The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin

We report here LC-MS data, used in conjunction with NMR analysis, to elucidate the specificity and structure of interstrand crosslinks (ICL) of DNA resulting from the genotoxin colibactin. The measured masses of 14- and 25-mer double strand DNA oligomers exposed to colibactin provided for the determination of the chemical structure of colibactin-ICL. It revealed an α-ketoiminium in the central region of colibactin that likely serves as a key DNA recognition element, explaining colibactin’s sequence selectivity. A strand cleavage assay with high resolution LC-MS detection was used to study the site-specific products of various base sequences of 25mer double-strand DNA oligomer sequences containing colibactin ICLs. This data was used to understand how and when colibactin-ICLs form.
, , # Data from: The specificity and structure of DNA crosslinking by the gut bacterial genotoxin colibactin

Dataset DOI: [10.5061/dryad.vmcvdnd5g](https://doi.org/10.5061/dryad.vmcvdnd5g)

## Description of the data and file structure

Data was acquired on Thermo Scientific Orbitrap Fusion and Lumos mass spectrometers and therefore the files are the vendors .raw data format. It can be processed directly using the vendors Xcalibur FreeStyle or Qualbrowser (older but still functional). An alternative free software which could be used is OpenChrom - an open-source alternative that can handle various mass spectrometry data formats.

The samples with names containing \"clb-\" in the name are control samples which were exposed to e.coli which do not have the clb gene and therefore do not produce colibactin. The samples with \"clb+\" in the name are those which do produce colibactin. The data which was collected in triplicate has the each individual replicates indicated in its name so the first repl...,

本研究报道了与核磁共振（NMR）分析联用的液相色谱-质谱（LC-MS）数据，用于阐明由基因毒素大肠杆菌素（colibactin）诱导产生的DNA链间交联（ICL）的特异性与结构。经大肠杆菌素处理的14聚体与25聚体双链DNA寡核苷酸的实测质量数，可用于确定大肠杆菌素诱导链间交联（colibactin-ICL）的化学结构。研究发现，大肠杆菌素的中心区域存在α-酮亚胺鎓（α-ketoiminium）结构，该结构或为关键的DNA识别元件，这也解释了大肠杆菌素的序列选择性。本研究采用高分辨率液相色谱-质谱检测的链裂解实验，对含大肠杆菌素诱导链间交联的25聚体双链DNA寡核苷酸的不同碱基序列的位点特异性产物进行了分析。该数据用于解析大肠杆菌素诱导链间交联的形成方式与时机。
# 数据来源：肠道细菌基因毒素大肠杆菌素诱导DNA交联的特异性与结构
数据集DOI：[10.5061/dryad.vmcvdnd5g](https://doi.org/10.5061/dryad.vmcvdnd5g)

数据与文件结构说明
本研究的数据采集使用赛默飞世尔科技（Thermo Scientific）Orbitrap Fusion与Lumos质谱仪，因此原始数据文件为厂商专属的.raw格式。可直接使用厂商提供的Xcalibur FreeStyle或Qualbrowser（虽为旧版但仍可正常运行）进行数据处理。另有一款免费开源替代软件OpenChrom，可兼容多种质谱数据格式。
名称中含"clb-"的样本为对照组样本，其对应的大肠杆菌（E. coli）不含clb基因，因此无法合成大肠杆菌素；名称中含"clb+"的样本则可合成大肠杆菌素。采用三次重复实验采集的数据，其文件名会标注各次重复的信息，例如第一个重复……