RM+First+Semester+Milestone+Report

RM's Logbook

This page reveals the stepping stones of making a scientifc journey using the Atomic Force Microscope and DNA, but specifically for DNA scaffolding. These individual points mark the goals that need to be accomplished before moving on. The subheadings denote the subject of the milestones; however, the milestones are preferably accomplished in the given order.

The Fundamentals: Describe the goal of this project and its application to future technologies. Describe the functions of the AFM. Explain the tapping, contact, and non-contact scanning modes. Explain what APTES stands for and its function between silicon and DNA. Describe what a DNA plasmid is and why it is used for research. Explain why we want "linearized" DNA. Describe the functions of restriction enzymes, which type is used in this project, and why. Explain the plasmids' relationship to the silicon surface and APTES.

The Technology Explain the necessary steps to set-up the AFM and insert a sample. Describe some of the features of the Nanoscope(III) program. Explain the steps needed to obtain an image and capture it.

Independent Preparation Describe how to clean mica surfaces. Describe how to clean silicon surfaces. Describe how to prepare the APTES solution. Describe how to prepare the DNA plasmid solution. Describe how to deposit solutions on the surface, and the difference between the deposition on silicon and mica surfaces.

The Future Learn how to view different aspects of the sample using Nanoscope (3-D images, cross sections, etc.) Learn different techniques of deposition on different surfaces (gallium nitride, gold, other semiconductors). Learn how to measure monolayers. Learn how to mix monolayers, in order to create monolayers such as PEG and OTS. Learn how to measure the contact angle. Learn how to test samples in an oxygen-free environment.

Taking on a different project using the AFM-CFM, I would need to: Apply for a mentor with connections to the biology building at Notre Dame (where an AFM-CFM is kept). Learn the differences between using the AFM-CFM and just the AFM.