  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.
