Anomalous electrophoresis of deoxyribonucleic acid restriction fragments on polyacrylamide gels

A detailed study has been made of the polyacrylamide gel electrophoresis of DNA restriction fragments obtained from two plasmids, pBR322 and p82-6B. Variables studied were molecular weight, gel concentration, temperature, and electric field strength. The retardation coefficients of the larger fragments (greater than 800 base pairs) were independent of molecular weight. The retardation coefficients of the smallest fragments (less than or equal to 300 base pairs) were proportional to Mr1/3, and therefore to the mean geometric radii of the fragments. The logarithm of the relative mobility of all fragments was also proportional to Mr1/3. The anomalous migration of certain fragments on polyacrylamide gels was found to be "transportable" into fragments generated by different restriction enzymes. Anomalous migration was enhanced at lower temperatures and disappeared upon increasing the temperature. A fragment which migrated anomalously slowly migrated even more anomalously when dimerized; dimerizing a normally migrating fragment resulted in the normal migration of the dimerized fragment. Anomalously migrating fragments were found to be localized in distinct regions of the pBR322 circle.     

Transfer of small DNA fragments from polyacrylamide gels to diazobenzyloxymethyl-paper and detection by hybridization with DNA probes.

A method for transferring small DNA fragments from composite polyacrylamide-agarose gels to diazobenzyloxymethyl (DBM)-paper is described. DNA fragments are separated by electrophoresis in polyacrylamide-agarose gels crosslinked with N,N′-diallyltartardiamide instead of N,N′-methylenebis-acrylamide. The crosslinks are cleaved by treating the gel with periodic acid after electrophoresis and the DNA is denatured with alkali. After neutralization, the single stranded DNA fragments are transferred to DBM-paper and detected by hybridization with labeled DNA probes. The procedure has been used to transfer and visualize unlabeled SV40 DNA fragments in the size range 28 to 1790 base pairs.     

Strand separation of DNA fragments and their isolation from nondenaturing polyacrylamide gels

A technique for rapidly and quantitatively denaturing double-stranded DNA employing urea and moderate heat is described. The single DNA strands are resolved on high-percentage nondenaturing polyacrylamide gels from which they can be recovered for Maxam-Gilbert sequence analysis.     

A hybridization method for autoradiographic visualization of small unique sequence fragments resolved on polyacrylamide gels

A useful method is described for sequence-specific visualization of small nucleic acid fragments on polyacrylamide gels. Excess highly radioactive probe is annealed in solution to smaller fragments. The resulting hybrids are trimmed (under appropriate conditions) with S1 nuclease to yield duplex fragments whose sizes are determined by the strand contributed by the smaller unlabeled fragment, but which also contain a labeled strand from the radioactive probe. These fragments can then be resolved on polyacrylamide gels and visualized by drying the gel and subjecting it to autoradiography. This method is shown to visualize fragments as small as 40 base pairs.     

Separation of the complementary strands of DNA fragments on polyacrylamide gels.

32P-labeled (in vivo) phiX174 RFI DNA was restricted by Hinc II. Three aliquots of the same digest: a) nondenatured, b) heat denatured, and c) denatured by 5 mM Me-HgOH were analyzed on 3-15% acrylamide gel gradients or on 3% gels with reduced N,N'-methylene-bis-acrylamide. The autoradiography of the gels showed that the nondenatured sample migrates two times faster than the denatured samples. After denaturation each original fragment appeared as a doublet. Using in vitro synthesized RFI DNA labeled only in negative strand with 32P we could identify the position of the negative strand in each denatured doublet. The single strand DNA fragments could be recovered from the gel slices on a semi-preparative scale by electrophoresis into dialysis tubing.     

Electrophoresis of DNA restriction fragments in poly-N-acryloyl-tris gels

Poly-N-acryloyl-tris(hydroxymethyl)aminomethane (NAT) gels were evaluated as a matrix for DNA electrophoresis. The resolution of DNA restriction fragments in three poly(NAT)-N,N'-methylenebisacrylamide (Bis) gels (4, 5, and 6%) was compared with the resolution in polyacrylamide (AA)-Bis gels of the same percentage. Poly(NAT) gels were found to give a substantially improved separation of DNA fragments larger than 200 bp. In contrast to poly(AA) gels, DNA fragments of up to 4 kbp were well resolved in the new matrix. By pulse-field electrophoresis the useful separation range of poly(NAT) gels was expanded to at least 23 kbp. For DNA fragments below 10 kbp, the resolution was better than that in a 0.7% agarose gel. Thus poly(NAT) gels are most suitable for the electrophoretic separation of DNA molecules whose size is out of the optimal fractionation range of poly(AA) or agarose gels.     

A simple method for filter hybridization of labeled restriction fragments excised from gels

Labeled DNA restriction fragments excised from agarose or bisacrylylcystamine-acrylamide gels can be used for hybridization to nitrocellulose-bound DNA without eliminating the gel matrix. A gel slice containing the labeled fragment is excised, dissolved by heating at 105 degrees C (in the presence of beta-mercaptoethanol for bisacrylylcystamine-acrylamide gels), and added to the hybridization mixture. The presence of agarose or polyacrylamide in the solution does not inhibit hybridization. The method is simple, rapid, and allows complete recovery of the probe.     

Quantitative electrophoretic transfer of DNA from polyacrylamide or agarose gels to nitrocellulose

A method for efficient electrophoretic transfer of DNA fragments from polyacrylamide gels to nitrocellulose sheets was developed. Hybridization to these fragments can be performed by standard techniques. The method is also applicable to agarose gels, allowing this transfer method to be used for DNA ranging from 40 to at least 23,000 bp.     

Quantification of small amounts of hemoglobin in polyacrylamide gels with benzidine.

Benzidine-hydrogen peroxide is a sensitive blood stain. Since benzidine is carcinogenic, less hazardous substitutes have been sought which retain the specificity and sensitivity of benzidine. We have tested two benzidine derivatives, 3,3′-dimethoxybenzidine and 3,3′, 5,5′-tetramethylbenzidine, reported to be satisfactory substitutes, but have found both to be unsatisfactory for quantifying small amounts of hemoglobin (Hb) on polyacrylamide gels. However, our data show that benzidine stains gels with an intensity proportional to the amount of Hb present when the staining time and temperature are controlled. The stain is fast, sensitive, and specific for Hb, gives very little background stain, and is stable if the gels are thoroughly rinsed and stored in distilled-deionized water. The relative amounts of Hb in different bands or different gels may be quantified later by densitometry. Procedures are suggested for using benzidine while giving adequate attention to governing regulations and personnel safety.     

Two-dimensional restriction mapping by digestion with restriction endonucleases of DNA in agarose and polyacrylamide gels

We have studied with a number of bacterial restriction enzymes the conditions for digestion of DNA in agarose and polyacrylamide gels. The restriction endonucleases HpaII, MspI, HaeIII, HindIII, TaqI, HhaI, AluI, BamHI, EcoRI and SalI are capable of digesting DNA in agarose gels of low electroendosmosis and low sulfate concentration. All enzymes, except BamHI, are also capable of digesting DNA in polyacrylamide gels. With this method, rapid two-dimensional restriction mapping of genomes with low and high sequence complexity is possible.     

Rapid and inexpensive recovery method of DNA fragments from agarose and polyacrylamide gels by a cotton-wool column tube.

We developed a rapid, convenient, simple, and inexpensive method for isolating pure DNA from agarose and polyacrylamide gels using cotton wool tubes. DNA fragments ranging in size from 193-23,130 bp can be easily recovered within 2 hours by centrifugation through cotton wool from gel slices. The recovery rate of this method is 35% to 50%, when estimated for isolation of lambda DNA-HindIII fragments. We have also recovered 700-bp polymerase chain reaction (PCR) products using cotton wool tubes from electrophoresis on both a 0.8% agarose gel and a 6% polyacrylamide gel, in which satisfactory yields of more than 50% were obtained. The DNA thus recovered in this way is biologically active and can be used as a substrate for further experimental procedures without additional purification steps.     

A novel procedure for separating small peptides on polyacrylamide gels

A simple and fast procedure that allows the separation of small(1–3 kDa) peptides on glycine-SDS gels is described. Peptideswere separated by glycine-SDS/PAGE as a result of in situ complexation of peptide/SDS during electrophoretic migration and visualized by Coomassie blue staining. The data presented here shows the separation of small peptides of different isoelectric points, sizes, and hydrophobicity on polyacrylamidemini gels. Ten different peptides have been tested with this method. The data suggest the dependence of SDS/peptide complex formation and migration due to the number of basic amino acid residues, length of peptide and the hydrophobicity/hydrophilicity ratio.     

A novel procedure for separating small peptides on polyacrylamide gels

Summary A simple and fast procedure that allows the separation of small (1–3 kDa) peptides on glycine-SDS gels is described. Peptides were separated by glycine-SDS/PAGE as a result ofin situ complexation of peptide/SDS during electrophoretic migration and visualized by Coomassie blue staining. The data presented here shows the separation of small peptides of different isoelectric points, sizes, and hydrophobicity on polyacrylamide mini gels. Ten different peptides have been tested with this method. The data suggest the dependence of SDS/peptide complex formation and migration due to the number of basic amino acid residues, length of peptide and the hydrophobicity/hydrophilicity ratio.     

Ultramicrodetection of proteins in polyacrylamide gels.

Here we report the development of a highly sensitive procedure to detect proteins within separation matrices which should facilitate the characterization of rare proteins. The procedure is based on photochemical reactions where very low amounts of silver are deposited around proteins and in a series of steps are converted to silver sulfide. When this conversion is carried out in the presence of [35S]thiourea the resulting radioactive silver sulfide allows detection down to femtogram quantities of protein. In this work we applied the above principle to proteins separated on sodium dodecyl sulfate-polyacrylamide gels, thus not influencing physical and chemical parameters which are important for separation. This procedure should find application in any technique where detection of very low or limited amounts of proteins are required.     

Detection of copper on polyacrylamide gels.

A color test for the localization of copper on polyacrylamide gels is described. The test is based upon the quenching of fluorescence of bathocuproine sulfonate by Cu¹⁺ and is sensitive to 0.1 nmol of free or protein-bound copper. There is no false positive reaction with 10 nmol of hemeprotein, free Fe³⁺, Fe²⁺, Co²⁺, or Mn²⁺.     

Two methods for electrophoretic elution of proteins from polyacrylamide gels.

An apparatus is described which improves an earlier technique for eluting proteins from polyacrylamide-gel slabs by electrophoresis against a sucrose gradient. Another elution method where the components are concentrated electrophoretically in a collodion bag by altering the current density is described. This method enables the elution of small amounts of sample, free from disturbing background material arising from the gel, and also permits subsequent dialysis and ultrafiltration without transfer losses. It can be used with alkaline and acidic buffers and has been applied in the purification of human pituitary thyrotropin (TSH).