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Calculate persistence length from force extension data of a single DNA

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  1. Aug 29, 2014 #1

    pen

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    Hello!

    From a data set of F-x measurements of a single dsDNA molecule I want to calculate the persistence length [itex] P [/itex]. So I plotted [itex] \frac {1} {\sqrt{(F)}}[/itex] vs. [itex]x[/itex] and fitted these data points (linear).

    According to an interpolation formula the extension [itex]x[/itex] of a worm like chain with contour length [itex]L_0 [/itex] (Bustamante et al.,1994) is:

    [itex] \frac{FP}{k_BT}= \frac{1}{4} \Big( 1-\frac{x}{L_0}\Big)^{-2} -\frac{1}{4} + \frac{x}{L_0}[/itex], applicable for extensions [itex]\frac{x}{L_0}<0.97[/itex]

    Thus the y-intercept of the straight line fitted to the data as described above is [itex] 2\sqrt{\frac{P}{k_BT}}[/itex].

    When I calculate [itex] P [/itex] this way, I get values between ~2.7 nm (when I choose a force range beween ~6-17pN, which is roughly linear, and the dsDNA molecule behaves as a Hookean spring). However these values are far below the expected value for the persistence length of dsDNA (50nm).

    Does anyone see what' s wrong with my approach ?


    Thanks a lot for help

    Pen


    P.S. please find attached the F-x-graph and the 1/sqrt(F)-x-graph
     

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    Last edited: Aug 29, 2014
  2. jcsd
  3. Aug 30, 2014 #2

    NascentOxygen

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    Staff: Mentor

    I find your 1/√F plot to have a y-intercept of 1.4
     
  4. Aug 31, 2014 #3

    pen

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    then unfortunately the plot was for a different force range, however in case the intercept is 1.4, the persistence length would be ~2nm (still much too low).
     
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