Internet-scale discovery of RNA bioengineering rules

描述（由申请人提供）：生物学基础非编码rna的最新发现激发了新的抗菌、抗肿瘤和抗病毒疗法，这些疗法可能会使相关分子失效或被操纵。然而，在硅折叠模型还不能自信地预测体外RNA构象，减缓了这些潜在的拯救生命的努力的发展。为了开发下一代强大且经过严格测试的RNA生物工程规则，我们正在探索一种非常规的策略：去年，我们发布了一个公民科学项目，使非专家能够在互联网规模的RNA设计竞赛中开发和测试折叠假设，并通过湿实验室反馈进行严格评分。在2011年初启动的EteRNA项目中，25000个参与者已经超越了现有的设计新型RNA结构的方法，这些结构可以在体外正常折叠。关键的下一个阶段是维持和形式化保存在EteRNA社区中的RNA纳米工程见解。我们建议采取步骤，将社区的实验验证的人类计算整合到一套自动化设计算法（EteRNAbot）中，供整个RNA纳米工程社区使用。除了汇编这样的案例，我们还将通过成千上万的新实验，对计算机和体外设计失败的严格搜索和解决方案进行众包。最后，我们将为专家和众包三维设计部署EteRNA- 3D界面，利用不断增长的3D构建模块数据库和ROSETTA RNA折叠/设计算法。我们将通过我们的高通量湿实验室管道，通过新设计的合成和单核苷酸分辨率化学作图来评估每个目标的成功。更一般地说，我们将通过评估自动化设计工具的使用和引用程度来评估成功；为该项目生成的可公开获取的RNA制图数据库的挖掘和引用程度；以及在核酸设计之外的生物医学计算问题中采用EteRNA范式进行互联网规模的科学发现。

DESCRIPTION (provided by applicant): Recent discoveries of biologically fundamental non-coding RNAs are inspiring novel antibacterial, antitumor, and antiviral therapies that might disable or manipulate the molecules involved. However, in silico folding models cannot yet confidently predict RNA conformations in vitro, slowing the development of these potentially life-saving efforts. To develop the next-generation of robust and rigorously tested RNA bioengineering rules, we are exploring an unconventional strategy: last year, we released a citizen science project enabling non-experts to develop and test folding hypotheses in internet-scale RNA design competitions that are rigorously scored through wet-lab feedback. Launched in early 2011, the 25,000-player EteRNA project already outperforms existing previous methods for designing novel RNA structures which fold properly in vitro. The critical next stage is to sustain and formalize the RNA nanoengineering insights preserved within the EteRNA community. We propose steps to consolidate the community's experimentally validated human computation into a suite of automated design algorithms (EteRNAbot) usable by the entire RNA nanoenginering community. Beyond compiling such cases, we will crowd-source the rigorous search and resolution of in silico and in vitro design failures with thousands of new experiments. Finally, we will deploy the EteRNA- 3D interface for both expert and crowd-sourced three-dimensional design, leveraging a growing database of 3D building blocks and the ROSETTA RNA folding/design algorithms. We will evaluate success in each aim via synthesis and single-nucleotide- resolution chemical mapping of novel designs through our high-throughput wet-lab pipeline. More generally, we will evaluate success by assessing the extent of utilization and citation of the automated design tools; the extent of mining and citation of the publically available RNA Mapping Database generated for the project; and the adoption of the EteRNA paradigm for Internet-scale scientific discovery in biomedical computation problems beyond nucleic acid design.