i-Motifs: Sequence, Structure and Function in Ageing

DNA通常被认为是一种双螺旋结构，即由Watson和Crick在1953年首次提出的“扭曲梯形”结构。然而，鲜为人知的是，DNA可以采用不同的形状，这些形状可以作为开关来控制它的工作方式。DNA由四个碱基组成，通常被描述为生命的“构件”，因为它们编码了构建和维持有机体所需的所有信息。这四种碱基(腺嘌呤、鸟嘌呤、胸腺嘧啶和胞嘧啶)的序列决定了我们是人类，也是我们区别于细菌、酵母和植物的原因。含有大量碱基胞嘧啶的DNA序列可以形成另一种二级结构，而不是看起来像正常的两条链的“扭曲的梯子”，而是一个非常紧密地包裹着四条DNA的“结”。我们称这些结构为I-基元。这种类型的序列在纳米技术中被用作pH依赖的开关，但也广泛存在于人类基因组中，存在于细胞中，并已被证明在基因表达和定义我们的细胞寿命方面发挥作用。尽管最近取得了这些进展，但我们缺乏关于这些结构如何在体内发挥作用的细节。我们知道，对于DNA的某些区域，这些类型的序列可能在我们患某些疾病的易感性中发挥作用，例如糖尿病。我们还知道，随着我们年龄的增长，以及在癌症等疾病中，这些序列会发生活跃的突变和缺失。为了能够理解这些结构对疾病的影响，我们需要了解它们如何被改变，以及这对它们在生物学中的工作方式有什么不同。这可能会给我们提供诊断或治疗某些遗传病的方法。这项建议的中心目的是研究DNA I基序结构在开启和关闭基因方面的序列、结构和功能之间的关系，以及这种关系如何在衰老过程中发生变化。我们将使用广泛的计算、生物学和生物物理技术来研究这一点。我们以前的工作让我们了解了哪些类型的序列可能折叠成I-基序结构。我们将利用生物物理学和分子生物学的方法，研究I基序结构在人类中的重要性及其在控制基因切换中的精确影响。这将给我们提供关于I-基序的结构对功能有多重要的信息。我们有初步数据表明，随着年龄的增长，I基序形成序列会发生突变和缺失，这可能会影响疾病的进展。我们的目标是破译基因组的关键区域中是否存在受突变严重影响的“热点”。最后，我们将对人类细胞中存在I-基序结构的位置进行全球研究，并观察它们的分布是否随着细胞年龄的变化而变化。这将涉及到一种新技术的开发，该技术基于观察这些结构所具有的“足迹”。该项目将促进我们对I-基序在生物学中的工作方式以及它们如何受到衰老过程影响的突变的控制的理解。这项工作的结果也将提高我们对不同条件下I-基序折叠的理解，使我们能够更好地预测基于DNA序列的调节特性。这将影响基于DNA/RNA的纳米技术的设计和创造。开发一种新的工具来研究人类细胞中I-基序结构的普遍性，将能够应用于任何其他生物体，这将把我们的研究范围扩大到植物学家和微生物学家。

DNA is often assumed to be a double helix, the "twisted ladder" structure which was first proposed by Watson and Crick in 1953. However, it is less well known that DNA can adopt different shapes and these can be used as switches to control how it works. DNA is comprised of four bases, often described as the "building blocks" for life because they encode all the information required to build and maintain an organism. The sequence of these four bases (adenine, guanine, thymine and cytosine) is what defines us as humans and what makes us different to bacteria, yeast and plants. DNA sequences which contain lots of the base cytosine can form alternative secondary structures which instead of appearing like the normal "twisted ladder" of two strands, are a very tightly packed "knot" of four strands of DNA. We call these structures i-motifs. Sequences of this type have been used as pH-dependent switches in nanotechnology but are also widespread throughout the human genome, exist in cells and have been shown to play a role in gene expression and defining how long our cells live. Despite these recent advances, we lack the detail about how these structures work in the body. We know that for some regions of DNA, these types of sequences may play a role in our predisposition to getting certain diseases, such as Diabetes. We also know that these sequences are actively mutated and deleted as we age and in diseases such as Cancer. To be able to understand the effects of these structures have on disease, we need to understand how they can be changed and what difference this makes to how they work in biology. This could potentially give us ways to diagnose or treat certain genetic diseases. The central aim of this proposal is to investigate the relationship between sequence, structure and function of DNA i-motif structures in switching genes on and off and how this changes during ageing. We will examine this using a wide range of computational, biological and biophysical techniques. Our previous work has given us an understanding of which types of sequences could potentially fold into i-motif structures. Using biophysical and molecular biology methods, we will investigate the importance of the structure of i-motif in humans and their precise influence in controlling gene switching. This will give us information about how important the structure of i-motif is to function. We have preliminary data to show that i-motif forming sequences are mutated and deleted as we age, and this can affect the progression of disease. We aim to decipher whether there are "hot spots" in critical regions of the genome that are critically affected by mutations. Finally, we will perform a global study of where i-motif structures are present in human cells and observe whether their distribution changes as cells age. This will involve development of a new technique, based on looking at a "footprint" these structures have.The project will advance our understanding of how i-motifs work in biology and how they are controlled by mutations affected by the ageing process. The outcomes of the work will also improve our understanding about the folding of i-motifs under different conditions, allowing better prediction of regulating properties based on DNA sequence. This will impact the design and creation of DNA/RNA based nanotechnologies. The development of a new tool to study the prevalence of i-motif structures in human cells will be able to be applied to any other organism, which will expand the scope of our research to plant scientists and microbiologists.