Compression and Stretching of Single DNA Molecules under Channel Confinement.

We study the compression and extension response of single dsDNA (double-stranded DNA) molecules confined in cylindrical channels by means of Monte Carlo simulations. The elastic response of micrometer-sized DNA to the external force acting through the chain ends or through the piston is markedly affected by the size of the channel. The interpretation of the force ()-displacement () functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement Δ into the confinement contribution Δ and the force contribution Δ. The external stretching of confined DNA results in a characteristic pattern of - functions involving their shift to the larger extensions due to the channel-induced pre-stretching Δ. A smooth end-chain compression into loop-like conformations observed in moderately confined DNA can be accounted for by the relationship valid for a Gaussian chain in bulk. In narrow channels, the considerably pre-stretched DNA molecules abruptly buckle on compression by the backfolding into hairpins. On the contrary, the piston compression of DNA is characterized by a gradual reduction of the chain span and by smooth - functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the - and - functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.