Modeling and design of complex RNA structures

项目总结 RNA的不断发现及其在细胞和病毒机制中的关键作用 是鼓舞人心的新型抗菌、抗肿瘤、抗病毒和基因组编辑疗法 基于禁用、操作和重新调整所涉及的RNA的用途。不幸的是， 我们对RNA如何工作的生物物理理解很差，这正在减缓 这些可能挽救生命的努力。一个关键的瓶颈是不适用于 结晶学、核磁共振、系统发育分析和生化方法来确定 非编码RNA在其所有功能状态下的部分有序构象。至 为了解决这一瓶颈，我们将生物物理建模、电子显微镜、 高通量生化/测序实验，机器学习，湿法实验室- 集成众包，以及广泛的协作网络。当前的项目 例如，我们的做法涉及新冠肺炎大流行。我们的RiBosolve混合动力车 结构确定管道，我们正在发现许多片段的 SARS-CoV-2 RNA基因组形成明确的3D结构，其靶向 反义寡核苷酸可抑制病毒复制。在OpenVaccine挑战中，我们 正在开发高结构的新冠肺炎基因疫苗，在体外有足够的 稳定性，使预充式注射器中的信使核糖核酸能够在全球范围内运输。这个新冠肺炎 研究受益于我们的敏捷方法和Mira允许的灵活性 支持；我们现在使用的许多计算和实验方法都不存在 在大流行之前。因为RNA是生命的基础，解决了许多科学问题 如果我们能够想象和发现人类疾病中的更多“大问题”，那么人类疾病的进一步“大问题”可能会加速 设计任何核糖核酸。我的实验室试图创造出计算和实验的RNA 基金会需要在接下来的几年里让我们所有人都去那里。

PROJECT SUMMARY The continuing discoveries of RNAs and their critical roles in cellular and viral machinery are inspiring novel antibacterial, antitumor, antiviral, and genome-editing therapies based on disabling, manipulating, and repurposing the RNAs involved. Unfortunately, our poor biophysical understanding of `how RNAs work' is slowing the development of these potentially life-saving efforts. A critical bottleneck has been the inapplicability of crystallography, NMR, phylogenetic analysis, and biochemical methods to determine the partly ordered conformations of non-coding RNAs in all their functional states. To address this bottleneck, we bring together biophysical modeling, electron microscopy, high throughput biochemical/sequencing experiments, machine learning, wet-lab- integrated crowdsourcing, and a wide collaborative network. Current projects that exemplify our approach involve the COVID-19 pandemic. With our Ribosolve hybrid structure determination pipeline, we are discovering that numerous segments of the SARS-CoV-2 RNA genome form well-defined 3D structures whose targeting by antisense oligonucleotides inhibits viral replication. In the OpenVaccine challenge, we are developing highly structured COVID-19 mRNA vaccines with sufficient in vitro stability to enable world-wide shipping of mRNA in prefilled syringes. This COVID-19 research has benefited from our agile approach and the flexibility allowed by MIRA support; many of the computational and experimental methods we use now did not exist before the pandemic. Because RNA is so fundamental to life, tackling many of science's further `big questions' in human disease could be accelerated if we could visualize and design any RNA. My lab seeks to create the RNA computational and experimental foundation needed to get all of us there in upcoming years.