Hello!
1. The problem statement and all variables
AIM: Calculating persistence length [itex]P[/itex] of a single dsDNA molecule from a data set of force [itex]F[/itex] (to the molecule) vs. extension [itex]x[/itex] measurements. Experimental background: pN forces were applied to a single dsDNA molecule spanned between two μm-beads using an optical tweezer.
PROBLEM: When I calculate [itex]P[/itex], I get values of about 2.9 nm, which is far below the expected value for [itex]P[/itex] of dsDNA, which is about 50nm.
2. Relevant equations
The calculation was done as follows: For a chosen force range the [itex]F[/itex]-data were converted to [itex]F^{-1/2} [/itex] and plotted vs. [itex]x[/itex]. The data points were fitted linearly.
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}(1−\frac{x}{L_0})−2−\frac{1}{4}+\frac{x}{L_0 }[/itex],
applicable for a force range of ~5-15pN, where the molecule reveals a linear [itex]F-x[/itex] relationship (like a Hookean spring).
From that follows that the y-intercept of the straight line fitted to the data points is [itex]2\sqrt{\frac{P}{k_BT}}[/itex].
3. The attempt at a solution
The problem is (as I think) that the slope of the fitted straight line is too low. So I chose different force-ranges, as I thought, that the chosen force range might be wrong. But that didnt work. In the attachement of the thread "Calculate persistence length from force extension data of a single DNA" one can find the force curve and a [itex]F^{-1/2}-x[/itex] graph, plotted for a force range of 6-16pN, with the linear fit: slope of -1.5151, the y-intercept at 1.6931 and a calculated persistence length of 2.9455 nm
I really would appreciate some help
Pen
1. The problem statement and all variables
AIM: Calculating persistence length [itex]P[/itex] of a single dsDNA molecule from a data set of force [itex]F[/itex] (to the molecule) vs. extension [itex]x[/itex] measurements. Experimental background: pN forces were applied to a single dsDNA molecule spanned between two μm-beads using an optical tweezer.
PROBLEM: When I calculate [itex]P[/itex], I get values of about 2.9 nm, which is far below the expected value for [itex]P[/itex] of dsDNA, which is about 50nm.
2. Relevant equations
The calculation was done as follows: For a chosen force range the [itex]F[/itex]-data were converted to [itex]F^{-1/2} [/itex] and plotted vs. [itex]x[/itex]. The data points were fitted linearly.
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}(1−\frac{x}{L_0})−2−\frac{1}{4}+\frac{x}{L_0 }[/itex],
applicable for a force range of ~5-15pN, where the molecule reveals a linear [itex]F-x[/itex] relationship (like a Hookean spring).
From that follows that the y-intercept of the straight line fitted to the data points is [itex]2\sqrt{\frac{P}{k_BT}}[/itex].
3. The attempt at a solution
The problem is (as I think) that the slope of the fitted straight line is too low. So I chose different force-ranges, as I thought, that the chosen force range might be wrong. But that didnt work. In the attachement of the thread "Calculate persistence length from force extension data of a single DNA" one can find the force curve and a [itex]F^{-1/2}-x[/itex] graph, plotted for a force range of 6-16pN, with the linear fit: slope of -1.5151, the y-intercept at 1.6931 and a calculated persistence length of 2.9455 nm
I really would appreciate some help
Pen
0 commentaires:
Enregistrer un commentaire