Elongational-flow-induced scission of DNA nanotubes in laminar flow

The length distributions of polymer fragments subjected to an elongational-flow-induced scission are profoundly affected by the fluid flow and the polymer bond strengths. In this paper, laminar elongational flow was used to induce chain scission of a series of circumference-programmed DNA nanotubes. The DNA nanotubes served as a model system for semiflexible polymers with tunable bond strength and cross-sectional geometry. The expected length distribution of fragmented DNA nanotubes was calculated from first principles by modeling the interplay between continuum hydrodynamic elongational flow and the molecular forces required to overstretch multiple DNA double helices. Our model has no-free parameters; the only inferred parameter is obtained from DNA mechanics literature, namely, the critical tension required to break a DNA duplex into two single-stranded DNA strands via the overstretching B-S DNA transition. The nanotube fragments were assayed with fluorescence microscopy at the single-molecule level and their lengths are in agreement with the scission theory

Applications of nonequilibrium Kubo formula to the detection of quantum noise

The Kubo fluctuation-dissipation theorem relates the current fluctuations of a system in an equilibrium state with the linear AC-conductance. This theorem holds also out of equilibrium provided that the system is in a stationary state and that the linear conductance is replaced by the (dynamic) conductance with respect to the non equilibrium state. We provide a simple proof for that statement and then apply it in two cases. We first show that in an excess noise measurement at zero temperature, in which the impedance matching is maintained while driving a mesoscopic sample out of equilibrium, it is the nonsymmetrized noise power spectrum which is measured, even if the bare measurement, i.e. without extracting the excess part of the noise, obtains the symmetrized noise. As a second application we derive a commutation relation for the two components of fermionic or bosonic currents which holds in every stationary state and which is a generalization of the one valid only for bosonic currents. As is usually the case, such a commutation relation can be used e.g. to derive Heisenberg uncertainty relationships among these current components.Comment: 10 pages, Invited talk to be given by Y. I. at the SPIE Noise Conference, Grand Canary, June 2004. Added reference and 2 footnotes, corrected typo in Eq.

Catalyzed relaxation of a metastable DNA fuel

Practically all of life's molecular processes, from chemical synthesis to replication, involve enzymes that carry out their functions through the catalytic transformation of metastable fuels into waste products. Catalytic control of reaction rates will prove to be as useful and ubiquitous in nucleic-acid-based engineering as it is in biology. Here we report a metastable DNA "fuel" and a corresponding DNA "catalyst" that improve upon the original hybridization-based catalyst system (Turberfield et al. Phys. Rev. Lett. 90, 118102-1118102-4) by more than 2 orders of magnitude. This is achieved by identifying and purifying a fuel with a kinetically trapped metastable configuration consisting of a "kissing loop" stabilized by flanking helical domains; the catalyst strand acts by opening a helical domain and allowing the complex to relax to its ground state by a multistep pathway. The improved fuel/catalyst system shows a roughly 5000-fold acceleration of the uncatalyzed reaction, with each catalyst molecule capable of turning over in excess of 40 substrates. With k_(cat)/K_M ≈ 10^7/M/min, comparable to many protein enzymes and ribozymes, this fuel system becomes a viable component enabling future DNA-based synthetic molecular machines and logic circuits. As an example, we designed and characterized a signal amplifier based on the fuel-catalyst system. The amplifier uses a single strand of DNA as input and releases a second strand with unrelated sequence as output. A single input strand can catalytically trigger the release of more than 10 output strands

Bell's inequalities, multiphoton states and phase space distributions

The connection between quantum optical nonclassicality and the violation of Bell's inequalities is explored. Bell type inequalities for the electromagnetic field are formulated for general states of quantised radiation and their violation is connected to other nonclassical properties of the field. This is achieved by considering states with an arbitrary number of photons and carefully identifying the hermitian operators whose expectation values do not admit any local hidden variable description. We relate the violation of these multi-photon inequalities to properties of phase space distribution functions such as the diagonal coherent state distribution function and the Wigner function. Finally, the family of 4-mode states with Gaussian Wigner distributions is analysed, bringing out in this case the connection of violation of Bell type inequalities with the nonclassical property of squeezing.Comment: 16-pages in revtex with three ps figure included using eps

Nonlocality of Hardy type in experiments using independent particle sources

By applying Hardy's argument, we demonstrate the violation of local realism in a gedanken experiment using independent and separated particle sources.Comment: 9 pages, 1 fig, revtex, title change

On the Biophysics and Kinetics of Toehold-Mediated DNA Strand Displacement

Dynamic DNA nanotechnology often uses toehold-mediated strand displacement for controlling reaction kinetics. Although the dependence of strand displacement kinetics on toehold length has been experimentally characterized and phenomenologically modeled, detailed biophysical understanding has remained elusive. Here, we study strand displacement at multiple levels of detail, using an intuitive model of a random walk on a 1D energy landscape, a secondary structure kinetics model with single base-pair steps and a coarse-grained molecular model that incorporates 3D geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Two factors explain the dependence of strand displacement kinetics on toehold length: (i) the physical process by which a single step of branch migration occurs is significantly slower than the fraying of a single base pair and (ii) initiating branch migration incurs a thermodynamic penalty, not captured by state-of-the-art nearest neighbor models of DNA, due to the additional overhang it engenders at the junction. Our findings are consistent with previously measured or inferred rates for hybridization, fraying and branch migration, and they provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems