A one step method for isolation of genomic DNA using multi-amino modified magnetic nanoparticles

A simple and efficient approach for the rapid extraction of genomic DNA from blood using various amino-modified magnetic nanoparticles (AMNPs) has been described. The salmon sperm DNA was isolated from aqueous solution based on electrostatic interaction between the positively charged amino-groups of AMNPs and the negatively charged phosphate groups of the DNA. The results of ultraviolet-visible (UV-Vis) spectrometry showed that increasing number of amino groups on the AMNPs surface resulted in an improvement in DNA adsorption efficiency. Several variables including the extraction pH, adsorption time, ionic strength and quantity of AMNPs were optimized to achieve the best extraction efficiency with the proposed method. Acceptable adsorption efficiency of 92% and recovery of 91% were achieved using multi-amino modified MNPs (mAMNPs) with an extraction time of 10 min and an overall processing time of 30 min. The mAMNPs enabled genomic DNA capture from human whole blood, and the resulting mAMNP/DNA complexes could be directly used as templates for PCR amplification without the need for complex and time-consuming DNA elution and purification steps. Our results imply that this method can be used as an effective strategy for genomic DNA extraction and may be extended to other types of biological samples.

Selective hybridization and capture of KRAS DNA from plasma and blood using ion-tagged oligonucleotide probes coupled to magnetic ionic liquids

Detection of circulating tumor DNA (ctDNA) presents several challenges due to single-nucleotide polymorphisms and large amounts of background DNA. Previously, we reported a sequence-specific DNA extraction procedure utilizing functionalized oligonucleotides called ion-tagged oligonucleotides (ITOs) and disubstituted ion-tagged oligonucleotides (DTOs). ITOs and DTOs are capable of hybridizing to complementary DNA for subsequent capture by a magnetic ionic liquid (MIL) through hydrophobic interactions, π-π stacking, and fluorophilic interactions. However, the performance of the ITOs and DTOs in complex sample matrices has not yet been evaluated. In this study, we compare the amount of KRAS DNA extracted using ITO and DTOs from saline, 2-fold diluted plasma, 10-fold diluted plasma, and 10-fold diluted blood. We demonstrate that ITO/DTO-MIL extraction is capable of selectively preconcentrating DNA from diluted plasma and blood without additional sample preparation steps. In comparison, streptavidin-coated magnetic beads were unable to selectively extract DNA from 10-fold diluted plasma and 10-fold diluted blood without additional sample clean-up steps. Significantly more DNA could be extracted from 2-fold diluted plasma and 10-fold diluted blood matrices using the DTO probes compared to the ITO probes, likely due to stronger interactions between the probe and MIL. The ability of the DTO-MIL method to selectively preconcentrate small concentrations of DNA from complex biological matrices suggests that this method could be beneficial for ctDNA analysis.

Review on sample preparation methods for oligonucleotides analysis by liquid chromatography

Antisense oligonucleotides have been successfully investigated for the treatment of different types of diseases. Detection and determination of antisense oligonucleotides and their metabolites are necessary for drug development and evaluation. This review focuses mainly on the first step of the analysis of oligonucleotides i.e. the sample preparation stage, and in particular on the techniques used for liquid chromatography and liquid chromatography coupled with mass spectrometry. Exceptional sample preparation techniques are required as antisense oligonucleotides need to be determined in complex biological matrices. The text discusses general issues in oligonucleotide sample preparation and approaches to their solution. The most popular techniques i.e. protein precipitation, protein enzyme digestion and liquid-liquid extraction are reviewed. Solid phase extraction methods are discussed and the issues connected with the application of each method are highlighted. Other newly reported promising techniques are also described. Finally, there is a summary of actually used techniques and the indication of the direction of future research.

Liquid-liquid extraction of enzymatically synthesized functional RNA oligonucleotides using reverse micelles with a DNA-surfactant

We successfully implemented solvent extraction of short, single-stranded RNA using reverse micelles (water-in-oil microemulsions) with a DNA-surfactant. A thrombin-binding RNA aptamer was enzymatically synthesized and purified by extraction using the reverse micellar system. The extracted RNA aptamer retained thrombin-binding activity after the extraction procedure.

DNA-mediated phase transfer of DNA-functionalized quantum dots using reverse micelles

We report the selective phase transfer of DNA-functionalized CdTe quantum dots (DNA-QDs) from an aqueous phase to an organic phase using reverse micelles and a DNA surfactant.

A hybrid lipid oligonucleotide: a versatile tool for supramolecular chemistry

Lipid oligonucleotides (LONs) self-assemble into supramolecular structures. This property has an impact on the biological effects of the oligonucleotide sequences.

Fluorochrome-functionalized magnetic nanoparticles for high-sensitivity monitoring of the polymerase chain reaction by magnetic resonance

Easy to find: magnetic nanoparticles bearing fluorochromes (red) that intercalate with DNA (green) form microaggregates with DNA generated by the polymerase chain reaction (PCR). These aggregates can be detected at low cycle numbers by magnetic resonance (MR).

His-tagged protein purification by metal-chelate affinity extraction with nickel-chelate reverse micelles

Di(2-ethylhexyl) phosphoric acid (HDEHP) was used as a transition metal ion chelator and introduced to the nonionic reverse micellar system composed of equimolar Triton X-45 and Span 80 at a total concentration of 30 mmol/L. Ni(II) ions were chelated to the HDEHP dimers in the reverse micelles, forming a complex denoted as Ni(II)R(2). The Ni(II)-chelate reverse micelles were characterized for the purification of recombinant hexahistidine-tagged enhanced green fluorescent protein (EGFP) expressed in Escherichia coli. The affinity binding of EGFP to Ni(II)R(2) was proved by investigation of the forward and back extraction behaviors of purified EGFP. Then, EGFP was purified with the affinity reverse micelles. It was found that the impurities in the feedstock impeded EGFP transfer to the reverse micelles, though they were little solubilized in the organic phase. The high specificity of the chelated Ni(2+) ions toward the histidine tag led to the production of electrophoretically pure EGFP, which was similar to that purified by immobilized metal affinity chromatography. A two-stage purification by the metal-chelate affinity extraction gave rise to 87% recovery of EGFP. Fluorescence spectrum analysis suggests the preservation of native protein structure after the separation process, indicating the system was promising for protein purification.

Characterization of the nanostructure of complexes formed by single- or double-stranded oligonucleotides with a cationic surfactant

We report the use of dynamic light scattering (DLS), small-angle neutron scattering (SANS), and small-angle X-ray scattering (SAXS) to characterize the nanostructure of complexes formed by either single- or double-stranded oligonucleotides with a cationic surfactant (cetyltrimethylammonium bromide, CTAB) in aqueous solution (1 mM Li(2)SO(4)). For single-stranded oligonucleotides 5'-A(20)-3' and 5'-CCCCATTCTAGCAGCCCGGG-3', both the appearance of two Bragg peaks (at 0.14 and 0.28 Å(-1)) in SAXS spectra with a spacing of 1:2 and form factor fits to SANS spectra are consistent with the presence of multilamellar vesicles (with, on average, 6-9 layers with a periodicity of 45-48 Å). Some samples showed evidence of an additional Bragg peak (at 0.20 Å(-1)) associated with periodic packing (with a periodicity of 31 Å) of the oligonucleotides within the lamellae of the nanostructure. The nucleotide composition of the single-stranded oligonucleotides was also found to impact the number and size of the complexes formed with CTAB. In contrast to 5'-A(20)-3' and 5'-CCCCATTCTAGCAGCCCGGG-3', 5'-T(20)-3' did not change the state of aggregation of CTAB (globular micelles) over a wide range of oligonucleotide:CTAB charge ratios. These results support the proposition that hydrophobic interactions, as well as electrostatics, play a central role in the formation of complexes between cationic amphiphiles and single-stranded oligonucleotides and thus give rise to nanostructures that depend on nucleotide composition. In contrast to the single-stranded oligonucleotides, for double-stranded oligonucleotides mixed with CTAB, three Bragg peaks (0.13, 0.23, and 0.25 Å(-1)) in SAXS spectra with a spacing ratio of 1:√3:√4 and characteristic changes in SANS spectra indicate formation of a hexagonal nanostructure. Also, the composition of the double-stranded oligonucleotides did not measurably impact the nanostructure of complexes formed with CTAB, suggesting that electrostatic interactions dominate the formation of these complexes. Overall, these results provide insights into the intermolecular interactions that occur between cationic amphiphiles and oligonucleotides and establish that single and double-stranded oligonucleotides form complexes with cationic surfactants that differ in nanostructure. The results also provide guidance for the design of oligonucleotide complexes with cationic amphiphiles.

A metal-chelate affinity reverse micellar system for protein extraction

A new nonionic reverse micellar system is developed by blending two nonionic surfactants, Triton X-45 and Span 80. At total surfactant concentrations lower than 60 mmol/L and molar fractions of Triton X-45 less than 0.6, thermodynamically stable reverse micelles of water content (W(0)) up to 30 are formed. Di(2-ethylhexyl) phosphoric acid (HDEHP; 1-2 mmol/L) is introduced into the system for chelating transition metal ions that have binding affinity for histidine-rich proteins. HDEHP exists in a dimeric form in organic solvents and a dimer associated with one transition metal ion, including copper, zinc, and nickel. The copper-chelate reverse micelles (Cu-RM) are characterized for their W(0), hydrodynamic radius (R(h)), and aggregation number (N(ag)). Similar with reverse micelles of bis-2-ethylhexyl sodium sulfosuccinate (AOT), R(h) of the Cu-RM is also linearly related to W(0). However, N(ag) is determined to be 30-90 at W(0) of 5-30, only quarter to half of the AOT reverse micelles. Then, selective metal-chelate extraction of histidine-rich protein (myoglobin) by the Cu-RM is successfully performed with pure and mixed protein systems (myoglobin and lysozyme). The solubilized protein can be recovered by stripping with imidazole or ethylinediaminetetraacetic acid (EDTA) solution. Because various transition metal ions can be chelated to the reverse micelles, it is convinced that the system would be useful for application in protein purification as well as simultaneous isolation and refolding of recombinant histidine-tagged proteins expressed as inclusion bodies.

Imidazolium bromide-based ionic liquid assisted improved activity of trypsin in cationic reverse micelles

The present work reports the imidazolium-based ionic liquids (ILs) assisted enhancement in activity of water-pool solubilized enzyme trypsin in cationic reverse micelles of CTAB. A set of imidazolium ILs (1-alkyl-3-methyl imidazolium bromides) were prepared with varying lengths of their side arm which results in the differential location of these organic salts in the reverse micelles. The different ILs offered varied activating effects on the biocatalyst. The activity of trypsin improved approximately 30-300% in the presence of 0.1-10 mM of different ILs in reverse micelles of CTAB. Trypsin showed approximately 300% (4-fold) increment in its activity in the presence of IL 2 (1-ethyl-3-methyl imidazolium bromide, EMIMBr) compared to that observed in the absence of IL in CTAB reverse micelles. The imidazolium moiety of the IL, resembling the histidine amino acid component of the catalytic triad of hydrolases and its Br(-) counterion, presumably increases the nucleophilicity of water in the vicinity of the enzyme by forming a hydrogen bond that facilitates the enzyme-catalyzed hydrolysis of the ester. However, the ILs with increasing amphiphilic character had little to no effect on the activity of trypsin due to their increased distance from the biocatalyst, as they tend to get localized toward the interfacial region of the aggregates. Dynamic light scattering experimentation was carried out in the presence of ILs to find a possible correlation between the trypsin activity and the size of the aggregates. In concurrence with the observed highest activity in the presence of IL 2, the circular dichroism (CD) spectrum of trypsin in CTAB reverse micelles doped with IL 2 exhibited the lowest mean residue ellipticity (MRE), which is closest to that of the native protein in aqueous buffer.

Superior activity of structurally deprived enzyme-carbon nanotube hybrids in cationic reverse micelles

In the present work, we report the superior activity of hydrophobically adsorbed enzymes onto single-walled carbon nanotubes (SWNTs) in the reverse micelles of cationic surfactants. Horseradish peroxidase and soybean peroxidase adsorbed onto SWNTs endure a notable loss in secondary structure and catalytic activity. This structurally and functionally deformed enzyme-SWNT when confined in CTAB reverse micelles showed approximately 7-9-fold enhancement in activity compared to that was in water and also importantly approximately 1500-3500 times higher activity than that of the enzymes in aqueous-organic biphasic mixtures. The activation observed for this nanobiocomposite is due to the (i) possible localization of enzyme-SWNT hybrid at the micellar interface; (ii) facile transport of substrates across the microscopic interface of reverse micelles; and (iii) greater local concentration of substrates at the augmented interfacial space in the presence of SWNT. This interfacial localization of the SWNT-protein hybrid was tested using FITC-tagged protein (BSA) by fluorescence spectroscopy. FTIR and CD spectroscopy established that the enzyme notably loses its native structure as it gets adsorbed onto the CNTs. However, this loss in the secondary structure is neither aggravated nor recovered when the enzyme-SWNT resides at the reverse micellar interface. So, localization of the surface-active peroxidase-CNT hybrids at the interface is the main reason for significant enzyme activation. The generality of the activation of the enzyme-CNT hybrid by reverse micelles was tested using amphiphiles with varying headgroup sizes, where an overall enhancement in activity was observed with an increase in headgroup size. Activation of this nanobiocomposite would find utmost importance in material science as the activity of structurally deprived enzyme in reverse micelles surpassed (approximately 1.7-fold) even the activity of the native enzyme in water.

Conjugation of DNA with protein using His-tag chemistry and its application to the aptamer-based detection system

We propose a novel method to prepare a DNA-protein conjugate using histidine-tag (His-tag) chemistry. Oligo-DNA was modified with nitrilotriacetate (NTA), which has high affinity to a His-tag on recombinant protein via the complexation of Ni(2+). Investigations using a microplate which displayed a complementary DNA-strand revealed that a NTA-modified DNA-protein conjugate was formed and immobilized in the presence of Ni(2+) on the microplate. We then adopted alkaline phosphatase (AP) as a model protein, and application of the DNA-AP conjugate was demonstrated in a thrombin aptamer-based detection system with a detection limit of approximately 10 nM.

Nucleoside, nucleotide and oligonucleotide based amphiphiles: a successful marriage of nucleic acids with lipids

Amphiphilic molecules based on nucleosides, nucleotides and oligonucleotides are finding more and more biotechnological applications. This Perspective highlights their synthesis, supramolecular organization as well as their applications in the field of biotechnology.