The size standards can be generated either by PCR amplification with different sets of primers amplifying varying size products or by cutting a plasmid with restriction endonucleases and end labeling the fragments with a fluorescent tag. We adopted the latter approach with certain modifications. We surpassed the requirement of restriction digestion and used commercially available size standards that were PCR amplified and fluorescently labeled. The latter procedure reduced the cost as well as time needed for designing primers for generation of different size standards. Commercially available 100 bp DNA ladder (Medox Biotech India Pvt. Ltd.) was used as the source of size standards (100-1000 bp) consisting of standards having 100 bp increment in size.
About 2 μg of the DNA was precipitated by adding 1/25th volume of 5 M NaCl and 2 volumes of cold ethanol and incubated at -20°C for 2 hours. The DNA was pelleted at 12,000 rpm for 15 min at 4°C followed by 70% ethanol wash. The pellet was air dried and dissolved in 10 μl sterile water. Addition of deoxyadenosine residues at the 3' ends of the size standards was done prior to cloning. The standards were incubated with 1 μl of 10 mM dATP, 1.5 μl of 10× PCR buffer (100 mM Tris, 500 mM KCl, 15 mM MgCl2, 0.1% (w/v) gelatin, 0.05% (v/v) Tween-20, 0.05% (v/v) NP-40, pH 8.8), 0.20 μl Taq DNA polymerase (in-house isolated) in a total volume of 15 μl at 72°C for 15 min. The pool of DNA size standards carrying A at their 3' ends were ligated to pGEM®-T Easy Vector (3015 bp, Promega) carrying M13 forward and reverse sequencing primer binding sites. The ligated product was transformed in ultra-competent E. coli DH5α cells followed by plating on Luria Bertani agar plates supplemented with 50 μg/ml ampicillin and incubated at 37°C overnight. Transformants were analyzed by colony PCR using M13F (TGTAAAACGACGGCCAGT) and M13R (AGGAAACAGCTATGACCAT) primers. Plasmid DNA was isolated from the positive clones by alkali lysis method and purified by PEG 8000. The pellet was air-dried and dissolved in 20 μl sterile water.
The plasmids having the desired inserts were amplified with unlabeled M13 forward and reverse primers. The PCR reaction contained 20-25 ng of plasmid DNA, 1× PCR buffer, 200 μM dNTPs, 3 pmoles each of M13 forward and reverse primers (unlabeled) and 0.18 μl of Taq DNA polymerase in a total volume of 20 μl. After confirmation of PCR amplification on agarose gel, the products were 2-fold diluted with sterile water. PCR reaction with labeled M13F and M13R primers (MWG) was carried out on individual amplified products in two sets. The first set of PCR reaction contained about 1 μl of the diluted amplified product, 1× PCR buffer, 200 μM dNTPs, 1 pmole each of M13 forward primer (7:3 ratio of IR dye labeled and unlabeled), M13 reverse primer (unlabeled) and 0.18 μl of Taq DNA polymerase. The second set PCR was similar as described above except that M13 forward primer (unlabeled) and M13 reverse primers (7:3 ratio of IR dye labeled and unlabeled) were used. The cycling conditions were 94°C for 4 min; 35 cycles of 94°C for 20 sec, 60°C for 30 sec, 72°C for 1.5 min; 72°C for 10 min followed by 4°C forever. 5 μl aliquots from each reaction were mixed with 2 μl formamide loading buffer {37% (v/v) deionized formamide, 1 mM EDTA and 0.02% (w/v) bromophenol blue}. To generate a cocktail of different size standards, an aliquot from all of the above PCR amplifications were pooled for usage as labeled size standard for Li-COR without any further purification. The cocktails of above products (0.3-0.5 μl) was electrophoresed on 6.5% (w/v) denaturing polyacrylamide gel in 0.8% TBE buffer at 1500 V, 40 mA and 40 V setting on 4300 Li-COR Analyzer for 4 hours. The TIFF images of 700 and 800 channels respectively, were analyzed in Adobe Photoshop software (Adobe Systems Inc.).
To determine the exact molecular size of the standards generated using M13 forward and reverse unlabeled primers, the PCR products were sequenced by ABI Big dye terminator chemistry (v 3.0) {Applied Biosystems}. Figure 1A shows the molecular size of the generated standards in the ladder and its comparison with the commercially available size standards from Li-COR. Figure 1B shows a part of the polyacrylamide gel with in-house generated size standards loaded adjacent to mutant DNA samples showing the complementary cut products in the 700 and 800 channels. One of the advantages of custom labeled standards is that these can be used to demarcate the left and right sides of gel. For this, two different cocktails of size standards can be made by mixing individual standards. The left side markers can contain all the standards whereas the right side markers can have just few of the standards. Employing two sets of standards can eliminate any error that may occur due to accidental flipping of paper combs. Using two different cocktails the left and right side of the gel can be visually detected during electrophoresis. In addition, a single size standard such as of 200 or 300 bp size can be loaded in every 8th lane to aid precise identification of lane with an increment of 8 numbers during mutation/SNP analysis.
Occasionally some faint spurious bands may appear along with the size standards on Li-COR. Primarily these bands arise due to some degree of mispriming during PCR amplifications with M13 forward and reverse primers. Though these bands are undetectable on agarose gels but owing to the sensitive nature of laser detection are visible during run on Li-COR machine. In such case, the given size standard can be diluted to a level allowing only the standard of interest to be visible on Li-COR machine.
