Silicon Nanotweezers Research Articles

Direct measurement of the mechanical properties of a chromatin analog and the epigenetic effects of para-sulphonato-calix[4]arene

By means of Silicon Nano Tweezers (SNTs) the effects on the mechanical properties of λ-phage DNA during interaction with calf thymus nucleosome to form an artificial chromatin analog were measured. At a concentration of 100 nM, a nucleosome solution induced a strong stiffening effect on DNA (1.1 N m−1). This can be compared to the effects of the histone proteins, H1, H2A, H3 where no changes in the mechanical properties of DNA were observed and the complex of the H3/H4 proteins where a smaller increase in the stiffness is observed (0.2 N m−1). Para-sulphonato-calix[4]arene, SC4, known for epigenetic activity by interacting specifically with the lysine groups of histone proteins, was studied for its effect on an artificial chromatin. Using a microfluidic SNT device, SC4 was titrated against the artificial chromatin, at a concentration of 1 mM in SC4 a considerable increase in stiffness, 15 N m−1, was observed. Simultaneously optical microscopy showed a physical change in the DNA structure between the tips of the SNT device. Electronic and Atomic Force microscopy confirmed this structural re-arrangement. Negative control experiments confirmed that these mechanical and physical effects were induced neither by the acidity of SC4 nor through nonspecific interactions of SC4 on DNA.

Urface modification on probes of Silicon nanotweezers for cell trapping and releasing

urface modification on probes of Silicon nanotweezers for cell trapping and releasing

Direct measurement of the mechanism by which magnesium specifically modifies the mechanical properties of DNA.

We examine the effect of physiological cations Na+, K+, Mg2+, and Ca2+ on the mechanical properties of bundles of λ-phage DNA using silicon nanotweezers (SNTs). Integrating SNTs with a microfluidic device allows us to perform titration experiments while measuring the effect in real-time. The results show that only for Mg2+ and in particular, at the intra-nuclear concentration (100 mM), the interaction occurs.

Real-time mechanical characterization of DNA degradation under therapeutic X-rays and its theoretical modeling.

The killing of tumor cells by ionizing radiation beams in cancer radiotherapy is currently based on a rather empirical understanding of the basic mechanisms and effectiveness of DNA damage by radiation. By contrast, the mechanical behaviour of DNA encompassing sequence sensitivity and elastic transitions to plastic responses is much better understood. A novel approach is proposed here based on a micromechanical Silicon Nanotweezers device. This instrument allows the detailed biomechanical characterization of a DNA bundle exposed to an ionizing radiation beam delivered here by a therapeutic linear particle accelerator (LINAC). The micromechanical device endures the harsh environment of radiation beams and still retains molecular-level detection accuracy. In this study, the first real-time observation of DNA damage by ionizing radiation is demonstrated. The DNA bundle degradation is detected by the micromechanical device as a reduction of the bundle stiffness, and a theoretical model provides an interpretation of the results. These first real-time observations pave the way for both fundamental and clinical studies of DNA degradation mechanisms under ionizing radiation for improved tumor treatment.

Direct electrical and mechanical characterization of in situ generated DNA between the tips of silicon nanotweezers (SNT).

Previously, we reported the application of micromachined silicon nanotweezers (SNT) integrated with a comb-drive actuator and capacitive sensors for capturing and mechanical characterization of DNA bundles. Here, we demonstrate direct DNA amplification on such a MEMS structure with subsequent electrical and mechanical characterization of a single stranded DNA (ssDNA) bundle generated between the tips of SNT via isothermal rolling circle amplification (RCA) and dielectrophoresis (DEP). An in situ generated ssDNA bundle was visualized and evaluated via electrical conductivity (I-V) and mechanical frequency response measurements. Colloidal gold nanoparticles significantly enhanced (P < 0.01) the electrical properties of thin ssDNA bundles. The proposed technology allows direct in situ synthesis of DNA with a predefined sequence on the tips of a MEMS sensor device, such as SNT, followed by direct DNA electrical and mechanical characterization. In addition, our data provides a "proof-of-principle" for the feasibility of the on-chip label free DNA detection device that can be used for a variety of biomedical applications focused on sequence specific DNA detection.

Silicon Nano Tweezers are reaching clinical research

Silicon Nano Tweezers are reaching clinical research

Improvement of Silicon Nanotweezers Sensitivity for Mechanical Characterization of Biomolecules Using Closed-Loop Control

In this paper, we show that closed-loop control can be advantageously used for the characterization of mechanical properties of biomolecules using silicon nanotweezers (SNT). SNT have already been used in open-loop mode for the characterization of mechanical properties of DNA molecules. Up to now, such an approach allows the detection of stiffness variations equivalent to about 15 DNA molecules. Here, it is shown that this resolution is inversely proportional to the resonance frequency of the whole system and that real-time feedback control with state observer can drastically improve the performances of the tweezers used as biosensors. Such improvement is experimentally validated in the case of the manipulation of fibronectin molecules. The results are promising for the accurate characterization of biopolymers such as DNA molecules.

Real-time Measurement of DNA Degradation under Radiation by Silicon Nanotweezers Coupled with Microfluidic Cavity

Real-time Measurement of DNA Degradation under Radiation by Silicon Nanotweezers Coupled with Microfluidic Cavity

Silicon nanotweezers for biomechanical and bioelectrical assays

In modern life, technologies enabling detection of biological molecules at a low threshold, for health and ecological concerns, are in high demand. Directly interrogating the molecules is a promising direction to clarify the noisy response of conventional assays arising from simultaneous different reactions. Besides sophisticated biophysical instrument such as the atomic force microscope, this paper proposes silicon nanotweezers (SNT) as a new microsystem for molecular manipulation. SNT can trap molecules and sense their biomechanical and bioelectrical response in minute operations. In this review SNT characteristics are overviewed; their operation modes are illustrated by molecule and cell trapping, manipulation and characterization in air and in solution. As they are tiny and can be mass produced by highly parallel microsystem technology, SNT can be seen as a potential molecular and cellular probe for routine analysis and bio detection.

Four-Terminal Electrical Measurement of a DNA Molecular Bundle Captured by Silicon Nanotweezers

We measured the electrical characteristics of DNA molecular bundles that were 25-µm long and had a diameter of 100-500 nm. We captured the bundle between the tips of silicon nanotweezers by dielectrophoresis. The two-terminal measurement, which used only the tweezers, failed because of the contact resistance between the bundle and the tips. We adopted a four-terminal measurement that eliminated the effect of the contact resistance. We fabricated potential measurement probes, which consisted of 2-µm-wide line electrodes with a 4-µm separation. The captured DNA bundle was pressed against the probes, and the potential drop associated with the current in the bundle was measured. We successfully determined the conductivity of the bundle.

Single-DNA-molecule trapping with silicon nanotweezers using pulsed dielectrophoresis

DNA manipulation based on dielectrophoresis between microfabricated electrodes is one of the most efficient methods for the physical handling of molecules. Dielectrophoresis is routinely used for stretching and trapping DNA molecules between the opposing tips of silicon nanotweezers. However, the precise number of trapped molecules is difficult to predict, as a continuous application of ac voltage continually attracts the molecules while the electric-field-induced fluid flow prevents them from bridging the tips. To circumvent this difficulty, the dielectrophoresis signal is applied during very short intervals. In this pulsed mode, the electrohydrodynamic fluid flow is lessened and the molecule trapping success rate is greatly enhanced. A fluorescently labeled single λ-DNA molecule was successfully stretched and captured by the silicon nanotweezers with 50 ms pulses of a 1 MHz, 1 MV m−1 ac dielectrophoresis voltage. This single-molecule trapping between the tweezers' tips is monitored, in real time, under fluorescence imaging.

Trapping of hyaluronic acid molecule by metal-coated silicon nanotweezers

We describe the trapping characteristic of hyaluronic acid (HA) molecules using silicon micromachined nanotweezers having two opposed needle tips (3-7 µm gap) that were coated with Al, Au, and Pt thin films. In an aqueous HA solution, ac voltage (20 Vpp, sine wave) was applied between the nanotweezer tips. In the experiments using the Al-coated nanotweezers, HA molecules were successfully trapped as a thin string bridged between the tips of the nanotweezers when the frequency of applied ac voltage was 500 Hz or higher. The diameter of the trapped string tended to decrease when the frequency of the applied ac voltage was increased. A molecular string with a diameter of 30 nm consisting of a bundle of multiple HA molecules was obtained when the frequency of the applied ac voltage was 3 kHz. In addition to the Al-coated nanotweezers, HA molecules were also successfully trapped as a string using the nanotweezers with tips coated with Au and Pt thin films.

Silicon Nanotweezers With Subnanometer Resolution for the Micromanipulation of Biomolecules

The metabolism and toxicity of dapsone was compared in vitro and in vivo in rat, mouse and man. Metabolism was assessed by high-pressure liquid chromatography-mass spectrometry and methemoglobin formation has been used as a toxic endpoint. The greatest toxicity in vitro was seen in microsomes prepared from male Wistar rats (36.6 +/- 1.5% methemoglobin), although toxicity was also seen in microsomes from the female rat (8.2 +/- 1.3%), male CD1 (4.2 +/- 1.6%) and human (10. 9 +/- 1.1%). The rank order of toxicity agreed with the formation of the hydroxylamine metabolite in vitro. All microsomes were also capable of catalyzing the reverse reaction, i.e., reduction of the hydroxylamine to dapsone. However, in vivo administration of dapsone resulted in significant (P < 0.05) methemoglobinemia only in male rats and humans. This species difference in the susceptibility to dapsone toxicity could not be attributed solely to the sensitivity of the target erythrocytes, because the order of sensitivity to dapsone hydroxylamine was human > mouse > rat. Analysis of bile and urine revealed the formation of dapsone hydroxylamine and its glucuronide in male rats and humans, but not in female rats or mice. This species difference in the metabolism and toxicity of dapsone has important implications in the safety evaluation of related compounds for man.

FEM Analysis of Mechanical Characteristics of Nano Tweezers with MemsOne

In this study, we investigate improvements in silicon nanotweezers used to handle DNA molecules. We analyzed the deformation and frequency properties of the nanotweezers by finite element method (FEM) analysis. From this analysis, we determined the appropriate operation area of the nanotweezers.