Nucleic acid ion structures in the gas phase

Abi-Ghanem, Joséphine; Gabelica, Valérie

doi:10.1039/c4cp02362e

Cited by 27 publications

(24 citation statements)

References 164 publications

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“…However due to the gentleness and ease of ionizing DNA in negative ion mode, ESI-MS has long been used to detect delicate DNA bindings, including non-covalent attachment of molecules to DNA [28] and for investigation of binding stoichiometries to DNA [29]. Gas phase ESI-MS data for binding stoichiometry studies has also been experimentally shown to agree with high fidelity to solution phase data [30], though some fragmentation of canonically paired DNA oligomers may occur depending on the instrumental conditions employed [31,32]. Due to the considerably higher strength of Ag + -mediated pairings than WC pairings [23], we expect minimal fragmentation for these non-canonical, metal-bridged products and gas-phase distributions that are good approximations to solution phase abundances.…”

Section: Resultsmentioning

confidence: 99%

Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

Swasey

Gwinn

2016

New J. Phys.

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The thermal and chemical fragility of DNA nanomaterials assembled by Watson-Crick (WC) pairing constrain the settings in which these materials can be used and how they can be functionalized. Here we investigate use of the silver cation, Ag + , as an agent for more robust, metal-mediated self-assembly, focusing on the simplest duplex building blocks that would be required for more elaborate Ag + -DNA nanostructures. Our studies of Ag + -induced assembly of non-complementary DNA oligomers employ strands of 2-24 bases, with varied base compositions, and use electrospray ionization mass spectrometry to determine product compositions. High yields of duplex products containing narrowly distributed numbers of Ag + can be achieved by optimizing solution conditions. These Ag +mediated duplexes are stable to at least 60 mM Mg 2+ , higher than is necessary for WC nanotechnology schemes such as tile assemblies and DNA origami, indicating that sequential stages of Ag + -mediated and WC-mediated assembly may be feasible. Circular dichroism spectroscopy suggests simple helical structures for Ag + -mediated duplexes with lengths to at least 20 base pairs, and further indicates that the structure of cytosine-rich duplexes is preserved at high urea concentrations. We therefore propose an approach towards dynamic DNA nanomaterials with enhanced thermal and chemical stability through designs that combine sturdy silver-mediated 'frames' with WC paired 'pictures'.

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Section: Resultsmentioning

confidence: 99%

Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

Swasey

Gwinn

2016

New J. Phys.

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“…Indeed, besides the classical and widely known double‐stranded DNA sequence (duplex), a plethora of other helical structures can be found, such as hairpin, pseudoknot, triplex, cruciform (Holliday junction), and G‐quadruplex structures. Most of these DNA conformations have been studied by IM–MS and molecular dynamics, highlighting a more dynamic and complex behavior in the gas‐phase as compared to proteins .…”

Section: Application Of Ion Mobility Spectrometry To the Characterizamentioning

confidence: 99%

Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry?

D’Atri

Causon

Hernandez‐Alba

et al. 2017

J of Separation Science

148

142

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* These authors contributed equally.Ion mobility spectrometry is an analytical technique known for more than 100 years, which entails separating ions in the gas phase based on their size, shape, and charge. While ion mobility spectrometry alone can be useful for some applications (mostly security analysis for detecting certain classes of narcotics and explosives), it becomes even more powerful in combination with mass spectrometry and high-performance liquid chromatography. Indeed, the limited resolving power of ion mobility spectrometry alone can be tackled when combining this analytical strategy with mass spectrometry or liquid chromatography with mass spectrometry. Over the last few years, the hyphenation of ion mobility spectrometry to mass spectrometry or liquid chromatography with mass spectrometry has attracted more and more interest, with significant progresses in both technical advances and pioneering applications. This review describes the theoretical background, available technologies, and future capabilities of these techniques. It also highlights a wide range of applications, from small molecules (natural products,

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“…One chain terminus then gets expelled into the vapor phase, followed by stepwise sequential ejection of the remaining protein and separation from the droplet [19, 20]. Despite its success in explaining the ionization of unfolded protein chains, the CEM is unlikely to apply to nucleic acid chains because their hydrophobic and hydrophilic moieties are homogenously distributed along the chain [21]. …”

Section: Introductionmentioning

confidence: 99%

Assessing the Interplay between the Physicochemical Parameters of Ion-Pairing Reagents and the Analyte Sequence on the Electrospray Desorption Process for Oligonucleotides

Basiri

Murph

Bartlett

2017

J. Am. Soc. Mass Spectrom.

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Alkylamines are widely used as ion-pairing agents during LC-MS of oligonucleotides. In addition to a better chromatographic separation, they also assist with the desorption of oligonucleotide ions into the gas phase, cause charge state reduction and decrease cation adduction. However, the choice of such ion-pairing agents has considerable influence on the MS signal intensity of oligonucleotides as they can also cause significant ion suppression. Interestingly, optimal ion-pairing agents should be selected on a case by case basis as their choice is strongly influenced by the sequence of the oligonucleotide under investigation. Despite imposing major practical difficulties to analytical method development, such a highly variable system that responds very strongly to the nuances of the electrospray composition provides an excellent opportunity for a fundamental study of the electrospray ionization process. Our investigations using this system quantitatively revealed the major factors that influenced the ESI ionization efficiency of oligonucleotides. Parameters such as boiling point, proton affinity, partition coefficient, water solubility and Henry’s law constants for the ion-pairing reagents and the hydrophobic thymine content of the oligonucleotides were found to be the most significant contributors. Identification of these parameters also allowed for the development of a statistical predictive algorithm that can assist with the choice of an optimum IP agent for each particular oligonucleotide sequence. We believe that research in the field of oligonucleotide bioanalysis will significantly benefit from this algorithm (included in supplementary material) as it advocates for the use of lesser-known but more suitable ion-pair alternatives to TEA for many oligonucleotide sequences.

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Nucleic acid ion structures in the gas phase

Cited by 27 publications

References 164 publications

Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

Silver-mediated base pairings: towards dynamic DNA nanostructures with enhanced chemical and thermal stability

Adding a new separation dimension to MS and LC–MS: What is the utility of ion mobility spectrometry?

Assessing the Interplay between the Physicochemical Parameters of Ion-Pairing Reagents and the Analyte Sequence on the Electrospray Desorption Process for Oligonucleotides

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