DYNAMICS OF ADSORBED DNA
a nanoscale view
My group and I are using nanoscale techniques in combination with environmental samples to unravel the DNA-mineral affinities at different environmental settings. Our main approach is atomic force microscopy. With my Young Investigator Funding provided by the VILLUM FOUNDATION I have been fortunate to purchase the instrument of my dreams: The Cypher VRS atomic force microscope
Atomic force microscopy
We use atomic force microscopy (AFM) to study the associations between a surface and single DNA molecules. We do imaging in liquid to study adsorption dynamics dynamics and chemical force microscopy or dynamic force spectroscopy to study interactions strengths or to quantify binding parameters.
DNA adsorbed to steps
Following the Villum Young Investigator funding (2019-23023) I have been able to take on a range of projects where we exploit our view into the nanoscale to understand which minerals offer DNA preservation across time and space and why.
FINISHED MSCA PROJECT: DENMARK
Ioannis Kontopolos has started his postdoctoral experience in April 2020 to work on reaction kinetics of DNA-mineral associations in the environment. He was awarded a Marie Skłodowska-Curie Individual Fellowship (H2020-MSCA-IF-EF-ST) for our DENMARK project:
Environmental DNA (eDNA) is trace amounts of DNA released by organisms into water and sediments. It has recently attracted a lot of attention as it can be a valuable tool for detecting present and past organisms without the need to directly sample them. However, biotic and abiotic decay has severe effects on DNA survival. The adsorption of DNA to mineral surfaces in sediments have been shown to protect DNA molecules and decrease the DNA decay rate. Understanding which minerals and environmental conditions provide the best preservation of adsorbed DNA can thus allow us to:
a) target such environments for paleoecological and palaeogenetic studies;
b) serve as a quantitative tool for assessing DNA migration, i.e. is the recovered eDNA autochthonous?
c) significantly advance eDNA extraction and analysis protocols by targeting and extracting eDNA from specific minerals.
Ioannis approaches will include extraction techniques, atomic force microscopy, and in-situ liquid cell FTIR