Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry

Wenjuan Zeng; Yanyan Zhang; Wei Zheng; Qun Luo; Juanjuan Han; Jian'an Liu; Yao Zhao; Feifei Jia; Kui Wu; Fuyi Wang

doi:10.3390/molecules24101852

Discovery of Cisplatin Binding to Thymine and Cytosine on a Single-Stranded Oligodeoxynucleotide by High Resolution FT-ICR Mass Spectrometry

Molecules. 2019 May 14;24(10):1852. doi: 10.3390/molecules24101852.

Authors

Wenjuan Zeng^{1

2}, Yanyan Zhang³, Wei Zheng⁴, Qun Luo^{5

6}, Juanjuan Han⁷, Jian'an Liu⁸, Yao Zhao⁹, Feifei Jia¹⁰, Kui Wu¹¹, Fuyi Wang^{12

13

14}

Affiliations

¹ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. zengwj2014@iccas.ac.cn.
² University of Chinese Academy of Sciences, Beijing 100049, China. zengwj2014@iccas.ac.cn.
³ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. zhangyy0816@iccas.ac.cn.
⁴ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. zhengwei0246@iccas.ac.cn.
⁵ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. qunluo@iccas.ac.cn.
⁶ University of Chinese Academy of Sciences, Beijing 100049, China. qunluo@iccas.ac.cn.
⁷ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. hjuan@iccas.ac.cn.
⁸ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. lja@iccas.ac.cn.
⁹ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. yaozhao@iccas.ac.cn.
¹⁰ Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. poppyjff@iccas.ac.cn.
¹¹ Key Laboratory of Hubei Province for Coal Conversion and New Carbon Materials, School of Chemistry and Chemical Engineering, Wuhan University of Science and Technology, Wuhan 430081, China. wukui@wust.edu.cn.
¹² Beijing National Laboratory for Molecular Sciences, National Centre for Mass Spectrometry in Beijing, CAS Key Laboratory of Analytical Chemistry for Living Biosystems, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, China. fuyi.wang@iccas.ac.cn.
¹³ University of Chinese Academy of Sciences, Beijing 100049, China. fuyi.wang@iccas.ac.cn.
¹⁴ Basic Medical College, Shandong University of Chinese Traditional Medicine, Jinan 250355, China. fuyi.wang@iccas.ac.cn.

Abstract

The clinically widely-used anticancer drug, cisplatin, binds strongly to DNA as a DNA-damaging agent. Herein, we investigated the interaction of cisplatin with a 15-mer single-stranded C,T-rich oligodeoxynucleotide, 5'-CCTT₄CTT₇G₈C₉T₁₀TCTCC-3' (ODN15), using ultra-high resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) in conjunction with tandem mass spectrometry (top-down MS). Top-down MS analysis with collision-induced dissociation (CID) fragmentation of the mono-platinated and di-platinated ODN15 provided abundant and informative Pt-containing or Pt-free a/[a - B], w and internal fragments, allowing the unambiguous identification of T₄, T₇, C₉, and T₁₀ as the platination sites on the cisplatin-ODN15 adducts. These results revealed that, in addition to the well-established guanine site, the unexpected thermodynamic binding of cisplatin to cytosine and thymine bases was also evident at the oligonucleotide level. Furthermore, the binding models of cisplatin with cytosine and thymine bases were built as the Pt coordinated to cytosine-N(3) and thymine-N(3) with displacement of the proton or tautomerization of thymine. These findings contribute to a better understanding of the mechanism of action of cisplatin and its preference for gene loci when the drug binds to cellular DNA, and also demonstrate the great potential and superiority of FT-ICR MS in studying the interactions of metallodrugs with large biomolecules.

Keywords: FT-ICR MS; binding sites; cisplatin; cytosine; oligodeoxynucleotide; thymine.

MeSH terms

Cisplatin / pharmacology*
Cytosine / metabolism
Models, Molecular
Oligodeoxyribonucleotides / chemistry*
Oligodeoxyribonucleotides / metabolism*
Tandem Mass Spectrometry
Thymine / metabolism

Substances

Oligodeoxyribonucleotides
Cytosine
Cisplatin
Thymine

Grants and funding

21575145, 21635008, 21621062, 21790390, 21790392 and 21505141/National Natural Science Foundation of China