DNA-Based Soft Phases

Abstract

This chapter reviews the state-of-the-art in the study of molecular or colloidal systems whose mutual interactions are mediated by DNA molecules. In the last decade, the robust current knowledge of DNA interactions has enabled an impressive growth of self-assembled DNA-based structures that depend crucially on the properties of DNA-DNA interactions. In many cases, structures are built on design by exploiting the programmable selectivity of DNA interactions and the modularity of their strength. The study of DNA-based materials is definitely an emerging field in condensed matter physics, nanotechnology, and material science. This chapter will consider both systems that are entirely constructed by DNA and hybrid systems in which latex or metal colloidal particles are coated by DNA strands. We will confine our discussion to systems in which DNA-mediated interactions promote the formation of "phases," that is structures extending on length scales much larger than the building blocks. Their self-assembly typically involves a large number of interacting particles and often features hierarchical stages of structuring. Because of the possibility of fine-tuning the geometry and strength of the DNA-mediated interactions, these systems are characterized by a wide variety of patterns of self-assembly, ranging from amorphous, to liquid crystalline, to crystalline in one, two, or three dimensions.

Liquid crystal self-assembly of random-sequence DNA oligomers

“…Similar high levels of selectivity are exploited in genomic PCR, relying on the capacity of primers to target their complementary sequence within a full genome. Selective interactions of DNA oligomers have been exploited in the past years in a variety of strategies for the construction of designed self-assembled nanostructures (1)(2)(3)(4). Selectivity combines with self-assembly in the recent observation that short oligomers of nucleic acids having complementary sequences exhibit liquid crystal (LC) ordering (5)(6)(7).…”

Molecular Dynamics Simulation of High Density DNA Arrays

“…We have computed all three order parameters along the axis of a given DNA pair for water molecules located in a cuboid (defined by DNA-DNA interaxial spacing, DNA diameter, and its long axis) between a given DNA pair. We found that upon the increase of the DNA concentration the local ordering of water molecules, as quantified by the order parameters η (1,2,3) , shows distinct features as well as a noticeable symmetry. In particular, the η (2,3) are symmetric w.r.t.…”

“…We found that upon the increase of the DNA concentration the local ordering of water molecules, as quantified by the order parameters η (1,2,3) , shows distinct features as well as a noticeable symmetry. In particular, the η (2,3) are symmetric w.r.t. the midpoint and indicate progressive orientational layering, while η (1) is antisymmetric and quantifies the ordering strength of the opposed DNA surfaces.…”

“…Three different types of these order parametrers, η (1,2,3) , have been investigated in related contexts. They are defined as…”

“…The properties of dilute (double-stranded) dsDNA solutions do not really suffice in order to understand their behavior in vivo [1,2]. The internal environment of eukaryotic nuclei, bacterial nucleoids and/or viral capsids, is anything but dilute and the properties of DNA solutions in these environments can only be characterized by specifically invoking the fine details of molecular interactions between them at small intersurface spacings [3].…”