Recoiling DNA Molecule: Simulation & Experiment

Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the persistence length of single DNA molecules can also be measured based on the recoil dynamics of these DNA-microsphere complexes if appropriate corrections are made to the friction coefficient of the microsphere in the vicinity of the substrate. Comparison between computer simulated recoil curves, generated from the corresponding Langevin equation, and experimental recoils is used to assure the validity of data analysis.Comment: 14 pages (single column preprint), 7 figures. Major changes: data analysis method improved; dna-ethidium bromide results removed (dna-ethidium bromide protocol affected microspheres and coverglass behavior

Transition on the entropic elasticity of DNA induced by intercalating molecules

We use optical tweezers to perform stretching experiments on DNA molecules when interacting with the drugs daunomycin and ethidium bromide, which intercalate the DNA molecule. These experiments are performed in the low-force regime from zero up to 2 pN. Our results show that the persistence length of the DNA-drug complexes increases strongly as the drug concentration increases up to some critical value. Above this critical value, the persistence length decreases abruptly and remains practically constant for larger drug concentrations. The contour length of the molecules increases monotonically and saturates as drugs concentration increases. Measured in- tercalants critical concentrations for the persistence length transition coincide with reported values for the helix-coil transition of DNA-drug complexes, obtained from sedimentation experiments.Comment: This experimental article shows and discuss a transition observed in the persistence length of DNA molecules when studied as a function of some intercalating drug concentrations, like daunomycin and ethidium bromide. It has 15 pages and 4 figures. The article presented here is in preprint forma

DNA-psoralen: single-molecule experiments and first principles calculations

The authors measure the persistence and contour lengths of DNA-psoralen complexes, as a function of psoralen concentration, for intercalated and crosslinked complexes. In both cases, the persistence length monotonically increases until a certain critical concentration is reached, above which it abruptly decreases and remains approximately constant. The contour length of the complexes exhibits no such discontinuous behavior. By fitting the relative increase of the contour length to the neighbor exclusion model, we obtain the exclusion number and the intrinsic intercalating constant of the psoralen-DNA interaction. Ab initio calculations are employed in order to provide an atomistic picture of these experimental findings.Comment: 9 pages, 4 figures in re-print format 3 pages, 4 figures in the published versio

Towards absolute calibration of optical tweezers

Aiming at absolute force calibration of optical tweezers, following a critical review of proposed theoretical models, we present and test the results of MDSA (Mie-Debye-Spherical Aberration) theory, an extension of a previous (MD) model, taking account of spherical aberration at the glass/water interface. This first-principles theory is formulated entirely in terms of experimentally accessible parameters (none adjustable). Careful experimental tests of the MDSA theory, undertaken at two laboratories, with very different setups, are described. A detailed description is given of the procedures employed to measure laser beam waist, local beam power at the transparent microspheres trapped by the tweezers, microsphere radius and the trap transverse stiffness, as a function of radius and height in the (inverted microscope) sample chamber. We find generally very good agreement with MDSA theory predictions, for a wide size range, from the Rayleigh domain to large radii, including the values most often employed in practice, and at different chamber heights, both with objective overfilling and underfilling. The results asymptotically approach geometrical optics in the mean over size intervals, as they should, and this already happens for size parameters not much larger than unity. MDSA predictions for the trapping threshold, position of stiffness peak, stiffness variation with height, multiple equilibrium points and `hopping' effects among them are verified. Remaining discrepancies are ascribed to focus degradation, possibly arising from objective aberrations in the infrared, not yet included in MDSA theory.Comment: 15 pages, 20 figure

Fluctuations and transport in a stirred fluid with a mean gradient

The effective thermal diffusivity D* and the probability distribution of temperature fluctuations are measured in a stirred fluid across which a temperature gradient is maintained. A distinct mixing transition is observed for D* as a function of Reynolds number R. Above the transitions, the distribution is strongly non-Gaussian and approaches an exponential exp(-‖δT‖/βξ), where β is the local temperature gradient and ξ the correlation length

Involuntary sustained firing of plantar flexor motor neurones: effect of electrical stimulation parameters during tendon vibration

Purpose Simultaneous application of tendon vibration and neuromuscular electrical stimulation (NMES) induces an involuntary sustained torque. We examined the effect of different NMES parameters (intensity, pattern of stimulation and pulse width) on the magnitude of the evoked involuntary torque. Methods Plantar flexor torque was recorded during 33-s Achilles tendon vibration with simultaneous 20-Hz NMES bouts on triceps surae (n = 20; 13 women). Intensity was set to elicit 10, 20 or 30% of maximal voluntary contraction torque (MVC), pulse width was narrow (0.2 ms) or wide (1 ms), and the stimulus pattern varied (5 × 2-s or 10 × 1-s). Up to 12 different trials were performed in a randomized order, and then repeated in those who produced a sustained involuntary torque after the cessation of vibration. Results Six of 7 men and 5 of 13 women produced a post-vibration sustained torque. Eight of 20 participants did not complete the 30% trials, as they were perceived as painful. Torque during vibration at the end of NMES and the increase in torque throughout the trial were significantly higher in 20 than 10% trials (n = 11; 9.7 ± 9.0 vs 7.1 ± 6.1% MVC and 4.3 ± 4.5 vs 3.6 ± 3.5% MVC, respectively). Post-vibration sustained torque was higher in wide pulse-width trials (5.4 ± 5.9 vs 4.1 ± 4.3% MVC). Measures of involuntary torque were not different between 20 and 30% trials (n = 8). Conclusion Bouts of 5 × 2-s NMES with wide pulse width eliciting 20% MVC provides the most robust responses and could be used to maximise the production of involuntary torque in triceps surae