FIG. 6.

Significance of (AT)n and (AC)n (GT)n palindromes in rAAV-labeled palindromes susceptible to breakage. (A) Percentage of rAAV-labeled (AT)n palindromes among the 134 rAAV-labeled palindromes with an arm length of ≥20 bp is plotted as a function of n. Random integration-labeled palindromes are likewise plotted. Asterisks and solid triangles indicate statistical significance between rAAV and random integrations (*, P < 0.001 by χ² test; closed triangle, P < 0.001 by Fisher's exact test). (B) DNA sequences of six (AC)n (GT)n palindromes (numbered 1 to 6) labeled by rAAV integration. Black arrowheads indicate the positions at which joining to the rAAV vector genome occurred. Uppercase letters denote the portion of the palindrome sequence that was retained in each junction, while lowercase letters denote the nonretained portion. Underlined nucleotides are central spacer sequences. All six (AC)n (GT)n palindromes show a center-deleted pattern. Two representative (AT)n palindromes are shown as 7 and 8 for comparison. Coordinates of the palindromes numbered 1 to 8 (UCSC mm8) are chr 10: 38176562, chr 5: 118212140, chr 6: 7083048, chr 15: 29735040, chr 8: 120556025, chr 16: 69258562, chr X: 150903099, and chr 15: 3434443, respectively.