Probing confined DNA

30 Mar 2012, 10:00
45m
132:028 (Nordita)

132:028

Nordita

Speaker

Prof. Jonas Tegenfeldt (Department of Physics, Lund University and Department of Physics, University of Gothenburg)

Description

In my presentation I will touch on three topics with fundamental interest and with relevance to biomedical applications. All involve DNA stretched by confinement in nanofluidic channels: (1) orientational correlations, (2) force-extension measurements, and (3) barcode labeling. The behavior of DNA confined into a nanochannel with a effective cross sectional diameter less than the radius of gyration of the polymer have been described by two theories. For effective diameters less than the persistence length Odijk has devised a model where the DNA undulates between the walls. For effective diameters greater than the persistence length deGenne's blob theory predicts a powerlaw dependence of the extension as a function of the effective diameter with an exponent of -2/3. However, although deGennes blob theory correctly predict some of the characteristics of experimental results, the predicted exponent is not reproduced and with careful measurements we show that the behavior does not even follow a power law. Using Monte Carlo simulations together with a mean-field theory we develop a model based on local orientational correlations that better predict the global properties of the DNA that we observe in our measurements. Using force-extension measurements we probe the effect of confinement on the elastic properties of DNA. The results have strong biological relevance due to the high degree of crowding in natural environments. The measurements take place in a device with two microscale channels connected by a nano-slit. The DNA is attached to a magnetic bead and introduced into one of the microchannels. The DNA is subsequently allowed to pass through the nanoslit and finally bound to the surface of the opposite microchannel. With a magnetic tweezers a force is exerted on the DNA while the total extension is observed. For deep slits and for high forces the force extension curve follows the bulk Marco-Siggia model. However for strong confinement and for low forces the fluctuations in one dimension are suppressed, lowering the required force for a given extension. A modified Marco_Siggia model is developed and is found to be consistent with our observations. The direct visualization of DNA stretched in nanochannels opens up for interesting applications in genomics, oncology and infectious disease. We have developed a simple labeling technique that results in a pattern along the DNA that is based on the local melting and thus a function of the underlying sequence. I will discuss the prospects of this technique along with recent results.

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