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Biomedical subjects

C Dekker

Publications and source records attributed to C Dekker.

At least 19 recordsLinked to original sources
PubMed2006

Nanobubbles in solid-state nanopores.

From conductance and noise studies, we infer that nanometer-sized gaseous bubbles (nanobubbles) are the dominant noise source in solid-state nanopores. We study the ionic conductance through solid-state nanopores as they are moved through the focus of an infrared laser beam. The resulting conductance profiles show strong variations in both the magnitude of the conductance and in the low-frequency noise when a single nanopore is measured multiple times. Differences up to 5 orders of magnitude are found in the current power spectral density. In addition, we measure an unexpected double-peak ionic conductance profile. A simple model of a cylindrical nanopore that contains a nanobubble explains the measured profile and accounts for the observed variations in the magnitude of the conductance.

Electric Conductivity↗
PubMed2006

Tunneling in suspended carbon nanotubes assisted by longitudinal phonons.

Current-voltage characteristics of suspended single-wall carbon nanotube quantum dots show a series of steps equally spaced in voltage. The energy scale of this harmonic, low-energy excitation spectrum is consistent with that of the longitudinal low-k phonon mode (stretching mode) in the nanotube. Agreement is found with a Franck-Condon-based model in which the phonon-assisted tunneling process is modeled as a coupling of electronic levels to underdamped quantum harmonic oscillators. A comparison with this model indicates a rather strong electron-phonon coupling factor of order unity.

Journal Article↗
PubMed2005

Translocation of double-strand DNA through a silicon oxide nanopore.

We report double-strand DNA translocation experiments using silicon oxide nanopores with a diameter of about 10 nm . By monitoring the conductance of a voltage-biased pore, we detect molecules with a length ranging from 6557 to 48 500 base pairs. We find that the molecules can pass the pore both in a straight linear fashion and in a folded state. Experiments on circular DNA further support this picture. We sort the molecular events according to their folding state and estimate the folding position. As a proof-of-principle experiment, we show that a nanopore can be used to distinguish the lengths of DNA fragments present in a mixture. These experiments pave the way for quantitative analytical techniques with solid-state nanopores.

Biocompatible Materials↗
PubMed2005

Electronic transport spectroscopy of carbon nanotubes in a magnetic field.

We report magnetic field spectroscopy measurements in carbon nanotube quantum dots exhibiting fourfold shell structure in the energy level spectrum. The magnetic field induces a large splitting between the two orbital states of each shell, demonstrating their opposite magnetic moment and determining transitions in the spin and orbital configuration of the quantum dot ground state. We use inelastic cotunneling spectroscopy to accurately resolve the spin and orbital contributions to the magnetic moment. A small coupling is found between orbitals with opposite magnetic moment leading to anticrossing behavior at zero field.

Journal Article↗
PubMed2005

Single-molecule measurements of the persistence length of double-stranded RNA.

Over the past few years, it has become increasingly apparent that double-stranded RNA (dsRNA) plays a far greater role in the life cycle of a cell than previously expected. Numerous proteins, including helicases, polymerases, and nucleases interact specifically with the double helix of dsRNA. To understand the detailed nature of these dsRNA-protein interactions, the (bio)chemical, electrostatic, and mechanical properties of dsRNA need to be fully characterized. We present measurements of the persistence length of dsRNA using two different single-molecule techniques: magnetic tweezers and atomic force microscopy. We deduce a mean persistence length for long dsRNA molecules of 63.8 +/- 0.7 nm from force-extension measurements with the magnetic tweezers. We present atomic force microscopy images of dsRNA and demonstrate a new method for analyzing these, which yields an independent, yet consistent value of 62 +/- 2 nm for the persistence length. The introduction of these single-molecule techniques for dsRNA analysis opens the way for real-time, quantitative analysis of dsRNA-protein interactions.

Biophysics↗
PubMed2004

Electrical generation and absorption of phonons in carbon nanotubes.

The interplay between discrete vibrational and electronic degrees of freedom directly influences the chemical and physical properties of molecular systems. This coupling is typically studied through optical methods such as fluorescence, absorption and Raman spectroscopy. Molecular electronic devices provide new opportunities for exploring vibration-electronic interactions at the single molecule level. For example, electrons injected from a scanning tunnelling microscope tip into a metal can excite vibrational excitations of a molecule situated in the gap between tip and metal. Here we show how current directly injected into a freely suspended individual single-wall carbon nanotube can be used to excite, detect and control a specific vibrational mode of the molecule. Electrons tunnelling inelastically into the nanotube cause a non-equilibrium occupation of the radial breathing mode, leading to both stimulated emission and absorption of phonons by successive electron tunnelling events. We exploit this effect to measure a phonon lifetime of the order of 10 ns, corresponding to a quality factor of well over 10,000 for this nanomechanical oscillator.

Journal Article↗
PubMed2004

Joining of long double-stranded RNA molecules through controlled overhangs.

We describe two methods for creating long (>1 kb) dsRNA molecules with specific, user-controlled overhangs for efficient hybridization and ligation. The two methods create double-stranded RNA (dsRNA) molecules with 5' overhangs or with 3' overhangs using T7 RNA polymerase (T7 RNAP) in transcription reactions of carefully designed PCR products. Primers utilized in the PCR reactions provide the template for the desired dsRNA overhangs. These methods provide complete control of the length and the sequence of the overhangs. This supplies a tool which is particularly lacking in dsRNA biochemistry given the absence of restriction endonucleases active on these substrates.

DNA↗
PubMed2003

Fabrication of solid-state nanopores with single-nanometre precision.

Single nanometre-sized pores (nanopores) embedded in an insulating membrane are an exciting new class of nanosensors for rapid electrical detection and characterization of biomolecules. Notable examples include alpha-hemolysin protein nanopores in lipid membranes and solid-state nanopores in Si3N4. Here we report a new technique for fabricating silicon oxide nanopores with single-nanometre precision and direct visual feedback, using state-of-the-art silicon technology and transmission electron microscopy. First, a pore of 20 nm is opened in a silicon membrane by using electron-beam lithography and anisotropic etching. After thermal oxidation, the pore can be reduced to a single-nanometre when it is exposed to a high-energy electron beam. This fluidizes the silicon oxide leading to a shrinking of the small hole due to surface tension. When the electron beam is switched off, the material quenches and retains its shape. This technique dramatically increases the level of control in the fabrication of a wide range of nanodevices.

Crystallization↗
PubMed2002

Biochemical markers predicting survival in peroxisome biogenesis disorders.

OBJECTIVE: To identify prognostic markers reflecting the extent of peroxisome dysfunction in primary skin fibroblasts from patients with peroxisome biogenesis disorders (PBD). BACKGROUND: PBD are a genetically heterogeneous group of disorders due to defects in at least 11 distinct genes. Zellweger syndrome is the prototype of this group of disorders, with neonatal adrenoleukodystrophy and infantile Refsum disease as milder variants. Common to these three disorders are liver disease, variable neurodevelopmental delay, retinopathy, and perceptive deafness. Because genotype-phenotype studies are complicated by the genetic heterogeneity among patients with PBD, the authors evaluated a series of biochemical markers as a measure of peroxisome dysfunction in skin fibroblasts. METHODS: Multiple peroxisomal functions including de novo plasmalogen synthesis, dihydroxyacetonephosphate acyltransferase (DHAPAT) activity, C26:0/C22:0 ratio, C26:0 and pristanic acid beta-oxidation, and phytanic acid alpha-oxidation were analyzed in fibroblasts from a series of patients with defined clinical phenotypes. RESULTS: A poor correlation with age at death was found for de novo plasmalogen synthesis, C26:0/C22:0 ratio, and phytanic acid alpha-oxidation. A fairly good correlation was found for pristanic acid beta-oxidation, but the best correlation was found for DHAPAT activity and C26:0 beta-oxidation. A mathematic combination of DHAPAT activity and C26:0 beta-oxidation showed an even better correlation. CONCLUSIONS: DHAPAT activity and C26:0 beta-oxidation are the best markers in predicting life expectancy of patients with PBD. Combination of both markers gives an even better prediction. These results contribute to the management of patients with PBD.

Acyltransferases↗
PubMed2002

Correlated tunneling in intramolecular carbon nanotube quantum dots.

We investigate correlated electronic transport in single-walled carbon nanotubes with two intramolecular tunneling barriers. We suggest that below a characteristic temperature the long-range nature of the Coulomb interaction becomes crucial to determine the temperature dependence of the maximum G(max) of the conductance peak. Correlated sequential tunneling dominates transport yielding the power law G(max) proportional, variant T(alpha(end-end)-1), typical for tunneling between the ends of two Luttinger liquids. Our predictions are in agreement with recent measurements.

Journal Article↗
PubMed2001

Logic circuits with carbon nanotube transistors.

We demonstrate logic circuits with field-effect transistors based on single carbon nanotubes. Our device layout features local gates that provide excellent capacitive coupling between the gate and nanotube, enabling strong electrostatic doping of the nanotube from p-doping to n-doping and the study of the nonconventional long-range screening of charge along the one-dimensional nanotubes. The transistors show favorable device characteristics such as high gain (>10), a large on-off ratio (>10(5)), and room-temperature operation. Importantly, the local-gate layout allows for integration of multiple devices on a single chip. Indeed, we demonstrate one-, two-, and three-transistor circuits that exhibit a range of digital logic operations, such as an inverter, a logic NOR, a static random-access memory cell, and an ac ring oscillator.

Journal Article↗
PubMed2001

Two-dimensional imaging of electronic wavefunctions in carbon nanotubes.

The drive towards the development of molecular electronics is placing increasing demands on the level of control that must be exerted on the electronic structure of materials. Proposed device architectures ultimately rely on tuning the interactions between individual electronic states, which amounts to controlling the detailed spatial structure of the electronic wavefunctions in the constituent molecules. Few experimental tools are available to probe this spatial structure directly, and the shapes of molecular wavefunctions are usually only known from theoretical investigations. Here we present scanning tunnelling spectroscopy measurements of the two-dimensional structure of individual wavefunctions in metallic single-walled carbon nanotubes; these measurements reveal spatial patterns that can be directly understood from the electronic structure of a single graphite sheet, and which represent an elegant illustration of Bloch's theorem at the level of individual wavefunctions. We also observe energy-dependent interference patterns in the wavefunctions and exploit these to directly measure the linear electronic dispersion relation of the metallic single-walled carbon nanotube.

Journal Article↗
PubMed2001

Carbon nanotube single-electron transistors at room temperature.

Room-temperature single-electron transistors are realized within individual metallic single-wall carbon nanotube molecules. The devices feature a short (down to approximately 20 nanometers) nanotube section that is created by inducing local barriers into the tube with an atomic force microscope. Coulomb charging is observed at room temperature, with an addition energy of 120 millielectron volts, which substantially exceeds the thermal energy. At low temperatures, we resolve the quantum energy levels corresponding to the small island. We observe unconventional power-law dependencies in the measured transport properties for which we suggest a resonant tunneling Luttinger-liquid mechanism.

Journal Article↗
PubMed2001

Biophysical characterization of the influence of salt on tetrameric SecB.

SecB is a tetrameric chaperone, with a monomeric molecular mass of 17 kDa, that is involved in protein translocation in Escherichia coli. It has been hypothesized that SecB undergoes a conformational change as a function of the salt concentration. To gain more insight into the salt-dependent behavior of SecB, we studied the protein in solution by dynamic light scattering, size exclusion chromatography, analytical ultracentrifugation, and small angle neutron scattering. The results clearly demonstrate the large influence of the salt concentration on the behavior of SecB. At high salt concentration, SecB is a non-spherical protein with a radius of gyration of 3.4 nm. At low salt concentration the hydrodynamic radius of the protein is apparently decreased, whereas the ratio of the frictional coefficients is increased. The protein solution behaves in a non-ideal way at low salt concentrations, as was shown by the analytical ultracentrifugation data and a pronounced interparticle effect observed by small angle neutron scattering. A possible explanation is a change in surface charge distribution dependent on the salt concentration in the solvent. We summarize our data in a model for the salt-dependent conformation of tetrameric SecB.

Bacterial Proteins↗
PubMed2001

Human Rad50/Mre11 is a flexible complex that can tether DNA ends.

The human Rad50 protein, classified as a structural maintenance of chromosomes (SMC) family member, is complexed with Mre11 (R/M) and has important functions in at least two distinct double-strand break repair pathways. To find out what the common function of R/M in these pathways might be, we investigated its architecture. Scanning force microscopy showed that the complex architecture is distinct from the described SMC family members. R/M consisted of two highly flexible intramolecular coiled coils emanating from a central globular DNA binding domain. DNA end-bound R/M oligomers could tether linear DNA molecules. These observations suggest that a unified role for R/M in multiple aspects of DNA repair and chromosome metabolism is to provide a flexible, possibly dynamic, link between DNA ends.

DNA↗
PubMed2000

High-field electrical transport in single-wall carbon nanotubes

Using low-resistance electrical contacts, we have measured the intrinsic high-field transport properties of metallic single-wall carbon nanotubes. Individual nanotubes appear to be able to carry currents with a density exceeding 10(9) A/cm(2). As the bias voltage is increased, the conductance drops dramatically due to scattering of electrons. We show that the current-voltage characteristics can be explained by considering optical or zone-boundary phonon emission as the dominant scattering mechanism at high field.

Journal Article↗
PubMed2000

Direct measurement of electrical transport through DNA molecules.

Attempts to infer DNA electron transfer from fluorescence quenching measurements on DNA strands doped with donor and acceptor molecules have spurred intense debate over the question of whether or not this important biomolecule is able to conduct electrical charges. More recently, first electrical transport measurements on micrometre-long DNA 'ropes', and also on large numbers of DNA molecules in films, have indicated that DNA behaves as a good linear conductor. Here we present measurements of electrical transport through individual 10.4-nm-long, double-stranded poly(G)-poly(C) DNA molecules connected to two metal nanoelectrodes, that indicate, by contrast, large-bandgap semiconducting behaviour. We obtain nonlinear current-voltage curves that exhibit a voltage gap at low applied bias. This is observed in air as well as in vacuum down to cryogenic temperatures. The voltage dependence of the differential conductance exhibits a peak structure, which is suggestive of the charge carrier transport being mediated by the molecular energy bands of DNA.

DNA↗