Long‐Term Structural and Chemical Stability of DNA in Hydrated Ionic Liquids

Vijayaraghavan, R.; Izgorodin, Aleksey; Venkatraman, Ganesh; Surianarayanan, M.; MacFarlane, Douglas R.

doi:10.1002/ange.200906610

Cited by 176 publications

(18 citation statements)

References 26 publications

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“…24 The Journal of Physical Chemistry B Article stability is enhanced in the presence of IL, are in line with the earlier observations of enhanced thermal stability of DNA in choline and imidazole based ionic liquids. 7,19 The observation, i.e., an enhanced thermal stability of DNA in the presence of the IL, can be explained following the mechanism suggested by Auffinger and Jumbri. 19,44 According to them, the hydration shell around DNA is responsible for its thermal stability and with an increase in temperature an enhanced entropy of water molecules destabilizes the DNA.…”

Section: Fluorescence Correlation Spectroscopy Studymentioning

confidence: 87%

“…14 Exceptional stability of DNA in the presence of choline based ILs is attributed to the slow rate of hydrolytic reactions in the presence of ILs. 7 Ding et al studied the interaction between [Bmim][Cl] and DNA using several analytical techniques and concluded that both electrostatic and hydrophobic interactions play important roles in the binding of IL to DNA. 15 Pang and co-workers estimated the binding parameters of [Bmim][BF 4 ] with DNA using an electrochemical micromethod.…”

Section: Introductionmentioning

confidence: 99%

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Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid

Pabbathi

Samanta

2015

J. Phys. Chem. B

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The structural integrity of a nucleic acid under various conditions determines its utility in biocatalysis and biotechnology. Exploration of the ionic liquids (ILs) for extraction of DNA and other nucleic acid based applications requires an understanding of the nature of interaction between the IL and DNA. Considering these aspects, we have studied the interaction between calf-thymus DNA and a less toxic morpholinium IL, [Mor1,2][Br], employing fluorescence correlation spectroscopy (FCS), conventional steady state and time-resolved fluorescence, circular dichroism (CD) and molecular docking techniques. While the CD spectra indicate the stability of DNA and retention of its B-form in the presence of the morpholinium IL, the docking study reveals that [Mor1,2](+) binds to the minor groove of DNA with a binding energy of -4.57 kcal mol(-1). The groove binding of the cationic component of the IL is corroborated by the steady state fluorescence data, which indicated displacement of a known minor groove binder, DAPI, from its DNA-bound state on addition of [Mor1,2][Br]. The FCS measurements show that the hydrodynamic radius of DNA remains more or less constant in the presence of [Mor1,2][Br], thus suggesting that the structure of DNA is retained in the presence of the IL. DNA melting experiments show that the thermal stability of DNA is enhanced in the presence of morpholinium IL.

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Section: Fluorescence Correlation Spectroscopy Studymentioning

confidence: 87%

Section: Introductionmentioning

confidence: 99%

Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid

Pabbathi

Samanta

2015

J. Phys. Chem. B

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“…6 Furthermore, through careful selection of cation−anion combinations, the chemical and physical properties of ILs can be modulated for task-specific applications. 7 Hence, this class of "designer" solvents continues to find increasing use in an expanding number of areas, including polymer chemistry as self-assembly media; 8 material chemistry for catalysis and synthesis; 9 biotechnology for biocatalysis, 10 biomolecular dissolution 11−13 and stability; 14,15 and electrochemistry for sensors, biosensors, and in electrochemical storage devices; 16 etc.…”

Section: ■ Introductionmentioning

confidence: 99%

“…Likewise, DNA can be preserved for long-term usage under ambient conditions in hydrated ILs. 14 Similarly, the water content of hydrated ILs plays a crucial role in the dissolution and regeneration of cellulose from organic biomass. 17 The wide applications of IL/water binary mixtures have prompted many researchers to determine the thermophysical properties of this versatile solvent medium.…”

Section: ■ Introductionmentioning

confidence: 99%

Nanostructural Reorganization Manifests in Sui-Generis Density Trend of Imidazolium Acetate/Water Binary Mixtures

Ghoshdastidar

Senapati

2015

J. Phys. Chem. B

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Ionic liquids (ILs) are emerging as a novel class of solvents in chemical and biochemical research. Their range of applications further expands when a small quantity of water is added. Thus, the past decade has seen extensive research on IL/water binary mixtures. While the thermophysical properties of most of these mixtures exhibited the expected trend, few others have shown deviations from the general course. One such example is the increase in density of the 1-alkyl-3-methyl imidazolium acetate ([Rn mim][Ac])-based ILs with the addition of low to moderate concentrations of water. Although such a unique trend was observed for imidazolium cations of different tail lengths and also from independent experiments, the molecular basis of this unique behavior remains unknown. In this study, we examine the nanostructural reordering in [Rn mim][Ac] (n = 2-6) ILs due to added water by means of molecular dynamics simulations, and correlate the observed changes to the sui-generis density trend. Results suggest that the initial rise in density in these ILs mainly pertains to the water-induced increased spatial correlation among the polar components, where high basicity of the acetate anion plays a key role. At moderate water concentration, the density can rise further for ILs with longer cation tails due to hydrophobic clustering. Thus, while [emim][Ac]/water mixtures exhibit the density turnover at Xw = 0.5, [bmim][Ac] and [hmim][Ac] show the turnover at Xw = 0.7. The detailed understanding provided here could help the preparation of optimal IL/water binary mixtures for various biochemical applications.

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“…13 They pointed out that high stability in the solvation structure arises from the hydrogen-bonding interactions of the cations and anions with the DNA bases as well as interactions between the cations and P-O bonds of phosphates in the DNA strands. On the other hand, strong interactions of the solvent ions with enzymes make them less stable and reduce their activity.…”

Section: Introductionmentioning

confidence: 99%

Solvation of a Small Metal-Binding Peptide in Room-Temperature Ionic Liquids

Shim¹,

Kim

Jung

2012

Bulletin of the Korean Chemical Society

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Structural properties of a small hexapeptide molecule modeled after metal-binding siderochrome immersed in a room-temperature ionic liquid (RTIL) are studied via molecular dynamics simulations. We consider two different RTILs, each of which is made up of the same cationic species, 1-butyl-3-methylimidazolium (BMI + ), but different anions, hexafluorophosphate (PF6 − ) and chloride (Cl − ). We investigate how anionic properties such as hydrophobicity/hydrophilicity or hydrogen bonding capability affect the stabilization of the peptide in RTILs. To examine the effect of peptide-RTIL electrostatic interactions on solvation, we also consider a hypothetical solvent BMI − . This is ascribed to the good hydrogen-bond accepting power of chloride anions, which enables them to bind strongly to hydroxyl groups of the peptide and to stabilize its structure. Transport properties of the peptide are examined briefly. Translations of the peptide significantly slow down in highly viscous RTILs.

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Long‐Term Structural and Chemical Stability of DNA in Hydrated Ionic Liquids

Abstract: Sicher aufbewahrt: Es wurde gezeigt, dass DNA in einer Vielzahl Cholin‐basierter hydratisierter ionischer Flüssigkeiten (ILs) löslich ist (siehe Bild). Die gelöste DNA ist außergewöhnlich langzeitstabil und liegt auch nach über einem Jahr unverändert vor.

Cited by 176 publications

References 26 publications

Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid

Spectroscopic and Molecular Docking Study of the Interaction of DNA with a Morpholinium Ionic Liquid

Nanostructural Reorganization Manifests in Sui-Generis Density Trend of Imidazolium Acetate/Water Binary Mixtures

Solvation of a Small Metal-Binding Peptide in Room-Temperature Ionic Liquids

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