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. 2007 Jan 30;35(4):1198–1208. doi: 10.1093/nar/gkm036

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© 2007 The Author(s).

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Potential secondary structures formed by single-stranded PATRR sequences. Eight-hundred nucleotides containing each PATRR at the centre are analysed by mfold to demonstrate the putative stem-loop structures formed by intrastrand basepairing. The most prominent stem-loop structure for each sequence is formed by every PATRR sequence, whose length is indicated in parentheses. With regard to the PATRR22-pal and the PATRR22-quasi, sequences around the centre are indicated. The lowercase sequences are PATRR11-derived sequences in the junction fragment of the t(11;22) that provide the SnaBI site used to ligate the proximal and distal arms of the PATRR22-derived sequence. The PATRR22-pal is a perfect palindrome, whereas the PATRR22-quasi is a quasipalindrome having a spacer of 9 nt at the centre and four mismatched bases at 23, 27, 28 and 29 nt away from the hairpin tip.