DNA:

A programmable Force Sensor

Hauke Clausen-Schaumann et al. 2003

To directly quantify biomolecular interaction

General Goal:

Why?

“…it has become evident that bimolecular processes aregoverned by piconewton forces”

• Receptor-ligand interactions

•Protein and nucleic acid structures

•Covalent bonds

Examples:

The next goal:

To detect single-base pair mismatch using Single-molecular forces measurements

***Previous best was 10 base pairs***

Previous best method used Atomic Force Microscopy

AFM

or

The cantilever spring method:

Glass slide

Rudder stamp

The new method (differential force) :

Glass slide

Rudder stamp

The single-base pair mismatchchallenge:

PM > MM

Cy5 intensity = strength

Shear Geometry vs.

Zip Geometry

Have :

•Identical sequence•Binding energies•Thermal on/off rates

…but the zip 25-mer is 15 fold

more likely to rupture!

The Application:

A means of discriminating betweenspecific and non-specificantibody antigen interactions

Cy3 intensity = strength

False Positive detection:

• Protein array confirmation

• Since false positives increase geometrically as the number of spots increases.

• Could increase specificity

Questions:

1. Data is presented as intensity (probabilities), not forces

2. How complex are the mechanics of the tug-of-war?

3. How useful would it really be for “Precision SNP detection”?

4. Applications for DNA arrays

5. Chip design cost?

6. Cost of synthesizing antibodies couples to oligos on the rubber stamp thing?