Infrared Multiphoton Dissociation of Duplex DNA/Drug Complexes in a Quadrupole Ion Trap

• Published in: Analytical chemistry (Washington) Vol. 79; no. 5; pp. 2067 - 2077
• Main Authors: Wilson, Jeffrey J, Brodbelt, Jennifer S
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 01.03.2007
• Subjects: Analytical chemistry; Base Sequence; Chemistry; Chromatographic methods and physical methods associated with chromatography; Deoxyribonucleic acid; DNA; DNA - chemistry; Drugs; Exact sciences and technology; Gas chromatographic methods; Ions; Mass spectrometry; Pharmaceutical Preparations - chemistry; Photons; Spectrometric and optical methods; Spectrometry, Mass, Electrospray Ionization; Spectrophotometry, Infrared - methods; Drug; Phosphates; Collisional activation; Cross section; Laser irradiation; Multiphoton process; Quadrupole spectrometer; Fragmentation; Gas chromatography; Ion trap; Sensitivity; DNA; Mass spectrometry MS/MS; Dissociation; Mass spectrometry
• ISSN: 0003-2700; 1520-6882
• DOI: 10.1021/ac061946f

Noncovalent duplex DNA/drug complexes formed between one of three 14-base pair non-self-complementary duplexes with variable GC content and one of eight different DNA-interactive drugs are characterized by infrared multiphoton dissociation (IRMPD), and the resulting spectra are compared to conventional collisionally activated dissociation (CAD) mass spectra in a quadrupole ion trap mass spectrometer. IRMPD yielded comparable information to previously reported CAD results in which strand separation pathways dominate for complexes containing the more AT-rich sequences and/or minor groove binding drugs, whereas drug ejection pathways are prominent for complexes containing intercalating drugs and/or duplexes with higher GC base content. The large photoabsorptive cross section of the phosphate backbone at 10.6 μm promotes highly efficient dissociation within short irradiation times (<2 ms at 50 W) or using lower laser powers and longer irradiation times (<15 W at 15 ms), activation times on par with or shorter than standard CAD experiments. This large photoabsorptivity leads to a controllable ion activation method which can be used to produce qualitatively similar spectra to CAD while minimizing uninformative base loss dissociation pathways or instead be tuned to yield a high degree of secondary fragmentation. Additionally, the low-mass cutoff associated with conventional CAD plays no role in IRMPD, resulting in richer MS/MS information in the low m/z region. IRMPD is also used for multiadduct dissociation in order to increase MS/MS sensitivity, and a two-stage IRMPD/IRMPD method is demonstrated as a means to give specific DNA sequence information that would be useful when screening drug binding by mixtures of duplexes.