Dmitri V. Vezenov

Stretching and breaking duplex DNA by chemical force microscopy

BACKGROUND Specific interactions between complementary strands of DNA and other molecules are central to the storage, retrieval and modification of information in biological systems. Although in many cases the basic structures of duplex DNA and the binding energetics have been well characterized, little information is available about the forces in these systems. These forces are of critical importance because they must be overcome, for example, by protein machines during transcription and repair. Recent developments in atomic force microscopy make possible direct measurements of such forces between the individual oligonucleotide strands that form DNA duplexes. RESULTS We used the chemical force microscopy technique, in which oligonucleotides are covalently linked to the force microscope probe tip and the sample surface, to measure the elongation and binding forces of individual DNA duplexes. The separation forces between complementary oligonucleotide strands were found to be significantly larger than the forces measured between noncomplementary strands, and to be consistent with the unbinding of a single DNA duplex. With increasing applied force, the separation of complementary strands proceeded in a stepwise manner: B-form DNA was stretched, then structurally transformed to a stable form of DNA approximately twice the length of the B form, and finally separated into single-stranded oligonucleotides. These data provide a direct measurement of the forces required to elastically deform and separate double-stranded DNA into single strands. CONCLUSIONS Force microscopy provides a direct and quantitative measurement of the forces and energetics required to stretch and unbind DNA duplexes. Because the measurements can be carried out readily on synthetic oligonucleotides and in the presence of exogenous molecules, this method affords an opportunity for directly assessing the energetics of distorting and unbinding specific DNA sequences and DNA complexes. Such data could provide unique insights into the mechanistic steps following sequence-specific recognition by, for example, DNA repair and transcription factors.

Integrated fluorescent light source for optofluidic applications

This letter describes a simple fluidic light source for use “on-chip” in integrated microsystems. It demonstrates the feasibility of light sources based on liquid-core, liquid-cladding (L2) microchannel waveguides, with liquid cores containing fluorescent dyes. These fluorescent light sources, using both miscible and two-phase systems, are tunable in terms of the beam size, intensity and spectral content. The observed output intensity from fluorescent L2 light sources is comparable to standard fiber optic spectrophotometer light sources. Integration of fluorescent light sources during device fabrication removes both the need for insertion and alignment of conventional, optical-fiber light sources and the constraints on channel size imposed by fiber optics, albeit at the cost of establishing a microfluidic infrastructure.This letter describes a simple fluidic light source for use “on-chip” in integrated microsystems. It demonstrates the feasibility of light sources based on liquid-core, liquid-cladding (L2) microchannel waveguides, with liquid cores containing fluorescent dyes. These fluorescent light sources, using both miscible and two-phase systems, are tunable in terms of the beam size, intensity and spectral content. The observed output intensity from fluorescent L2 light sources is comparable to standard fiber optic spectrophotometer light sources. Integration of fluorescent light sources during device fabrication removes both the need for insertion and alignment of conventional, optical-fiber light sources and the constraints on channel size imposed by fiber optics, albeit at the cost of establishing a microfluidic infrastructure.

Optical waveguiding using thermal gradients across homogeneous liquids in microfluidic channels

This letter describes the design and operation of a liquid-core liquid-cladding (L2) optical waveguide composed of a thermal gradient across a compositionally homogeneous liquid flowing in a microfluidic channel at low Reynolds number. Two streams of liquid at a higher temperature (the cladding) sandwich a stream of liquid at a lower temperature (the core). This temperature difference results in a contrast in refractive index across the width of the channel that is sufficient to guide light. The use of a single homogeneous liquid in this L2 system simplifies recycling, and facilitates closed-loop operation. Furthermore, with radiative and inline heating of the liquids, it should be possible to reconfigure this optical system with considerable flexibility.

Chemical Force Microscopy: Probing Chemical Origin of Interfacial Forces and Adhesion

Intermolecular interactions between distinct chemical functionalities define a multitude of adhesion events in chemistry, biology and materials science. Modern techniques for measuring molecular level forces have allowed direct quantitative characterization of these interactions. In particular, chemical force microscopy (CFM), which uses the probe tip of a force microscope covalently modified with specific organic functional groups, provides a flexible approach for studying interactions between specific chemical functionalities. In this review, we survey the progress in CFM in recent years as it applies to adhesion of soft materials. We show how new developments in the experimental and theoretical approaches continue to build a realistic and detailed picture of adhesion interaction in condensed phases. We specifically highlight the importance of the kinetics of the unbinding processes and solvation effects in determining the strength of intermolecular interactions. We also describe some recent new directions in CFM, such as high-throughput adhesion measurements and mapping of full intermolecular potentials.

Diffusion-controlled optical elements for optofluidics

Diffusion at the interface between two streams of liquids with different refractive indices, flowing laminarly, creates a controllable concentration gradient and a corresponding refractive index gradient. Using flow rate to change the time over which diffusion occurs in a liquid-liquid (L2) optical waveguide, we demonstrate an optical splitter and a wavelength filter. The optical splitter comprises two parallel L2 waveguides which smoothly merge into a single L2 waveguide by diffusion. The wavelength filter comprises an optical splitter in which the two L2 waveguides contain an absorbing dye.

Optical waveguiding in suspensions of dielectric particles.

An optical waveguide formed by a suspension of dielectric nanoparticles in a microchannel is described. The suspensions, chosen for their guiding and scattering properties, are silica and polystyrene particles that have diameters of 30–900 nm and are dispersed in water with volume fractions up to 10%. Changing the diameter and concentration of the particles causes the suspensions to transition from Rayleigh to Mie scattering and from single to multiple scattering. The threshold for optical guiding in a waveguide core composed of these suspensions is set by the numerical aperture of the effective refractive-index difference introduced by the suspension and not by the average interparticle distance.