Direct Extraction of Double-Stranded DNA Into Ionic Liquid 1-Butyl-3-methylimidazolium Hexafluorophosphate and Its Quantification

Wang, Jianhua; Cheng, Dehong; Chen, Xuwei; Du, Zuliang; Fang, Zheng

doi:10.1021/ac061145c

Cited by 201 publications

(154 citation statements)

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“…The 65 DNA fluorescence in the aqueous phase remained quite constant for all the DNA sequences, suggesting that most of the DNA should still be in the aqueous phase. Since this observation is different from a published paper, 25 we performed back extraction ( Figure 3D). The aqueous phase 70 after mixing with IL shows roughly the same fluorescence intensity compared to the original DNA dispersed just in water (red and blue bars in Figure 3D).…”

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confidence: 59%

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Extraction of DNA staining dyes from DNA using hydrophobic ionic liquids

et al. 2013

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The partition of oligonucleotides and DNA staining dyes into a few hydrophobic ionic liquids has been studied, where the oligonucleotides remain in the aqueous phase and all the DNA staining dyes are extracted in the ionic liquid phase, allowing the separation of these two. 10DNA staining dyes are commonly used in molecular biology and analytical chemistry for detecting not only nucleic acids, but also metal ions, small molecules and proteins (e.g. with DNA aptamers). [1][2][3][4][5][6] Most DNA staining dyes are conjugated cationic molecules and they bind to DNA via electrostatic, - 15 stacking and intercalation interactions to produce strong fluorescence. The DNA/dye complex is very stable and can often survive gel electrophoresis. Therefore, one of the analytical challenges is to remove the dye after staining so that precious DNA samples might still be used for other 20 applications. So far, no attempts have been reported to achieve this goal.Ionic liquids (ILs) are molten salts at around room temperature. [7][8][9][10] ILs are comprised of cations and anions with low symmetry, disfavoring their packing into stable crystals. 25With very low vapor pressure, ILs are considered to be green solvents that may replace some of the conventional organic solvents. Recently, ILs have been shown to dissolve many biopolymers. 11-14 Some protein enzymes are more stable and active in ILs. 15 ILs can also provide long-term stability to 30 DNA. 16 Various studies have been carried out to understand the interaction between ILs and DNA. [17][18][19][20][21][22] There are two types of ILs; one type is hydrophilic and miscible with water while the other type is hydrophobic and forms a separate phase in water. We recently reported that 35 some hydrophilic ILs can either act as salt to increase the melting temperature (Tm) of DNA or as solvent to reduce its Tm. 22 Hydrophobic ILs, on the other hand, might be used for analyte enrichment and extraction. [23][24][25] Hydrophobic ILs have also been used for DNA separation, 26 translocation, 27 mass 40 spectrometry, 28 and DNA gel fiber formation. 29 We reason that hydrophobic ILs might interact with DNA staining dyes via electrostatic, hydrophobic and van der Waals interactions, which may be stronger than its interaction with DNA. In this work, we demonstrate extraction of DNA staining dye from 45 DNA using hydrophobic ILs.A total of four ILs were studied in this work ( Figure 1A As an initial test, we mixed a 24-mer single-stranded (ss) DNA with SYBR Green I dye (SG) in buffer (50 mM NaCl, 20 mM HEPES, pH 7.6). A strong green fluorescence was observed under UV excitation ( Figure 1B). We then added an equal volume of [Bmim][PF6]. After a 55 thorough mixing and then centrifugation to facilitate phase separation, the fluorescence disappeared. This suggests that the DNA and SG either are separated into different phases or are both extracted into the IL phase, where the fluorescence was quenched. 60To confirm the location of DNA, we repeated the experiment with a Cy3-labeled DNA ( Figu...

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confidence: 59%

“…[7][8][9][10] ILs are comprised of cations and anions with low symmetry, disfavoring their packing into stable crystals. 25 With very low vapor pressure, ILs are considered to be green solvents that may replace some of the conventional organic solvents. Recently, ILs have been shown to dissolve many biopolymers.…”

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confidence: 99%

Extraction of DNA staining dyes from DNA using hydrophobic ionic liquids

et al. 2013

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“…The separation and purification of DNA from real sample matrices is of great value, and the utilization of ILs may simplify this separation and purification process [88]. Without any other reagent, ds-DNA was rapidly and quantitatively extracted into [C 4 MIM][PF 6 ] from the aqueous phase, while part of the extracted DNA can be backextracted to phosphate-citrate buffer.…”

Section: Extraction Of Biomacromoleculesmentioning

confidence: 99%

Ionic liquids in sample preparation

et al. 2008

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Due to their unique properties, their good extractabilities for various target analytes, and the fact that many compounds are highly soluble in them, room-temperature ionic liquids (ILs) are used as promising alternatives to the traditional organic solvents employed in sample preparation. ILs have been used as extraction solvents for a wide range of analytes, from environmental contaminates to biomacromolecules and nanomaterials, and as dissolution solvents for various detection techniques. In this paper, the main applications of ILs in sample preparation are reviewed, and the problems and challenges in this area are described.

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“…Ionic liquids (ILs) are liquids composed completely of ions, and thus have unique physicochemical properties, including broad liquid range, low to negligible vapor pressures, high thermal stability, and high solubility for different classes of analytes [30][31][32][33][34][35][36][37][38][39][40][41][42]. Therefore, ILs environment is quite different from that of all polar or non-polar organic solvents [32], which is capable of forming virtually all possible types of interactions with solutes [33,34].…”

Section: Introductionmentioning

confidence: 99%

“…Due to the above-mentioned unique properties, ILs are regarded as a new class of green solvents [30,35] and have been successfully applied in sample extraction [31,36,37], chromatography separation [38,39], and MS identification [40][41][42]. Anderson et al [31] applied ILs containing tris(pentafluoroethyl)trifluorophosphate anion for the extraction of polycyclic aromatic hydrocarbons.…”

Section: Introductionmentioning

confidence: 99%

Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics

et al. 2010

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The solubility and digestion efficiency are two crucial factors that might affect the identification of integral membrane proteins (IMPs). In this work, 1% (v/v) ionic liquid (IL), 1-butyl-3-methyl imidazolium tetrafluoroborate (BMIM BF 4 ), added in NH 4 HCO 3 buffer (pH 8.3), was applied as a sample preparation buffer for IMPs analysis. Compared to the commonly used sodium dodecyl sulfate and methanol methods, the number of identified IMPs from rat brain by microcolumn reversed phase liquid chromatography (μRPLC)-electrospray ionization tandem mass spectrometry (ESI-MS/MS) was improved by over three times, which might be due to the fact that BMIM BF 4 offered high solubilizing ability for IMPs and good compatibility for tryptic digestion. Furthermore, compared to Rapigest and urea methods, with BMIM BF 4 method, the number of identified IMPs from rat brain could be improved 25% and 80%, respectively, which might be contributed to the good solubilizing ability and high thermal stability of such IL. With the sample treated by BMIM BF 4 method, by 2D-nanoSCX-RPLC-ESI-MS/MS, 1,450 non-redundant proteins and 7,978 unique peptides were identified from rat brain, and 418 proteins contained at least one predicted transmembrane domain, with false discovery rates of less than 1% for peptide identification, and at least two identified unique peptides per protein. All these results demonstrate that the BMIM BF 4 method is of high potential for the large-scale identification of IMPs.

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Direct Extraction of Double-Stranded DNA Into Ionic Liquid 1-Butyl-3-methylimidazolium Hexafluorophosphate and Its Quantification

Cited by 201 publications

References 46 publications

Extraction of DNA staining dyes from DNA using hydrophobic ionic liquids

Extraction of DNA staining dyes from DNA using hydrophobic ionic liquids

Ionic liquids in sample preparation

Ionic liquid 1-butyl-3-methyl imidazolium tetrafluoroborate for shotgun membrane proteomics

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