Figure 2

Amplicon range of inter-Alu PCR. The different lanes show gel electrophoretograms of amplicons obtained using different single primer or multiple primer sets: (A) AluJo56H16 alone; (B) AluJo232T16 alone; (C) AluSq56H16 alone; (D) AluSq263T16 alone; (E) AluJo56H16 and AluJo232T16; (F) AluJo56H16 and AluSq56H16; (G) AluJo56H16 and AluSq263T16; (H) AluJo232T16 and AluSq56H16; (I) AluJo232T16 and AluSq263T16; (J) AluSq56H16 and AluSq263T16; (K) AluJo56H16, AluSq56H16 and H-type L12A/8; (L) AluJo232T16, AluSq263T16 and T-type R12A/267, (N) AluY278T18, (P) AluY278T18 and AluY66H21, (Q)-(S) AluY278T18, AluY66H21 and R12A/267, (T) AluJo56H16, AluSq56H16 and AluSq263T16, (U) AluJo56H16, AluSq263T16 and AluJo232T16, (V) AluJo56H16, AluSq263T16 and L12A/8, and (M) M.W. markers. Notably, lanes E, G, H, J, P-V, where the inter-Alu PCR was performed using both H-type and T-type primers, gave rise to a largely smeared gel. Comparison of lanes N and P showed the conversion of a banded pattern obtained using a single T-type primer to a smeared one through the addition of an H-type primer. The much stronger staining intensity of lane S relative to lane R showed that the 0.30 μM concentrations of the same three primers in S compared to 0.10 μM in R resulted in increased amounts of amplicons. The primers AluJo56H16 (5'-GGCTCAAGCGATCCTC-3'), AluJo232T16 (5'-TATGATCGTGCCACTG-3'), AluSq56H16 (5'ACCTCAGGTGATCCAC-3'), and AluSq263T16 (5'-AACAAGAGCGAAACTC-3') were based on AluJo and AluSq consensus sequences [20]. H-type L12A/8 was an Alu consensus primer suggested earlier for inter-Alu PCR [15]. AluY278T18, AluY66H21 and T-type R12A/67 are described in Methods.