Biomedical subjects

Andrew J Spakowitz

Publications and source records attributed to Andrew J Spakowitz.

4 recordsLinked to original sources

PubMed2006

Effect of force on mononucleosomal dynamics.

Using single-molecule optical-trapping techniques, we examined the force-induced dynamic behavior of a single nucleosome core particle. Our experiments using the DNA construct containing the 601 nucleosome-positioning sequence revealed that the nucleosome unravels in at least two major stages. The first stage, which we attributed to the unraveling of the first DNA wrap around the histone octamer, could be mechanically induced in a reversible manner, and when kept at constant force within a critical force range, exhibited two-state hopping behavior. From the hopping data, we determined the force-dependent equilibrium constant and rates for opening/closing of the outer wrap. Our investigation of the second unraveling event at various loading rates, which we attributed to the inner DNA wrap, revealed that this unraveling event cannot be described as a simple two-state process. We also looked at the behavior of the mononucleosome in a high-salt buffer, which revealed that the outer DNA wrap is more sensitive to changes in the ionic environment than the inner DNA wrap. These findings are needed to understand the energetics of nucleosome remodeling.

Chemical Phenomena↗

PubMed2005

End-to-end distance vector distribution with fixed end orientations for the wormlike chain model.

We find exact expressions for the end-to-end distance vector distribution function with fixed end orientations for the wormlike chain model. This function in Fourier-Laplace space adopts the form of infinite continued fractions, which emerges upon exploiting the hierarchical structure of the moment-based expansion. Our results are used to calculate the root-mean-square end displacement in a given direction for a chain with both end orientations fixed. We find that the crossover from rigid to flexible chains is marked by the root-mean-square end displacement slowly losing its angular dependence as the coupling between chain conformation and end orientation wanes. However, the coupling remains strong even for relatively flexible chains, suggesting that the end orientation strongly influences chain conformation for chains that are several persistence lengths long. We then show the behavior of the distribution function by a density plot of the probability as a function of the end-to-end distance vector for a wormlike chain in two dimensions with one end pointed in a fixed direction and the other end free (in its orientation). As we progress from high to low rigidity, the distribution function shifts from being peaked at a location near the full contour length of the chain in the forward direction, corresponding to a straight configuration, to being peaked near zero end separation, as in the Gaussian limit. The function exhibits double peaks in the crossover between these limiting behaviors.

Journal Article↗

PubMed2005

Topological constraints in nucleic acid hybridization kinetics.

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of 'helix-driven wrapping'. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary 'kissing hairpins' demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.

Base Pairing↗

PubMed2003

Semiflexible polymer confined to a spherical surface.

We develop a formalism for describing the kinematics of a wormlike chain confined to the surface of a sphere that simultaneously satisfies the spherical confinement and the inextensibility of the chain contour. We use this formalism to study the statistical behavior of the wormlike chain on a spherical surface. In particular, we provide an exact, closed-form expression for the mean square end-to-end distance that is valid for any value of chain length L, persistence length l(p), and sphere radius R. We predict two qualitatively different behaviors for a long polymer depending on the ratio R/l(p). For R/l(p)>4, the mean square end-to-end distance increases monotonically with the chain length, whereas for R/l(p)<4, a damped oscillatory behavior is predicted.

DNA↗