Studies of translation , on the ensemble level using in vivo techniques and on the single molecule level using optical

With the evolution of single molecule techniques as force-scope optical tweezers, it has become possible to perform very accurate measurements of the elastic properties of biopolymers as e.g. DNA. Nucleic acid elasticity is important in the interaction of these molecules with proteins and protein complexes in the living cell. Mostexperimental and theoretical effort has been aimed at uncovering and understanding of the behavior of polymers with contour lengths significantly longer than their persistence length. The well-established Worm-Like-Chainmodel has been modified such that a satisfactory description of such long biopolymers is available. However,in many single molecule experiments, such as the unfolding of RNA stem-loops and RNA pseudoknots, one is dealing with biopolymers whose contour lengths are comparable to persistence lengths. A full understandingof such curves requires an understanding of the physics of short biopolymers. For such cases, theories are just beginning to emerge and there is hardly any experimental data available. We target this problem by optical tweezers quantitative force-extension measurements on short biopolymers. The biopolymers used are primarilydouble stranded DNA whose total length ( 300 nm) is comparable to their persistence length ( 50 nm). As a control of our equipment and methods, we also stretch longer dsDNA ( 1100 nm), the force-extension curves ofwhich resemble those in literature. For the short DNA the force-extension curves qualitatively resemble those predicted by WLC theories, but a reasonable fit can only be made if the persistence length is allowed to be a fitting parameter. If made a fitting parameter, the ’apparent persistence length’ is found as 8.7±4 nm, a numberwhich is significantly lower than the real physical value.