Department of Physics, Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.
Nat Struct Mol Biol. 2012 May 13;19(6):623-7. doi: 10.1038/nsmb.2294.
Sequence recognition through base-pairing is essential for DNA repair and gene regulation, but the basic rules governing this process remain elusive. In particular, the kinetics of annealing between two imperfectly matched strands is not well characterized, despite its potential importance in nucleic acid-based biotechnologies and gene silencing. Here we use single-molecule fluorescence to visualize the multiple annealing and melting reactions of two untethered strands inside a porous vesicle, allowing us to precisely quantify the annealing and melting rates. The data as a function of mismatch position suggest that seven contiguous base pairs are needed for rapid annealing of DNA and RNA. This phenomenological rule of seven may underlie the requirement for seven nucleotides of complementarity to seed gene silencing by small noncoding RNA and may help guide performance improvement in DNA- and RNA-based bio- and nanotechnologies, in which off-target effects can be detrimental.
碱基配对的序列识别对于 DNA 修复和基因调控至关重要，但控制这一过程的基本规则仍然难以捉摸。特别是，尽管两条不完全匹配的链之间的退火动力学在基于核酸的生物技术和基因沉默中具有潜在的重要性，但它仍未得到很好的描述。在这里，我们使用单分子荧光技术可视化了多孔囊泡内两个无束缚链之间的多次退火和熔化反应，从而能够精确地量化退火和熔化速率。作为错配位置函数的数据表明，DNA 和 RNA 的快速退火需要七个连续的碱基对。这个七的现象学规则可能是小非编码 RNA 引发基因沉默所必需的七个核苷酸互补的基础，并且可能有助于指导基于 DNA 和 RNA 的生物和纳米技术的性能改进，因为脱靶效应可能是有害的。
