Crisscross cooperative self-assembly of DNA
Abstract
RESEARCH PROBLEM AND OBJECTIVES. We propose to self-assemble DNA-based ???slats??? into criss-crossed layers that can propagate as 1D filaments, 2D sheets, 3D blocks. Slats are designed such that they only can interact when at a crossed angle, furthermore the base-pairing interaction strength between any two intersecting slats is designed to be very small. Therefore, association between any slats A and B only will persist if slat A already is part of a pre-existing filament that presents a large number of previously captured slats that can cooperatively engage slat B and prevent it from leaving. In turn, each freshly recruited slat then presents weak binding sites for assisting capture of a number of subsequent slats. As a consequence of this extreme cooperativity, initiation of filament growth can be made to require impossibly high concentrations of slats to overcome the entropic nucleation barrier, except in the presence of an introduced ???seed???. The seed can be designed as a folded nanostructure (e.g. DNA origami) that can engage a large number of individual slats each with a large interaction strength, and that can arrange them into a polymerization-competent terminus of a filament. We will compare and contrast crisscross growth across three distinct classes of DNA-based primitives. AIM I: Characterize crisscross growth with single-stranded, antiparallel-crossover slats (AXS). Each half-turn (i.e. 5 or 6 nt) of an AXS monomer constitutes an interaction domain, therefore this is a highly compact architecture. Assembly from relative short DNA strands should enable folding with up to high micromolar concentrations of rapidly diffusing monomers, and therefore may yield the most rapid overall assembly speeds. AIM II: Characterize crisscross growth with paranemic-crossover slats (PXS). Each PXS monomer is a folded-back strand that alternates fullturn duplex domains with half-turn single-stranded domains for cross-slat interactions. AIM III: Characterize crisscross growth with DNA-origami slats (OGS) consisting of six-helix bundles (6hb) or sixteen-helix bundles (16hb). These are much more rigid and massive than the AXS or PXS monomers, furthermore we can design them to interact with other OGS monomers via basepairing directly below and above. OGS monomers lend themselves to growth of more porous structures, and also provide a more conceptually straightforward path to 3D. TECHNICAL APPROACHES. To construct our devices, we will use DNA sequence design, enzymatic DNA synthesis and DNA purification, thermal ramps for self-assembly. To characterize our devices, we primarily will use agarose gel electrophoresis and transmission electron microscopy. EXPECTED OUTCOMES. We expect to achieve successful self-assembly of 1D filaments (ribbons and tubes), 2D sheets, 3D blocks. All assemblies will only initiate from provided seeds.We will learn the best architectures for achieving the fastest and most homogeneous growth. IMPACT ON DOD CAPABILITIES. This novel capability will prove especially important for applications in high-performance sensing and signal transduction, due to complete suppression of background nucleation, and for applications in optics, due to the larger sizes of nanostructures that will become accessible, with dimensions comparable to the wavelength of visible light. Rapid, on-demand production of increasingly large and robust DNA nanostructures could enable diverse applications, including the following: reconfigurable visible-light plasmonic metamaterials (e.g. applications to optical computing, adaptive coloration, cloaking); structuralscaffolding that adaptively strengthens in the direction of applied stress (e.g. application to wound healing); single-molecule sensing with nanopores or nanobarcodes; nanorobotics therapeutic-delivery vehicles; macromolecular structure determination; molecular information storage, retrieval, and manipulation.
Document Details
- Document Type
- DoD Grant Award
- Publication Date
- Jul 26, 2018
- Source ID
- N000141812566
Entities
People
- William M. Shih
Organizations
- Dana–Farber Cancer Institute
- Office of Naval Research
- United States Navy