Abstract: A heterochiral strand displacement molecular circuit generally includes an input oligonucleotide, a first translator, a second translator, and an output oligonucleotide. The first translator generally includes a domain that binds to the input binding oligonucleotide, at least a portion of which is complementary to, and has the same chirality as, the input oligonucleotide. The first translator also includes a translation domain having chirality opposite the chirality of the input oligonucleotide (and the binding domain). The second translator generally includes a nucleotide sequence, at least a portion of which is complementary to, and has the same chirality as, the translation domain of the first translator. The output oligonucleotide includes a nucleotide sequence, at least a portion of which is complementary to, and has the same chirality as, the second translator.

Abstract: The invention is directed to a hybrid architecture that comprises a stacked autoencoder and a deep echo state layer for temporal pattern discovery in high-dimensional sequence data. The stacked autoencoder plays a preprocessing role that exploits spatial structure in data and creates a compact representation. The compact representation is then fed to the echo state layer in order to generate a short-term memory of the inputs. The output of the network may be trained to generate any target output.

Abstract: This disclosure describes a structured polynucleotide, devices that include the structured polynucleotide, and methods involving the structured polynucleotide and/or devices. Generally, the structured polynucleotide includes five domains. A first domain acts as a toehold for an input DNA logic gate to initiate binding to an SCS biomolecule. A second domain acts as a substrate recognition sequence for an upstream DNA logic gate. A third domain acts as a toehold for a output DNA logic gate to initiate binding of the SCS biomolecule to the gate. A fourth domain acts as an effector sequence to alter the state of the output logic gate. A fifth domain acts as a cage sequence to lock the effector sequence in an inactive state until an input gate binds to the structured polynucleotide.

Abstract: The invention is directed to a hybrid architecture that comprises a stacked autoencoder and a deep echo state layer for temporal pattern discovery in high-dimensional sequence data. The stacked autoencoder plays a preprocessing role that exploits spatial structure in data and creates a compact representation. The compact representation is then fed to the echo state layer in order to generate a short-term memory of the inputs. The output of the network may be trained to generate any target output.

Abstract: This disclosure describes a structured polynucleotide, devices that include the structured polynucleotide, and methods involving the structured polynucleotide and/or devices. Generally, the structured polynucleotide includes five domains. A first domain acts as a toehold for an input DNA logic gate to initiate binding to an SCS biomolecule. A second domain acts as a substrate recognition sequence for an upstream DNA logic gate. A third domain acts as a toehold for a output DNA logic gate to initiate binding of the SCS biomolecule to the gate. A fourth domain acts as an effector sequence to alter the state of the output logic gate. A fifth domain acts as a cage sequence to lock the effector sequence in an inactive state until an input gate binds to the structured polynucleotide.

Abstract: This disclosure describes a structured polynucleotide, devices that include the structured polynucleotide, and methods involving the structured polynucleotide and/or devices. Generally, the structured polynucleotide includes five domains. A first domain acts as a toehold for an input DNA logic gate to initiate binding to an SCS biomolecule. A second domain acts as a substrate recognition sequence for an upstream DNA logic gate. A third domain acts as a toehold for a output DNA logic gate to initiate binding of the SCS biomolecule to the gate. A fourth domain acts as an effector sequence to alter the state of the output logic gate. A fifth domain acts as a cage sequence to lock the effector sequence in an inactive state until an input gate binds to the structured polynucleotide.

Abstract: The development of the first solution-phase molecular assembly comprising over 100 molecular logic gates, which more than quadruples the complexity performed by any previous system. “MAYA-II” is a second generation molecular automaton capable of playing a complete game of tic-tac-toe against a human opponent, and encompasses 76 permissible game plays. MAYA-II is more user-friendly than MAYA-I, as it signals both players move in a two-color output system and imposes no constraints on the position of the human player's first move. MAYA-II is constructed from three classes of stem-loop controlled deoxyribozyme-based logic gates that are allosterically modulated by input oligonucleotides to produce fluorescent output signals.

Abstract: Compositions and methods for optically detecting the presence of a plurality of oligonucleotides in a sample, wherein each oligonucleotide to be detected comprises consecutive nucleotides having a sequence different than the remaining oligonucleotides of the plurality are provided.