We introduce a new experimental technique for manipulating a segment of a charged macromolecule inside a transient nanogap between two fluidic reservoirs. This technique uses an FPGA-driven nanopositioner to control the coupling of a nanopipette with the liquid surface of a fluidic cell. We present results on creating a transient nanogap, triggered by a translocation of double-stranded DNA between a nanopipette and a fluidic cell, and measure the probability to find the molecule near the tip of the nanopipette after closing the gap. The developed platform will enable testing of our recent theoretical predictions for the behavior of charged macromolecule in a nanogap between two fluidic reservoirs. © 2014 AIP Publishing LLC.