Programmable energy landscapes for kinetic control of DNA strand displacement

DNA strand displacement reaction for programmable release of biomolecules.

Sample cleanup is a major processing step in many analytical assays. Here, we propose an approach to capture-and-release of analytes based on the DNA strand displacement reaction (SDR) and demonstrate its application to a fluoroimmunoassay on beads for a thyroid cancer biomarker, thyroglobulin. The SDR-based cleanup showed no interference from matrix molecules in serum.

Supporting Information DNA Strand Displacement Reaction for Programmable Release of biomolecules

Space and Energy Efficient Computation with DNA Strand Displacement Systems

Chemical reaction networks (CRN’s) are important models of molecular programming that can be realized by logically reversible, and thus energy efficient, DNA strand displacement systems (DSD’s). Qian et al., [12] showed that energy efficient DSD’s are Turing-universal; however their simulation of a computation requires space (or volume) proportional to the number of steps of the computation. He...

Control of DNA strand displacement kinetics using toehold exchange.

DNA is increasingly being used as the engineering material of choice for the construction of nanoscale circuits, structures, and motors. Many of these enzyme-free constructions function by DNA strand displacement reactions. The kinetics of strand displacement can be modulated by toeholds, short single-stranded segments of DNA that colocalize reactant DNA molecules. Recently, the toehold exchang...

Two-Domain DNA Strand Displacement

We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose restrictions on the single strands they interact with: we consider only two-domain single strands consisting of one toehold domain and one recognition domain. We study ...