This dissertation focuses on developing microfabricated components for stretching, immobilizing and cutting single DNA molecules. Towards this goal, a transpiration-based micropump was constructed for stretching DNA molecules using hydrodynamic forces. The developed micropump can deliver non-pulsatile, low-velocity (100 μm/s, 5 nl/min) flows and can be used in several other applications. Microfabricated devices incorporating gold electrodes were constructed for stretching DNA molecules using electrostatic forces in polymer-enhanced media. A ‘thiol-on-gold’ based immobilization chemistry was developed for fixing one end of a lambda DNA molecule (48500 bp) onto a pointed gold electrode. Once immobilized the lambda DNA molecule was stretched to its full length (21 μm) in the Linear polyacrylamide (3.75% by wt) enhanced medium placed between two gold electrodes (20 Pin apart), using a high frequency electric field (3x 105 v/m, 1 MHz). For cutting stretched lambda DNA molecules at precise locations using restriction enzymes, a photo-initiated reaction scheme was developed. In this scheme, magnesium ions necessary for the reaction are delivered as caged compounds (using DM Nitrophen as the caging complex) and later released at specific locations by shining 100 ms UV light pulse. Finally, an on-chip photodetection scheme was refined to detect DNA molecules at very low concentrations using high-sensitivity, low-noise PIN diodes. The several microfabricated components developed in this work can be used as tools for monitoring single molecule enzyme kinetics or studying structural conformations of single DNA molecules under applied forces. These components could also be integrated to perform the various single-molecular operations of stretching, fixing, and cutting on a single platform. Such a system holds great promise for the genome community towards developing a high throughput device for sequencing long DNA molecules with minimal post-processing.
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