4.8 Article

A pipeline for computational design of novel RNA-like topologies

Journal

NUCLEIC ACIDS RESEARCH
Volume 46, Issue 14, Pages 7040-7051

Publisher

OXFORD UNIV PRESS
DOI: 10.1093/nar/gky524

Keywords

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Funding

  1. National Institute of General Medical Sciences, National Institutes of Health (NIH) [GM100469, R35GM122562, GM101237, HG008133]
  2. National Institute of Child Health and Human Development, NIH [K08 HD069597]

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Designing novel RNA topologies is a challenge, with important therapeutic and industrial applications. We describe a computational pipeline for design of novel RNA topologies based on our coarse-grained RNA As-Graphs (RAG) framework. RAG represents RNA structures as tree graphs and describes RNA secondary (2D) structure topologies (currently up to 13 vertices, approximate to 260 nucleotides). We have previously identified novel graph topologies that are RNA-like among these. Here we describe a systematic design pipeline and illustrate design for six broad design problems using recently developed tools for graph partitioning and fragment assembly (F-RAG). Following partitioning of the target graph, corresponding atomic fragments from our RAG-3D database are combined using F-RAG, and the candidate atomic models are scored using a knowledge-based potential developed for 3D structure prediction. The sequences of the top scoring models are screened further using available tools for 2D structure prediction. The results indicate that our modular approach based on RNA-like topologies rather than specific 2D structures allows for greater flexibility in the design process, and generates a large number of candidate sequences quickly. Experimental structure probing using SHAPE-MaP for two sequences agree with our predictions and suggest that our combined tools yield excellent candidates for further sequence and experimental screening.

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