2003 Loading Rate Clamp Flow Chart supp to Koch and Wang PRL 2003

None
Share this:
Embed*
Cite this:
J. koch, Steven (2011): 2003 Loading Rate Clamp Flow Chart supp to Koch and Wang PRL 2003. figshare.
http://dx.doi.org/10.6084/m9.figshare.148
Retrieved 06:42, Sep 02, 2014 (GMT)

Description

This flow chart may help explain the "loading rate clamp" optical tweezers system used in the publication "Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA" by Koch and Wang, Phys. Rev. Lett. (2003). http://link.aps.org/doi/10.1103/PhysRevLett.91.028103 I was always disappointed that since we published in PRL we could not explain the loading rate clamp effectively because of page limits. I had drawn this figure to expalin to my advisor how the feedback system worked, but I never published it. The key to the system is that we know we are unzipping DNA and the polymer stiffness is dominated by the single-stranded DNA. Knowing the properties of the ssDNA (freely-jointed chain model), allowed me to calculate in real-time the number of nucleotides that had been unzipped. It also allowed for calculation of the instantaneous stiffness of the system, by taking analytical derivatives of the extensible freely-jointed chain model. I'll want to publish the derivatives someday, but they're not complicated. I did something like this: R = ( -B/((sinh(F*B))**2) + 1 / (B*F*F) ); G =(1 + 1 / (F*F*B))*(1+F/K) + (1 - 1 / (F*B) ) * (1 + 1 / K); Gp = (1-2/(F*F*F*B))*(1+F/K) + 2*(1+1/(F*F*B))*(1+1/K); where B is persistence length scaled by kT, F is force (pN), and K is stretch modulus for FJC model. The instantaneous length was calculated something like cotf = 1/tanh(f1); Lss = (x / (1+f2)) *( 1 / (cotf - 1/f1)); tp = (Lss) / a; /*tp is length of ssDNA in nucleotides*/

Comments (0)

You must be logged in to post comments.

Cite "Filename"

Place your mouse over the citation text to select it

Embed "2003 Loading Rate Clamp Flow Chart supp to Koch and Wang PRL 2003"

Place your mouse over the embed code to select and copy it

Claim article

You claim request was sent. I will be handled in the next 24 hours.

Close window

Feedback

We appreciate all your comments, questions, suggestions or gratitude.

Login

The username or password entered are wrong.

Reset password

Your password will be sent to your registered e-mail address.

Create account

I agree to the Terms & Conditions *