Table 1.

Secondary structure characteristics of 8q24.1 breakpoint relative to other junction sites involved in constitutional translocations involving LCR-B of 22q11.2

Sequences surrounding breakpoints involved in translocations with LCR-B of 22q11.2 were analyzed by M-Fold. Nucleotide sequence forming the primary stem–loop or 1200 nucleotides (nt) surrounding the breakpoint (600 nt on each side) was analyzed to determine melting temperature, the free energy of this single strand of sequence annealed to its complimentary strand (free energy of the double strand, G_DS), or that contained within the single-strand secondary structure (G_STRUC). Only structures having the greatest stability were included in this analysis (M-Fold frequently returns numerous potential structures for a given sequence). References for characterized breakpoint sequences: 22q11.2 (Kurahashi and Emanuel 2001), 11q23 (Edelmann et al. 1999; Kurahashi and Emanuel 2001), 17q11 (Kehrer-Sawatzki et al. 2002; Kurahashi et al. 2003), 4q35.1 (Nimmakayalu et al. 2003), 1q21.1 (Gotter et al. 2004).

^aNumber of nucleotides contained in the stem–loop region surrounding the indicated translocation breakpoint. This includes palindromic and loop sequence as well as mismatched bases.

^bΔG/nt: For a given sequence, the difference in free energy between that contained in the double-stranded and single-strand secondary structure configurations per nucleotide [(G_DS – G_STRUC) / (number of base pairs analyzed)].

^cOnly 878 bp of sequence surrounding the LCR-B breakpoint are currently known.

^d8q24.1 sequence surrounding the t(1;22) breakpoint in the current work was deduced from junction fragment sequence (see Figure 5B).