Fluorescence labeling of DNAs is broadly useful, but methods for labeling are expensive and labor-intensive. Here we describe a general method for fluorescence labeling of oligonucleotides readily and cost-efficiently via base excision trapping (BETr), employing deaminated DNA bases to mark label positions, which are excised by base excision repair enzymes generating AP sites. Specially designed aminooxy-substituted rotor dyes trap the AP sites, yielding high emission intensities. BETr is orthogonal to DNA synthesis by polymerases, enabling multi-uracil incorporation into an amplicon and in situ BETr labeling without washing. BETr also enables labeling of dsDNA such as genomic DNA at a high labeling density in a single tube by use of nick translation. Use of two different deaminated bases facilitates two-color site-specific labeling. Use of a multi-labeled DNA construct as a bright fluorescence tag is demonstrated through the conjugation to an antibody for imaging proteins. Finally, double-strand selectivity of a repair enzyme is harnessed in sensitive reporting on the presence of a target DNA or RNA in a mixture with isothermal turnover and single nucleotide specificity. Overall, the results document a convenient and versatile method for general fluorescence labeling of DNAs.

DNA 的荧光标记用途广泛，但标记方法昂贵且劳动密集。在这里，我们描述了一种通过碱基切除捕获 (BETr) 轻松且经济高效地对寡核苷酸进行荧光标记的一般方法，使用脱氨 DNA 碱基来标记标签位置，这些标签位置被产生 AP 位点的碱基切除修复酶切除。特别设计的氨氧基取代的转子染料捕获 AP 位点，产生高发射强度。BETr 与聚合酶的 DNA 合成是正交的，能够将多尿嘧啶掺入扩增子和原位 BETr 标记而无需洗涤。BETr 还可以通过使用缺口平移在单管中以高标记密度标记 dsDNA，例如基因组 DNA。使用两种不同的脱氨基碱基有助于双色位点特异性标记。通过与用于成像蛋白质的抗体结合，证明了使用多标记 DNA 构建体作为明亮的荧光标记。最后，利用修复酶的双链选择性敏感地报告目标 DNA 或 RNA 在具有等温转换和单核苷酸特异性的混合物中的存在。总的来说，结果记录了一种方便且通用的 DNA 一般荧光标记方法。