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Precise positioning of molecular objects from one location to another is important for nanomanipulation and is also involved in molecular motors. Here, we study single-polymer-based positioning on the basis of the exact solution to the realistic three-dimensional worm-like-chain (WLC) model. The results suggest the possibility of a surprisingly accurate flyfishing-like positioning in which tilting one end of a flexible short polymer enables positioning of the other diffusing end to a distant location within an error of ∼1 nm. This offers a new mechanism for designing molecular positioning devices. The flyfishing effect (and reverse process) likely plays a role in biological molecular motors and may be used to improve speed of artificial counterparts. To facilitate these applications, a new force–extension formula is obtained from the exact WLC solution. This formula has an improved accuracy over the widely used Marko–Siggia formula for stretched polymers and is valid for compressed polymers too. The new formula is useful in analysis of single-molecule stretching experiments and in estimating intramolecular forces of molecular motors, especially those involving both stretched and compressed polymer components.

A purely DNA nanomachine must support internal stresses across short DNA segments with finite rigidity, producing effects that can be qualitatively very different from experimental observations of isolated DNA in fixed-force ensembles. In this article, computational simulations are used to study how well the rigidity of a driving DNA duplex can rupture a double-stranded DNA target into single-stranded segments and how well this stress can discriminate between unzipping or shearing geometries. This discrimination is found to be maximized at an optimal length but deteriorates as the driving duplex is either lengthened or shortened. This differs markedly from a fixed-force ensemble and has implications for the design parameters and limitations of dynamic DNA nanomachines.