Assessment of the gas phase stability of quadruplex DNA using travelling wave ion mobility mass spectrometry

Porter, Karina C.; Beck, Jennifer L.

doi:10.1016/j.ijms.2010.10.033

Cited by 7 publications

(7 citation statements)

References 35 publications

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“…The ion [qDNA -5 H] 5-was the most abundant with the latter two ions present at lower, similar abundance. Circular dichroism (CD) spectra can be used to demonstrate the presence of qDNA and other nucleic acid structures in solution [29][30][31]. CD spectra of annealed solutions of qDNA used to obtain ESI mass spectra showed a maximum positive ellipticity at 290 nm, consistent with predominantly antiparallel qDNA [30] (Supplementary Figure S3a), confirming that qDNA was present in solution.…”

Section: Esi-ms Of Bimolecular Qdna and Dna/rna Hybridmentioning

confidence: 86%

“…The absence of ammonium ions from the bimolecular [qDNA -5 H] 5-(m/z 1501.5) suggests that they may have been lost during the ionization and/or mass analysis processes while the assembly of the two strands remained intact [11,29] with that previously obtained using a similar hybrid sequence [32]. Since the qDNA structure with two bound ammonium ions was more abundant in the ESI mass spectra acquired when the RF lens 1 voltage was lower (50 V), these conditions were applied to determine if they were also suitable for analysis of the hybrid DNA/RNA duplex.…”

Section: Esi-ms Of Bimolecular Qdna and Dna/rna Hybridmentioning

confidence: 99%

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ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

Birrento

Bryan

Samosorn

et al. 2015

J. Am. Soc. Mass Spectrom.

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, J. L. (2015). ESI-MS investigation of an equilibrium between a bimolecular quadruplex DNA and a duplex DNA/RNA hybrid. Journal of the American Society for Mass Spectrometry, 26 (7), 1165-1173.ESI-MS investigation of an equilibrium between a bimolecular quadruplex DNA and a duplex DNA/RNA hybrid AbstractElectrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the quadruplex DNA (qDNA) resulted in formation of the duplex DNA/ RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine (1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its circular dichroism (CD) melting temperature of 10°C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of (1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid. Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if telomeric DNA was folded into a qDNA structure, it is possible for a DNA/RNA hybrid to form as is required during template alignment. The discrimination of ligand (1) AbstractElectrospray ionization mass spectrometry (ESI-MS) conditions were optimized for simultaneous observation of a bimolecular qDNA and a Watson-Crick base-paired duplex DNA/RNA hybrid. The DNA sequence used was telomeric DNA, and the RNA contained the template for telomerase-mediated telomeric DNA synthesis. Addition of RNA to the qDNA resulted in formation of the duplex DNA/RNA hybrid. Melting profiles obtained using circular dichroism spectroscopy confirmed that the DNA/RNA hybrid exhibited greater thermal stability than the bimolecular qDNA in solution. Binding of a 13-substituted berberine (1) derivative to the bimolecular qDNA stabilized its structure as evidenced by an increase in its stability in the mass spectrometer, and an increase in its (CD) melting temperature of 10 C. The DNA/RNA hybrid did not bind the ligand extensively and its thermal stability was unchanged in the presence of (1). The qDNA-ligand complex resisted unfolding in the presence of excess RNA, limiting the formation of the DNA/RNA hybrid.Previously, it has been proposed that DNA secondary structures, such as qDNA, may be involved in the telomerase mechanism. DNA/RNA hybrid structures occur at the active site of telomerase. The results presented in the current work show that if tel...

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Section: Esi-ms Of Bimolecular Qdna and Dna/rna Hybridmentioning

confidence: 86%

Section: Esi-ms Of Bimolecular Qdna and Dna/rna Hybridmentioning

confidence: 99%

ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

Birrento

Bryan

Samosorn

et al. 2015

J. Am. Soc. Mass Spectrom.

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“…In contrast, published G-quadruplex MS spectra recorded in purely aqueous ammonium acetate solutions [34][35][36] often show lower signalto-noise ratio. Porter and Beck recently mentioned that slight solvent-induced changes in G-quadruplexes were evidenced by ion mobility spectrometry, but the solvent effect was not extensively studied [37]. It is therefore very tempting to systematically add low amounts of organic co-solvents to perform ESI-MS of nucleic acid complexes, and in our past methodological reviews we were also recommending adding 10-20% methanol ''just prior to ESI-MS analysis'' [10,38].…”

Section: Electrospray Ion Mobility Mass Spectrometry (Esi-ims-ms)mentioning

confidence: 99%

Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT)

Ferreira

Marchand

Gabelica

2012

Methods

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We survey here state of the art mass spectrometry methodologies for investigating G-quadruplexes, and will illustrate them with a new study on a simple model system: the dimeric G-quadruplex of the 12-mer telomeric DNA sequence d(TAGGGTTAGGGT), which can adopt either a parallel or an antiparallel structure. We will discuss the solution conditions compatible with electrospray ionisation, the quantification of complexes using ESI-MS, the interpretation of ammonium ion preservation in the complexes in the gas phase, and the use of ion mobility spectrometry to resolve ambiguities regarding the strand stoichiometry, or separate and characterise different structural isomers. We also describe that adding electrospray-compatible organic co-solvents (methanol, ethanol, isopropanol or acetonitrile) to aqueous ammonium acetate increases the stability and rate of formation of dimeric G-quadruplexes, and causes structural transitions to parallel structures. Structural changes were probed by circular dichroism and ion mobility spectrometry, and the excellent correlation between the two techniques validates the use of ion mobility to investigate G-quadruplex folding. We also demonstrate that parallel G-quadruplex structures are easier to preserve in the gas phase than antiparallel structures.

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“…In recent times, the coupling of (nano)ESI-MS with ion mobility mass spectrometry (IMMS) has offered the promise of adding to the structural information available from ESI-MS alone. IMMS can provide measurements of collisional cross-section (CCS) and can also be used to compare the conformations and unfolding of biomolecules [2] and biomolecular complexes under different conditions [3], and to characterize the quaternary structure of protein complexes [4].…”

Section: Introductionmentioning

confidence: 99%

Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS

Harrison

Kelso

Pukala

et al. 2018

J. Am. Soc. Mass Spectrom.

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Determination of collisional cross sections (CCS) by travelling wave ion mobility mass spectrometry (TWIM-MS) requires calibration against standards for which the CCS has been measured previously by drift tube ion mobility mass spectrometry (DTIM-MS). The different extents of collisional activation in TWIM-MS and DTIM-MS can give rise to discrepancies in the CCS of calibrants across the two platforms. Furthermore, the conditions required to ionize and transmit large, folded proteins and assemblies may variably affect the structure of the calibrants and analytes. Stable hetero-oligomeric phospholipase A 2 (PDx) and its subunits were characterized as calibrants for TWIM-MS. Conditions for acquisition of native-like TWIM (Synapt G1 HDMS) and DTIM (Agilent 6560 IM-Q-TOF) mass spectra were optimized to ensure the spectra exhibited similar charge state distributions. CCS measurements (DTIM-MS) for ubiquitin, cytochrome c, holo-myoglobin, serum albumin and glutamate dehydrogenase were in good agreement with other recent results determined using this and other DTIM-MS instruments. PDx and its β and γ subunits were stable across a wide range of cone and trap voltages in TWIM-MS and were stable in the presence of organic solvents. The CCS of PDx and its subunits were determined by DTIM-MS and were used as calibrants in determination of CCS of native-like cytochrome c, holo-myoglobin, carbonic anhydrase, serum albumin and haemoglobin in TWIM-MS. The CCS values were in good agreement with those measured by DTIM-MS where available. These experiments demonstrate conditions for analysis of native-like proteins using a commercially available DTIM-MS instrument, characterize robust calibrants for TWIM-MS, and present CCS values determined by DTIM-MS and TWIM-MS for native proteins to add to the current literature database.

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Assessment of the gas phase stability of quadruplex DNA using travelling wave ion mobility mass spectrometry

Cited by 7 publications

References 35 publications

ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

ESI-MS Investigation of an Equilibrium between a Bimolecular Quadruplex DNA and a Duplex DNA/RNA Hybrid

Mass spectrometry and ion mobility spectrometry of G-quadruplexes. A study of solvent effects on dimer formation and structural transitions in the telomeric DNA sequence d(TAGGGTTAGGGT)

Conditions for Analysis of Native Protein Structures Using Uniform Field Drift Tube Ion Mobility Mass Spectrometry and Characterization of Stable Calibrants for TWIM-MS

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