Bottom-up Fabrication of Functional DNA Nanostructures
Doctoral thesis, 2012

This thesis demonstrates bottom-up fabrication of a fully addressable non-repetitive network on the nanometer scale, assembled by synthetic DNA molecules. Each side constitutes a unique sequence of 10 bases, i.e. 3.4 nm in length, and can be considered the smallest practical unit of DNA in a nanotechnological context. Working with units of this length scale ensures a system fit for non-mundane molecular nanotechnology. The thesis features a progressive growth of the nanostructure, from the formation of the single-ringed hexagonal unit-cell to an asymmetric four-ring network of 17 nodes. Each structure is formed in a one-step self-assembly reaction. Alongside construction of the DNA-based nanostructural template, the thesis also illustrates three different aspects of functionalization. Firstly, a fixation strategy infusing stability in the delicate network by chemical ligation. The click chemistry based strategy will pave the way for modular build-up of larger nanostructures. Results show that multiple site-specific click reactions can perform simultaneously and independently of each other on a hybridized DNA template. Fixated modules are resistant to denaturing agent and can be freeze-dried. The second important aspect is incorporation of these DNA nanoconstructs onto lipid bilayers, for development of soft-surface nanotechnology. This creates controllable new interfaces in an aspiration towards membrane-integrated applications, e.g. mimicking a photosynthetic reaction centre. This thesis features two different molecular anchors: a multi-functional porphyrin moiety and a more universal lipid anchor. Both anchors are shown to align a DNA nanostructure with the membrane surface, a conformational arrangement that also depends on position of anchoring points. The last theme of this thesis is triplex recognition as a method for site-specific functionalization of preformed DNA nanostructures. The specific function of energy transfer is demonstrated in a simple photonic device, which can be switched ON and OFF by slight adjustment of pH. This DNA-based nanoscopic system is envisioned as a platform for high-precision control over molecular processes towards nanotechnological applications. It is part of an ambition in molecular nanoscience to fabricate systems from the bottom-up, based on principles of self-assembly and with functional complexity on levels not achievable by a conventional top-down perspective to nanoscience. The great leap of molecular nanoscience stems from inspiration of biological systems. New advancement in technological progress is possible by harvesting benefits of Darwinian evolution.

click chemistry

gel electrophoresis



lipid membrane


linear dichroism





triplex recognition

Opponent: Professor Friedrich C. Simmel


Erik Lundberg

Chalmers, Chemical and Biological Engineering, Physical Chemistry

A new fixation strategy for addressable nano-network building blocks

Chemical Communications,; Vol. 46(2010)p. 3714-3716

Journal article

Soft-Surface DNA Nanotechnology: DNA Constructs Anchored and Aligned to Lipid Membrane

Angewandte Chemie - International Edition,; Vol. 50(2011)p. 8312-8315

Journal article

Addressable high-information-density DNA nanostructures

Chemical Physics Letters,; Vol. 440(2007)p. 125-129

Journal article

Triplex addressability as a basis for functional DNA nanostructures

Nano Letters,; Vol. 7(2007)p. 3832-3839

Journal article

Jag visar i den här avhandlingen hur vi genom smart molekylär design kan konstruera ett DNA-baserat ”nano-pussel” som lägger sig självt. De unika molekylära byggstenarna som utgör grunden för dessa strukturer är organiska DNA-molekyler som är programmerade att organisera sig i specifika sexkantsmönster. Genom att använda minsta möjliga byggstenar har jag skapat strukturer som tänjer på den undre gränsen av vad som tidigare varit möjligt. Syftet med dessa nanostrukturer är att skapa ett intelligent material som kan fungera som ramverk för många molekylära processer, exempelvis artificiell fotosyntes för miljövänlig bränsleproduktion. Jag demonstrerar därför bland annat hur energi kan transporteras mellan olika specifika punkter i strukturen, något som också skulle kunna leda till ljusbaserade kretsar. Inspirerad av hur naturen knyter många biokemiska processer till lipidmembran, har jag även tagit fram metoder att integrera DNA-nanostrukturer med sådana ytor vilket skapar nya intressanta möjligheter för att exempelvis skapa syntetiska reaktionscentra. (ej fulltext)

Areas of Advance

Nanoscience and Nanotechnology (2010-2017)

Subject Categories

Chemical Sciences



Doktorsavhandlingar vid Chalmers tekniska högskola. Ny serie: 3328


Opponent: Professor Friedrich C. Simmel

More information