Journal
JOURNAL OF PHYSICAL CHEMISTRY B
Volume 124, Issue 9, Pages 1691-1702Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jpcb.9b11602
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Funding
- COST Action [CA17139]
- [SRDA-15-0323]
- [VEGA 2/0055/16]
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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 (f)-displacement (R) functions under quasi-one-dimensional confinement is facilitated by resolving the overall change of displacement Delta R into the confinement contribution Delta R-D and the force contribution Delta R-f. The external stretching of confined DNA results in a characteristic pattern of f-R functions involving their shift to the larger extensions due to the channel-induced pre-stretching Delta R-D. 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 S and by smooth f-S functions in the whole spatial range from the 3d near to 1d limits. The observed discrepancy between the shape of the f-R and f-S functions from two compression methods can be important for designing nanopiston experiments of compaction and knotting of single DNA in nanochannels.
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