Reconfigurable DNA triplex structure for pH responsive logic gates

Abstract

We constructed pH-responsive logic gates through substrate conformational change that uses two types of logic calculations, ‘AND’ and ‘OR’. Our logic gates necessitate fewer substrates when two types of logic calculations are needed.

Dynamics of terminal fraying–peeling and hydrogen bonds dictates the sequential vs. cooperative melting pathways of nanoscale DNA and PNA triplexes

“…The ultimate goal is to understand the behavior and dynamics of interactions in more intricate self-assembly and disassembly of nanostructures toward their applications for constructing nucleic acid based functional nanodevices. 78–83…”

Lipid vesicle-based molecular robots

“…Importantly, the group demonstrated the circuit's ability to compute the floor of the square root of a four-bit binary number, enabling digital logic networks to be compiled into DNA-based implementations. Moreover, circuits with unique functions, for example, DNA circuits with enhanced reaction speed, responsiveness, and robustness using the cationic polymer, poly( l -lysine)- graft -dextran, 200 in addition to temporal DNA circuits that can respond to both the presence and history of a molecular environment, 201 and pH-responsive switchable DNA circuits 202 have all been reported. Through such cascading, scaling, and additional functionalization, DNA circuits can potentially attain the capabilities of reliable computation, precise error correction, and automated circuit compilers, ultimately achieving a computational behaviour reminiscent of electronic computers in wet biological environments.…”

DNA Logic Gates Integrated on DNA Substrates in Molecular Computing

“…Most common Boolean logic gates accept one or more inputs and produce ON or OFF output signals, conditioned by a set of rules known as truth table (Figure 2e). Even though DNA logic gates can identify as inputs a myriad of biomolecules (ions, [42] small molecules, [43] nucleic acids, [11] and peptides [41] ) as well as non‐molecular stimulus (temperature, [44] electromagnetic force, [45] and pH [46] ), input and output homogeneity are necessary among each logic gate for their intercommunication. DNA allows for this input/output homogeneity using DNA sequences as inputs and outputs, which interact with the DNA logic gates by formation and/or dissociation of base pairs.…”