Abstract: DNA is a crucial construction
material for molecular scale objects with nano-scale features. Diverse
synthetic DNA objects hold great potential for applications such as nano-fabrication,
nano-robotics, nano-computing, and nano-electronics. The construction
of DNA objects is generally carried out via self-assembly. During self-assembly,
DNA strands are guided by their sequence information into secondary structures
to maximize Watson-Crick pairing of their bases and thus minimize the
free energy of the resultant structures. A crucial computational problem
in constructing DNA objects is the design of DNA sequences that can correctly
assemble into desired DNA secondary structures. However, existing software
packages only provide unintuitive text-line interfaces and generally require
the user to step through the entire sequence selection process, which could
be time-consuming and tedious. In contrast, TileSoft described here
deliver the following features: 1) Its graphical user interface renders
the molecular architect the ability to define DNA secondary structure and
accompanying designing constraints directly on the interface as well as
the ability to view the optimized sequence information pictorially. 2) Its
fully automatic optimization module relieves the user of the drudgery of
manually dictating the sequence selection process, and its evolutionary algorithm
produces satisfactory results efficiently. 3) Its graphical user interface
and its optimization module are smoothly integrated from user's perspective,
while they are at the same time well separated in terms of software architecture,
making each amenable to future improvements without negatively affecting
the other. The figure shows the default window of TileSoft.
The design engine of TileSoft is built upon an earlier
version of DNADesign
authored by Erik Winfree
at CalTech.