First Direct Measurement of DNA Stacking Forces

DNA is one of the most important and studied molecules around, and yet only now has a team of scientists, working at Duke University, succeeded in measuring the force between the nucleotides in a single-stranded DNA (ssDNA) molecule, using an atomic force microscope (AFM).

A double-stranded DNA is characterized by two principal forces---the stacking force between base units along the length of the double helix and the pairing force (Watson-Crick pairing) between the opposing base units forming the rungs of the helix. Measurements of DNA elasticity dating back to the 1990s (http://www.aip.org/pnu/1997/split/pnu312-1.htm) were done with double-stranded DNA, and it is difficult to separate the effects of the pairing and stacking forces.

That's why Piotr E. Marszalek (pemar@duke.edu) and his colleagues (Changhong Ke, Michael Humeniuk, and Hanna S-Gracz) turned to ssDNA. They rigged an artificial ssDNA consisting only of adenine base units attached to a gold substrate, and then pulled it with an AFM tip.

With a force resolution of about 1 pico-Newton, the Duke apparatus detected one plateau in elasticity (of the stacking force) at around 23 pN, which was expected, and then a second plateau around 113 pN. (Ke et al. Physical Review Letters, upcoming article)( a paper measuring forces for a single RNA molecule, finding a single force plateau at 20 pN, appeared in Seol et al., Phys Rev Lett, 13 April 2007)