Single-Molecule AFM Characterization of Individual Chemically Tagged DNA Tetrahedra

Institute for Biophysics, Johannes Kepler University, A-4040 Linz, Austria.
ACS Nano (Impact Factor: 12.88). 08/2011; 5(9):7048-54. DOI: 10.1021/nn201705p
Source: PubMed


Single-molecule characterization is essential for ascertaining the structural and functional properties of bottom-up DNA nanostructures. Here we enlist three atomic force microscopy (AFM) techniques to examine tetrahedron-shaped DNA nanostructures that are functionally enhanced with small chemical tags. In line with their application for biomolecule immobilization in biosensing and biophysics, the tetrahedra feature three disulfide-modified vertices to achieve directed attachment to gold surfaces. The remaining corner carries a single bioligand that can capture and present individual cargo biomolecules at defined lateral nanoscale spacing. High-resolution AFM topographic imaging confirmed the directional surface attachment as well as the highly effective binding of individual receptor molecules to the exposed bioligands. Insight into the binding behavior at the single-molecule level was gained using molecular recognition force spectroscopy using an AFM cantilever tip with a tethered molecular receptor. Finally, simultaneous topographic and recognition imaging demonstrated the specific receptor-ligand interactions on individual tetrahedra. In summary, AFM characterization verified that the rationally designed DNA nanostructures feature characteristics to serve as valuable immobilization agents in biosensing, biophysics, and cell biology.

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    • "Through chemical modification of the 5' end of each DNA strand, they were able to append a disulfide molecule on each of three vertices, with either a biotin or Cy3 dye on the fourth (Scheme 1a ii).The three disulfide tags permitted strong adhesion to gold surfaces (Scheme 1a iii).A kinetic dissociation experiment determined that only 5% of triple-tagged tetrahedra were displaced after 2 hours, whereas 50% of doubly-tagged and 90% of singly-tagged tetrahedra were lost.AFM experiments with the biotin functionalized molecule confirmed that the fourth vertex was vertically oriented and remained accessible for complexation with streptavidin.[10] [11]. "
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