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

2011-12-30T13:45:26Z (GMT) by Steven J. koch
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*/
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