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Fig. 1. The loop formation patterns of the lambda phage insert and the S/MAR-IFNB1 insert. Integrated lambda loops (A) and the integrated IFNBI construct loops (B) visualized with FISH probes to compare the loop size. (A) The lambda phage insertion (an example of non-S/MAR integrated construct) is shown as a green color that illustrates a large extended loop; the red color distinguishes the nuclear matrix. The integrated lambda loop detected as large released loops seems to lack endogenous MARs, and the fortuitous genomic MARs adjacent to the integrated sites are probably serving as anchoring sites. (B) The S/MAR-containing IFNB construct is shown as red and green signals (two-color FISH) in loop patterns closely resembling the endogenous loop pattern. The darker DAPI staining region in (B) represents the nuclear matrix and the lighter blue surrounding area illuminates the loop region. The IFNB1 construct displayed considerably smaller loop sizes than that of the lambda phage insert even though the total size of the insert was the same as the lambda insert. This is most probably due to the availability of S/MAR sequences within the IFNB1 construct.

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