Jump to main content
Jump to site search
PLANNED MAINTENANCE Close the message box

Scheduled maintenance work on Wednesday 27th March 2019 from 11:00 AM to 1:00 PM (GMT).

During this time our website performance may be temporarily affected. We apologise for any inconvenience this might cause and thank you for your patience.

Issue 11, 2012
Previous Article Next Article

Atomic force microscopy of arrays of asymmetrical DNA motifs

Author affiliations


DNA can easily be assembled into wide and relatively flat nanostructures that lend themselves to study viaAtomic Force Microscopy (AFM). It is often important to know which side of an assembly the AFM is imaging. This is particularly crucial for characterizing nanomachines, where the movement must be measured relative to fiducial features visible to the AFM. We have developed a cheap and simple technique for building DNA arrays with distinguishable sides, a technique requiring 10 or fewer strands – dozens or hundreds of strands fewer than used for these purposes previously. Our approach involves constructing arrays out of DNA tiles that have low apparent symmetry when imaged viaAFM. We have surveyed the effects of varying degrees of motif asymmetry in AFM micrographs. Even at resolutions where the individual tiles cannot be resolved (either because of sub-optimal tip quality, or very gentle tapping by the AFM tip) the larger scale features of the arrays have predictable structures that allow the determination of which side of the array is facing up. We have used this information to verify that DNA hairpins attached to either the up- or down-facing side of an array on mica can be detected in AFM height scans. We have also characterized differences in appearance between hairpins attached to different sides of the arrays.

Graphical abstract: Atomic force microscopy of arrays of asymmetrical DNA motifs

Back to tab navigation

Publication details

The article was received on 17 Nov 2011, accepted on 12 Jan 2012 and first published on 02 Feb 2012

Article type: Paper
DOI: 10.1039/C2SM07205J
Citation: Soft Matter, 2012,8, 3094-3104

  •   Request permissions

    Atomic force microscopy of arrays of asymmetrical DNA motifs

    T. K. Mudalige and W. B. Sherman, Soft Matter, 2012, 8, 3094
    DOI: 10.1039/C2SM07205J

Search articles by author