DNA Tug-of-War at Micro-Nanofluidic Interfaces

Entropy-driven polymer dynamics at the nanoscale is fundamentally important in biological systems but the dependence of the entropic force on the nano-confinement remains elusive. Here we establish entropy-driven single DNA tug-of-war (TOW) at two micro-nanofluidic interfaces bridged by a nanoslit and present both theoretical and experimental study for the TOW and the conformation recovery through entropic recoiling. Using photolithography nanoslits have been fabricated that vary in height from 110 nm down to 15 nm and length from 30 micrometer to 4 micrometer. During retracting-recoiling (RR) phase, the turning points between elastic and recoil phase were determined various slit height, close to pure recoil as slit height shallower. Our force analysis from a modified worm-like chain relation in the TOW scenario and the entropic recoiling process provides direct experimental evidence that the entropic forces in these two regimes, though unequal, are essentially constant at a de ned slit height, irrespective of the slit length and the DNA segments within. We also determined the dependence of free energy change under strong confinement (h persistence length, P) and Odijk regime (h < persistence length, P) under slit-like confinements. Furthermore, we directly observed the tube-like motion (reptation) of DNA in ultra-thin nanoslits as h < 25 nm where it normally occurs in 2D-confined environments. Our experimental results show that the tube-like DNA motion is caused by strong confinement effect which enforces the interaction between DNA and the slit surface (roughness ~2 nm measured by AFM) with or without passivated PVP molecules in nanoslits, but not related to the bonding methods (PSQ or fusion bonding techniques) or DNA-conjugating fluorescent dyes (YOYO-1 and SYBR-Gold). DNA tube-like motion in nanoslits could be applied to DNA mapping and bionanotechnology. Our findings have implications to polymer transport in biological processes, the interface interactions in nanofluidic systems, device design for single molecule analysis and nanobiotechnological applications