Kidd Lab 

Alu site

Template: Genomic DNA 100-200 ng/reaction volume of 25 µl

Primer 1. CD4 4104: 5'-AGG CCT TGT AGG GTT GGT CTG ATA-3'              100 ng/reaction
Primer 2. CD4 R105: 5'-TGC AGC TGC TGA GTG AAA GAA CTG-3'            100 ng/reaction

dNTPs: Final Concentration 200 µM each

Buffer: Final Concentration 2.25 mM MgCl₂, 50 mM KCl, 10 mM Tris-HCl pH 8.4

Taq DNA Polymerase: 0.625 Units/reaction
                                 (Perkin-Elmer Amplitaq DNA polymerase 5 U/µl, Cat. No. N808-0145)

PCR Cycling Profile:  94^oC (5')
                               94^oC (1'), 58^oC (1.5'), 72^oC (1.5')  × 30 cycles

Product size:
                     1500 bp—Alu present
                     1200 bp—Alu absent

[NB: There is preferential amplification of the smaller product.  This can be minimized by limiting genomic DNA to 100 ng/reaction volume of 25 µl.]

Reference: Edwards and Gibbs, Genomics 14: 590-597 (1992).
 
 

Kidd Lab Histograms for Allele Frequencies