DNA Tiling and the AFM By Alexi Lykoudis

DNA versus DNA Tiling DNA is a nucleic acid formed by a double helix DNA is a nucleic acid formed by a double helix DNA is also made of a negatively charged phosphate backbone, base pairs and bonds between those bases DNA is also made of a negatively charged phosphate backbone, base pairs and bonds between those bases DNA tiling is the analyzing and the engineering of DNA and its structures DNA tiling is the analyzing and the engineering of DNA and its structures DNA plasmids are circular double-stranded molecules DNA plasmids are circular double-stranded molecules

DNA Structure

The AFM The Atomic Force Microscope, or AFM is a scanning probe microscope The Atomic Force Microscope, or AFM is a scanning probe microscope On the cantilever is a tip that scans back and forth the surface of your sample On the cantilever is a tip that scans back and forth the surface of your sample The microscope gives you enlarged images of the DNA on the sample surface The microscope gives you enlarged images of the DNA on the sample surface

Reasons for AFM Advantages: Advantages: Can create detailed, true 3-D images of surfaces unlike the electron microscopeCan create detailed, true 3-D images of surfaces unlike the electron microscope Works in a normal environment with little to no sanitary measures being taken in the environmentWorks in a normal environment with little to no sanitary measures being taken in the environment Disadvantages: Disadvantages: Cannot scan a very large surface in comparison to the STMCannot scan a very large surface in comparison to the STM Scans relatively slowly and the tip used to scan is easily breakableScans relatively slowly and the tip used to scan is easily breakable

Silicon Wafers Silicon is used as a surface for the DNA plasmids to sit on while being analyzed by the AFM Silicon is used as a surface for the DNA plasmids to sit on while being analyzed by the AFM For plain imaging on the AFM, Silicon does not have to be used For plain imaging on the AFM, Silicon does not have to be used Then why is silicon emphasized? Then why is silicon emphasized?

The Adhesive Monolayer The silane layer on the silicon is negative The silane layer on the silicon is negative The phosphate backbone of the DNA plasmid is also negative The phosphate backbone of the DNA plasmid is also negative A molecule known as aminopropyltriethoxys ilane, or APTES is used as an adhesive A molecule known as aminopropyltriethoxys ilane, or APTES is used as an adhesive

DNA Structures In DNA there are unpaired bases that stick out of the structure In DNA there are unpaired bases that stick out of the structure They can be used to attach other DNA sticky ends to them, creating a larger structure They can be used to attach other DNA sticky ends to them, creating a larger structure Other tile-like but more complex DNA structures can be used in nanotechnology Other tile-like but more complex DNA structures can be used in nanotechnology

Nanotechnology Nanotechnology is the building of structures in the range of nanometers Nanotechnology is the building of structures in the range of nanometers One example of the power of nanotechnology is the image to the right One example of the power of nanotechnology is the image to the right

Why DNA Tiling? One main goal is to use DNA as a programmable component with other nanostructures One main goal is to use DNA as a programmable component with other nanostructures DNA can be used to act as scaffolding to hold molecules in an organized crystalline pattern DNA can be used to act as scaffolding to hold molecules in an organized crystalline pattern DNA can be engineered to act as circuitry for computers DNA can be engineered to act as circuitry for computers