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Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

D'Atri V, Porrini M, Rosu F, Gabelica V - J Mass Spectrom (2015)

Bottom Line: The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data.Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)?Which one(s) can I apply to my systems?

View Article: PubMed Central - PubMed

Affiliation: Univ. Bordeaux, IECB, ARNA laboratory, Pessac, F-33600, France.

No MeSH data available.


Related in: MedlinePlus

What is a G-quadruplex? (A) Four guanines forming a G-quartet via Hoogsteen H-bonds, involving N1-O6 and N2-N7 atoms. (B) Sequences containing consecutive guanines form G-quartets core stabilized by the coordination of monovalent cations in-between G-quartets. (C) 3-D crystal structure of the DNA G-quadruplex [dTGGGGT]4; cations shown as orange spheres; PDB reference 352D.[11]
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fig01: What is a G-quadruplex? (A) Four guanines forming a G-quartet via Hoogsteen H-bonds, involving N1-O6 and N2-N7 atoms. (B) Sequences containing consecutive guanines form G-quartets core stabilized by the coordination of monovalent cations in-between G-quartets. (C) 3-D crystal structure of the DNA G-quadruplex [dTGGGGT]4; cations shown as orange spheres; PDB reference 352D.[11]

Mentions: On the calculation side, we will discuss the choice of the starting model(s), the methods for three-dimensional structure calculation in the gas phase, the sampling of structures in the gas phase and the different methods available to calculate CCSs. To assess the errors and biases pertaining to modelling, we needed a system with limited conformational diversity in the gas phase. We chose the parallel-stranded [dTGGGGT]4 G-quadruplex DNA structure (Fig.1) because (1) starting atomic coordinates of [dTGGGGT]4 are available from X-ray crystallography,[11–14] (2) the same molecular assembly was studied by nuclear magnetic resonance (NMR) as well and presents the same G-quadruplex core arrangement, although the thymine placement differs, with evidence for T–T interactions,[15–17] and (3) the central guanine-rich core remains very rigid in the gas phase, [18–21] thanks to the preservation of the G-quartet hydrogen bonds and to the coordination of three ammonium cations in-between the four guanine G-quartets. Only the position of thymines in the gas phase is less certain.


Linking molecular models with ion mobility experiments. Illustration with a rigid nucleic acid structure.

D'Atri V, Porrini M, Rosu F, Gabelica V - J Mass Spectrom (2015)

What is a G-quadruplex? (A) Four guanines forming a G-quartet via Hoogsteen H-bonds, involving N1-O6 and N2-N7 atoms. (B) Sequences containing consecutive guanines form G-quartets core stabilized by the coordination of monovalent cations in-between G-quartets. (C) 3-D crystal structure of the DNA G-quadruplex [dTGGGGT]4; cations shown as orange spheres; PDB reference 352D.[11]
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4440389&req=5

fig01: What is a G-quadruplex? (A) Four guanines forming a G-quartet via Hoogsteen H-bonds, involving N1-O6 and N2-N7 atoms. (B) Sequences containing consecutive guanines form G-quartets core stabilized by the coordination of monovalent cations in-between G-quartets. (C) 3-D crystal structure of the DNA G-quadruplex [dTGGGGT]4; cations shown as orange spheres; PDB reference 352D.[11]
Mentions: On the calculation side, we will discuss the choice of the starting model(s), the methods for three-dimensional structure calculation in the gas phase, the sampling of structures in the gas phase and the different methods available to calculate CCSs. To assess the errors and biases pertaining to modelling, we needed a system with limited conformational diversity in the gas phase. We chose the parallel-stranded [dTGGGGT]4 G-quadruplex DNA structure (Fig.1) because (1) starting atomic coordinates of [dTGGGGT]4 are available from X-ray crystallography,[11–14] (2) the same molecular assembly was studied by nuclear magnetic resonance (NMR) as well and presents the same G-quadruplex core arrangement, although the thymine placement differs, with evidence for T–T interactions,[15–17] and (3) the central guanine-rich core remains very rigid in the gas phase, [18–21] thanks to the preservation of the G-quartet hydrogen bonds and to the coordination of three ammonium cations in-between the four guanine G-quartets. Only the position of thymines in the gas phase is less certain.

Bottom Line: The collision cross sections of candidate molecular models have to be calculated, and the resulting Ω(CALC) are compared with the experimental data.Researchers who want to apply this strategy to a new type of molecule face many questions: (1) What experimental error is associated with Ω(EXP) determination, and how to estimate it (in particular when using a calibration for traveling wave ion guides)?Which one(s) can I apply to my systems?

View Article: PubMed Central - PubMed

Affiliation: Univ. Bordeaux, IECB, ARNA laboratory, Pessac, F-33600, France.

No MeSH data available.


Related in: MedlinePlus