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The couple Calix[4]arene-1,3-O-diphosphorous acid (C4diP) and zinc ions (Zn 2+ ) acts as a synergistic DNA binder. Silicon NanoTweezer (SNT) measurements show an increase in the mechanical stiffness of DNA bundles by a factor of >150, at Zn 2+ to C4diP ratios above 8, as compared to Zinc alone whereas C4diP alone decreases the stiffness of DNA. Electroanalytical measurements using 3D printed devices demonstrate a progression of events in the assembly of C4diP on DNA promoted by zinc ions. A mechanism at the molecular level can be deduced in which C4diP initially coordinates to DNA by phosphate-phosphate hydrogen bonds or in the presence of Zn 2+ by Zn 2+ bridging coordination of the phosphate groups. Then, at high ratios of Zn 2+ to C4diP, interdigitated dimerization of C4diP is followed by cross coordination of DNA strands through Zn 2+ /C4diP inter-strand interaction. The sum of these interactions leads to strong stiffening of the DNA bundles and increased inter-strand binding.

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., Competing Interests: The authors declare no conflict of interest.

Monitoring biological reactions using the mechanical response of macromolecules is an alternative approach to immunoassays for providing real-time information about the underlying molecular mechanisms. Although force spectroscopy techniques, e.g. AFM and optical tweezers, perform precise molecular measurements at the single molecule level, sophisticated operation prevent their intensive use for systematic biosensing. Exploiting the biomechanical assay concept, we used micro-electro mechanical systems (MEMS) to develop a rapid platform for monitoring bio/chemical interactions of bio macromolecules, e.g. DNA, using their mechanical properties. The MEMS device provided real-time monitoring of reaction dynamics without any surface or molecular modifications. A microfluidic device with a side opening was fabricated for the optimal performance of the MEMS device to operate at the air-liquid interface for performing bioassays in liquid while actuating/sensing in air. The minimal immersion of the MEMS device in the channel provided long-term measurement stability (>10 h). Importantly, the method allowed monitoring effects of multiple solutions on the same macromolecule bundle (demonstrated with DNA bundles) without compromising the reproducibility. We monitored two different types of effects on the mechanical responses of DNA bundles (stiffness and viscous losses) exposed to pH changes (2.1 to 4.8) and different Ag(+) concentrations (1 μM to 0.1 M).

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.

This paper describes an integrated biomechanical platform for real-time molecular or cellular assays. This platform is composed of silicon nanotweezers to manipulate the biological samples and an open microfluidic to handle solution and reactive agents. The tweezers are fabricated by standard Silicon-On-Insulator based micromachining processes (2 masks +1 additional mask for special tips) and integrate actuator, trapping tips and sensor. The microfluidic device is produced from common polydimethylsiloxane (PDMS) micromolding and integrates active valves for controlling the biological medium. Combining both technologies, a versatile experimental setup, built up in an enclosed space (< 10 cm(3)), enables direct interrogation of molecules or cells in solution. The silicon nanotweezers sense slight biological modifications of the trapped molecules or cell by monitoring the mechanical resonance response, which keeps a high Q factor (over 20) in liquid. Biomolecular assays (molecule trapping and enzymatic reaction kinetics) as well as characterizations of cells are reported here. The system provide molecular level resolution and is sensitive enough to capture cell biomechano-transduction activities. Moreover as the system is handy, it may be an easy, fast and quantitative alternative to existing methods.

We report the biomechanical characterization of λ-DNA bundle exposed to a therapeutic radiation beam by silicon Nanotweezers. The micromechanical device endures the harsh environment of radiation beams, and still retains molecular-level detection accuracy. The real-time DNA bundle degradation is observed in terms of biomechanical stiffness and viscosity reduction, both in air and in solution. These results pave the way for both fundamental and clinical studies of DNA degradation mechanisms under ionizing radiation for improved tumor treatment.