Stretching of a single-stranded DNA: Evidence for structural transition

Recent experiments have shown that the force-extension (F-x) curve for single-stranded DNA (ssDNA) consisting only of adenine [poly(dA)] is significantly different from thymine [poly(dT)]. Here, we show that the base stacking interaction is not sufficient to describe the F-x curves as seen in the experiments. A reduction in the reaction co-ordinate arising from the formation of helix at low forces and an increase in the distance between consecutive phosphates of unstacked bases in the stretched state at high force in the proposed model, qualitatively reproduces the experimentally observed features. The multi-step plateau in the F-x curve is a signature of structural change in ssDNA.Comment: 10 pages, 4 figure

Respondents, Operants, and Emergents: Toward an Integrated Perspective on Behavior

A triarchic organization of behavior, building on Skinner's description of respondents and operants, is proposed by introducing a third class of behavior called 'emergents.' Emergents are new responses, never specifically reinforced, that require operations more complex than association. Some of these operations occur naturally only in animals above a minimum level of brain complexity, and are developed in an interaction between treatment and organismic variables. (Here complexity is defined in terms of relative levels of hierarchical integration made possible both by the amount of brain, afforded both by brain-body allometric relationships and by encephalization, and, also, the elaboration of dendritic and synaptic connections within the cortex and connections between various parts/regions of the brain.) Examples of emergents are discussed to advance this triarchic view, of behavior. The prime example is language. This triarchic view reflects both the common goals and the cumulative nature of psychological science

Helicase on DNA: A Phase coexistence based mechanism

We propose a phase coexistence based mechanism for activity of helicases, ubiquitous enzymes that unwind double stranded DNA. The helicase-DNA complex constitutes a fixed-stretch ensemble that entails a coexistence of domains of zipped and unzipped phases of DNA, separated by a domain wall. The motor action of the helicase leads to a change in the position of the fixed constraint thereby shifting the domain wall on dsDNA. We associate this off-equilibrium domain wall motion with the unzipping activity of helicase. We show that this proposal gives a clear and consistent explanation of the main observed features of helicases.Comment: Revtex4. 5 pages. 4 figures. Published versio

Elongation dynamics of amyloid fibrils: a rugged energy landscape picture

Protein amyloid fibrils are a form of linear protein aggregates that are implicated in many neurodegenerative diseases. Here, we study the dynamics of amyloid fibril elongation by performing Langevin dynamic simulations on a coarse-grained model of peptides. Our simulation results suggest that the elongation process is dominated by a series of local minimum due to frustration in monomer-fibril interactions. This rugged energy landscape picture indicates that the amount of recycling of monomers at the fibrils' ends before being fibrilized is substantially reduced in comparison to the conventional two-step elongation model. This picture, along with other predictions discussed, can be tested with current experimental techniques

Induction of respiratory control in submitochondrial particles by dicyclohexylcarbodiimide

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/33289/1/0000681.pd

Dielectric relaxation of DNA aqueous solutions

We report on a detailed characterization of complex dielectric response of Na-DNA aqueous solutions by means of low-frequency dielectric spectroscopy (40 Hz - 110 MHz). Results reveal two broad relaxation modes of strength 20<\Delta\epsilon_LF<100 and 5<\Delta\epsilon_HF<20, centered at 0.5 kHz<\nu_LF<70 kHz and 0.1 MHz<\nu_HF<15 MHz. The characteristic length scale of the LF process, 50<L_LF<750nm, scales with DNA concentration as c_DNA^{-0.29\pm0.04} and is independent of the ionic strength in the low added salt regime. Conversely, the measured length scale of the LF process does not vary with DNA concentration but depends on the ionic strength of the added salt as I_s^{-1} in the high added salt regime. On the other hand, the characteristic length scale of the HF process, 3<L_HF<50 nm, varyes with DNA concentration as c_DNA^{-0.5} for intermediate and large DNA concentrations. At low DNA concentrations and in the low added salt limit the characteristic length scale of the HF process scales as c_DNA^{-0.33}. We put these results in perspective regarding the integrity of the double stranded form of DNA at low salt conditions as well as regarding the role of different types of counterions in different regimes of dielectric dispersion. We argue that the free DNA counterions are primarily active in the HF relaxation, while the condensed counterions play a role only in the LF relaxation. We also suggest theoretical interpretations for all these length scales in the whole regime of DNA and salt concentrations and discuss their ramifications and limitations.Comment: 15 pages, 9 figure

The Force-Velocity Relation for Growing Biopolymers

The process of force generation by the growth of biopolymers is simulated via a Langevin-dynamics approach. The interaction forces are taken to have simple forms that favor the growth of straight fibers from solution. The force-velocity relation is obtained from the simulations for two versions of the monomer-monomer force field. It is found that the growth rate drops off more rapidly with applied force than expected from the simplest theories based on thermal motion of the obstacle. The discrepancies amount to a factor of three or more when the applied force exceeds 2.5kT/a, where a is the step size for the polymer growth. These results are explained on the basis of restricted diffusion of monomers near the fiber tip. It is also found that the mobility of the obstacle has little effect on the growth rate, over a broad range.Comment: Latex source, 9 postscript figures, uses psfig.st

Hysteresis in Pressure-Driven DNA Denaturation

In the past, a great deal of attention has been drawn to thermal driven denaturation processes. In recent years, however, the discovery of stress-induced denaturation, observed at the one-molecule level, has revealed new insights into the complex phenomena involved in the thermo-mechanics of DNA function. Understanding the effect of local pressure variations in DNA stability is thus an appealing topic. Such processes as cellular stress, dehydration, and changes in the ionic strength of the medium could explain local pressure changes that will affect the molecular mechanics of DNA and hence its stability. In this work, a theory that accounts for hysteresis in pressure-driven DNA denaturation is proposed. We here combine an irreversible thermodynamic approach with an equation of state based on the Poisson-Boltzmann cell model. The latter one provides a good description of the osmotic pressure over a wide range of DNA concentrations. The resulting theoretical framework predicts, in general, the process of denaturation and, in particular, hysteresis curves for a DNA sequence in terms of system parameters such as salt concentration, density of DNA molecules and temperature in addition to structural and configurational states of DNA. Furthermore, this formalism can be naturally extended to more complex situations, for example, in cases where the host medium is made up of asymmetric salts or in the description of the (helical-like) charge distribution along the DNA molecule. Moreover, since this study incorporates the effect of pressure through a thermodynamic analysis, much of what is known from temperature-driven experiments will shed light on the pressure-induced melting issue