The Role of DNA dynamics in damage recognition

细胞忠实地复制和传递它们的遗传信息(它们的DNA)的能力在所有活着的有机体中都是必不可少的。这一过程需要准确地将数十亿个核苷酸单位的序列复制成两个相同的副本。此外，自然的细胞过程和环境因素可能会导致必须修复的DNA损伤。如果不能准确复制和/或修复遗传物质，可能会导致包括癌症在内的疾病。在DNA复制过程中，会形成偏离双螺旋的DNA结构，这些结构必须由专门的酶处理才能使DNA恢复到正常的双螺旋状态。另一类酶修复化学损伤的DNA。在这个项目中，我们想要了解这些不同类别的酶是如何在浩瀚的正常DNA海洋中识别异常DNA的。这是修复过程的第一步，因此至关重要。许多人从蛋白质的角度来看待这一过程，但我们将寻求发现DNA动态的差异是否也是重要的。具体地说，我们将发现DNA灵活性的变化是否可能是修复酶快速定位其底物的一种机制。要做到这一点，我们将逐一观察单个DNA分子的构象(形状)(从而克服任何整体平均)。我们还将实施一种新的方法，X射线散射干涉技术(英国尚未使用)，它的工作原理是测量附着在DNA上的微小金晶体之间的距离。这种测量速度如此之快，以至于它提供了DNA在溶液中采用的所有不同形状的快照，即未平均的构象整体。我们将比较这些正常双链和一系列异常DNA的构象集合，以了解灵活性在基因组稳定中的作用。在人类细胞中，DNA被包装在蛋白质(组蛋白)周围，形成称为核小体的颗粒。在项目的最后部分，我们将看看异常的DNA结构是否与正常的双链DNA包装不同，可能会使自己更容易与修复蛋白相互作用。我们的项目将使用尖端的实验方法，结合计算机模拟来了解构象动力学在异常DNA识别中的作用。

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.