The impact of substrate on the measurement of DNA complex morphology

A problem presented at the UK MMSG Nottingham 2002.

Presented by:
Dr Stephanie Allen (School of Pharmaceutical Sciences, University of Nottingham)
S Allen, GW Richardson, JAD Wattis

Problem Description

In-vivo, deoxyribonucleic acid (DNA) molecules rarely exist on their own, and are normally complexed with a range of molecules ranging from small inorganic molecules to large proteins. The formed complexes and molecular condensates are integral to many cellular processes including DNA replication and molecular compaction within the nucleosome. Implicit to many of the microscopic techniques required to visualize these molecules is their deposition or immobilization onto a flat surface. The impact of the surface upon the morphology of the condensate however, remains poorly understood.

The study group is thus asked to develop mathematical models to tackle the following problems:

  1. Do the structures of the molecules visualized on the surface reflect those in solution?
  2. For a given population of DNA molecular complexes (with a range of charges/charge densities) is there any preferential adsorption of a particular species on to a defined surface?

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Study Group Report

After describing the physical set-up of an AFM cell and giving the relevant parameters, we describe simple ODE models which aim to answer the former of these two questions. These models are described and solved. A complete model of the system is then derived comprising a system of PDEs, through which we aim to answer both the above questions. It was not possible to solve this model during the week, though some preliminary results and ideas for further work are discussed.

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