Silver staining method for DNA in polyacrylamide gels using eriochrome black T as a silver-ion sensitizer

A highly sensitive nucleic acid stain based on amino-modified tetraphenylethene: the influence of configuration

We designed and synthesized a new amino-functionalized tetraphenylethene (TPE) derivative as a highly sensitive dye for the detection of dsDNA and oligonucleotide in both solution and a gel matrix. We further revealed that the cis configuration dye showed a much higher sensitivity than its trans isomer for the first time.

A method for sensitive staining of DNA in polyacrylamide gels using basic fuchsin

BACKGROUND

PAGE is a widely used analytical method to resolve components of a DNA mixture based on their size. Various DNA visualization methods including fluorescence, visible dye and silver have been used for the detection of gel-separated DNA, with each having different advantages and disadvantages in terms of sensitivity, safety and simplicity.

RESULTS

A fast and sensitive visible dye-based staining method for DNA in polyacrylamide gels using basic fuchsin (BF) is described. As low as 10-20 pg of DNA can be visualized within 10 min; the sensitivity is fourfold more sensitive than that of SYBR® Gold stain, the most sensitive commercial fluorescent probe, but similar to silver staining kit from GE Healthcare. In addition, the mechanism studies suggest that the interaction of BF with DNA is mainly contributed by non-intercalative binding mode.

CONCLUSION

By comprehensive studies of this visible dye-based protocol, we concluded that BF stain is a fast and sensitive method currently available for detecting DNA in polyacrylamide gels.

PDMS-glass bonding using grafted polymeric adhesive--alternative process flow for compatibility with patterned biological molecules

We report a novel modification of silicone elastomer polydimethylsiloxane (PDMS) with a polymer graft that allows interfacial bonding between an elastomer and glass substrate to be performed without exposure of the substrate to harsh treatment conditions, such as oxygen plasma. Organic molecules can thus be patterned within microfluidic channels and still remain functional post-bonding. In addition, after polymer grafting the PDMS can be stored in a desiccator for at least 40 days, and activated upon exposure to acidic buffer for bonding. The bonded devices remain fully bonded in excess of 80 psi driving pressure, with no signs of compromise to the bond integrity. Finally, we demonstrate the compatibility of our method with biological molecules using a proof-of-concept DNA sensing device, in which fluorescently-labelled DNA targets are successfully captured by a patterned probe in a device sealed using our method, while the pattern on a plasma-treated device was completely destroyed. Therefore, this method provides a much-needed alternative bonding process for incorporation of biological molecules in microfluidic devices.

A Note on Development of a Low-cost and High-throughput SSR-based Genotyping Method in Peanut (Arachis hypogaea L.)

Peanut cultivar development has been dominated by conventional breeding methods, which have and will continue to play an important role. Applications of marker-assisted selection (MAS) have been used in peanut breeding selection but the cost of genotyping is still a considerable factor. The objective of this study was to introduce a simple, low-cost, and high-throughput protocol for peanut community. The developed system was based on a smaller (10.5 cm in length) polyacrylamide gel size system to separate PCR amplified DNA fragments and silver staining to visualize the bands. This system is very easy to operate, having one electrophoresis unit holds two vertical 52-sample gels, and the cost for purchasing the unit is less than $200. For instance, the electrophoresis runs about 1 hr and 40 min at 180 V for 9% polyacrylamide gel to separate small to medium sized DNA bands (< 500 bp) or 1 hr and 20 min at 160 V for 6% polyacrylamide gel preferably for larger band separation (≥ 500 bp), but the gel concentrations and running times could be adjusted according to the polymorphic banding patterns and sizes to mitigate the drawback of this system of small gel-size. The silver staining takes about 30 min. After staining, the gels are placed on a light-box for genotype scoring and then photographed using a digital camera. The cost per gel is estimated at $0.54 and the cost for silver staining is estimated at $0.37. Therefore, the cost could be as low as $0.018 per data point, excluding PCR reaction and DNA preparation cost. A scientist has the potential to generate over 1,200 data points per day. This method has been used in the construction of a peanut genetic linkage map and QTL studies in our laboratory in conjunction with other methods.

Improved conditions for silver-ammonia staining of DNA in polyacrylamide gel

An improved silver-ammonia staining method for DNA on polyacrylamide gels is described. In this method, staining of DNA using silver-ammonia complex allows high sensitivity, low cost, low toxicity, and simple protocol without requiring fixation and sensitization steps. The protocol takes less than 40 min to complete, with a detection limit of 1.5 pg of single DNA band on polyacrylamide gels, approximately 30-fold higher than that of original silver-ammonia staining method. Furthermore, this novel technique not only exhibits high sensitivity for large DNA fragment, but also shows a better trend to detect low-base-pair DNA compared with other silver staining methods.

A user-friendly alternative to formaldehyde-based DNA silver-staining method on polyacrylamide gels

We have developed a practical, cost-effective and user-friendly protocol to meet the needs of nucleic acids research, particularly in respect of DNA detection on polyacrylamide gels. In this method, the most commonly used alkaline formaldehyde developer in DNA silver stain, which does harm to operator, is first replaced by glucose in alkaline borate buffer. In addition, the effects of six reducing sugars on the quality of DNA visualization were investigated. Consequently, the optimal protocol using glucose takes about 45 min to complete all the procedures, with a detection limit of 5 pg of single DNA band on polyacrylamide gels, was developed. The results indicate that this user-friendly and economic protocol could be a good choice for routine use in DNA visualization on polyacrylamide gels.