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. 2006 Jun 6;34(10):3139–3149. doi: 10.1093/nar/gkl405

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© 2006 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-commerical use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Analysis of hairpin opening products. (A) Effect of hairpin loop length. Transposition reactions were performed as in Figure 5. Hairpin opening products of hairpin donors having variable loop length were analyzed by denaturing urea–PAGE and visualized by autoradiography. The length of the expected opening product is 50 nt. The secondary bands seen in several lanes probably represent DNA synthesis impurities or they (mutually not exclusively) may represent DNA migrating in several major conformations, possibly influenced by the presence of hairpin ends. Minor products seen below 50 nt products (lanes 6 and 7) most probably represent cleavage from the (n − 1) synthesis impurities. Several bands seen in the top part of lane 1 represent strand transfer products. (B) Kinetics of hairpin opening reaction. Transposition reaction with HP13A donor was performed, and samples (taken after incubation of 0, 10, 30 and 90 min) were analyzed by urea–PAGE and autoradiography.