Massively Parallel DNA Computing Based on Domino DNA Strand Displacement Logic Gates

DNA computing has
gained considerable attention due to the characteristics
of high-density information storage and high parallel computing for
solving computational problems. Building addressable logic gates with
biomolecules is the basis for establishing biological computers. In
the current calculation model, the multiinput AND operation often
needs to be realized through a multilevel cascade between logic gates.
Through experiments, it was found that the multilevel cascade causes
signal leakage and affects the stability of the system. Using DNA
strand displacement technology, we constructed a domino-like multiinput
AND gate computing system instead of a cascade of operations, realizing
multiinput AND computing on one logic gate and abandoning the traditional
multilevel cascade of operations. Fluorescence experiments demonstrated
that our methods significantly reduce system construction costs and
improve the stability and robustness of the system. Finally, we proved
stability and robustness of the domino AND gate by simulating the
tic-tac-toe process with a massively parallel computing strategy.

DNA计算（DNA computing）因兼具高密度信息存储与高并行计算的特性，在求解计算问题的领域中受到了广泛关注。利用生物分子构建可寻址逻辑门，是实现生物计算机的基础。在当前的计算模型中，多输入与运算往往需要通过逻辑门间的多级级联来完成。实验发现，多级级联会引发信号泄漏，进而影响系统的稳定性。本研究借助DNA链置换（DNA strand displacement）技术，构建了类多米诺结构的多输入与门计算系统，摒弃了传统的多级级联运算模式，在单个逻辑门上即可实现多输入与运算。荧光实验结果表明，该方法显著降低了系统的构建成本，并提升了系统的稳定性与鲁棒性。最后，本研究通过采用大规模并行计算策略模拟井字棋（tic-tac-toe）博弈过程，验证了该类多米诺与门的稳定性与鲁棒性。