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. 2011 Mar 15;6(3):e16890. doi: 10.1371/journal.pone.0016890

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Su et al.

This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.

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Inline graphic — The contour lengths of the DNA are (A) m, (B) m, (C) m and (D) nm. For a long DNA (A and B), data from internal segments of various locations of the chain collapse on the a curve with power law (light green). The result agrees with Eq.9 (blue), which is derived for the end-to-end fluctuation of a confined DNA. For short DNA however (C and D), no power law is found as data from various locations of the chain do not collapse onto a single curve (light green). Therefore, formulae derived for the end-to-end fluctuation of the confined DNA, such as Eq.9 (blue), cannot be used for internal fluctuation. The boundary effect is so significant that the rms fluctuation not only depends on , but also on the location of the internal segments.

The contour lengths of the DNA are (A) m, (B) m, (C) m and (D) nm. For a long DNA (A and B), data from internal segments of various locations of the chain collapse on the a curve with power law (light green). The result agrees with Eq.9 (blue), which is derived for the end-to-end fluctuation of a confined DNA. For short DNA however (C and D), no power law is found as data from various locations of the chain do not collapse onto a single curve (light green). Therefore, formulae derived for the end-to-end fluctuation of the confined DNA, such as Eq.9 (blue), cannot be used for internal fluctuation. The boundary effect is so significant that the rms fluctuation not only depends on , but also on the location of the internal segments.