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

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.

DNA Functional Materials Assembled from Branched DNA: Design, Synthesis, and Applications

“…Dong et al developed a strategy of step-by-step amplification based on branched DNA (Figure 35C). 391 In the presence of target DNA, X-shaped DNA specifically and rapidly polymerized into DNA dendrimers without the involvement of any enzymes. By alternatively introducing two kinds of X-DNA, the frequency signals and corresponding dissipative signals presented a trend of stepwise change for enhanced detection sensitivity (Figure 35D).…”

“…Copyright 2018, Elsevier Publishing Group. (C) Cascade-amplification detection platform based on two kinds of X-DNA as signal amplifiers . (D) Frequency response curves presenting stepped decreasing when alternately introducing two kinds of X-DNA.…”

“…On the basis of one-step amplification, a strategy of multistep amplification has been developed to further improve detection performance. Dong et al developed a strategy of step-by-step amplification based on branched DNA (Figure C) . In the presence of target DNA, X-shaped DNA specifically and rapidly polymerized into DNA dendrimers without the involvement of any enzymes.…”

Construction of Branched DNA‐based Nanostructures for Diagnosis, Therapeutics and Protein Engineering

“…In addition, the length of the branching arm can be adjusted as required to control the size of branched DNA monomer. The expansion area can be flexibly designed as a functional motif, which is conducive to subsequent high-graded assembly or application [11] . These characteristics fully reflect the sequence designability, structure controllability and functional customizability of branched DNA monomer.…”

“…A kind of branched DNA-based nanosphere was designed and synthesized to distinguish the sites of base mutation and the number of mutated bases (Figure 6a). The strategy of target-triggered polymerization was introduced into the formation of DNA nanosphere, which facilitated the signal amplification of target molecule, and effectively improved the specificity and sensitivity of signal detection [11] . Branched DNA as a basic construction unit could polymerize into DNA nanosphere only under the trigger of specific target DNA, while remained an isolated state in the absence of target DNA.…”