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We demonstrate direct visualization of melting mapping of DNA stretched in nanoscale channels[1] using standard staining methods and epifluorescence microscopy to gain information on the local AT/GC ratio along large DNA molecules. Our development opens up a novel route to mapping of large-scale genomic variations.
The local alignment of DNA stretched in nanofluidic channels is measured using polarization sensitive detection. With increased degree of stretching the polarization anisotropy increases both in the deGennes and the Odijk regime. The technique is expected to find use in studies of, for example, local conformational changes in polymer physics in confined spaces, studies of protein-DNA interactions
In this work, the near-field and far-field electric magnetic (EM) wave distributions of metallic slits was observed using tapered fiber probe and modelled using finite difference time domain (FDTD) computer simulations. The EM wave field distribution from rectangular slits with widths 100 nm, 300 nm, and 500 nm was mapped with excitation wavelength λ = 532 nm. λ/2 can be considered a characteristi
Chip based bio/chemical analysis relies on networks of fluidic channels that are connected to reaction chambers and sensors. For sensitive detection it is important to scale down the size of the channels so that they approach the relevant length scales of the molecules of interest. Here we have made sealed channels on the 100 nm scale using nanoimprinting to pattern the sacrificial polymer polynor
Recently, we reported a microfabricated "DNA prism" device that continuously sorts large DNA molecules (61 kilobase pair to 209 kb) according to size in 15 seconds. In this paper, we develop models to understand and optimize the device. The device's complicated characteristics are explained poorly by a simple model based on the assumption that DNA molecules are fully stretched. Assuming DNA molecu
It is difficult to introduce long genomic DNA molecules into nanometer scale fluidic channels directly from the macroscale world because of the steep entropic barrier caused by necessary stretching of the polymer. We present a very simple technique using optical lithography to fabricate continuous spatial gradient structures which smoothly narrow the cross section of a volume from the micron to th
We made uniform arrays of nanometer scale structures using nanoimprint lithography over large areas (100 mm wafers). The nanofluidic channels were further narrowed and sealed by techniques that are based on nonuniform deposition. The resulting sealed channels have a cross section as small as 10 nm by 50 nm, of great importance for confining biological molecules into ultrasmall spaces. These techni
Long double-stranded DNA molecules were separated in microfabricated hexagonal arrays in less than 1 min, several orders of magnitude faster than by using conventional technology. DNA samples were first concentrated at the entrance to the array in a thin band by entropic focusing. They were then separated by pulsed field electrophoresis. T4 (168.9 kbp) and λ (48.5 kbp) DNAs could be resolved into
A new technology that provides high optical resolution as well as very high data rates for moving molecules is presented. An important aspect of the device is the dependence of both the near-field radiation pattern and the far-field transmission of a thin slit on the polarization of the incident light.
We show that a careful analysis of the Navier-Stokes equation in the low Reynolds number limit has two distinct solutions, one valid for a deep, thin curtain of flow and the other for a thin wide flow. We derive a solution to the latter situation and use the results to develop a new way to control fluid flows in thin, wide sheet flow.
Micro- and nanofabrication techniques have provided an unprecedented opportunity to create a designed world in which separation and fractionation technologies which normally occur on the macroscopic scale can be optimized by designing structures which utilize the basic physics of the process, or new processes can be realized by building structures which normally do not exist without external desig
Micro and nano fabrication techniques have provided an unprecedented opportunity to create a designed world in which separation and fractionation technologies which normally occur on the macroscopic scale can be optimized by designing structures which utilize the basic physics of the process, or new processes can be realized by building structures which normally do not exist without external desig
Object. The pathogenesis of cerebrospinal fluid (CSF) shunt infection is characterized by staphylococcal adhesion to the polymeric surface of the shunt catheter. Proteins from the CSF-fibronectin, vitronectin, and fibrinogen-are adsorbed to the surface of the catheter immediately after insertion. These proteins can interfere with the biological systems of the host and mediate staphylococcal adhesi
Quantitation of microbes adhering to a surface is commonly used in studies of microbial adhesion to different surfaces. We have quantified different staphylococcal strains adhering to polymer surfaces by measuring bacterial ATP (adenosine triphosphate) by bioluminescence. The method is sensitive, having a detection limit of 104 bacterial cells. Viable counting of bacterial cells may yield falsely
Biomaterials are commonly used in modern medicine. Proteins are adsorbed to the surface of the biomaterial immediately after insertion. This report demonstrates the presence of adsorbed proteins in one infected cerebrospinal shunt from a child with hydrocephalus and on fifteen temporary ventricular catheters from adult patients with spontaneous or traumatic brain injuries. Depositions of vitronect
The interest in miniaturization of modern chemical and medical sensors is steadily increasing. However, when employing methods and fabrication procedures especially developed for microelectronics, one may encounter new and unpredictable problems for applications in aqueous media. For instance, in microelectronics often a dual metal layer system is employed for making electrical contacts. In a solu
As the tip in the atomic force microscope is scanned over the sample surface an image results which contains information from the sample as well as from the tip. This mainly results in an increase of the apparent size of the sample. If the tip is reasonably sharp the contribution from the tip is small. In some cases the widening still persists in spite of a very sharp tip. In this letter, a model
We have fabricated nanometer-sized interdigitated electrode patterns using electron beam lithography and liftoff techniques. The aim of the investigation was to find out whether the dimensions (i.e., the electrode separations) of the pattern would affect the admittance signal of the biomolecules in between the electrodes. Since the admittance signal scales with the geometrical factor A/d, where A
In this study we report on the first direct observation of the real shape of the atomic force microscopy (AFM) tip using the AFM technique itself, utilizing a specially designed sample geometry. This is the first report of the so-called inverse AFM mode in which the tip is actually used as the sample and vice versa. We propose how this method can, with a very high accuracy, be used for studying ob
In this economic evaluation, conducted alongside a randomized, double-blind clinical trial, economic data were collected from 339 patients with moderate-persistent asthma randomized to receive twice-daily, double-blind treatment with budesonide/formoterol 160/4.5 μg in a single inhaler (n = 166) or fluticasone propionate 250 μg (n = 173) for 12 weeks. The mean number of episode-free days (EFD) per
