(548d) Rapid Screening of DNA Due to Differences In the Viscoelastic Properties

As the role of disease causing genetic mutations are more clearly understood, the need for quick DNA screening is rapidly increasing. Here we show a rapid characterization technique which makes use of the single strand DNA's ability to form a particular configuration in aqueous solution which is directly related to its base sequence. When immobilized onto a substrate, the film formed will have viscoelastic properties which are characteristic of the base sequence in the ssDNA.

In this study we evaluate the differences in the viscoelastic properties between the P53 Wild type DNA molecule and the P53 mutant R type DNA molecule using a QCM-D. The QCM-D is a surface acoustic wave based sensor which can measure extremely low masses with very high precision. It makes use of a quartz crystal with a resonant frequency of around 5 Mhz (crystals with different resonant frequencies can also be used). For a rigid film depositing on the crystal, the frequency of resonance decreases linearly with the amount of mass deposited according to the Saurberey's equation and so, a highly sensitive measurement of frequency would enable us to calculate the amount of mass deposited in the order of ngs per square cm. By measuring the energy dissipation of the film at very short intervals, the instrument enables us to evaluate the viscoelastic properties of the film. For a film that is viscoelastic (not rigid with an appreciable energy dissipation), the Saurberey's equation becomes insufficient and viscoelastic modeling (usually the Voight Maxwell model) becomes necessary.

We have studied the viscoelastic properties of the film formed by the deposition of biotinylated P53 ssDNA, both wild type and the mutant type by immobilizing it via Avidin to a biotin-thiol surface. We have shown that the wild type and the mutant type ssDNA form films of different properties which are due to interactions between the bases in single strand DNA molecules in aqueous solution leading to the formation of particular configurations.

The value of the shear modulus was evaluated for the film formed by the wild type DNA and the film formed by the mutant DNA. The appreciable difference in the values suggests that this method of rapid screening has much promise.