Calculate persistence length from force extension data of a single DNA

In summary, the conversation discusses a method for calculating the persistence length of a single dsDNA molecule using F-x measurements. The conversation includes an interpolation formula and a plot of 1/√F vs. x, which should have a y-intercept of 1.4. However, the calculated values for the persistence length are much lower than the expected value of 50nm. The speaker asks for help in identifying the mistake in their approach.
  • #1
pen
6
0
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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  • #2
I find your 1/√F plot to have a y-intercept of 1.4
 
  • #3
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).
 

1. How is the persistence length of DNA calculated from force extension data?

The persistence length of DNA can be calculated using the worm-like chain model, which assumes that DNA behaves like a flexible polymer, and the force-extension data can be fit to this model using statistical analysis.

2. What is the worm-like chain model?

The worm-like chain model is a mathematical model that describes the behavior of flexible polymers, such as DNA. It takes into account the bending and stretching of the polymer chain under applied force.

3. What type of force-extension data is needed to calculate the persistence length of DNA?

The force-extension data should be obtained from single molecule stretching experiments using techniques like atomic force microscopy or optical tweezers. These experiments measure the force required to stretch a single DNA molecule and the resulting extension.

4. Can the persistence length of DNA vary?

Yes, the persistence length of DNA can vary depending on various factors such as the sequence of the DNA, the ionic strength of the solution, and the presence of other molecules that can interact with DNA.

5. What is the significance of calculating the persistence length of DNA?

The persistence length of DNA is an important physical parameter that can provide insights into the structural properties and behavior of DNA. It can also help in understanding the interactions of DNA with other molecules and their effects on DNA stability and function.

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