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. Author manuscript; available in PMC: 2014 Dec 15.
Published in final edited form as: Anal Biochem. 2013 Jun 14;443(2):10.1016/j.ab.2013.06.001. doi: 10.1016/j.ab.2013.06.001

Figure 7.

Figure 7

The model.

(A) Migration of DNA through the agarose gel as shown by [48; 57]. In this model, DNA undergoes cyclic motion of alternating elongated and compact conformations, the duration of which depends upon the size of the DNA. The elongated confirmation, in the form of U-shaped structure, is assumed when the DNA molecule is transiently ‘hooked around’ the gel fiber. The small arrows show the direction of DNA sliding off the hook.

(B) Breakage of the transiently trapped DNA at nicks. Nicked DNA stays in the elongated confirmation (I) until a nick reaches the vertex at the hook (II). Subsequent local unraveling of the DNA structure from the nick leads to the formation of SS ends that pull apart, anchoring the DNA at the hook (III). When the electric field-caused unraveling of the DNA duplex reaches another nick in the opposite DNA strand, a double-strand break is formed (IV), and the broken DNA can now slide off the hook (V).