RUI: Comparative Analysis of Small RNA Motifs

RNA由四种核苷酸碱基组成：腺嘌呤(A)、鸟嘌呤(G)、尿嘧啶(U)和胞嘧啶(C)。这四种碱基在RNA中的排列顺序称为RNA序列。这些碱基相互作用，A与U （A-U）和G与C （G-C）形成标准碱基对。RNA中存在许多独特的相互作用组合，例如G与A （G.A）或G与U （G.U）形成非规范碱基对。其他相互作用也会发生，例如，几个a可以堆叠在一起，或者未配对的U可以与a -U对相互作用，形成U - a -U碱基三元组。目前，当RNA使用已知的相互作用规则折叠时，RNA的许多区域留在“凸起”和“环”中。这些地区的构造形成规律尚不清楚；然而，已知这些位点与蛋白质、RNA和药物的相互作用有关。这个项目将专注于在许多不同的RNA中发现的小凸起结构，并且在没有大RNA的情况下是稳定的。其中一种结构是三核苷酸凸起，通常存在于许多RNA的重要区域，如核糖体RNA，引起艾滋病的人类免疫缺陷病毒1型（HIV-1），以及称为微RNA的小RNA中。有许多问题需要回答：是否所有的三核苷酸凸起RNA都形成了相似的结构？如果凸起序列变大或变小，RNA的结构和稳定性会发生什么变化？这些凸起的核苷酸是否与RNA的其他邻近部分相互作用？如果一个凸起序列的存在导致RNA弯曲，我们能预测弯曲的角度和所需的能量吗？凸起序列与金属离子结合吗？金属结合是否有助于稳定或拉直RNA？为了了解短凸起RNA的结构和功能，将测量“撤消”该结构所需的能量；结构越坚固，展开所需的能量就越多。凸起内部和周围的RNA序列将被改变，以确定展开RNA所需的相应能量变化。由于RNA的形状决定了它如何在基质中移动或吸收某些类型的光，这些技术将用于研究RNA的弯曲。某些金属离子和其他分子与RNA结合的紧密程度也将被测量。这项研究的重要性首先在于了解RNA形成的基本结构。这项研究将确定小凸起序列的一般模式。这些“规则”可以被包括在目前用于预测RNA结构的计算机程序中。由于这些凸起序列来源于功能重要的RNA，本研究将改善这些RNA的结构和功能之间的联系。许多生物体的DNA和RNA的核苷酸序列目前是可用的。因此，提高将这些信息与分子的结构和功能联系起来的能力将增强基因组数据库的有用性。例如，许多新的病原体，包括用于生物恐怖主义的生物体，现在可以快速测序。为了设计基于RNA的药物来中和病原体，需要非常详细地了解病原体和宿主的功能重要RNA的局部和全局结构。这项研究更广泛的影响是，它将在本科生中进行。学生们将在大学一年级就开始从事独立的研究项目。本研究也将纳入核酸生物化学课程。通过参与，对生物科学感兴趣的学生将学习定量研究方法，并提高他们的数学技能。在课程中学习的抽象概念在应用于实际生活问题时会变得更加有趣。学生将在当地社区和K-12学校系统参加与课程相关的外展活动。学生将利用他们的知识为他们的社区提供疾病和药物的生物化学信息，这反过来又将使科学与他们自己的生活相关。学生将与K-12学校系统合作，提供指导和指导以科学为基础的活动，以保持年轻学生对科学的好奇心。学生将有机会与三个不同国家的科学家一起工作，体验研究的国际性。这些项目将把令人兴奋的研究带到本科环境中。设备和专业知识将与邻近的学校共享，这将使每个参与其中的人受益。学生研究人员将被鼓励成为专业学会的成员，如美国生物化学和分子生物学学会（ASBMB），并将有机会在地区、国家和国际会议上展示他们的研究成果。为此，ASBMB创建了大学生联盟网络（UAN），学生们已经建立了一个地方分会。研究和推广经验将帮助学生看到科学与现实世界问题的相关性，并意识到他们作为科学家可以在他们的社区中发挥作用。

RNA is made up of four nucleotide bases: adenine (A), guanine (G), uracil (U) and cytosine (C). The order in which these four bases are found in any RNA is called its sequence. These bases interact with each other, A with U (A-U) and G with C (G-C) to form canonical base pairs. Many unique combinations of interactions occur in RNA, for example, G with A (G.A) or G with U (G.U) to form non-canonical base pairs. Other interactions also occur, for example, a few A's can stack on top of each other or an unpaired U can interact with an A-U pair to form U.A-U base triple. Currently, when RNA is folded using the known rules of interactions, many regions of RNA are left in "bulges" and "loops". The rules for structure formation within these regions are not known; however, these sites are known to be involved in interactions with proteins, RNA, and drugs. This project will focus on small bulge structures that are found in many different RNA and are stable in the absence of the large RNA. One such structure is a three-nucleotide bulge that is commonly found in important regions of many RNA, such as ribosomal RNA, AIDS-causing human immunodeficiency virus type 1 (HIV-1), and in small RNA called micro-RNA. There are many questions that need to be answered : are all three-nucleotide bulge RNA forming similar structures? What happens to the structure and stability of RNA if the bulge sequences become slightly bigger or smaller? Do these bulge nucleotides interact with other neighboring portions of RNA? If the presence of a bulge sequence causes RNA to bend, can we predict the bend angle and the energy required to do so? Do the bulge sequences bind to metal ions? Does the metal binding help stabilize or straighten the RNA? To understand the structure and function of short bulged RNA, the energy required to "undo" the structure will be measured; the stronger the structure, the more energy it will take to unfold. The RNA sequence in and around the bulge will be altered to determine the corresponding changes in energy required to unfold the RNA. Since the shape of RNA determines how it moves through a matrix or absorbs certain types of light, these techniques will be used to study bending of RNA. How tightly certain metal ions and other molecules bind to RNA will also be measured. The importance of this study is first and foremost to understand the basic structures that form in RNA. This research will determine general patterns that are to be expected for small bulged sequences. These "rules" can then be included in computer programs that are currently used to predict RNA structures. As these bulge sequences are derived from functionally important RNA, this study will improve the link between the structure and function of these RNA. The nucleotide sequence for DNA and RNA of many organisms is currently available. Thus, improving the ability to link this information to the structure and function of molecules will enhance the usefulness of the genome databases. For example, many new pathogens, including organisms used in bio-terrorism, can now be sequenced quickly. To design RNA-based drugs to neutralize a pathogen will require a very detailed understanding of local and global structures of functionally important RNA for both the pathogen and the host.The broader impact of this research is that it will be done with undergraduate students. Students will start working on independent research projects starting as early as their first year of college. This research will also be incorporated into nucleic acid biochemistry courses. By participating, students interested in the biological sciences will learn quantitative research methods and will improve their mathematical skills. Abstract concepts learned in courses will become more interesting when applied to real life problems. Students will participate in course-linked outreach activities in their local communities and K-12 school system. Students will use their knowledge to provide information on biochemistry of diseases and drugs to their communities, which in turn will make science relevant to their own lives. Students will work with K-12 school system to provide mentoring and to direct science-based activities to keep the younger students curious about science. Students will get an opportunity to work with scientists in three different countries and will experience the international nature of research. These projects will bring the excitement of research into the undergraduate environment. The equipment and expertise will be shared with neighboring schools and it will benefit everyone involved. Student researchers will be encouraged to become members of professional societies, such as the American Society for Biochemistry and Molecular Biology (ASBMB), and will be given opportunities to present their research at regional, national, and international meetings. Towards this end, Undergraduate Affiliate Network (UAN) has been created by ASBMB and students have started a local chapter. The research and outreach experiences will help students to see the relevance of science to real world problems, and to realize that they, as scientists, can make a difference in their communities.