Compression and Free Expansion of Single DNA Molecules in Nanochannels

Christian H. Reccius, John T. Mannion, Joshua D. Cross

Our goal is to understand the mechanical properties of single DNA strands under high compression forces in confined environments. Characterization of these properties is important for an understanding of DNA packing into chromatin or bacteriophage heads as well as the verification of theoretical biopolymer models. We are currently investigating the compression and subsequent free expansion of DNA molecules in artificial nanofluidic devices.[1] Our method stands in contrast to established techniques for investigating single DNA strands [2], for example the stretching by an external force, which was used to study the elasticity of DNA molecules.[3]

Our microfluidic devices consist of parallel fused silica nanochannels (diameter 90-130nm) which have a narrow constriction for blocking electrophoretically driven DNA. The structures were fabricated by sealing a structured wafer (500 microns) with a thin cover wafer (170 microns). The nanochannels were built by deep reactive ion etching using a chromium or aluminum mask which was patterned by electron beam lithography.

In our experiments, single lambda DNA multimers were first driven into the nanofluidic channels by an electric field. Since the radius of gyration of the biomolecules was bigger than the channel diameter, their equilibrium state was no longer a sphere but instead an elongated cylinder.[4] Forcing the stretched DNA into a channel constriction led to a compression of the molecule into a tight conformation. When the electric field was turned off, the DNA molecule slowly expanded back to the energetically favorable stretched out conformation. This expansion can be interpreted with the help of a simple polymer model based on self-avoidance effects.

Figure 1. Schematic of a DNA strand entering into a nanochannel (1-3), its compression (4-6) and its relaxation (7-9).

Figure 2. Constriction inside an open fused silica 130nm channel.

References:

[1] C. H. Reccius, J. T. Mannion, J. D. Cross, and H. G. Craighead, Compression and Free Expansion of Single DNA Molecules in Nanochannels, Phys. Rev. Lett., 95, 268101 (2005).

[2] T. R. Strick, M-N. Dessinges, G. Charvin, N. H. Dekker, J-F. Allemand, D. Bensimon, and V. Croquette, Stretching of macromolecules and proteins, Rep. Prog. Phys., 66, 1-45 (2003).

[3] S. B. Smith, L. Finzi, and C. Bustamente, Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads, Science, 258, 1122-1126 (1992).

[4] J. O. Tegenfeldt, C. Prinz, H. Cao, S. Chou, W. W. Reisner, R. Riehn, Y. M. Wang, E. C. Cox, J. C. Sturm, P. Silberzan, and R. H. Austin, The dynamics of genomic-length DNA molecules in 100-nm channels, Proc. Natl. Acad. Sci. U. S. A. 101, 10979 (2004).