Simple Single-Legged DNA Walkers at Diffusion-Limited Nano-Interfaces of Gold Nanoparticles Driven by DNA Circuit Mechanism.

07:00 EST 13th February 2020 | BioPortfolio

Summary of "Simple Single-Legged DNA Walkers at Diffusion-Limited Nano-Interfaces of Gold Nanoparticles Driven by DNA Circuit Mechanism."

We designed and prepared a single-legged DNA walker that relies on the creation of a simple diffusion limited nano-interface on a gold nanoparticle (DNA/PEG(+)-GNP) track co-modified with fluorescence-labelled hairpin DNA and poly(ethylene glycol) (PEG) containing a positively charged amino group at one end. The movement of our single-legged DNA walker is driven by an enzyme-free DNA circuit mechanism through cascading toehold mediated DNA displacement reactions (TMDRs) using fuel hairpin DNAs. The acceleration of TMDRs was observed for the DNA/PEG(+)-GNP track through electrostatic interaction between the positively charged track and negatively charged DNAs, resulting in the acceleration of the DNA circuit and amplification of the fluorescence signal. Furthermore, the DNA/PEG(+)-GNP track allowed autonomous and persistent movement of a walker DNA strand on the same GNP track, because the intraparticle DNA circuit occurred preferentially by preventing diffusion of the negatively charged free walker DNA strand from near the positively charged tracks into solution through electrostatic interaction. Based on comparative study of kinetics of TMDRs and DNA walking behaviors, it is to be noted that the DNA/PEG(+)-GNP track showed the fastest DNA circuit reaction (walking rate) and the largest number of steps taken by the walker DNA strand compared to other GNP tracks with varying nano-interfaces that differ in terms of their type of charges (non- and negative charges), density of positive charges, and number of hairpin DNAs per GNP track. These facts reveal that the positive charges on the GNP track play an important role in the acceleration of the DNA circuit, as well as the successful walking motion of the single-legged DNA strand. By using the fluorescence signal amplification functions, our single-legged DNA walker could be applied directly and successfully to enzyme-free miRNA-detection systems. The miRNA-detection system provided higher discrimination of other mismatched miRNAs, and higher sensitivity (the lowest
4.0 pM) when compared to other miRNA-detection systems based on other GNP tracks without positive charges. Unlike existing single-legged DNA walkers, our single-legged DNA walkers do not require complex processes, such as immobilization of the walker DNA strand on the tracks and precise adjustment of the sequence of walker DNA. Therefore, our strategy, based on the creation of diffusion limited nano-interfaces, has enormous potential for the applications of single-legged DNA walkers to biosensors, bioimaging, and computing.


Journal Details

This article was published in the following journal.

Name: ACS nano
ISSN: 1936-086X


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The passive movement of molecules exceeding the rate expected by simple diffusion. No energy is expended in the process. It is achieved by the introduction of passively diffusing molecules to an enviroment or path that is more favorable to the movement of those molecules. Examples of facilitated diffusion are passive transport of hydrophilic substances across a lipid membrane through hydrophilic pores that traverse the membrane, and the sliding of a DNA BINDING PROTEIN along a strand of DNA.

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Uptake of substances by the body, tissues, or cells. The uptake may occur by various forms of BIOLOGICAL TRANSPORT or by simple DIFFUSION.

The tendency of a gas or solute to pass from a point of higher pressure or concentration to a point of lower pressure or concentration and to distribute itself throughout the available space. Diffusion, especially FACILITATED DIFFUSION, is a major mechanism of BIOLOGICAL TRANSPORT.

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