Nucleic acids solvent extraction

Nucleic acids, DNA and RNA, are attractive biopolymers that can be used for biomedical applications [175,176], nanostructure fabrication [177,178], computing [179,180], and materials for electron-conduction [181,182]. Immobilization of DNA and RNA in well-defined nanostructures would be one of the most unique subjects in current nanotechnology. Unfortunately, a silica surface cannot usually adsorb duplex DNA in aqueous solution due to the electrostatic repulsion between the silica surface and polyanionic DNA. However, Fujiwara et al. recently found that duplex DNA in protonated phosphoric acid form can adsorb on mesoporous silicates, even in low-salt aqueous solution [183]. The DNA adsorption behavior depended much on the pore size of the mesoporous silica. Plausible models of DNA accommodation in mesopore silica channels are depicted in Figure 4.20. Inclusion of duplex DNA in mesoporous silicates with larger pores, around 3.8 nm diameter, would be accompanied by the formation of four water monolayers on the silica surface of the mesoporous inner channel (Figure 4.20A), where sufficient quantities of Si—OH groups remained after solvent extraction of the template (not by calcination). 

Treatment with hot organic solvents was the next step in the tissue fractionation, to remove lipid-phosphorous and breakdown lipid-protein interactions. In the Schneider procedure, nucleic acids were then extracted in hot dilute trichloroacetic or perchloric acid, leaving a protein residue with any phosphoprotein links still intact. This method was to become particularly useful when 3H thymidine became the preferred label for DNA in the early 1960s. For investigations where both RNA and DNA were to be examined the Schmidt-Thannhauser process was often chosen. Here the lipid-extracted material was hydrolyzed with dilute sodium hydroxide releasing RNA nucleotides and any hydroxyamino acid bound phosphorus. DNA could be precipitated from the extract but the presence in the alkaline hydrolysate of the highly labeled phosphate released from phosphoprotein complicated... 

When plant or animal tissues are extracted with nonpolar solvents, a portion of the material dissolves. The components of this soluble fraction are called lipids and include fatty acids, triacylglycerols, waxes, terpenes, postagladins, and steroids. The insoluble portion contains the more polar plant components including carbohydrates, lignin, proteins, and nucleic acids. 

With additional information, including the heat capacity of the buffer solvent, the partial specific volumes (volume per gram of the solute), and the specific volume of the solvent, one can extract the partial specific heat capacity (J K 1g I) of the solute. Privalov has summarized these calculations.8 Because the solutions are studied at very low concentrations, it is assumed that the contribution to the total heat capacity from the solvent cancels out when one calculates the excess heat capacity. With only minor exceptions, the procedures used to calculate parameters associated with the transformations in nucleic acids and in proteins are the same and yield quantities that are interpreted in similar ways, although researchers in these two fields may use a different notation for the same quantity. 

Phenolic extraction of cell lysates is one of the oldest techniques in DNA preparation. Examples of these have been presented in Chapters 6 and 7. Single cells in suspension are lysed with a detergent, and a proteinase enzyme is used to break down the protein molecules. Non-nucleic acid components are then extracted into an organic (phenol-chloroform) solvent, leaving nucleic acids in the aqueous layer. Two volumes of isopropanol are added to the isolated aqueous phase to precipitate the high-molecular-weight nucleic acids as a white mass. These are then treated with DNase-free ribonuclease (RNase) to remove the RNA. This is followed by a second treatment with proteinase, phenol extraction, and isopropanol precipitation. After precipitation, the DNA is separated from the isopropanol by... 

To extract DNA and RNA from serum samples or from culture supernatant fractions which contain a low level of proviral DNA, the IsoQuick extraction kit (a modified guanidinium salt-organic solvent extraction method) by MicroProbe Corporation (Bothell, WA) has been used successfully by our group. Following the manufacturer s recommended procedures for total nucleic acid extraction, the final DNA-RNA suspension can be amplified directly to detect proviral DNA. Using cDNA templates synthesized from total nucleic acids with random hexamer priming generally increases the PCR product yield. 

Lipids are defined as water-insoluble compounds extracted from living organisms by weakly polar or nonpolar solvents. This definition is based on a physical property, in contrast to the definitions of proteins, carbohydrates, and nucleic acids, which are based on chemical structure. Consequently, the term lipid covers a structurally diverse group of compounds, and there is no universally accepted scheme for classifying lipids. 

Diethylene glycol (2,2 -oxydiethanol) was selected, from a number of glycols tested, as a suitable solvent for the O antigen of ShigeUa dysen-anhydrous solvent should be used for extracting dried cells because, in the presence of water, proteins and nucleic acids are not left... 

For the determination of metal cations, chelates are created with oxine (8-hydroxyquinoline), alizarine or benzoin, then extracted by organic solvents. In biochemistry, fluorescence has numerous applications for the quantification of proteins or nucleic acids by means of reagents which can affix with specificity to these compounds. This approach, sometimes very elaborate, in association with electrophoresis constitutes a more sensitive and less restricting method than detection by radioactive substrates. 

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