SECTION C
DNA nanopores are synthetic analogues of biological transmembrane protein pores, whichhave been designed for applications in single-molecule sensing and drug delivery. The behaviour of novel DNA nanostructures in the presence of lipid membranes is difficult to predict due to their high charge density and the flexibility of DNA.
Describe a protocol for simulating a large heterogeneous DNA nanopore/membrane system, and discuss the structural features of the nanopore that could be characterised at different stages of the simulation protocol. Make use of figures provided in the Supplementary Information as you deem appropriate. Your answer should include:•
A description of the appropriate force-fields for these simulations, and a short summary of their advantages and disadvantages. [9marks]
•The function of the DNA nanopore in drug delivery and single-molecule sensing systems, and how the structural properties of the nanopores influence their functional propertiesindrugdelivery and small molecule sensingapplications.[9marks]•
A discussion of the difficulties that are commonly encountered when simulating DNA and where specifically they arise, and the limitations these difficulties impose on the kind of structural informationthat may be obtained. [6marks]
•How might these limitations be circumvented?
