LM-PCR detects ongoing TCR gene rearrangement in pediatric and adult thymocytes. (a) LM-PCR detects free signal ends generated by dsDNA breaks 3′ and 5′ of the Dβ2.1 TCR gene segment, corresponding to D-J and V-DJ rearrangements, respectively. (b) Specific LM-PCR products obtained from thymocytes from 2 normal individuals less than 6 months old, indicating ongoing V-DJ (lanes 1 and 3; 409 bp) and D-J (lanes 9 and 11; 492 bp) rearrangement. Controls with non–linker-ligated DNA amplified with primers 3 and 5 (lane 17) or 2 and 4 (lane 18) demonstrate the appropriately sized germline bands (868 and 956 bp, respectively). Lanes using mock-ligated DNA (lanes 2, 4, 10, and 12), DNA lacking the TCR loci (bacterial DNA ± linker ligation; lanes 5, 6, 13, and 14), linker alone (lanes 7 and 15), and PCR blanks (lanes 8 and 16) are negative. The higher molecular weight bands seen in lanes 1 and 11 probably represent dsDNA breaks corresponding to additional (nonproductive) rearrangements in cells with a rearranged Dβ2.1 locus. However, this remains to be formally demonstrated using probes and primers specific for sequences unique to these downstream regions. (c) LM-PCR signals generated from thymocytes obtained from a 24-year-old male. Eight-fold dilutions of DNA (decreasing concentration left to right) were linker ligated and subjected to LM-PCR as described. Signals corresponding to both D-J and V-DJ rearrangements were detected in 5 of 8 samples (donor age and gender: 24 M, 29 F, 27 F, 41 F, 42 F). Only D-J signals were detected in 3 samples (donor age and gender: 28 F, 34 F, 46 M). All tissues tested had immunohistologic evidence for thymopoiesis, with at least small foci of CD1a+, mib-1+ lymphocytes within a loose network of thymic epithelial cells. Template control reactions using primers 2 and 4 amplified the appropriately sized germline band.