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Differentiation and Distributions of DNA/Cisplatin Crosslinks by Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation Mass Spectrometry

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Journal of The American Society for Mass Spectrometry

Abstract

Liquid chromatography-electrospray ionization-infrared multiphoton dissociation (IRMPD) mass spectrometry was developed to investigate the distributions of intrastrand crosslinks formed between cisplatin and two oligodeoxynucleotides (ODNs), d(A1T2G3G4G5T6A7C8C9C10A11T12) (G3-D) and its analog d(A1T2G3G4G5T6T7C8C9C10A11T12) (G3-H), which have been reported to adopt different secondary structures in solution. Based on the formation of site-specific fragment ions upon IRMPD, two isobaric crosslink products were differentiated for each ODN. The preferential formation of G3G4 and G4G5 crosslinks was determined as a function of reaction conditions, including incubation temperature and presence of metal ions. G3-D consistently exhibited a greater preference for formation of the G4G5 crosslink compared with the G3-H ODN. The ratio of G3G4:G4G5 crosslinks increased for both G3-D and G3-H at higher incubation temperatures or when metal salts were added. Comparison of the IRMPD fragmentation patterns of the unmodified ODNs and the intramolecular platinated crosslinks indicated that backbone cleavage was significantly suppressed near the crosslink.

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Acknowledgments

Funding from NIH (RO1 GM65956) and the Welch Foundation (F1155) is gratefully acknowledged.

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Authors and Affiliations

  1. Department of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, TX, 78712, USA

    Zhe Xu & Jennifer S. Brodbelt

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  1. Zhe Xu
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  2. Jennifer S. Brodbelt
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Correspondence to Jennifer S. Brodbelt.

Electronic supplementary material

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Supplemental Figure 1

Oligonucleotide fragmentation nomenclature. Internal fragments result from a double backbone cleavage. The internal ions have a phosphate at their 5′ end and a furan at the 3′ terminal. (PDF 62 kb)

Supplemental Figure 2

Expanded regions of IRMPD spectra for (A) G3-D/cisplatin and (B) G3-H/cisplatin adducts showing some of the diagnostic fragment ions that allow differentation of the adducts. (PDF 46 kb)

Supplemental Figure 3

Relative abundances of IRMPD fragment ions at each backbone cleavage site for (a) all fragments of [G3-D-3H]3-; (b) all fragments of [G3-H-3H]3-. (PDF 53 kb)

Supplemental Table 1

The relative abundances of fragments upon IRMPD for G3-D/cisplatin cross-links (3-) (PDF 56 kb)

Supplemental Table 2

The relative abundances of fragments upon IRMPD for G3-H/cisplatin cross-links (3-). (PDF 57 kb)

Supplemental Table 3

The relative abundances of fragments upon IRMPD for unmodified G3-D and G3-H (3-). (PDF 57 kb)

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Xu, Z., Brodbelt, J.S. Differentiation and Distributions of DNA/Cisplatin Crosslinks by Liquid Chromatography-Electrospray Ionization-Infrared Multiphoton Dissociation Mass Spectrometry. J. Am. Soc. Mass Spectrom. 25, 71–79 (2014). https://doi.org/10.1007/s13361-013-0755-1

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  • DOI: https://doi.org/10.1007/s13361-013-0755-1

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