Vortex fluidics-mediated DNA rescue from formalin-fixed museum specimens

DNA from formalin-preserved tissue could unlock a vast repository of genetic information stored in museums worldwide. However, formaldehyde crosslinks proteins and DNA, and prevents ready amplification and DNA sequencing. Formaldehyde acylation also fragments the DNA. Treatment with proteinase K proteolyzes crosslinked proteins to rescue the DNA, though the process is quite slow. To reduce processing time and improve rescue efficiency, we applied the mechanical energy of a vortex fluidic device (VFD) to drive the catalytic activity of proteinase K and recover DNA from American lobster tissue (Homarus americanus) fixed in 3.7% formalin for >1-year. A scan of VFD rotational speeds identified the optimal rotational speed for recovery of PCR-amplifiable DNA and while 500+ base pairs were sequenced, shorter read lengths were more consistently obtained. This VFD-based method also effectively recovered DNA from formalin-preserved samples. The results provide a roadmap for exploring DNA from millions of historical and even extinct species.福尔马林固定组织中的DNA，有望解锁全球博物馆馆藏中蕴藏的海量遗传信息宝库。然而，甲醛会使蛋白质与DNA发生交联，阻碍DNA的便捷扩增与测序；同时甲醛酰化反应还会导致DNA片段化。采用蛋白酶K（proteinase K）处理可水解交联蛋白以回收DNA，但该过程耗时极长。为缩短处理时长并提升回收效率，本研究借助涡旋流体装置（vortex fluidic device, VFD）的机械能强化蛋白酶K的催化活性，从经3.7%福尔马林固定超过1年的美洲螯龙虾（Homarus americanus）组织中成功回收DNA。通过对VFD转速的筛选，确定了可回收经PCR扩增的DNA的最优转速；尽管测序可获得500碱基对以上的序列，但更稳定获取的仍是较短的读长。该基于VFD的方法同样可高效回收福尔马林固定样品中的DNA。本研究结果为探索数百万份历史标本乃至已灭绝物种的DNA提供了可行路径。