Self-Assembly of DNA Arrays into Multilayer Stacks

• Published in: Langmuir Vol. 25; no. 2; pp. 1091 - 1096
• Main Authors: Koyfman, Alexey Y, Magonov, Sergei N, Reich, Norbert O
• Format: Journal Article
• Language: English
• Published: Washington, DC American Chemical Society 20-01-2009
• Subjects: Aluminum Silicates - chemistry; Chemistry; Colloidal state and disperse state; DNA - chemistry; Exact sciences and technology; General and physical chemistry; Lipid Bilayers - chemistry; Magnesium - chemistry; Materials: Nano-and Mesostructured Materials, Polymers, Gels, Liquid Crystals, Composites; Microscopy, Atomic Force; Oligonucleotide Array Sequence Analysis - methods; Particle Size; Surface physical chemistry; Surface Properties; Self assembly; Atomic force microscopy; Shape; Multilayer; Multiple layer; Bilayer; Rotation; Close packing; Stack; Packing; DNA; Aggregate; Structure; Pattern analysis; Mica
• ISSN: 0743-7463; 1520-5827
• DOI: 10.1021/la801306j

We describe the self-assembly of multilayer hexagonal DNA arrays through highly regular interlayer packing. Slow cooling of a mixture of three single-stranded DNA sequences with various Mg2+ concentrations leads to the self-assembly of diverse multilayer architectures. The self-assembled aggregates were deposited onto mica surfaces and examined with atomic force microscopy. The size of the two-dimensional arrays and subsequent stacking to form multilayer structures are highly dependent on Mg2+ concentration. DNA bilayers and multilayers of defined shape are favored in 2−5 mM Mg2+ with an average lateral size of 700 nm. Arrays are much larger (up to 20 μm across) in 10−15 mM Mg2+, although multiple layers still make up 20−60% of the observed structures. Domains within single layer architectures were identified using Moiré pattern analysis. Distinct structural phases within the multilayer assemblies include two layers translated by 17.5 nm and interlayer rotations of 20° and 30°. Three layer assemblies have cubic close packing and taller multilayer architectures of 2D DNA sheets were also identified.