Eliminating unwanted patterns with minimal interference

Abstract: Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence patterns that correspond to binding sites of restriction enzymes or transcription factors. While many design tools address this problem, no adequate formal solution exists for the pattern elimination problem. In this work, we present a formal description of the elimination problem and suggest efficient algorithms that eliminate unwanted patterns and allow optimization of other objectives with minimal interference to the desired DNA functionality. Our approach is flexible, efficient, and straightforward, and therefore can be easily incorporated in existing DNA design tools, making them considerably more powerful.