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
Article

DOI: 10.1016/j.jasms.2006.09.021

Cite this article as:
Mazzitelli, C.L., Chu, Y., Reczek, J.J. et al. J Am Soc Mass Spectrom (2007) 18: 311. doi:10.1016/j.jasms.2006.09.021

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.

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Copyright information

© American Society for Mass Spectrometry 2007

Authors and Affiliations

  • Carolyn L. Mazzitelli
    • 1
  • Yongjun Chu
    • 1
  • Joseph J. Reczek
    • 1
  • Brent L. Iverson
    • 1
  • Jennifer S. Brodbelt
    • 1
  1. 1.Department of Chemistry and BiochemistryUniversity of Texas at AustinAustinUSA

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