Screening of Threading Bis-Intercalators Binding to Duplex DNA by Electrospray Ionization Tandem Mass Spectrometry

Carolyn L. Mazzitelli, Yongjun Chu, Joseph J. Reczek, Brent L. Iverson, Jennifer S. Brodbelt

Research output: Contribution to journalArticle

27 Citations (Scopus)

Abstract

The DNA binding of novel threading bis-intercalators V1, trans-D1, and cis-C1, which contain two naphthalene diimide (NDI) intercalation units connected by a scaffold, was evaluated using electrospray ionization mass spectrometry (ESI-MS) and DNAse footprinting techniques. ESI-MS experiments confirmed that V1, the ligand containing the -Gly3-Lys- peptide scaffold, binds to a DNA duplex containing the 5′-GGTACC-3′ specific binding site identified in previous NMR-based studies. The ligand formed complexes with a ligand/DNA binding stoichiometry of 1:1, even when there was excess ligand in solution. Trans-D1 and cis-C1 are new ligands containing a rigid spiro-tricyclic scaffold in the trans- and cis- orientations, respectively. Preliminary DNAse footprinting experiments identified possible specific binding sites of 5′-CAGTGA-5′ for trans-D1 and 5′-GGTACC-3′ for cis-C1. ESI-MS experiments revealed that both ligands bound to DNA duplexes containing the respective specific binding sequences, with cis-C1 exhibiting the most extensive binding based on a higher fraction of bound DNA value. Cis-C1 formed complexes with a dominant 1:1 binding stoichiometry, whereas trans-D1 was able to form 2:1 complexes at ligand/DNA molar ratios ≥1 which is suggestive of nonspecific binding. Collisional activated dissociation (CAD) experiments indicate that DNA complexes containing V1, trans-D1, and cis-C1 have a unique fragmentation pathway, which was also observed for complexes containing the commercially available bis-intercalator echinomycin, as a result of similar binding interactions, marked by intercalation in addition to hydrogen bonding by the scaffold with the DNA major or minor groove.

Original languageEnglish (US)
Pages (from-to)311-321
Number of pages11
JournalJournal of the American Society for Mass Spectrometry
Volume18
Issue number2
DOIs
StatePublished - Feb 1 2007

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Intercalating Agents
Electrospray ionization
Electrospray Ionization Mass Spectrometry
Tandem Mass Spectrometry
Mass spectrometry
Screening
Ligands
DNA
Scaffolds
Intercalation
Stoichiometry
Echinomycin
Experiments
Binding Sites
Hydrogen Bonding
Hydrogen bonds
Nuclear magnetic resonance
Peptides

ASJC Scopus subject areas

  • Structural Biology
  • Spectroscopy

Cite this

Screening of Threading Bis-Intercalators Binding to Duplex DNA by Electrospray Ionization Tandem Mass Spectrometry. / Mazzitelli, Carolyn L.; Chu, Yongjun; Reczek, Joseph J.; Iverson, Brent L.; Brodbelt, Jennifer S.

In: Journal of the American Society for Mass Spectrometry, Vol. 18, No. 2, 01.02.2007, p. 311-321.

Research output: Contribution to journalArticle

Mazzitelli, Carolyn L. ; Chu, Yongjun ; Reczek, Joseph J. ; Iverson, Brent L. ; Brodbelt, Jennifer S. / Screening of Threading Bis-Intercalators Binding to Duplex DNA by Electrospray Ionization Tandem Mass Spectrometry. In: Journal of the American Society for Mass Spectrometry. 2007 ; Vol. 18, No. 2. pp. 311-321.
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