Meller Group : Single Molecule Biophysics & Nano-biotechnologyTechnion Logo

Atto-mole detection of DNA using salt gradients

The DNA capture into solid-state nanopores involves two main steps: First, long-range electrostatic forces pull the DNA coil towards the pore, thus transitioning its motion from a purely diffusive to a biased one. Subsequently, a DNA coil experiencing this field is ‘funneled’ towards the pore mouth. Second, once the DNA coil is in contact with the pore, the local field pulls one of the DNA ends and threads it into the pore. This process involves crossing a free-energy barrier (see Figure 1).

 

The DNA funneling effect gives rise to a seemingly surprising result, where the likelihood of high molecular-weight DNA (longer molecules) to approach the pore and hence get captured is larger relative to short DNA molecules. This is a highly advantageous feature, since it permits the effective analyses of extremely long DNA molecules. Figure 2 shows the dependence of the capture rate of DNA molecules having different lengths. The data show that longer DNAs are captured by the nanopores at a constant or a growing rate compared with the shorter ones, despite the fact that the longer DNAs diffuse slower. Read more about this topic in our Nature Nanotechnology paper.

 

The DNA capture rate can be further increased by introducing salt concentration gradient across the two sides of the membrane in which the pore is made. When the concentration of salt ions in the Trans chamber is higher than in the Cis side (see Figure 1), we observe an increase in the DNA capture rate. This effect can be used to enhance the sensitivity of the nanopore method. For example, maintaining the DNA capture rate at 1 capture event per second, enables reduction of the DNA concentration in the Cis side down to a few Atto-moles (about 100,000 copies) or less. More details can be found here.

References:

  1. Wanunu M, Morrison W, Rabin Y, Grosberg AY, & Meller A (2010) Electrostatic Focusing of Unlabeled DNA into Nanoscale Pores using a Salt Gradient. Nature Nanotechnology 5:160-165.

 

Salt Gradient

Figure 1

cap[ture vs N