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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. 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 approximately constant for larger drug concentrations, at least in the concentration range used in our experiments. Measured intercalators critical concentrations for the persistence length transition coincide with the reported values for the helix-coil transition of DNA-drug complexes obtained from sedimentation experiments. The contour length of the molecules increases monotonically and saturates as the drug concentration increases. The neighbor exclusion model fits to our results for the total drug concentration as a function of the relative increase of the contour length. [ABSTRACT FROM AUTHOR]

By attaching one end of a single λ-DNA molecule to a microscope coverslip and the other end to a polystyrene microsphere trapped by an optical tweezers, we can study the entropic elasticity of the λ-DNA by measuring force versus extension as we stretch the molecule. This powerful method permits single molecule studies. We are particulary interested in the effects of the photosensitive drug psoralen on the elasticity of the DNA molecule. We have illuminated the sample with different light sources, studying how the different wavelengths affect the psoralen-DNA linkage. To do this, we measure the persistence length of individual DNA-psoralen complexes. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We introduce Defocusing Microscopy (DM), a bright-field optical microscopy technique able to perform total three-dimensional (3D) imaging of transparent objects. By total 3D imaging, we mean the determination of the actual shapes of the upper and lower surfaces of a phase object. We propose a methodology using DM and apply it to red blood cells subject to different osmolality conditions: hypotonic, isotonic, and hypertonic solutions. For each situation, the shapes of the upper and lower cell surface-membranes (lipid bilayer/cytoskeleton) are completely recovered, displaying the deformation of red blood cell (RBC) surfaces due to adhesion on the glass-substrate. The axial resolution of our technique allowed us to image surface-membranes separated by distances as small as 300 nm. Finally, we determine the volume, surface area, sphericity index, and RBC refractive index for each osmotic condition. [ABSTRACT FROM AUTHOR]

We have studied the interaction between the anticancer drug Actinomycin D (ActD) and the DNA molecule by performing single molecule stretching experiments and atomic force microscopy (AFM) imaging. From the stretching experiments, we determine how the mechanical properties of the DNA–ActD complexes vary as a function of drug concentration, for a fixed DNA concentration. We have found that the persistence lengths of the complexes formed behave non-monotonically: at low concentrations of ActD they are more flexible than the bare DNA molecule and become stiffer at higher concentrations. On the other hand, the contour length increases monotonically as a function of ActD concentration. Using a two-sites quenched disorder statistical model recently developed by us, we were able to extract chemical parameters such as the intrinsic binding constant and the degree of cooperativity from these pure mechanical measurements, thus performing a robust characterization of the interaction. The AFM images, otherwise, were used to measure the bending angle size distribution that ActD introduces on the double-helix structure and the average number of bendings per DNA molecule as a function of drug concentration, two quantities that cannot be determined from the stretching experiments. [ABSTRACT FROM AUTHOR]

We discuss measurements of the laser power at the focus of high numerical aperture objectives used in optical microscopy and optical tweezers. For a given power, the focused incident laser beam heats a small mercury bead that jumps when it reaches the boiling temperature of water, the medium used in the experiments. From the size of the mercury beads, the heat conductivities of water and glass-slide, and the absorption coefficient of mercury for the laser wavelength used, the incident power can be obtained using the solution of the associated heat problem. This problem is mapped onto the problem of a charged conducting sphere embedded in a semi-infinite medium of dielectric constant ϵ1, separated from another semi-infinite medium of dielectric constant ϵ2. [ABSTRACT FROM AUTHOR]

Recent theoretical proposals concerning non-Gaussian statistics of passive scalars in random velocity fields are tested experimentally, by measuring the probability distributions of fluctuating temperature in an oscillating grid flow across which a steady temperature gradient is maintained. Pronounced exponential tails occur at sufficiently high Reynolds number R, and predominantly Gaussian statistics at low R. When the extended tails are present for the passive scalar, the corresponding velocity power spectrum shows reasonable scaling, and the velocity distribution is not far from Gaussian. The present paper provides a more complete characterization of the flow field than an earlier brief report [Phys. Rev. Lett. 67, 3507 (1991)], and also contains a description of additional features, such as the skewness of the distributions. Finally, the effective or eddy diffusivity of both heat and a molecular impurity are measured and compared. [ABSTRACT FROM AUTHOR]

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 interaction. Ab initio calculations are employed in order to provide an atomistic picture of these experimental findings. [ABSTRACT FROM AUTHOR]

We show that a bright-field defocused microscope is effectively a phase-contrast microscope, but with advantages over the conventional one and maintaining the same optical resolution. In a multilayered transparent object, the height amplitude (static and dynamic) of each interface can be measured separately with nanometer sensitivity. By scanning the position of the objective focal plane in relation to the surfaces of a red blood cell, we obtain quantitative information on height fluctuations from each surface individually, which can be analyzed with our model of a defocused microscope and compared with theoretical models. [ABSTRACT FROM AUTHOR]

As a step toward absolute calibration of optical tweezers, a first-principles theory of trapping forces with no adjustable parameters, corrected for spherical aberration, is experimentally tested. Employing two very different setups, we find generally very good agreement for the transverse trap stiffness as a function of microsphere radius for a broad range of radii, including the values employed in practice, and at different sample chamber depths. The domain of validity of the WKB (“geometrical optics”) approximation to the theory is verified. Theoretical predictions for the trapping threshold, peak position, depth variation, multiple equilibria, and “jump” effects are also confirmed. [ABSTRACT FROM AUTHOR]

We built a simple mercury-based microbolometer to measure "in situ" laser power at the focus of high numerical aperture objectives used in optical microscopy and optical tweezers. With an optical microscope equipped with a high numerical aperture objective, we visualize a mercury droplet immersed in water that is heated by an infrared laser, whose power we want to determine. For a given laser power the mercury droplet reaches the boiling temperature of the water and then jumps, making a precise determination of this point very easy. We solve the heat equation for this system and, using known material parameters and the size of the mercury droplet, we determine the local power of the infrared laser. [ABSTRACT FROM AUTHOR]

Binding of ligands to DNA can be studied by measuring the change of the persistence length of the complex formed, in single-molecule assays. We propose a methodology for persistence length data analysis based on a quenched disorder statistical model and describing the binding isotherm by a Hill-type equation. We obtain an expression for the effective persistence length as a function of the total ligand concentration, which we apply to our data of the DNA-cationic β-cyclodextrin and to the DNA-HU protein data available in the literature, determining the values of the local persistence lengths, the dissociation constant, and the degree of cooperativity for each set of data. In both cases the persistence length behaves nonmonotonically as a function of ligand concentration and based on the results obtained we discuss some physical aspects of the interplay between DNA elasticity and cooperative binding of ligands. [ABSTRACT FROM AUTHOR]