DNA condensation in one dimension

Abstract

DNA can be programmed to assemble into a variety of shapes and patterns on the nanoscale and can act as a template for hybrid nanostructures such as conducting wires, protein arrays and field-effect transistors. Current DNA nanostructures are typically in the sub-micrometre range, limited by the sequence space and length of the assembled strands. Here we show that on a patterned biochip, DNA chains collapse into one-dimensional (1D) fibres that are 20 nm wide and around 70 µm long, each comprising approximately 35 co-aligned chains at its cross-section. Electron beam writing on a photocleavable monolayer was used to immobilize and pattern the DNA molecules, which condense into 1D bundles in the presence of spermidine. DNA condensation can propagate and split at junctions, cross gaps and create domain walls between counterpropagating fronts. This system is inherently adept at solving probabilistic problems and was used to find the possible paths through a maze and to evaluate stochastic switching circuits. This technique could be used to propagate biological or ionic signals in combination with sequence-specific DNA nanotechnology or for gene expression in cell-free DNA compartments.

Heterogeneous Morphology and Dynamics of Polyelectrolyte Brush Condensates in Trivalent Counterion Solution

“…As reported by the experiments [7,13], different modes of incorporating spermidine into brush (e.g., the rate by which trivalent counterions are added) lead to slightly different critical concentrations, different collapse dynamics, and different morphologies. All these kinetic effects of spermidine addition are closely linked to the ultra-slow dynamics of brush condensates at q 3+ ≈ 1, underscored in Fig.8, and are of great interest for the future study.…”

“…The heterogeneous morphology of DNA condensate points to polyamine-mediated regulation of local DNA configuration and gene expression [8,9], underscoring the importance of understanding the effects of multivalent counterions on polyelectrolyte brush [10,11]. Compared with uncharged polymer brushes in good or poor solvent, the electrostatic interaction and osmotic pressure, which are readily controlled by the salt concentration and pH, yield additional flexibilities in manipulating polyelectrolyte brushes, and thus holding promise for its wide applications [12,13].Conventional theoretical approaches, successful in explaining the behaviors of polyelectrolytes in monovalent salt solutions [11,14,15], are of limited use, particularly, when multivalent counterions are at work. For example, the solution to the mean-field PoissonBoltzmann theory [16] fails to account for phenomena such as ion condensation, charge over-compensation, and collapse of like-charged polymers [17][18][19][20].…”

Gene Expression on DNA Biochips Patterned with Strand‐Displacement Lithography

“…[15] Figure 3illustrates the attachment of DIS strands to areas or lines exposed to various electron doses (electrons per area or length). Since this technique does not require am ask and is not restricted by the diffraction limit of light, ebeam lithography is especially suited for fast prototyping of fine patterns with line widths on the order of around 100 nm.…”

Genexpression auf DNA‐Biochips: Strukturierung durch Strangverdrängungs‐Lithographie

“…Bephore kann außerdem mit noch höherer Auflösung mittels Elektronenstrahllithographie strukturiert werden. Da diese Technik keine Masken benötigt und in der Auflösung nicht durch die Beugung von Licht beschränkt ist, eignet sie sich im Besonderen zur schnellen Erzeugung von feinen Teststrukturen mit Linienbreiten in der Größenordnung von ≈100 nm . Abbildung zeigt die Anbindung von DIS‐Strängen an Flächen und Linien, die mit verschiedenen Elektronendosen (Elektronen pro Fläche bzw.…”