Reversibly switchable DNA nanocompartment on surfaces: experiments, applications, and theory

Abstract

This paper summarizes our studies of DNA nanocompartement in recent years. Biological macromolecules have been used to fabricate many nanostructures, bio-devices, and biomimetics because of their physical and chemical properties. But dynamic nanostructure and bio-machinery that depend on collective behavior of biomolecules have not been demonstrated. Here, we report the design of DNA nanocompartment on surfaces that exhibit reversible changes in molecular mechanical properties. Such molecular nanocompar- tment is served to encage molecules, switched by the collective effect of Watson-Crick base- pairing interactions. This effect is used to investigate the dynamic process of nanocompartment switching and molecular thermosensing, as well as perform molecular recognition. Further, we found that ‘fuel’ strands with single-base variation cannot afford an efficient closing of nanocompartment, which allows highly sensitive label-free DNA array detection. Theoretical analysis and computer simulations confirm our experimental observations, which are discussed in this review paper. Our results suggest that DNA nanocompartment can be used as building blocks for complex biomaterials, because its core functions are independent of substrates and mediators.

Keywords

DNA nanocompartment, DNA array, Molecular collective behavior, molecular channel