Article

Submicrometre geometrically encoded fluorescent barcodes self-assembled from DNA

1] Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
Nature Chemistry (Impact Factor: 21.76). 10/2012; 4(10):832-839. DOI: 10.1038/nchem.1451

ABSTRACT The identification and differentiation of a large number of distinct
molecular species with high temporal and spatial resolution is a major
challenge in biomedical science. Fluorescence microscopy is a powerful
tool, but its multiplexing ability is limited by the number of
spectrally distinguishable fluorophores. Here, we used
(deoxy)ribonucleic acid (DNA)-origami technology to construct
submicrometre nanorods that act as fluorescent barcodes. We demonstrate
that spatial control over the positioning of fluorophores on the surface
of a stiff DNA nanorod can produce 216 distinct barcodes that can be
decoded unambiguously using epifluorescence or total internal reflection
fluorescence microscopy. Barcodes with higher spatial information
density were demonstrated via the construction of super-resolution
barcodes with features spaced by ˜40 nm. One species of the
barcodes was used to tag yeast surface receptors, which suggests their
potential applications as in situ imaging probes for diverse
biomolecular and cellular entities in their native environments.

1 Bookmark
 · 
48 Views
  • [Show abstract] [Hide abstract]
    ABSTRACT: With the advent of deoxyribonucleic acid (DNA) nanotechnology, the Y-shaped DNA nanostructure (Y-DNA) as a basic block was first created. Due to their characteristic selectivity and specificity, Y-DNA-based materials have been utilized in a variety of scientific fields including multiplexed nanobarcoding. Basically, the tripod DNA nanostructure was prepared by simple hybridization of three different single stranded DNA (ssDNA). Before the synthetic process, the optical densities (OD) of the three ssDNAs were measured to accurately estimate the concentration. Through repeated temperature fluctuations, three ssDNAs were hybridized into a Y-shaped block with both a central junction and three blunt ended arms. After the reaction, the ODs of the synthesized DNA products were measured and compared with the theoretical OD values calculated by a MATLAB program (‘matrix laboratory’) with different molar concentrations and volumes to predict the presence of Y-DNA. Simultaneously, the product was analyzed by agarose gel electrophoresis to confirm the YDNA structure. The measured ODs of the solutions with confirmed Y-DNA structures were close to the theoretical maximum OD values. This article provides means to help understand and prepare Y-DNA by performing OD measurements. It is highly expected that this guide will be an excellent starting point for structural DNA nanotechnology.
    Biotechnology and Bioprocess Engineering 03/2014; 19(2):262-268. DOI:10.1007/s12257-013-0626-4 · 1.22 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: Toxicology is the highly interdisciplinary field studying the adverse effects of chemicals on living organisms. It requires sensitive tools to detect such effects. After their initial implementation during the 1990s, single-molecule fluorescence detection tools were quickly recognized for their potential to contribute greatly to many different areas of scientific inquiry. In the intervening time, technical advances in the field have generated ever-improving spatial and temporal resolution and have enabled the application of single-molecule fluorescence to increasingly complex systems, such as live cells. In this review, we give an overview of the optical components necessary to implement the most common versions of single-molecule fluorescence detection. We then discuss current applications to enzymology and structural studies, systems biology, and nanotechnology, presenting the technical considerations that are unique to each area of study, along with noteworthy recent results. We also highlight future directions that have the potential to revolutionize these areas of study by further exploiting the capabilities of single-molecule fluorescence microscopy.
    Archive für Toxikologie 09/2014; 88(11). DOI:10.1007/s00204-014-1357-9 · 5.08 Impact Factor
  • [Show abstract] [Hide abstract]
    ABSTRACT: DNA nanotechnology, which uses DNA as a material to self-assemble designed nanostructures, including DNA 2D arrays, 3D nanostructures, DNA nanotubes and DNA nanomechanical devices, has showed great promise in biomedical applications. Various DNA nanostructures have been used for protein characterization, enzyme assembly, biosensing, drug delivery and biomimetic assemblies. In this review, we will present recent advances of DNA nanotechnology and its applications in biomedical research field.
    Journal of Biomedical Nanotechnology 09/2015; 10(9). DOI:10.1166/jbn.2014.1930 · 7.58 Impact Factor

Full-text (2 Sources)

Download
24 Downloads
Available from
May 26, 2014