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Electrophoresis was performed in a 12% polyacrylamide running gel and a 4% stacking gel, with a 0.025 M Tris 0.19 M glycine buffer pH 8.3, and 100 μL of a sucrose buffer (50 mM Tris HCl, pH 8; 40 mM EDTA, pH 8; 0.75 M sucrose).
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) was performed in a Minigel-Twin (Biometra, Goetttingen, Germany) using a 10% polyacrylamide running gel [ 45].
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Samples were run through a polyacrylamide stacking gel at 20 mA and through a 13% polyacrylamide gel running at 30 mA.
Each extract (15 μl) was boiled and separated on an SDS 10% polyacrylamide gel (running buffer: 25 m M Tris-HCl, pH 8.3; 190 m M glycine, 0.1% w/v SDS) before electrotransfer onto Hybond-P membranes (Amersham Pharmacia Biotech, Pittsburgh, PA, USA).
RNA and RNA-protein complexes were separated in 0.5 TBE 6% native polyacrylamide gels run at 100V in the cold room.
For analysis of insertion/deletion (in/del) variations PCR products were analyzed on 15% (29∶1 acrylamide; bis-acrylamide) polyacrylamide gels run in 50 mM Tris-Borate EDTA buffer.
Size fractionation and purification of ligation products were performed using a 5% polyacrylamide gel run in TBE at 180 V for 120 min. Gel slices were cut containing DNA in the 10 to 500 bp range.
The complexes were fractionated on 6% native polyacrylamide gels run in 1× TBE buffer (89 mM Tris, 89 mM boric acid, and 2.0 mM EDTA), dried, and exposed to Kodak X-AR film at −70°C.
Products were resolved on 0.2× TBE 5% native polyacrylamide gels run for 3 hr at 300 V at 4°C.
PCR products were separated on 6% denaturing polyacrylamide gels, run in TBE buffer at 60 watts for 3 4 hours and visualized using silver stain procedures.
SSCP was performed in 12% polyacrylamide gels run at 200V for 2-4 hrs in 4°C followed by silver staining, as previously described [ 15].
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