Analysis of multiple gene expression array experiments after repetitive hybridizations on nylon membranes

Nylon membrane-based macroarrays form a widely available alternative to microarrays for the collection of large-scale gene expression data. To carry out repetitive hybridization experiments with nylon cDNA arrays, we used phosphorothioate 33P-cDNA, followed by stripping under relatively mild conditions. We were able to use the same membranes more than 10 times without a measurable reduction in their performance. Thus, our protocol allowsfor more comparative studies of multiple data sets obtained from sequential hybridizations of the same set of membranes. We demonstrate how to analyze repetitive macroarray experiments and to determine the reliability or statistical significance of the gene expression data obtained. Both the averaging of signals per gene and the reversal of nylon membranes had a favorable effect on accuracy. By self-self comparisons, we show that in a duplicate experiment with four membranes, a 2-fold change in the gene expression can be measured reliably.     

Anionic exchange nylon laminated membranes for enzyme immobilization

Summary This work presents the optimization of the chemical steps involved in nylon modification with dimethyl sulphate, polyethyleneimine, glutaraldehyde and 2-diethyl aminoethylamine to obtain a weak basic anion exchange support. Activated nylon laminated membranes were utilized for aminoacylase immobilization, allowing an ionically adsorbed enzyme derivative with high activity (0.16 U/mg E·cm²) and low removed activity (<1%). Optimum immobilization conditions and kinetic parameters were also determined. This immobilized enzyme can be used in laminated enzyme membrane reactors.     

Quantitative molecular hybridization on nylon membranes

A study of DNA hybridization to DNA covalently bound to nylon membranes was made in order to develop a quantitative method for molecular hybridization using a nylon-based matrix. Chloroplast DNA was covalently attached to nylon membranes by irradiation at 254 nm. Under hybridization conditions the initial rate of DNA loss from the nylon membranes was 5-10% per 24 h, while under comparable conditions DNA bound to nitrocellulose membranes was lost at a rate of 38 to 61% per 24 h. Several sets of hybridization conditions were examined to select one giving reasonable hybridization rates and minimal loss of bound DNA. Under the conditions selected [Denhardt's solution (D. Denhardt, 1966, Biochem. Biophys. Res. Commun. 23, 641-646), 0.5 M NaCl, 0.1% sodium dodecyl sulfate, and 31.4% formamide at 50 degrees C for 92 h], hybridization was observed to be 29% more efficient on nylon membranes than on nitrocellulose. Several attempts to remove previously hybridized DNA from nylon membranes proved only partially successful. Reuse of the membranes, therefore, was of limited value. Quantitative hybridization of total radiolabeled tobacco cellular DNA to cloned tobacco chloroplast DNA attached to nylon yielded results similar to those previously reported using nitrocellulose membranes. However, use of nylon membranes greatly facilitated the manipulations required in the procedure.     

Ultraviolet shadowing nucleic acids on nylon membranes

We describe a method for the direct visualization of nucleic acids on nylon membranes. Nylon is weakly fluorescent under short wave ultraviolet light allowing membrane-bound nucleic acids to be detected with a sensitivity of 10 ng. This procedure involves no staining or destaining of the gels prior to transfer, does not require duplicate sample lanes or blots, and does not interfere with transfer of the nucleic acid to the membrane or subsequent hybridization.     

Nick translation of DNA immobilized on nylon membranes

Nick translation of DNA bound to nylon membranes is described. Phage lambda DNA was digested with restriction endonuclease HindIII. The fragments were separated by agarose electrophoresis and electrophoretically transferred to Zeta-Probe nylon membranes. After being air-dried, the areas with DNA fragments attached were cut out and subjected to nick translation. The labeled fragments, removed from the membranes by a single wash step, can be used as specific hybridization probes. Currently used methods require time-consuming electroelution and often additional purification procedures if a specific DNA fragment, separated by gel electrophoresis, is to be labeled by nick translation. With the procedure described it is possible to label many DNA fragments in parallel in a time- and cost-saving manner.     

Chemiluminescent detection of DNA on nylon membranes.

Two types of nonradioactive DNA detection systems were optimized for use with nylon membranes in Southern transfers. A luminol substrate system (consisting of an enhanced chemiluminescent reaction utilizing luminol enzyme substrate) was used with peroxidase-labeled probe DNA, and a dioxetane-based substrate was used with alkaline phosphatase/antibody and digoxigenin-labeled probe DNA. Chemiluminescence was detected by autoradiography. Methods for reprobing the membranes were also optimized for both systems; blots could be reprobed at least ten times. Results showed that excellent sensitivity and low background can be achieved on both amphoteric and positively charged nylon membranes, using either detection system.     

Sensitive fluorescent detection of protein on nylon membranes

Detection of antigen immobilized on membranes, as in Western transfers and dot enzyme linked immunosorbent assays (ELISAs), often employ antibody-enzyme conjugates and chemiluminescent or precipitated colored reaction products. Although chemiluminescent markers are sensitive, they are time-consuming because of their required exposure to X-ray film and the presence of background artifacts sometimes limits their use. This report demonstrates that direct fluorescent detection technique using nylon membranes that has higher sensitivity than chemiluminescent methods is easier to perform and has a uniform, low background. An alkaline phosphatase conjugated antibody was compared with antibody conjugated to a fluorescent phycobiliprotein (allophycocyanin) for sensitivity in both Western transfers and dot ELISA assays using mouse IgG as the membrane-bound antigen. Direct fluorescent detection of antigen-antibody complexes on positively charged nylon membrane provided better sensitivity and lower background than similar conditions using enzyme amplification and chemiluminescent detection on either nylon or PVDF membranes. Processing time was reduced by the elimination of steps associated with substrate incubation, washing and X-ray film exposures required for chemiluminescence detection. These data support the view that direct fluorescent detection can represent a significant improvement in assay sensitivity and reduction in time compared with more traditional chemiluminescent detection techniques employed in the conduct of Western transfers and dot ELISA studies.     

Southern transfer of native DNA using nylon membranes

Transfer of native or denatured DNA from gels or filter manifolds was compared using nylon or nitrocellulose membranes. The results were comparable when denatured DNA was used, but only nylon membranes were able to retain native DNA. Although retention of the native DNA was less efficient the bound DNA could be rapidly denatured in situ, avoiding the need to soak gels in alkaline denaturation solution and neutralizing buffer.     

India ink staining of proteins on nylon and hydrophobic membranes

India ink was found to be an acceptable stain for proteins blotted or dotted onto positively charged nylon or hydrophobic membranes. The hydrophobic membrane, Immobilon, was an outstanding matrix for binding proteins and displayed low levels of background staining. The least amount of protein detected by india ink staining was between 1.0 and 10 ng. India ink staining of proteins on nylon membranes is an easy, inexpensive, and quick method for the unequivocal detection of both standards and unknowns in the same blot. However, inks, ink concentrations, fixing conditions, staining times, pH, washing conditions, and membrane lots all need to be controlled to achieve maximum sensitivity for protein detection following india ink staining.     

Adsorption of bilirubin with polylysine carrying chitosan-coated nylon affinity membranes

Microporous polyamide membranes were activated by bisoxirane and subsequently bound with chitosan (CS) to amplify reactive groups. Then polylysine (PLL) as ligand was immobilized onto the CS-coated nylon membranes. The contents of CS and PLL of PLL-attached membranes were 93.2 and 90.4 mg/g nylon membrane, respectively. Such PLL-attached membranes were used to adsorb bilirubin from the bilirubin-phosphate solution and bilirubin-albumin solution. The adsorption mechanism of bilirubin and the effects of temperature, initial concentration of bilirubin, albumin concentration and ionic strength on adsorption were investigated by batch experiments. The results showed that the adsorption capacity increased with increasing the temperature while decreased with increasing the NaCl concentration and albumin concentration, and the adsorption isotherm fitted the Freundlich model well. The result of dynamic experiment showed PLL-attached membranes can well remove the bilirubin from the bilirubin-albumin solution.     

Diagnostic nucleic acid hybridizations for infectious diseases

The use of nucleic acid hybridization techniques has expanded into many areas, including studies of gene structure and function, routine diagnosis of human, animal and plant diseases, and also forensic science. In situ hybridization is one of the techniques currently available for nucleic acid hybridization and has some distinct advantages compared with standard techniques such as dot-blot, Southern or Northern hybridization, in which the histological structure is lost during extraction of nucleic acids. On the other hand, immunohistochemical staining is one branch of histochemistry that has received considerable attention in recent years as a very sensitive method for localization of specific proteins and other antigenic macromolecules within tissues and cells. This technique has also been widely used for clinical diagnosis and in various fields of research in medical science and biology. Automation of colorimetric in situ hybridization and immunohistochemistry would greatly contribute to the ease of introducing these techniques for routine pathological diagnosis and would improve the reproducibility of the assay. In this review, author will describe the development of an automated method for in situ hybridization and immunohistochemical staining using an automatic machine for both procedures.     

A common reference for cDNA microarray hybridizations

Comparisons of expression levels across different cDNA microarray experiments are easier when a common reference is co-hybridized to every microarray. Often this reference consists of one experimental control sample, a pool of cell lines or a mix of all samples to be analyzed. We have developed an alternative common reference consisting of a mix of the products that are spotted on the array. Pooling part of the cDNA PCR products before they are printed and their subsequent amplification towards either sense or antisense cRNA provides an excellent common reference. Our results show that this reference yields a reproducible hybridization signal in 99.5% of the cDNA probes spotted on the array. Accordingly, a ratio can be calculated for every spot, and expression levels across different hybridizations can be compared. In dye-swap experiments this reference shows no significant ratio differences, with 95% of the spots within an interval of ±0.2-fold change. The described method can be used in hybridizations with both amplified and non-amplified targets, is time saving and provides a constant batch of common reference that lasts for thousands of hybridizations.     

"Pocket blotting": a method for transferring nucleic acids onto nylon membranes

We have developed a fast and efficient method for transferring nucleic acids onto nylon membranes. This method requires less DNA for transfer; no decrease in efficiency is observed after successive probing, and several gels can be processed simultaneously. We believe that this techniques is of general interest in routine analysis of multiple samples in population genetic studies or in diagnosis purposes.     

Rapid transfer of DNA from agarose gels to nylon membranes.

The unique properties of nylon membranes allow for dramatic improvement in the capillary transfer of DNA restriction fragments from agarose gels (Southern blotting). By using 0.4 M NaOH as the transfer solvent following a short pre-treatment of the gel in acid, DNA is depurinated during transfer. Fragments of all sizes are eluted and retained quantitatively by the membrane; furthermore, the alkaline solvent induces covalent fixation of DNA to the membrane. The saving in time and materials afforded by this simple modification is accompanied by a marked improvement in resolution and a ten-fold increase in sensitivity of subsequent hybridization analyses. In addition, we have found that nylon membrane completely retains native (and denatured) DNA in transfer solvents of low ionic strength (including distilled water), although quantitative elution of DNA from the gel is limited to fragments smaller than 4 Kb. This property can be utilized in the direct electrophoretic transfer of native restriction fragments from polyacrylamide gels. Exposure of DNA to ultraviolet light, either in the gel or following transfer to nylon membrane, reduces its ability to hybridize.     

Vacuum blotting: a simple method for transferring DNA from sequencing gels to nylon membranes

We describe a vacuum blotting procedure for transferring DNA fragments from conventional polyacrylamide sequencing gels to nylon membranes. The method employs a combination of vacuum-assisted diffusion (effected by a standard gel drier) and an osmotic gradient (effected by over- and underlying filters presoaked in ammonium acetate). Fragments up to 310 nucleotides in length transfer at 40–60% efficiency within 90 min. When combined with indirect end-labelling, the method allows genomic sequencing of a single-copy gene of Saccharomyces cerevisiae employing as little as 5 μg DNA per lane.     

Parameters affecting hybridization of nucleic acids blotted onto nylon or nitrocellulose membranes

Nine different nylon and nitrocellulose membranes were compared utilizing four different methods of attaching the nucleic acid target. Nylon membranes repeatedly demonstrated increased sensitivity as compared to nitrocellulose membranes. Sensitivity could also be enhanced by mildly denaturing the target prior to attachment onto the membrane. This was achieved by either UV cross-linking or baking.     

Non-isothermal cephalexin hydrolysis by penicillin G acylase immobilized on grafted nylon membranes

A new catalytic membrane has been prepared using a nylon membrane grafted by γ-radiation with methylmethacrylate (MMA) and using hexamethylenediamine (HMDA) as spacer. Penicillin G acylase (PGA) and cephalexin were employed as catalyst and substrate, respectively. Cephalexin hydrolysis was studied in bioreactors operated under isothermal and non-isothermal conditions. A hydrolysis increase was found when the temperature of the warm membrane surface was kept constant and the temperature of the other membrane surface was kept at a lower value. The hydrolysis increase was linearly proportional to the applied temperature difference. Cephalexin hydrolysis increased to about 10% when a temperature difference of 1°C was applied across the catalytic membrane. These results have been attributed to the non-isothermal cephalexin transport across the membrane, i.e., to the process of thermodialysis. In this way, the enzyme immobilized on and into the membrane reacts with a substrate concentration higher than that produced by simple diffusion under isothermal conditions.     

Hydroxyapatite-mediated transfer of DNA from diluted solutions to nitrocellulose or nylon membranes

Transfer of DNA (from 0.1 to 10 micrograms) from diluted solutions of variable volumes (1-10 ml) and various composition (2 M NaCl; 4 M LiCl, 8 M urea; 4 M CsCl; 20% sucrose) to nitrocellulose or nylon membranes was achieved with the use of hydroxyapatite. This absorbent that binds nucleic acids effectively and independently of ionic strength and composition of solution (except for chelators and phosphate ions) easily dissolves in small volumes of acids (for example, in 10% TCA). This phenomenon provides the opportunity to deliver the acid-insoluble precipitates to membrane filters. After alkaline denaturation on the filter followed by a fixation step (baking or UV irradiation for nitrocellulose or nylon filters, respectively), DNA hybridizes effectively with nick-translated DNA probes. The method is simple, reproducible, sensitive, and useful for working with diluted DNA solutions containing interfering substances.     

Protein binding to nitrocellulose, nylon and PVDF membranes in immunoassays and electroblotting

A selection of different membranes commonly used to bind proteins in blotting and dot binding assays were investigated for a range of properties which would influence their performance. Large differences were observed in the membranes' ability to bind increasing amounts of protein, the effect of incubation times on the quantity of protein bound and the loss of proteins from the membranes following their incubation with different detergents or protein blocking agents. These differences could only partially explain the observed performance of the membranes when used as protein adsorbants in immunoassays and when different buffers were used for the electro-transfer of several different proteins to a range of membranes.