Building-block dynamics play an important role in RNA nanostructure design and modeling

Tuesday, October 25, 2011 — Poster Session II
Noon – 2:00 p.m.	Natcher Conference Center	NCI	STRUCTBIO-4

Authors

• WK Kasprzak
• AR Diehl
• E Bindewald
• T-J Kim
• MT Zimmermann
• RL Jernigan
• BA Shapiro

Abstract

Our research focuses on methodology and computer tools development to automate the design of RNA-based nanostructures envisioned as delivery vehicles and therapeutic agents. We draw building blocks from RNAJunction, our database of n-way junctions and kissing-loops, and link them together with idealized helices, utilizing our programs NanoTiler and RNA2D3D (and other tools) to create 3D nanostructure models. Nanostructure building blocks are treated as rigid objects at first. However, based on our modeling experience and experimental evidence for the RNA shape adjustment to the constraints of larger structural context, we are now including the structural flexibility information in the design and modeling process. Experimental data as well as computational structure dynamics at the atomic resolution or coarse-grained level can be used to that end. Here we present examples of modeling methods which include flexibility data to bring the modeling results to agreement with experimental data. We focus on the benefits of a coarse-grained methodology based on the elastic network modeling which provides sufficiently accurate structure flexibility information at low computational cost and makes it feasible to design and characterize much larger structures than those which can be evaluated with the atomic resolution Molecular Dynamics simulations. Funded in part by HHSN261200800001E

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