The effects of pH and salts on nucleic acid partitioning during phenol extraction

The partitioning of nucleic acids is sensitive to pH during phenol extraction. However, the exact effects of pH on phenol extraction had not been systematically investigated, and the mechanism of which were not fully elucidated. In this paper, we showed that the partitioning of nucleic acids was determined neither solely by the pH of the aqueous buffer being used, nor by the “pH of the phenol”; the latter is a completely wrong conception. We demonstrated that a key determinant for nucleic acid partitioning during phenol extraction was the equilibrated pH of the aqueous phase, which should be defined as the pH of phenol extraction. For example, when 50?mM NaAc-HAc buffer at pH of 3.47 was mixed with an equal volume of water-saturated phenol, the equilibrated pH of aqueous phase would be raised to ～3.84. At this pH, almost all of genomic DNA partitioned into the phenol phase, and genomic DNA-free total RNA was retained in the aqueous phase. Several salts were found affecting the partitioning of nucleic acids during phenol extraction in different manners. Based on these results, a low-cost and efficient method for genomic DNA-free total RNA extraction was developed.     

Segregative phase separation in agarose/whey protein systems induced by sequence-dependent trapping and change in pH

The structural properties and morphology of mixed gels made of aqueous preparations of agarose and whey protein were modified by changing thermal treatment and pH. The conformationally dissimilar polymers phase separated and this process was followed by small-deformation dynamic oscillation in shear, differential scanning calorimetry and environmental scanning electron microscopy. Experimental protocol encourages formation of a range of two-phase systems from continuous agarose matrices perforated by liquid-like whey protein inclusions to phase inverted preparations where a soft protein matrix suspends hard agarose-filler particles. These distinct morphologies have widely different mechanical moduli, which were followed by adapting a theoretical analysis (isostress-isostrain and Lewis-Nielsen blending laws) from the literature in synthetic block polymers and polyblends. Based on this framework of thought, reasonable predictions of the elastic moduli in the composite gels were made that led to patterns of solvent partition between the two polymeric networks. It was shown that proteins, in mixture with polysaccharide, exhibit favorable relative affinity (P-factor) for water molecules at a pH above their isoelectric point. This is an unexpected outcome that adds to the central finding of a single P value for the distribution of solvent between the continuous matrix and discontinuous inclusions of binary gels. It was thus proposed that phase continuity and solvent distribution in agarose/whey protein systems are under kinetic control that can be heavily governed by pH changes in the aqueous environment.     

Hybridization of nucleic acids directly in agarose gels

Nucleic acids, both DNA and RNA, separated on agarose gels can be visualized by direct hybridization of the dried gel with appropriate radioactive probes. This method does not involve the transfer of the nucleic acid from the gel. The method requires less manipulation than other procedures; it is extremely rapid, sensitive, and inexpensive. These attributes make this procedure a valuable alternative or supplement to the commonly used methods for visualization by hybridization of nucleic acids separated on agarose gels.     

A simple method to recover intact high molecular weight RNA and DNA after electrophoretic separation in low gelling temperature agarose gels.

Defined RNA fractions can be recovered from low gelling temperature agarose gels by a combination of agarose melting at 65°C and phenol extraction. By this approach RNA molecules up to a size of 37 kb can be eluted undegraded with a recovery of 60–90%. The method is applicable also to DNA and the eluted DNA can be correctly cleaved with restriction endonucleases as shown for λDNA using EcoRI.     

Quantitative aspects of mercurial-agarose gel electrophoresis

Single-stranded nucleic acids are capable of extensive intramolecular base pairing as well as intermolecular aggregation. Consequently, electrophoretic studies of single-stranded nucleic acids are most effective when conducted under denaturing conditions. A number of techniques are available for nucleic acid denaturing gel electrophoresis (1–3). In this paper we describe certain quantitative features of one of these techniques, mercurial-agarose gel electrophoresis (4–7). Specifically, we address the questions of resolution and base composition dependence and we introduce a new mercurial for agarose gel electrophoresis, p-chloromercuriphenyl-sulfonic acid.In a previous publication we demonstrated that methylmercury was an effective denaturant in an agarose gel (4). The mechanism of denaturation is presumably the disruption of hydrogen bonding by the reversible binding of methylmercury to uridine and guanosine imino nitrogens. At saturating mercurial concentrations accurate molecular weights can be determined, free of conformation effects. The presence of methylmercury has no observable effect on the mechanical properties of the gel. Hence the denaturing power of the gel can be readily varied. The strength and rigidity of agarose gels make them considerably easier to handle than acrylamide gels, and the large pore size ensures a system compatible with high molecular weight RNA.     

An apparatus for the fluorescence scanning of ethidium bromide-stained gels

An apparatus has been constructed which permits a conventional gel-scanning apparatus to be used for the fluorescence scanning of nucleic acid bands in either agarose or polyacrylamide gels stained with ethidium bromide. The method involves the use of an ultraviolet (uv) light source perpendicular to the plane of the photodetector and a filter system to remove uv light. It is demonstrated that the method yields quantitative results and has a fourfold greater sensitivity than absorbance scanning for agarose gels.     

Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts

Nucleic acids were found to partition into the phenol phase during phenol extraction in the presence of guanidinium at certain concentrations under acidic conditions. The guanidinium-concentration-dependent nucleic acid partitioning patterns were analogous to those of the nucleic acid adsorption/partitioning onto silica mediated by guanidinium, which implied that phenol and silica interact with nucleic acids through similar mechanisms. A competition effect was observed in which the nucleic acids that had partitioned into the phenol phase or onto the silica solid phase could be recovered to the aqueous phases by potassium in a molecular weight–salt concentration-dependent manner (the higher molecular weight nucleic acids needed higher concentrations of potassium to be recovered, and vice versa). Methods were developed based on these findings to isolate total RNA from Escherichia coli. By controlling the concentrations of guanidinium and potassium salts used before phenol extraction or silica adsorption, we can selectively recover total RNA but not the high molecular weight genomic DNA in the aqueous phases. Genomic DNA-free total RNA obtained by our methods is suitable for RT-PCR or other purposes. The methods can also be adapted to isolate small RNAs or RNA in certain molecular weight ranges by changing the salt concentrations used.     

Mammalian expression cloning of nucleic acid binding proteins by agarose thin-layer gelshift clone selection

Here we report a functional screening technique to identify cDNAs encoding mammalian nucleic acid binding proteins. We have combined cDNA expression cloning with the agarose thin-layer gelshift assay technique to detect specific nucleic acid binding proteins from a mammalian expression library. We divided this cDNA expression library into multiple pools and transfected mammalian cells with the individual pools. Following transfection, we tested the expressed proteins for DNA-binding activity by agarose thin-layer electrophoretic gelshift assay. After we identified a single expression poolfor the presence of a DNA-binding protein, the corresponding cDNA pool was further divided into smaller aliquots. Then, the cDNA expression and gelshift clone selection was repeated until a single clone was isolated In contrast to traditional polyacrylamide gels, the agarose thin-layer is significantly faster and resolves larger DNA-protein complexes. This method can be widely used for the cDNA cloning of DNA- and RNA-binding proteins from various mammalian host cells.     

Isotachophoresis of nucleic acids in agarose gel rods

A new method of electrophoresis (isotachophoresis in agarose gel rods) in which nucleic acid molecules are not separated but, oppositely, are brought together into one band, was elaborated. Heterogeneous in size DNA and RNA polymers present in a few milliliters of a solution at so low concentration that their isolation by other methods is hardly attainable and fraught with losses are brought together into one visible narrow band when put in a discontinuous electric field. Polynucleotides migrate in dilute (0.1%) semifluid agarose gel that permits easy quantitative isolation of the band of interest. Resulting DNA can be used directly in PCR. The suggested method for isolation of micro amounts of nucleic acids from dilute solutions can be applied to forensic and clinical research and cancer gene diagnostics by the analysis of fragmented circulating DNA from bodily fluids.     

GelStar nucleic acid gel stain: high sensitivity detection in gels.

GelStar nucleic acid gel stain can be used for sensitive fluorescent detection of both double-stranded (ds) and single-stranded (ss) DNAs, oligonucleotides and RNA in gels. The stain can be added to agarose gels at casting for immediate imaging after electrophoresis or can be used after electrophoresis with both agarose and acrylamide gels. GelStar stain is highly fluorescent only when bound to nucleic acids thus giving superior signal-to-noise ratios and obviating the need to destain the gel. The detection limits of GelStar strain are 20 pg for dsDNA, 25 pg for ssDNA and 10 ng for native or glyoxal-treated RNA.     

A characterization of ribonucleic acid in the myxomycete Physarum polycephalum

This report deals with the quantitative extraction of total nucleic acid (TNA) containing undegraded RNA from the slime mold Physarum polycephalum. With the use of a three-step phenol extraction technique, approx. 95 % of the nucleic acid optical density and 90 % of the ³H-uridine incorporated radioactivity were routinely recovered in the extracts. With the use of this technique it was shown that (1) the TNA mg dry wt of the mold did not change throughout the mitotic cycle, even though the dry wt doubled; this indicates a continual net synthesis of nucleic acid throughout the cycle; (2) the relative proportions of the various nucleic acid components did not change significantly during the cycle and were found to be DNA, 6 %; rRNA, 82 %; and sRNA, 12 %; (3) RNA molecules with mol wts of 4.1 m and 1.9 m, which exhibit properties of rRNA precursors were found in plasmodia labeled for 20 min with ³H-uridine. Furthermore, there appears to be an RNA fraction, found only in nucleic acid preparations presumably enriched in nuclear RNA components, which is heat-labile, does not enter 2.6 % acrylamide gels during 4 h of electrophoresis, and has a uridine/methyl ratio different from the presumed rRNA precursors and mature rRNA.     

Rapid agarose gel electrophoretic mobility shift assay for quantitating protein: RNA interactions

Interactions between proteins and nucleic acids are frequently analyzed using electrophoretic mobility shift assays (EMSAs). This technique separates bound protein:nucleic acid complexes from free nucleic acids by electrophoresis, most commonly using polyacrylamide gels. The current study utilizes recent advances in agarose gel electrophoresis technology to develop a new EMSA protocol that is simpler and faster than traditional polyacrylamide methods. Agarose gels are normally run at low voltages (∼10 V/cm) to minimize heating and gel artifacts. In this study we demonstrate that EMSAs performed using agarose gels can be run at high voltages (≥20 V/cm) with 0.5 × TB (Tris-borate) buffer, allowing for short run times while simultaneously yielding high band resolution. Several parameters affecting band and image quality were optimized for the procedure, including gel thickness, agarose percentage, and applied voltage. Association of the siRNA-binding protein p19 with its target RNA was investigated using the new system. The agarose gel and conventional polyacrylamide gel methods generated similar apparent binding constants in side-by-side experiments. A particular advantage of the new approach described here is that the short run times (5–10 min) reduce opportunities for dissociation of bound complexes, an important concern in non-equilibrium nucleic acid binding experiments.     

Electrophoretic elution of nucleic acids from acrylamide and agarose gels

A simple method for electrophoretic elution of nucleic acids from gel slices is described. The procedure utilizes a standard tube gel system and can be completed in as little as one hour. Nucleic acids are recovered in a small volume with almost 100% efficiency. The procedure is applicable equally to acrylamide and agarose gels, and small as well as large RNA and DNA molecules. The eluted nucleic acids are essentially undegraded and are suitable for a variety of structural and biological analyses.     

Efficient extraction of RNA from mammalian tissue

RNA extraction from mammalian tissue has been compared using the different deproteinizing agents: a) guanidine-HCl, b) guanidinium-thiocyanate, c) buffer-saturated phenol, or d) buffer-saturated phenol followed by a proteinase K digestion of the aqueous phase. Both solid tissues (first, second, and third trimester fetal bovine pancreas), and human white blood cell populations were studied. Degradation, as seen in citric acid-urea agarose gels, and the ability to serve as templates for cell-free protein synthesis were used as criteria to assess the efficiency of the different methods. We conclude that employing buffer-saturated phenol with proteinase K digestion is a superior method for consistent extraction of relatively undegraded RNA in quantitative amounts from mammalian tissue.     

Detection of proteolytic enzymes in polyacrylamide gels

Aminopeptidases (1), dipeptidyl aminopeptidases (2), pyrrolidonyl peptidases (3), and carboxypeptidases (4,5) can be detected in polyacrylamide gels with appropriate-β-naphthylamide or carbonaphthoxyamino acid substrates while dipeptidases, tripeptidases (6), carboxypeptidases (7), and aminopeptidases can be detected by the coupled l-amino acid oxidase-peroxidase method of Lewis and Harris (6).In contrast, fewer methods are available for the detection of proteinases in gels. Trypsin-like (8,9) and chymotrypsin-like (5,10) proteinases can be detected with chromogenic β-naphthylamide and β-naphthol ester substrates, but proteinases such as thermolysin (11) and other bacterial neutral metal chelator-sensitive proteinases (12) cannot. For these latter proteinases, whose specificities are directed towards the amino acid residue containing the amino group of the bond to be hydrolyzed, and for proteinases, whose specificities remain to be determined, other methods of detection have to be employed.Uriel and Avrameas (13) detected proteinases in agarose gels by overlaying these gels with a second agarose gel mixture containing the substrate and a suitable pH indicator. However, the method suffers from interference by gel buffers and the instability of the pattern developed. Another procedure is to bring the gel in contact with a gelatinous layer of film material (14,15). This has been done successfully with tissue sections (16), paper electrophoretograms (17) and agarose gel separations (18).The most suitable approach is to diffuse an appropriate protein substrate into the gel after electrophoresis and detect the proteinase activity directly. Several variations of this method have been published (19–22), each with its own advantages and disadvantages. In this report a simple, sensitive method using cytochrome c as substrate, and requiring no staining, is described. This report describes its application to the detection of thermolysin and trypsin in anionic and cationic gel systems, respectively. The method has also been routinely used to locate bacterial and insect proteinases after electrophoresis.     

Evidence for restricted oligosaccharide mobility at the erythrocyte membrane surface: A fluorescence study

The glycophorins of whole, human erythrocytes were labeled at their sialic acid residues with one of three fluorescent probes. After preparation of the erythrocyte ghosts, the mobility of each fluorescent probe on the intact membrane was compared with its mobility on the isolated, labeled glycopeptides dissolved in aqueous buffer. A four- to ninefold decrease in the rotational relaxation time, as defined by the Perrin equation, accompanied the proteolytic removal of the labeled glycopeptides from the membrane. This suggests that the fluorescent probes, and by extrapolation, the sugars to which they are immediately attached, are restricted in their mobility at the membrane surface. A crude model of the carbohydrate layer of the erythrocyte surface was constructed by incorporating the labeled, tryptic glycopeptides into agarose gels of different agarose content. A decrease in the probe's mobility was observed as agarose content was raised. This indicates that the high oligosaccharide density at the erythrocyte membrane surface may contribute to the observed immobilization of the fluorescent probes in situ.     

Survey of the year 2009: applications of isothermal titration calorimetry

Isothermal titration calorimetry (ITC) is now an established and invaluable method for determining the thermodynamic constants, association constant and stoichiometry of molecular interactions in aqueous solutions. The technique has become widely used by biochemists to study protein interaction with other proteins, small molecules, metal ions, lipids, nucleic acids and carbohydrates; and nucleic acid interaction with small molecules. The drug discovery industry has utilized this approach to measure protein (or nucleic acid) interaction with drug candidates. ITC has been used to screen candidates, guide the design of potential drugs and validate the modelling used in structure-based drug design. Emerging disciplines including nanotechnology and drug delivery could benefit greatly from ITC in enhancing their understanding and control of nano-particle assembly, and drug binding and controlled release.     

A simple and fast electrophoretic method for elution of nucleic acids from gels

A very convenient electrophoretic procedure for DNA or RNA elution from agarose or polyacrylamide gels is described. The gel piece with nucleic acid to be eluted is contained in a dialysis bag filled with buffer and elution is carried out in a horizontal electrophoresis apparatus. The nucleic acid is recovered with a high yield and can be used, without prior treatment, in further enzymatic or chemical reactions. Results obtained with DNA are presented here.     

A new continuous, monodimensional electrophoretic system for the separation and quantitation of individual glycosaminoglycans

A rapid and sensitive method for agarose gel electrophoresis is described. By simply miniaturizing a conventional gel electrophoresis apparatus, we have decreased the time necessary for the separation of nucleic acid molecules by a factor of 10. The ability to detect DNA molecules by ethidium bromide fluorescence has simultaneously been increased fivefold. Transfer of DNA from these “minigels” onto nitrocellulose filters followed by hybridization using the procedure of C. M. Southern (1975, J. Mol. Biol.98, 503–517) was found to be efficient and rapid. This technique is sufficiently sensitive to detect radioactive quantities of [³²P]phosphate-labeled DNA or RNA microinjected into 500 chick embryo fibroblasts.     

Rapid isolation of high-molecular-weight DNA from agarose gels

We have developed a simple, reliable, and rapid method for recovering DNA from agarose gels. While many methods for DNA extraction have already been described, few provide quantitative recovery of large DNA molecules. These procedures generally require costly apparatus, extended elution times, or considerable handling of the sample after elution. Our method employs a novel electroelution chamber constructed from acrylic plastic. Gel slices containing DNA are placed in the chamber between platinum electrodes. Voltage is applied and a continuous flow of buffer sweeps the eluted DNA from the chamber into an external receptacle. Elution is complete in 7 min. Concentrated DNA is obtained by butanol extraction and alcohol precipitation in 1 h. Recoveries, quantitated by counting radiolabeled DNA or by densitometry of analytical gels, were 94 to 100% for fragments of 4 to 50 kb. The eluted DNA was undegraded and could be digested with restriction enzymes, ligated, end-labeled, or used to transform cells as efficiently as noneluted DNA. Complete elution of a 100-kb plasmid, a 194-kb concatemer of bacteriophage lambda, and of 440- and 550- chromosomes of Saccharomyces cerevisiae was also achieved using the same process. This method is suitable for routine use in a wide range of cloning applications, including the electrophoretic isolation of large DNA molecules.