ArticleJournal of the American Society for Mass Spectrometry2007
Gas-phase stability of G-quadruplex DNA determined by electrospray ionization tandem mass spectrometry and molecular dynamics simulations.
Article in Journal of the American Society for Mass Spectrometry, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 37 citations in OpenAlex.
- Negative Electron Transfer Collision-Induced Dissociation of G-Quadruplexes: Uncovering the Guanine Radical Anion Loss Pathway.Journal of the American Society for Mass Spectrometry · 2024Article
- Gas-Phase Fragmentation as a Probe of G-Quadruplex Formation.Analytical chemistry · 2023Article
- Antiparallel RNA G-quadruplex Formed by Human Telomere RNA Containing 8-Bromoguanosine.Scientific reports · 2017Article
- The Role of Fluorinated Alcohols as Mobile Phase Modifiers for LC-MS Analysis of Oligonucleotides.Journal of the American Society for Mass Spectrometry · 2017Article
- Tuning supramolecular G-quadruplexes with mono- and divalent cations.Supramolecular chemistry · 2015Article
- ESI mass spectrometric exploration of selective recognition of G-quadruplex in c-myb oncogene promoter using a novel flexible cyclic polyamide.Journal of the American Society for Mass Spectrometry · 2014Article
- Ammonium ion binding to DNA G-quadruplexes: do electrospray mass spectra faithfully reflect the solution-phase species?Journal of the American Society for Mass Spectrometry · 2013Article
- Examination of the effect of the annealing cation on higher order structures containing guanine or isoguanine repeats.Chemistry (Weinheim an der Bergstrasse, Germany) · 2009Article
- Interactions of sulfur-containing acridine ligands with DNA by ESI-MS.The Analyst · 2009Article
- Evaluation of binding selectivities and affinities of platinum-based quadruplex interactive complexes by electrospray ionization mass spectrometry.Biopolymers · 2009Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The relative gas-phase stabilities of seven quadruplex DNA structures, [d(TG(4)T)](4), [d(T(2)G(3)T)](4), [d(G(4)T(4)G(4))](2), [d(T(2)AG(3))(2)](2), d(T(2)AG(3))(4), d(T(2)G(4))(4), and d(G(2)T(4))(4), were investigated using molecular dynamics simulations and electrospray ionization mass spectrometry (ESI-MS). MD simulations revealed that the G-quadruplexes maintained their structures in the gas phase although the G-quartets were distorted to some degree and ammonium ions, retained by [d(TG(4)T)](4) and [d(T(2)G(3)T)](4), played a key role in stabilizing the tetrad structure. Energy-variable collisional activated dissociation was used to assess the relative stabilities of each quadruplex based on E(1/2) values, and the resulting order of relative stabilities was found to be [d(TG(4)T)](4) >> d(T(2)AG(3))(4) approximately d(T(2)G(4))(4) > [d(T(2)G(3)T)](4) > [d(T(2)AG(3))(2)](2) approximately d(G(2)T(4))(4) approximately [d(G(4)T(4)G(4))](2.) The stabilities from the E(1/2) values generally paralleled the RMSD and relative free energies of the quadruplexes based on the MD energy analysis. One exception to the general agreement is [d(G(4)T(4)G(4))](2), which had the lowest E(1/2) value, but was determined to be the most stable quadruplex according to the free-energy analysis and ranked fourth based on the RMSD comparison. This discrepancy is attributed to differences in the fragmentation pathway of the quadruplex.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.