Book of Abstracts: Albany 2003
June 17-21 2003
GIDEON, A Program for Design and Sequence Optimization in Structural Nucleic Acid Technology
Structural Nucleic Acid Nanotechnology (SNANT) originated from immobile branched junctions, analogs of the Holliday junction. The junctions were easily comprehended as a set of arms flanking a branch point. The design of objects based on combinations of junctions proved tractable to existing software throughout the 1990's.
Over the years, the challenge of SNANT design has increased. In particular, the generalization of motif generation by reciprocal exchange led to structures in which the junctions were very close to one another (1). Motifs began to contain sets of many closely spaced junctions. SEQUIN. the main sequence design program (2), has a structure based on individual arms, rather than on strands. This leads to a an unwieldy data structure when crossover points are in close proximity to each other. In addition, DNA tiles leading to 2D and 3D periodic arrays need to be designed. DNA nanomechanical devices present a further design challenge. These developments have led to a need for a more sophisticated design technology.
GIDEON provides a more convenient way of handling a structure, using a set of associated strands, rather than linked arms. It integrates several development tools into a single environment centered on the strand-based concept. GIDEON simplifies many complex development steps: Designing the system?s structure; analyzing the system?s stability; generating its component strand sequences that lead to proper self-assembly; analyzing existing sequences. GIDEON encapsulates the unique function of each tool, presenting many features: Familiar user interface throughout the design process; easily comprehended visual representation for each design step; simplified revision of the system; reliable communication of the system?s specifications (e.g., sending the strand sequences to the synthetic facility). A flexible architecture will allow GIDEON to expand as SNANT moves forward. Overall, GIDEON allows the users to focus on the implementation of their concepts with an obvious and direct approach.
This research supported by NIGMS, ONR, DARPA/AFOSR, and NSF.
Jeffrey J. Birac
Department of Chemistry