When the Second Circuit decided McKithen v. Brown, it joined an ever-growing list of courts faced with a difficult and pressing issue of both constitutional and criminal law: is there a federal constitutional right of post-conviction access to evidence for DNA testing? This issue, which sits at the intersection of new forensic technologies and fundamental principles of constitutional due proces...

This paper describes a new method of retroactively programming a genetic circuit to exhibit the behavior of one of four logic gates (AND, OR, NAND, and NOR) using pulses of light. These pulses must occur after DNA transfection into the host cell. The pulses of light deactivate a photosensitive kinase, inhibiting phosphorylation. Using this effect, we can control the transcription of recombinase...

Gene regulatory circuits with different architectures (patterns of regulatory interactions) can generate similar dynamics. This raises the question of why a particular circuit architecture is selected to implement a given cellular process. To investigate this problem, we compared the Bacillus subtilis circuit that regulates differentiation into the competence state to an engineered circuit with...

Epigenetics is the study of heritable changes in gene expression without concomitant changes in DNA sequence. Due to its relevance in development, differentiation and human health, epigenetics has recently become an emerging area of science with regard to eukaryotic organisms and has shown enormous potential in synthetic biology. However, significant examples of epigenetic regulation in bacteri...

DNA circuits have proven to be useful amplifiers for diagnostic applications, in part because of their modularity and programmability. In order to determine whether different circuits could be modularly stacked, we used a catalytic hairpin assembly (CHA) circuit to initiate a hybridization chain reaction (HCR) circuit. In response to an input nucleic acid sequence, the CHA reaction accumulates ...

Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching transition between those states are compared with the theoretical estimation of the switching rate derived from the idea similar to the transition state theory. Eve...

We investigate computing models that are presented as families of finite computing devices with a uniformity condition on the entire family. Examples of such models include Boolean circuits, membrane systems, DNA computers, chemical reaction networks and tile assembly systems, and there are many others. However, in such models there are actually two distinct kinds of uniformity condition. The f...

The cover picture shows an enzyme-free nucleic acid synthetic circuit constructed by the toehold-mediated DNA strand displacement reaction, where a fold-change input (top left) elicits similar response (bottom right). This work is anticipated to shed new light on design of dynamic circuits. More information can be found in Research Article Hao Pei, Tong Zhu, and co-workers.

This paper presents a DNA based classification technique. It exploits the properties of the DNA as a quaternary logic with the advantages of better storage, better accuracy, and shorter time compared to binary logic. Several examples are employed to demonstrate using the DNA as a new classification method for differentiation between closely related objects such as boys and girls also we used ne...

Simple computations can be performed using the interactions between single-stranded molecules of DNA. These interactions are typically toehold-mediated strand displacement reactions in a well-mixed solution. We demonstrate that a DNA circuit with tethered reactants is a distributed system and show how it can be described as a stochastic Petri net. The system can be verified by mapping the Petri...