An Algorithm-optimized Scheme for In situ Synthesis of DNA Microarrays

Abstract

Background: The cost of synthetic DNA has limited applications in frontier science and technology fields such as synthetic biology, DNA storage, and DNA chips.

Objective: The objective of this study is to find an algorithm-optimized scheme for the in situ synthesis of DNA microarrays, which can reduce the cost of DNA synthesis.

Methods: Here, based on the characteristics of in situ chemical synthesis of DNA microarrays, an optimization algorithm was proposed. Through data grading, the sequences with the same base at as many different features as possible were synthesized in parallel to reduce synthetic cycles.

Results and discussion: The simulation results of 10 and 100 randomly selected sequences showed that when level=2, the reduction ratio in the number of synthetic cycles was the largest, 40% and 32.5%, respectively. Subsequently, the algorithm-optimized scheme was applied to the electrochemical synthesis of 12,000 sequences required for DNA storage. The results showed that compared to the 508 cycles required by the conventional synthesis scheme, the algorithmoptimized scheme only required 342 cycles, which reduced by 32.7%. In addition, the reduced 166 cycles reduced the total synthesis time by approximately 11 hours.

Conclusions: The algorithm-optimized synthesis scheme can not only reduce the synthesis time of DNA microarrays and improve synthesis efficiency, but more importantly, it can also reduce the cost of DNA synthesis by nearly 1/3. In addition, it is compatible with various in situ synthesis methods of DNA microarrays, including soft-lithography, photolithography, a photoresist layer, electrochemistry and photoelectrochemistry. Therefore, it has very important application value.

Keywords: DNA microarrays; High-throughput DNA synthesis; application value; low cost; optimization algorithm; photolithography.