Observation of Duplex DNA-Drug Noncovalent Complexes by Electrospray Ionization Mass Spectrometry

Gale, David C.; Light-Wahl, Karen J.; Smith, Richard D.

doi:10.1021/ja00092a087

Cited by 109 publications

(85 citation statements)

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“…During the last decade the development of electrospray ionisation mass spectrometry (ESI-MS) has allowed accurate mass measurements to be performed on relatively large oligonucleotides including plasmid DNA. [15][16][17][18][19] ESI-MS has also been used for the characterisation of covalent [20][21][22][23][24] and non-covalent [25][26][27][28] drug-DNA complexes. For example, ESI-MS studies on DNA bound to the antibiotic hedamycin revealed that the drug selectively binds to specific DNA sequences and significantly increased the stability of duplex DNA in the gas phase.…”

Section: Introductionmentioning

confidence: 99%

Electrospray ionisation mass spectrometry of ruthenium and palladium complexes with oligonucleotides

Beck¹,

Humphries²,

Sheil³

et al. 1999

Eur. J. Mass Spectrom.

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Electrospray ionisation mass spectrometry (ESI-MS) was used to characterise complexes formed in reactions between[Pd(en)Cl 2 ] reacted more extensively with 5′-GGCTAGCC-3′ than the ruthenium complexes, since ESI mass spectra showed ions arising from complexes containing two, three and four Pd(en) moieties bound to the oligonucleotide. Mass spectra obtained after purifying the reaction mixture by HPLC indicated that the major complex contained only two Pd(en) units bound to the oligonucleotide, suggesting that ions containing three or four Pd(en) units were formed predominantly by gas-phase chemistry in the ion source.

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Section: Introductionmentioning

confidence: 99%

Electrospray ionisation mass spectrometry of ruthenium and palladium complexes with oligonucleotides

Beck¹,

Humphries²,

Sheil³

et al. 1999

Eur. J. Mass Spectrom.

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confidence: 99%

“…The binding selectivity and the stoichiometry of noncovalent complexes formed by DNA [22][23][24][25][26][27][28] and RNA [29 -32] substrates with a variety of small organic molecules can be determined unambiguously from di-rect mass determinations, rather than from curve fitting of bulk data provided by spectroscopic and calorimetric methods. Relative and absolute binding affinities are readily attainable by strategies that rely on the ability of ESI-MS to resolve complexes with very close physicalchemical characteristics, which are not easily discriminated by other established techniques.…”

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confidence: 99%

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

Turner

Hagan

Kohlway

et al. 2006

J. Am. Soc. Mass Spectrom.

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The binding modes and structural determinants of the noncovalent complexes formed by aminoglycoside antibiotics with conserved domains of the HIV-1 packaging signal (⌿-RNA) were investigated using electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). The location of the aminoglycoside binding sites on the different stemloop structures was revealed by characteristic coverage gaps in the ion series obtained by sustained off-resonance irradiation collision induced dissociation (SORI-CID) of the antibiotic-RNA assemblies. The site positions were confirmed using mutants that eliminated salient structural features of the ⌿-RNA domains. The effects of the mutations on the binding properties of the different substrates served to validate the position of the aminoglycoside site on the wild-type structures. Additional information was provided by docking experiments performed on the different aminoglycoside-stemloop complexes. The results have shown that, in the absence of features disrupting the regular A-helix of the double-stranded stem, aminoglycosides tend to bind in an area situated between the upper stem and the loop regions, as demonstrated for stemloop SL3. The presence of a tandem wobbles motif in SL4 modifies the regular geometry of the upper stem, which does not affect the general site location, but greatly increases its solution binding affinity compared with SL3. The platform motif in SL2 locates the binding site in the stem midsection and confers upon this stemloop an intermediate affinity toward aminoglycosides. In SL3 and SL4, the extensive overlap of the antibiotic site with the region used to bind the nucleocapsid (NC) protein provides the basis for a competition mechanism that could explain the aminoglycoside inhibition of the NC·SL3 and NC·SL4 assemblies. In contrast, the minimal overlap between the aminoglycoside and the NC sites in SL2 accounts for the absence of inhibition of the NC·SL2 complex. . The relatively low mutation frequency of this ϳ120 nt stretch of genomic RNA makes the packaging signal a very promising target for the development of new therapeutic strategies to contend with the rapid emergence of drug resistant strains [7,8]. For this reason, steps have been made toward the identification of possible inhibitors that may bind specific ⌿-RNA structures and disrupt their normal functions [9 -11]. In a systematic investigation of classic nucleic acid ligands, we have recently shown that aminoglycosidic antibiotics are not only capable of binding individual domains of ⌿-RNA, but can also inhibit their interactions with NC in a structure-specific fashion [12]. Initial tests to locate the actual binding sites on the different RNA substrates, which is crucial to explain the mechanism of preferential inhibition, were based on the analysis of mutant-ligand complexes performed by electrospray ionization (ESI) [13,14] and Fourier transform mass spectrometry (FTMS) [15,16].The favorable energetics characteristic of ESI enable the analysis of relatively labile noncovalent complex...

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“…Mass spectrometry has evolved to contribute to biological research on many frontiers (Ganem et al, 1991;Goodlett et al, 1993;Light-Wahl et al, 1993;Gale et al, 1994;Verentchikov et al, 1994;Little et al, 1995;Liu et al, 1995;Loo, 1995;Fitzgerald et al, 1996;Muddiman et al, 1996;Smith et al, 1996). The analysis of many types of biomolecules, including DNA, RNA, proteins, and their noncovalent complexes with mass spectrometry is rapidly becoming of great utility.…”

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confidence: 99%

The observation of chaperone‐ligand noncovalent complexes with electrospray ionization mass spectrometry

et al. 1998

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Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) was applied for the study of noncovalent chaperone SecB-ligand complexes produced in solution and examined in the gas phase with the aid of electrospray ionization (ESI). Since chaperone proteins are believed to recognize and bind only with ligands with nonnative tertiary structure, this work required careful unfolding of the ligand and subsequent reaction with the intact chaperone (the noncovalent tetrameric protein, SecB). A high denaturant concentration was employed to produce nonnative structures of the OppA, and microdialysis of the resulting solutions containing the chaperone-ligand complexes was camed out to rapidly remove the denaturant prior to analysis. Multistage mass spectrometry was essential to the successful study of these complexes since the initial mass spectra indicated extensive adduction that precluded mass measurements, even after microdialysis. However, low energy collisional activation of the ions in the FTICR trap proved useful for adduct removal, and careful control of excitation level preserved the intact complexes of interest, revealing a 1 : 1 SecB:OppA stoichiometry. To our knowledge, these results present the first direct observation of chaperone-ligand noncovalent complexes and the highest molecular weight heterogeneous noncovalent complex observed to date by mass spectrometry. Furthermore, these results highlight the capabilities of FTICR for the study of such complex systems, and the development of a greater understanding of chaperone interactions in protein export.Keywords: dissociation; Fourier transform ion cyclotron resonance; MS/MS; OppA; protein export; SecB; stoichiometry Mass spectrometry has evolved to contribute to biological research on many frontiers (Ganem et al

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Observation of Duplex DNA-Drug Noncovalent Complexes by Electrospray Ionization Mass Spectrometry

Cited by 109 publications

References 0 publications

Electrospray ionisation mass spectrometry of ruthenium and palladium complexes with oligonucleotides

Electrospray ionisation mass spectrometry of ruthenium and palladium complexes with oligonucleotides

Mapping noncovalent ligand binding to stemloop domains of the HIV-1 packaging signal by tandem mass spectrometry

The observation of chaperone‐ligand noncovalent complexes with electrospray ionization mass spectrometry

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