DNA Tiling and the DNA Tiling and the AFMAFM

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Alexi LykoudisAlexi Lykoudis

DNA versus DNA TilingDNA versus DNA Tiling DNA is a nucleic acid formed by DNA is a nucleic acid formed by

a double helixa double helix DNA is also made of a DNA is also made of a

negatively charged phosphate negatively charged phosphate backbone, base pairs and backbone, base pairs and bonds between those basesbonds between those bases

DNA tiling is the analyzing and DNA tiling is the analyzing and the engineering of DNA and its the engineering of DNA and its structuresstructures

DNA plasmids are circular DNA plasmids are circular double-stranded moleculesdouble-stranded molecules

DNA StructureDNA Structure

The AFMThe AFM The Atomic Force The Atomic Force

Microscope, or AFM is a Microscope, or AFM is a scanning probe microscope scanning probe microscope

On the cantilever is a tip On the cantilever is a tip that scans back and forth that scans back and forth the surface of your samplethe surface of your sample

The microscope gives you The microscope gives you enlarged images of the enlarged images of the DNA on the sample surfaceDNA on the sample surface

Reasons for AFMReasons for AFM Advantages:Advantages:

• Can create detailed, true 3-Can create detailed, true 3-D images of surfaces unlike D images of surfaces unlike the electron microscopethe electron microscope

• Works in a normal Works in a normal environment with little to environment with little to no sanitary measures being no sanitary measures being taken in the environmenttaken in the environment

Disadvantages:Disadvantages:• Cannot scan a very large Cannot scan a very large

surface in comparison to surface in comparison to the STMthe STM

• Scans relatively slowly and Scans relatively slowly and the tip used to scan is the tip used to scan is easily breakableeasily breakable

Silicon Wafers Silicon Wafers

Silicon is used as a Silicon is used as a surface for the DNA surface for the DNA plasmids to sit on plasmids to sit on while being while being analyzed by the AFManalyzed by the AFM

For plain imaging on For plain imaging on the AFM, Silicon the AFM, Silicon does not have to be does not have to be usedused

Then why is silicon Then why is silicon emphasized?emphasized?

The Adhesive MonolayerThe Adhesive Monolayer

The silane layer on the The silane layer on the silicon is negativesilicon is negative

The phosphate The phosphate backbone of the DNA backbone of the DNA plasmid is also plasmid is also negativenegative

A molecule known as A molecule known as aminopropyltriethoxysaminopropyltriethoxysilane, or APTES is used ilane, or APTES is used as an adhesive as an adhesive

DNA StructuresDNA Structures In DNA there are unpaired In DNA there are unpaired

bases that stick out of the bases that stick out of the structurestructure

They can be used to attach They can be used to attach other DNA sticky ends to other DNA sticky ends to them, creating a larger them, creating a larger structurestructure

Other tile-like but more Other tile-like but more complex DNA structures complex DNA structures can be used in can be used in nanotechnologynanotechnology

NanotechnologyNanotechnology Nanotechnology is the Nanotechnology is the

building of structures building of structures in the range of in the range of nanometersnanometers

One example of the One example of the power of power of nanotechnology is the nanotechnology is the image to the rightimage to the right

Why DNA Tiling?Why DNA Tiling?

One main goal is to use DNA as a One main goal is to use DNA as a programmable component with other programmable component with other nanostructuresnanostructures

DNA can be used to act as DNA can be used to act as scaffolding to hold molecules in an scaffolding to hold molecules in an organized crystalline patternorganized crystalline pattern

DNA can be engineered to act as DNA can be engineered to act as circuitry for computerscircuitry for computers