Algorithms Seminar

Speaker: Abdulmelik Mohammed

Title: Designs and algorithms for folding DNA into custom
nanoscale polyhedra

Over the past 30 years, DNA has been adopted as a novel nanoscale construction material because of its programmable sequence and its exquisitely specific Watson-Crick base pairing rules. DNA origami is a popular recent technique in DNA nanotechnology for the design and
synthesis of nanoscale shapes and patterns. DNA origami operates by
the folding of a single long viral strand of DNA called a scaffold with the help of numerous shorter synthetic strands. Although DNA origami has been successfully employed for assembling a variety of 2D structures, its application to 3D structures so far has been
limited to one-off designs.

In this work, we introduce a general algorithmic approach and a
software pipeline for generating DNA origami strand designs of
user-presented polyhedral meshes.

One of the strengths of this approach lies in formulating the design
criteria in precise graph-theoretic terms, which in turn facilitates its
algorithmic treatment and full automation. In this regard, we show that
the problem of routing the scaffold according to the design criteria
relates to finding topologically restricted Eulerian circuits called
A-trails.

The overall success of the design strategy is validated by experimental synthesis of several irregular structures including the Stanford bunny, one of the most famous computer graphics 3D models.

Host: Petteri Kaski