Measure DNA / RNA Structural Dynamics with High Throughput

Part of: DNA/RNA Structural Mechanics

Force-extension and manipulation of DNA/RNA molecules

Multiple DNA or RNA molecules can be tethered between a bead and a glass surface. We can manipulate the molecules by pushing the beads away from the surface while the position of each bead is measured. In this way it is possible to obtain the characteristic force-extension curves of many DNA molecules in parallel.

The measurement data in Figure 1 shows the ability to apply various levels of tension on a single DNA molecule (8.4 kbp) tethered to a polystyrene bead (4.5 µm) while measuring its length. During the measurement we increased the acoustic force in four steps: 0 pN (A), 1.3 pN (B), 8.1 (C) and 15.8 pN (D). Increasing the acoustic force also increases the DNA extension and decreases the amount of thermal fluctuations so that a length accuracy of 12.7 nm (4) is achieved (standard deviation of the DNA extension at 60 Hz).

All AFS experiments can be performed on hundreds of biomolecules in parallel. Figure 2 shows the force-distance curves obtained by extending 20 individual DNA molecules in parallel. Moreover, each molecule can be (over)stretched many times as observed in Figure 3, which shows ten sequential overstretching measurements of the same DNA molecule.

1 Extension of DNA at an acoustic force of 0 pN (A), 1.3 pN (B), 8.1 (C) and 15.8 pN (D).

2 Force-distance curves of 20 dsDNA molecules in parallel.

3 Ten sequential overstretching measurements of the same DNA molecule.



Parallel Single-Molecule Force Spectroscopy

Acoustic Force Spectroscopy is a new single-molecule and single-cell manipulation method capable of applying acoustic forces on hundreds of biomolecules in parallel for precise experimentation with high throughput. It enables scientists to probe thousands of individual molecules in parallel (such as RNA, DNA, proteins, and living cells), allowing statistical analysis of the mechanical properties of biological properties of biological systems based on a single experiment.

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