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Sci Adv. 2017 Jan 20;3(1):e1601600. doi: 10.1126/sciadv.1601600. eCollection 2017 Jan.

Visible/near-infrared subdiffraction imaging reveals the stochastic nature of DNA walkers.

Author information

1
School of Mechanical Engineering, Purdue University, West Lafayette, IN 47907, USA.

Abstract

DNA walkers are designed with the structural specificity and functional diversity of oligonucleotides to actively convert chemical energy into mechanical translocation. Compared to natural protein motors, DNA walkers' small translocation distance (mostly <100 nm) and slow reaction rate (<0.1 nm s-1) make single-molecule characterization of their kinetics elusive. An important indication of single-walker kinetics is the rate-limiting reactions that a particular walker design bears. We introduce an integrated super-resolved fluorescence microscopy approach that is capable of long-term imaging to investigate the stochastic behavior of DNA walkers. Subdiffraction tracking and imaging in the visible and second near-infrared spectra resolve walker structure and reaction rates. The distributions of walker kinetics are analyzed using a stochastic model to reveal reaction randomness and the rate-limiting biochemical reaction steps.

KEYWORDS:

DNA nanotechnology; DNA walker; single molecule kinetics; subdiffraction imaging

PMID:
28116353
PMCID:
PMC5249260
DOI:
10.1126/sciadv.1601600
[Indexed for MEDLINE]
Free PMC Article

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