Stretching and Heating Single DNA Molecules with Optically Trapped Gold-Silica Janus Particles

Self-propelled micro- and nanoscale motors are capable of autonomous motion typically by inducing local concentration gradients or thermal gradients in their surrounding medium. This is a result of the heterogeneous surface of the self-propelled structures that consist of materials with different chemical or physical properties. Here we present a self-thermophoretically driven Au–silica Janus particle that can simultaneously stretch and partially melt a single double-stranded DNA molecule. We show that the effective force acting on the DNA molecule is in the ∼pN range, well suited to probe the entropic stretching regime of DNA, and we demonstrate that the local temperature enhancement around the gold side of the particle produces partial DNA dehybridization

The noisy and marvelous molecular world of biology

At the molecular level biology is intrinsically noisy. The forces that regulate the myriad of molecular reactions in the cell are tiny, on the order of piconewtons (10−12 Newtons), yet they proceed in concerted action making life possible. Understanding how this is possible is one of the most fundamental questions biophysicists would like to understand. Single molecule experiments offer an opportunity to delve into the fundamental laws that make biological complexity surface in a physical world governed by the second law of thermodynamics. Techniques such as force spectroscopy, fluorescence, microfluidics, molecular sequencing, and computational studies project a view of the biomolecular world ruled by the conspiracy between the disorganizing forces due to thermal motion and the cosmic evolutionary drive. Here we will digress on some of the evidences in support of this view and the role of physical information in biology

Manipulation of Polystyrene Microparticles on a Microchannel Glass

Bulk quantities of spherical microbeads have various applications in research and industrial fields. Simple techniques are required to be developed in order to manipulate and modify large numbers of these beads simultaneously. In our experiment, a microchannel glass-based microfluidic device is used to actuate large numbers of microbeads in parallel. The microchannel glass used in these experiments contains channels 4.1 μm in diameter. The microbeads are polystyrene beads which are superparamagnetic in nature and 5-6 μm in diameter. An aqueous suspension of microbeads is injected into a 2-chamber fluid cell that contains a separator, microchannel glass. The beads are reversibly immobilized on the surface of the microchannel glass by the application of suction with the help of a syringe pump. Assessment of bead movement is performed using optical microscopy. Optical micrographs and the live video for various experimental results are presented. Several experiments were performed by varying flow rates in order to manipulate the beads and the data of flow rates is tabulated. The speed of the beads is calculated and is correlated with flow rates in different chambers. The results were studied by plotting the flow rates and speed of the beads. Microbeads are also immobilized by applying pressure in fluid cell. The pressure is applied by weights suspended and held on syringes at respective positions. Several experiments are performed by applying varied pressures in different chambers and these pressures are plotted. Optical micrographs and the live video for various applied pressures are presented

Advanced Dual Beam Optical Tweezers for Undergraduate Biophysics Research

Optical tweezing is a modern physics technique which allows us to use the radiation pressure provided from laser beams to trap very small microscopic particles. In the last two decades optical tweezers have been used extensively in biophysics and atomic physics to study the building blocks of our world on the cellular and quantum levels. Our goal is to construct a dual beam optical tweezers for future undergraduate biophysical research. In this thesis we discuss how the construction and assembly of the dual beam optical tweezers is done from start to finish. Construction consisted of assembling a polarization maintaining laser. This was then split into two to create a dual beam effect. Directing both beams in symmetrical and equidistant paths with the help of optical elements, the beams were overlapped in a counter propagating orientation. Microscopes were then used to focus the lasers into the target flow cell. Another set of optics were used to image the inside of the flow cell so we could visualize the laser trapping. It was necessary to construct a custom compressed air system to isolate the optical table from surrounding vibration so that we can accurately measure the pico-newton scale forces that are observed in biological systems. In addition, the biomaterial flow system was designed to supply the flow cell with biological solutions essential for experimentation. Future plans for this project include developing the software in order to collect experimental data and run biophysics experiments. This optical tweezers apparatus will allow us to study potential cancer drug interactions with DNA at the single molecule level and be a powerful tool in promoting interdisciplinary research at the undergraduate level

NANOSCIENCE IN DIAGNOSTICS: A SHORT REVIEW

Nanoscience is at the leading edge of the rapidly developing field of nanotechnology. Nanosciences and nanotechnology are transforming a wide array of products and services that have the potential to enhance the practice of medicine and improve public health. Several areas of medical care are already benefiting from the advantages that nanotechnology can offer. Applications of nanoscience are in biotechnology, medicine, pharmaceuticals, physics, material science and also electronics. Nanotechnology extends the limits of molecular diagnostics to the nanoscale. Nanotechnology on a chip is one more dimension of microfluidic/lab on a chip technology. We still suffer serious and complex illnesses like cancer, cardiovascular diseases, multiple sclerosis, Alzheimer’s and Parkinson’s disease, and diabetes as well as different kinds of serious inflammatory or infectious diseases (e.g. HIV). It is of extreme importance to face these diseases with appropriate means. The interplay between nanoscience and biomedicine is the hallmark of current scientific research worldwide. The use of nanoscience may open new vistas of improving the effectiveness and efficiency of medical diagnosis and therapeutics, so called nanomedicine. An appealing example is the use of quantum dots as fluorescent labels. Despite recent progress in the treatment of cancer, the majority of cases are still diagnosed only after tumors metastasize, leaving the patient with a grim prognosis. Nanotechnology is in a unique position to transform cancer diagnostics and to produce a new generation of biosensors and medical imaging techniques with higher sensitivity and precision of recognition. Novel nanotechnologies can complement and augment existing genomic and proteomic techniques employed to analyze variations across different tumor types, thus offering the potential to distinguish between normal and malignant cells. This brief review tries to reiterate the most contemporary developments in the field of applied nanoscience, particularly in their relevance in diagnosis of various diseases and discuss their future prospects

Extracting physical chemistry from mechanics: a new approach to investigate DNA interactions with drugs and proteins in single molecule experiments

In this review we focus on the idea of establishing connections between the mechanical properties of DNAligand complexes and the physical chemistry of DNA-ligand interactions. This type of connection is interesting because it opens the possibility of performing a robust characterization of such interactions by using only one experimental technique: single molecule stretching. Furthermore, it also opens new possibilities in comparing results obtained by very different approaches, in special when comparing single molecule techniques to ensemble-averaging techniques. We start the manuscript reviewing important concepts of the DNA mechanics, from the basic mechanical properties to the Worm-Like Chain model. Next we review the basic concepts of the physical chemistry of DNA-ligand interactions, revisiting the most important models used to analyze the binding data and discussing their binding isotherms. Then, we discuss the basic features of the single molecule techniques most used to stretch the DNA-ligand complexes and to obtain force x extension data, from which the mechanical properties of the complexes can be determined. We also discuss the characteristics of the main types of interactions that can occur between DNA and ligands, from covalent binding to simple electrostatic driven interactions. Finally, we present a historical survey on the attempts to connect mechanics to physical chemistry for DNA-ligand systems, emphasizing a recently developed fitting approach useful to connect the persistence length of the DNA-ligand complexes to the physicochemical properties of the interaction. Such approach in principle can be used for any type of ligand, from drugs to proteins, even if multiple binding modes are present