Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure

Takahashi, Shuntaro; Bhowmik, Sudipta; Sugimoto, Naoki

doi:10.1016/j.jinorgbio.2016.08.011

Cited by 19 publications

(27 citation statements)

References 49 publications

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“…In this study, we set out to explore the combined effects of HHP and common co‐solvents such as trimethylamine N ‐oxide (TMAO), urea, and the macromolecular crowding agent Ficoll on the conformational landscape of the human telomeric oligonucleotide sequence [A(GGGTTA) 3 GGG]. The conformations of G4‐DNAs are generally investigated using ensemble techniques such as circular dichroism (CD), UV/Vis, and NMR spectroscopy . The single‐molecule fluorescence resonance energy transfer (smFRET) technique as used herein allows to distinguish different folded conformations .…”

Section: Figurementioning

confidence: 99%

“…[16] In this study,w es et out to explore the combined effects of HHP and commonc o-solvents such as trimethylamine N-oxide (TMAO), urea, and the macromolecular crowding agent Ficoll on the conformational landscapeo ft he human telomeric oligonucleotide sequence [A(GGGTTA) 3 GGG].T he conformations of G4-DNAs are generally investigated using ensemble techniques such as circulard ichroism (CD), UV/Vis, and NMR spectroscopy. [4,5,[17][18][19][20][21][22] The single-molecule fluorescence resonance energy transfer (smFRET) technique as used herein allows to distinguish different folded conformations. [23][24][25][26] Recently,w ew ere also able to setup aH HP smFRET stage ( Figure S1 in the Supporting Information) allowing us to reach pressures up tõ 2kbar (200 MPa), covering the whole relevant pressure range on Earth.…”

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confidence: 99%

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The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

Knop

Patra

Harish

et al. 2018

Chemistry A European J

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Organisms are thriving in the deep sea at pressures up to the 1 kbar level, which imposes severe stress on the conformational dynamics and stability of their biomolecules. The impact of osmolytes and macromolecular crowders, mimicking intracellular conditions, on the effect of pressure on the conformational dynamics of a human telomeric G-quadruplex (G4) DNA is explored in this study employing single-molecule Förster resonance energy transfer (FRET) experiments. In neat buffer, pressurization favors the parallel/hybrid state of the G4-DNA over the antiparallel conformation at ≈400 bar, finally leading to unfolding beyond 1000 bar. High-pressure NMR data support these findings. The folded topological conformers have different solvent accessible surface areas and cavity volumes, leading to different volumetric properties and hence pressure stabilities. The deep-sea osmolyte trimethylamine N-oxide (TMAO) and macromolecular crowding agents are able to effectively rescue the G4-DNA from unfolding in the whole pressure range encountered on Earth.

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Section: Figurementioning

confidence: 99%

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confidence: 99%

The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

Knop

Patra

Harish

et al. 2018

Chemistry A European J

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“…The six variables (ɛ C , ɛ Q , b C , b Q , H°, and S°) can be calculated by curve fitting using Equations 17.9.2 to 17.9.5 on a computer equipped with a curve-fitting software such as IGOR Pro (WaveMetrics), KaleidaGraph (Synergy software), or ORIGIN (OriginLab), to derive the thermodynamic parameters from the shape of each melting curve. The G°2 5 value at 25°C is calculated using the following equation: Examples of thermodynamic parameters are listed in Table 17.9.1 (Takahashi et al, 2017).…”

Section: Analysis Of Uv Melting Curvesmentioning

confidence: 99%

“…The change in partial molar volume induced by a ligand, V b , can be considered as follows (Takahashi et al, 2017): in which V bM is the intrinsic volume change induced by the ligand, V bT is the thermal volume change induced by ligand binding, and V bI is the hydration volume change induced by ligand binding. The intrinsic volume is derived from the geometric volume of the solute molecules including void space inside the molecule (Likhodi & Chalikian, 1999).…”

Section: Background Informationmentioning

confidence: 99%

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G‐Quadruplexes

Takahashi

Sugimoto

2017

CP Nucleic Acid Chemistry

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Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate ΔV values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (ΔG, ΔH, ΔS, and ΔV) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley & Sons, Inc.

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“…For DNA, elevated pressure induced the B/Z conformational change and affected stability of non‐canonical structures (G‐quadruplex and i‐motif) . Such changes were found to be strongly dependent on the sequence and solvent .…”

Section: Introductionmentioning

confidence: 99%

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

Plamitzer

Bouř

2020

Chirality

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Change of molecular properties with pressure is an attracting means to regulate molecular reactivity or biological activity. However, the effect is usually small and so far explored rather scarcely. To obtain a deeper insight and estimate the sensitivity of vibrational optical activity spectra to pressure-induced conformational changes, we investigate small model molecules. The Ala-Ala dipeptide, isomaltose disaccharide and adenine-uracil dinucleotide were chosen to represent three different biomolecular classes. The pressure effects were modeled by molecular dynamics and density functional theory simulations. The dinucleotide was found to be the most sensitive to the pressure, whereas for the disaccharide the smallest changes are predicted. Pressure-induced relative intensity changes in vibrational circular dichroism and Raman optical activity spectra are predicted to be 2-3-times larger than for non-polarized IR and Raman techniques. K E Y W O R D S density functional theory, high pressure, molecular dynamics, spectra simulations, vibrational optical activity

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Volumetric analysis of formation of the complex of G-quadruplex DNA with hemin using high pressure

Cited by 19 publications

References 49 publications

The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

The Deep Sea Osmolyte TrimethylamineN‐Oxide and Macromolecular Crowders Rescue the Antiparallel Conformation of the Human Telomeric G‐Quadruplex from Urea and Pressure Stress

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G‐Quadruplexes

Pressure dependence of vibrational optical activity of model biomolecules. A computational study

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