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

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.

Tandem Mass Spectrometry Reveals Preferential Ruthenation of Thymines in Human Telomeric G-Quadruplex DNA by an Organometallic Ruthenium Anticancer Complex

“…During top-down MS analysis, the metalated products, for example, ruthenated DNA identified by the primary mass spectrometry analysis, can be exclusively selected and directly introduced into a dissociation cell for fragmentation followed by a secondary mass spectrometry detection. The binding site information can be obtained by the metalated or unmetalated sequential fragments generated from either the 3′- or 5′-terminal. , Recently, we demonstrated by tandem mass spectrometry analysis that the ruthenium arene complex [(η 6 -biphenyl)­Ru­(en)­(Cl)]­PF 6 ( 1 ) binds at T 2 or G 6 of a 6-mer human telomeric DNA model sequence, 5′-T 1 T 2 A 3 G 4 G 5 G 6 -3′ . This again confirmed the thermodynamic competition of thymine with guanine in a linear oligonucleotide for ruthenation.…”

Ruthenium Complexes: An Alternative to Platinum Drugs in Colorectal Cancer Treatment

“…Ru(III)-complexes also have been reported to bind to the N7 site of guanine [102] but in a less pronounced way than phosphate [101]. However, both Ru(II) and (III)-complexes have a common tendency to bind to the N7 site of guanine which is similar to CIS [103]. Some Ru-complexes such as Ru(III)-PTA compound trans-[RuCl 4 (1,3,5-triaza-7phosphaadamantane protonated at one N atom) 2 ]Cl (1a), η6-arene Ru-complexes particularly Ru-5-chloro-3-((5-(3-(4-methyl-1,4-diazepane-1-carbonyl)phenyl)furan-2-yl)methylene)indolin-2-one (1b), Ru(II) arene complexes including [(η6-fluorene)RuII(ethylenediamine)Cl] + (1c), and [(η6-9,10-dihydrophenanthrene)RuII(ethylenediamine)Cl] + (1d) mediated apoptosis in CRC cells by damaging DNA (Figure 4) [75][76][77].…”

“…Ru(III)-complexes also have been reported to bind to the N7 site of guanine [ 102 ] but in a less pronounced way than phosphate [ 101 ]. However, both Ru(II) and (III)-complexes have a common tendency to bind to the N7 site of guanine which is similar to CIS [ 103 ].…”

Towards Higher Sensitivity of Mass Spectrometry: A Perspective From the Mass Analyzers

“…FT-ICR analyzer has high mass accuracy and resolution (Bogdanov and Smith, 2005;Nagornov et al, 2014). It has become an important tool for the analysis of complex mixtures and molecular structures of large biomolecules (Sampson et al, 2009;Zeng et al, 2019). However, the instrument requires a strong magnetic field and an extremely high vacuum.…”