Sequence, Shape, Function: Synthetic Biology by DNA

Hendrik Dietz
Technische Universität München, Germany

Many processes in biology rely fundamentally on the relative position and orientation of interacting molecules. It is notoriously difficult to observe, let alone control, the position and orientation of molecules because of their small size and the constant thermal fluctuations that they experience in solution. Molecular self-assembly with DNA provides a route for placing molecules and constraining their fluctuations in user-defined ways, thereby opening attractive avenues for scientific and technological exploration. In the three parts of my talk I will provide evidence for this statement:
(1) Positional Control – The field has faced scepticism regarding its viability for creating objects with sufficient order and homogeneity to confer utility. I will present a high-resolution 3D structure of a discrete DNA based object that is twice the size of a prokaryotic ribosome [1]. The structure confirms structural order in synthetic DNA objects that is comparable to those found in proteins and supports a perspective in which chemical motifs may be arranged with precise structural specifications through an iterative strategy of DNA-templated design and 3D structural feedback. By using chemical groups attached to DNA strands or even reactive motifs formed by DNA itself, this strategy offers an attractive route to achieving complex functionalities known today only from natural nanomachines.
(2) Practical Assembly – In recent years, design strategies for encoding complex target shapes in DNA sequences have flourished, but the practical assembly of desired objects has often been quite difficult. I will show that, at constant temperature, hundreds of DNA strands can cooperatively fold a long template DNA strand within minutes into complex nanoscale objects [2]. Folding at optimized constant temperatures enabled the rapid production of DNA objects with yields that approached 100%, thereby opening attractive prospects for converting DNA-based self-assembly into a real-world manufacturing technique.
(3) Application – Finally, I will present synthetic lipid membrane channels that we created from self-assembled DNA nanostructures [3]. In single-channel electrophysiological measurements, we found similarities to the response of natural ion channels, such as conductances on the order of 1 nanosiemens and channel gating. More pronounced gating was seen for mutations in which a single DNA strand of the stem protruded into the channel. Single-molecule translocation experiments show that the synthetic channels can be used to discriminate single DNA molecules.
[1] Bai et al, PNAS, Dec 4 2012;
[2] Sobczak et al, Science, Dec 14, 2012;
[3] Langecker et al, Science, Nov 16 2012

Back to Molecular diagnostics (1)
Bookmark the permalink.

Comments are closed.