G‐Quadruplex formation of deoxyguanosine in the presence of alkaline earth metal ions studied by electrospray ionization mass spectrometry

Sravani, M.; Nagaveni, V.; Prabhakar, S.; Vairamani, M.

doi:10.1002/rcm.5082

Cited by 18 publications

(30 citation statements)

References 23 publications

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“…); (iv) the G-quadruplex was formed at the center of the incorporated strands, while leaving the duplex regions unaltered; (v) we could successfully monitor the conformational switching of the G-rich strands with as few as three contiguous G-repeats with concentrations in the nanomolar range of the strands in solution and roughly picomolar on the mica surface; (vi) in all cases, a minor but significant amount of X-shapes were formed in the K + -free condition, possibly 10 mM Mg 2+ present in the buffer may have induced a small amount of quadruplex structure. Note that previous studies using electrospray ionization mass spectrometry proved that the G-quadruplex can be formed in the presence of alkaline earth metal ions such as Mg 2+ , Ca 2+ , Sr 2+ and Ba 2+ (48). The stability order obtained was Sr 2+ > Ba 2+ > Ca 2+ >> Mg 2+ (48).…”

Section: Resultsmentioning

confidence: 94%

“…Note that previous studies using electrospray ionization mass spectrometry proved that the G-quadruplex can be formed in the presence of alkaline earth metal ions such as Mg 2+ , Ca 2+ , Sr 2+ and Ba 2+ (48). The stability order obtained was Sr 2+ > Ba 2+ > Ca 2+ >> Mg 2+ (48). Thus, we expect that the X-shape in the K + -free buffer could be the G-quadruplex induced by Mg 2+ ions.…”

Section: Resultsmentioning

confidence: 94%

“…Thus, we have performed our analyses within a nanovessel (46,47) constructed using the origami method. Cations such as K + and Na + are known to stabilize the G-quadruplex structures via binding at the center of the G-quadruplex, generally sandwiched between two consecutive quartets (48). Because of the high intracellular concentration of K + , we have used K + ions to mimic the cell-like condition and to execute the conformational switching.…”

Section: Introductionmentioning

confidence: 99%

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Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame

Rajendran¹,

Endo²,

Hidaka³

et al. 2013

Nucleic Acids Research

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Guanine-rich oligonucleotides often show a strong tendency to form supramolecular architecture, the so-called G-quadruplex structure. Because of the biological significance, it is now considered to be one of the most important conformations of DNA. Here, we describe the direct visualization and single-molecule analysis of the formation of a tetramolecular G-quadruplex in KCl solution. The conformational changes were carried out by incorporating two duplex DNAs, with G–G mismatch repeats in the middle, inside a DNA origami frame and monitoring the topology change of the strands. In the absence of KCl, incorporated duplexes had no interaction and laid parallel to each other. Addition of KCl induced the formation of a G-quadruplex structure by stably binding the duplexes to each other in the middle. Such a quadruplex formation allowed the DNA synapsis without disturbing the duplex regions of the participating sequences, and resulted in an X-shaped structure that was monitored by atomic force microscopy. Further, the G-quadruplex formation in KCl solution and its disruption in KCl-free buffer were analyzed in real-time. The orientation of the G-quadruplex is often difficult to control and investigate using traditional biochemical methods. However, our method using DNA origami could successfully control the strand orientations, topology and stoichiometry of the G-quadruplex.

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Section: Resultsmentioning

confidence: 94%

Section: Resultsmentioning

confidence: 94%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame

Rajendran¹,

Endo²,

Hidaka³

et al. 2013

Nucleic Acids Research

View full text Add to dashboard Cite

show abstract

“…This is a safe approximation since at a relatively basic solution pH, both species possess the same charge (although they differ structurally due to the coordination of a metal cation). Moreover, the deduction from these ESI MS screening experiments implies that any unaccounted artefact would similarly occur in all Be/ligand combinations, such that accurate trends in binding affinities can be obtained, as has been reported elsewhere , …”

Section: Resultsmentioning

confidence: 60%

Electrospray Ionisation Mass Spectrometric (ESI MS) Screening and Characterisation of Beryllium Complexes with Potentially Encapsulating Aminopolycarboxylate and Related Ligands

et al. 2018

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A fundamental issue in beryllium research is the search for suitable chelating ligands for environmental and biomedical application. In this paper, the speciation of beryllium ions with several multidentate aminopolycarboxylic acids, which are well‐known commercial and biomedical chelating agents, has been investigated using electrospray ionisation mass spectrometry (ESI MS). Stoichiometric information, which was readily obtained from the ESI mass spectra, was found to be effective for the preliminary screening of potential encapsulation by tetradentate coordination from a single ligand. Ions observed by ESI MS revealed that the pre‐existing solution species and binding affinity trends were preserved into the gas phase in good agreement with previous solution speciation data, suggesting the ability of ESI MS to be developed as a quick, sensitive and safe screening technique to observe beryllium speciation with ligands of interest at low concentrations. The disruption of beryllium‐ligand binding by addition of other di‐ or trivalent metal cations is also reported.

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“…The minor but significant amount of X-shapes observed under this condition could possibly because of the Mg 2+ ions present in the buffer which can induce small amount of quadruplex structure. 36,37 The parallel-shape was also obtained for all other sequences with different number of G-repeats such as four and three guanines (representative zoom-in images in Figure 3a) and different length of the strands such as 67 and 77 bp.…”

Section: Resultsmentioning

confidence: 79%

HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation

et al. 2013

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HIV-1 nucleocapsid proteins (NCps) facilitate remodeling of nucleic acids to fold thermodynamically stable conformations, and thus called nucleic acid chaperones. To date only little is known on the stoichiometry, NCp-NCp interactions, chaperone activity on G-quadruplex formation, and so on. We report here the direct and real-time analysis on such properties of proteolytic intermediate NCp15 and mature NCp7 using DNA origami. The protein particles were found to predominantly exist in monomeric form, while dimeric and multimeric forms were also observed both in free solution and bound to the quadruplex structure. The formation and the dissociation events of the G-quadruplexes were well documented in real-time and the intermediate-like states were also visualized. We anticipate that this pioneering study will strengthen our understanding on the chaperone activity of HIV-1 proteins which in turn will be helpful for the drug design based on G-quadruplex and also for the development of drugs against AIDS.

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G‐Quadruplex formation of deoxyguanosine in the presence of alkaline earth metal ions studied by electrospray ionization mass spectrometry

Cited by 18 publications

References 23 publications

Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame

Controlling the stoichiometry and strand polarity of a tetramolecular G-quadruplex structure by using a DNA origami frame

Electrospray Ionisation Mass Spectrometric (ESI MS) Screening and Characterisation of Beryllium Complexes with Potentially Encapsulating Aminopolycarboxylate and Related Ligands

HIV-1 Nucleocapsid Proteins as Molecular Chaperones for Tetramolecular Antiparallel G-Quadruplex Formation

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