Programmable DNA Lattices: Design Synthesis and Applications

Contract Plan for FY2004

Duke(Reif) Planned Work: Further development of novel DNA tiles to form patterned 2D and 3D DNA lattices. Experimental demonstration & comparison of various assembly techniques for patterned 2D DNA lattices of moderate size (over 512 tiles), using techniques of unmediated algorithmic self-assembly, step-wise assembly, and directed nucleation assembly.

We plan to continued work on experimental demonstration and comparison of a number of assembly techniques for constructing patterned 2D DNA lattices of modest size, using techniques of unmediated algorithmic self-assembly(programmed assembly via Wang tiles), step-wise assembly, and the directed nucleation assembly technique(where an input DNA strand is synthesized that encodes the required pattern, and then specified tiles assemble around blocks of this input DNA strand, forming the required 2D pattern of tiles). For the the directed nucleation assembly work, we intend to use Duke’s new 4 x 4 DNA tiles in this work. We will also apply newly developed error-resulent methods for our work on unmediated algorithmic self-assembly.

NYU(Seeman) Planned Work:

Improve 3D periodic assemblies with host-lattice crystals that diffract to 2.5 Å resolution or better, which is a resolution adequate for crystallography. Further work on tie down nanocrystals from the Alivisatos laboratory in a 2D DNA lattice.

We plan to continued work on design a variety of DNA motifs expected to form 3D lattices, both periodic and aperiodic. We plan to complete the DLS characterization of the melting behaviors of the aggregates so as (i) to determine proper temperature ranges and preferred lattice periodicities, and (ii) to establish a relationship between the melting temperatures established by the DLS and the proper temperature at which to attempt crystallization. We plan to continue to optimize thermal protocols for 3D assembly experiments so as to control assembly formation. We also plan to continue to examine the solid materials that we produce by means of X-ray diffraction experiments on synchrotron sources, to determine crystal quality.

Caltech(Winfree) Planned Work: Assessment of model parameters used in optimization algorithms by theoretical/experimental closed-loop design-test-recalibrate cycle; addition of geometric and structural energetic terms into the design models. Theoretical classification of reliable DNA lattice motifs, using existing experimental systems and mathematical framework. Design of an unbounded binary counter (a component of the RAM circuit pattern) and characterization of error rates during unmediated self-assembly of the binary counter.

We plan continued work to demonstrate algorithmic self-assembly of DNA and controlled nucleation of self-assembled structures using a binary counter design, which is an initial step toward the self-assembly of an important circuit element, a RAM memory array. We will experimentally determine error rates during unmediated self-assembly.

We will continue to develop software technology for design of DNA nanostructures. Optimization algorithms for DNA design will be implemented and tested. We plan to implement algorithms for prediction and design of partition functions for multi-stranded DNA complexes and DNA pseudo-knots, and for specifying and creating 3D molecular models of DNA structures.

Further Work Planned:

We will also continue to characterize various novel DNA tiles, and investigate the use of these and related tiles to form DNA lattices. We will continue investigation of modifications of the TX molecules with additional Holiday junctions between the top and bottom dsDNA, so the resulting tile, a “Cylindrical TX tile” (CTX), has a cylindrical conformation and we will investigate the use of these and related families of DNA tiles to form 3D DNA lattices based on hybrids of CTX plus more conventional DX and TX tiles. We will continue characterizion of 1 D tilings of CTX tiles; we expect these form long cylinders which may be able to capture linear structures (e.g., carbon nanotubes).We will continue design of DNA molecular building blocks (MBBs) that can be rigidly attached to DNA lattices with a known orientation, and of unbounded binary counter (a component of demultiplexing RAM lattice).