The Role of DNA dynamics in damage recognition

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The ability of cells to faithfully replicate and transmit their genetic information (their DNA) is essential in all living organisms. The process requires accurately reproducing a sequence of billions of nucleotide units into two identical copies. In addition, natural cellular processes and environmental factors can result in damage to the DNA that must be repaired. Failing to precisely duplicate and/or repair the genetic material can result in diseases including cancer. During DNA replication, DNA structures deviating from the double helix are formed that must be processed by specialized enzymes to return the DNA to its normal double helical state. Another class of enzymes repair chemically damaged DNA. In this project we want understand how these different classes of enzymes recognize aberrant DNA within a vast sea of normal DNA.This is the very first step in the repair process, and as such is of central importance. Many people have looked at this process from the point of view of the proteins, but we will seek to discover if differences in the dynamics of the DNA are also important.Specifically, we will discover if changes in DNA flexibility could be one mechanism by which repair enzymes quickly locate their substrates. To do this, we will look at the conformations (shapes) of individual DNA molecules, one at a time (and so overcome any ensemble averaging). We will also implement a new method, X-ray scattering interferometry technique (that has not yet been used in the UK) which works by measuring the distances between tiny gold crystals attached to the DNAs. This measurement is so fast that it provides a snapshot of all the different shapes a DNA adopts in solution i.e. the un-averaged, conformational ensemble. We will compare these conformational ensembles for normal duplexes and a range of aberrant DNAs, to understand the role of flexibility in genome stability.In human cells, DNA is packed around proteins (histones), into particles called nucleosomes. In the last part of the project we will see if aberrant DNA structures pack differently to normal duplex DNAs, possibly leaving themselves more open for repair proteins to interact with.Our project will use cutting-edge experimental methods, combined with computer simulations to understand the role of conformational dynamics in aberrant DNA recognition.