The Tom Perkins group is working on the development of DNA and DNA hairpins as a force standard for the nanoworld. Polymers of DNA act like well-calibrated springs. DNA hairpins flicker between open and closed states at a characteristic force. In addition, DNA undergoes a sharp phase transition at ~65 pN. DNA’s unique mechanical properties plus the simplicity and fidelity with which it can be produced and distributed, make it an excellent candidate for a force standard.
To explore this idea further, the group is tackling the challenge of precisely measuring the elasticity of short strands (~630 nm) of DNA. Initial experimental measurements revealed that short strands of DNA had systematic errors of up to 18%—which is poor for a precision measurement. By teaming up with theorists from the Universities of Colorado and Pennsylvania, the group showed that the elasticity measurements were not the origin of the problem; rather the classic description of DNA elasticity was responsible. The Perkins team incorporated corrections into the original model to account for boundary conditions that become important at these small length scales. With this improved model, the researchers were able to reduce the systematic error of their elasticity measurements by threefold.
Next they undertook the challenge of measuring a tiny force with high precision. The group adopted laser stabilization techniques developed in JILA and applied them to optical-trapping microscopy. Using DNA hairpins, the researchers showed that with their improved instrumentation, they could measure a 20% change in the probability of a DNA hairpin being open due to a 0.1 pN (<1%) force change, proving that biomolecules are indeed very sensitive to force.
Recently, the group used two entirely different methods to precisely measure the force required to initiate the sharp phase transition in DNA at ~65 pN. In the first experiment, researchers bound a piece of DNA at both ends, then slowly stretched it with an optical trap by moving the stage. The overstretching force for intact DNA was measured to be 65.2 ± 0.5pN. However, a single nick in the DNA resulted in an over stretching force of 64.8 ± 0.5 N. As part of this work, the researchers showed that DNA overstretching does not require peeling from free ends or nicks, a characteristic that may increase its value as a force standard. In a second experiment, the group used high-force optical trapping (with DNA anchored to a gold nanopost) to measure an overstretching force of 64.9 ± 0.5 pN.
The success of these two efforts inspired the group to test the effects of optimizing bead size on force errors in measurements of DNA hairpins. Optimizing bead size not only reduced the force measurement errors by twofold, but may also improve force accuracy. With the recent successes in precision measurement of forces on DNA hairpins and in DNA overstretching, it is increasingly clear that DNA holds great promise as an intrinsic biological force standard.
In the future, the group plans to continue to improve the accuracy of DNA elasticity measurements to complement optical trapping’s increasingly high precision. The development of even more precise and accurate measurements of single DNA molecules may soon enable detection of biological motion with atomic-scale sensitivity (0.1 nm).