiliations

¹ Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China.
² Department of Biological & Environmental Engineering, Cornell University, Ithaca, NY 14853, USA; CAS Key Laboratory of Nano-Bio Interface, Suzhou Institute of Nano-Tech and Nano-Bionics, Chinese Academy of Sciences, Suzhou 215123, P. R. China.
³ Frontier Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China. Electronic address: dayong.yang@tju.edu.cn.

Abstract

Single-base changes lead to important biological and biomedical implications; however, the discrimination of single-base changes from normal DNA always remains a grand challenge. Herein we developed a DNA recognition and amplification system based on artificial branched DNA, namely, target-triggered polymerization (TTP), to realize enzyme-free and fast discrimination of single-base changes. Branched DNA as monomers rapidly polymerized into DNA nanospheres only with the trigger of specific DNA. Our TTP system worked reliably over a wide range of conditions. Remarkably, our TTP system was capable of discriminating base-changing DNA from normal DNA, including distinguishing 1-4 nucleotide changes and positions of single base, which was attributed to the significant amplification of small differences in hybridization thermodynamics and kinetics. We further proposed a theoretical method for calculating the hybridization probability of nucleic acids, which performed highly consistent with experimental results.

Keywords: Nanostructure; Nanotechnology; Thermodynamics.