Dec 20, 2013
Short DNA molecules reveal ion patches
The ion exchange properties of the surface structure of mica have been known for many years, but it is difficult to determine how ions are spatially distributed on the nanoscale in this material. A team at Leeds University in the UK has now employed atomic force microscopy (AFM) to image how different length fragments of double-stranded DNA bind to mica ion-exchanged with nickel. The researchers used polymer chain statistics to quantify whether the DNA was in one of two conformations as determined by the binding mechanisms. Long fragments on nickel-mica behaved as expected but shorter ones (below 800 base pairs) behaved in a way that shows that nickel ions are distributed on the mica on characteristic length scales of around 100 nm.
Mica is a naturally abundant crystal and its layered structure means that it is strongly insulating. Mica consists of 1 nm thick layers of silicate ionically bonded by a group I cation (usually K+). Cleaving open a fresh surface requires that half the K+ ions stay on one surface and half on the other. These ions can be exchanged with other ions by immersing the surface in salt solutions but exchange times can last hours and it is difficult to see how the ions are distributed. This is because surface science techniques such as X-ray photoelectron spectroscopy (XPS), secondary ion mass spectroscopy (SIMS), low-energy electron diffraction (LEED) and Auger electron spectroscopy (AES) in their standard formats typically lack adequate spatial resolution and surface sensitivity.
Freshly cleaved mica is a commonly used support surface for imaging biological molecules because it provides an atomically flat uncontaminated surface. To bind DNA strongly, the surface exchanges with divalent cations, in this case, nickel ions. While imaging DNA under aqueous solutions, we noticed that sections of the DNA were still moving, which should not be the case if the DNA molecules were strongly bound to the nickel. This observation led us to carry out the detailed study described in this work using a range of DNA fragment lengths from 200 base pairs long upwards and quantify how ions are distributed along different distances on the mica. Our findings might be used to improve how DNA binds to inroganic surfaces in general with a view to patterning high-density arrays.
More information about the research can be found in the journal Nanotechnology 25 025704.
About the author
Daniel Billingsley, PhD, is a recent graduate funded on an EPSRC doctoral training centre at the physical-life science interface. He acquired the majority of the data and performed the quantitative analysis of the polymer chain statistics.
Andrew Lee is a PhD student on a current EPSRC funded centre for Doctoral Training in Molecular Scale Engineering. He carried out the kinetic study on the nickel ion exchange.
August Johansson and Leigh Stanger were final-year undergraduate project students who made independent AFM measurements to verify the length dependent behaviour of DNA.
Alex Walton carried out the XPS experiments and is currently a postdoc at the iNano centre in Aarhus, Denmark.
Neil Thomson is a reader in Biological Physics and Bionanotechnology, Molecular and Nanoscale Physics Group, School of Physics and Astronomy at Leeds University.