TileSoft: Sequence Optimization Software for Designing DNA Secondary Structures

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 nanofabrication, 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 WatsonCrick 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. TileSoft described in this manuscript improves on previous software by delivering 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.