pH-responsive and switchable triplex-based DNA hydrogels

New methods for the preparation of reversible pH-responsive DNA hydrogels based on Hoogsteen triplex structures are described. One system consists of a hydrogel composed of duplex DNA units that bridge acrylamide chains at pH = 7.4 and undergoes dissolution at pH = 5.0 through the reconfiguration of one of the duplex bridging units into a protonated CG·C⁺ triplex structure. The second system consists of a hydrogel consisting of acrylamide chains crosslinked in the presence of an auxiliary strand by Hoogsteen TA·T triplex interaction at pH = 7.0. The hydrogel transforms into a liquid phase at pH = 10.0 due to the separation of the triplex bridging units. The two hydrogel systems undergo reversible and cyclic hydrogel/solution transitions by subjecting the systems to appropriate pH values. The anti-cancer drug, coralyne, binds specifically to the TA·T triplex-crosslinked hydrogel thereby increasing its stiffness. The pH-controlled release of the coralyne from the hydrogel is demonstrated.     

Logic gates and elementary computing by enzymes

Different selected enzymes, glucose oxidase (GOx), catalase (Cat), glucose dehydrogenase (GDH), horseradish peroxidase (HRP), and formaldehyde dehydrogenase (FDH), are used alone or coupled to construct eight different logic gates. The added substrates for the respective enzymes, glucose and H(2)O(2), act as the gate inputs, while the biocatalytically generated gluconic acid or NADH are the output signals that follow the operation of the gates. Different enzyme-based gates are XOR, INHIBIT A, INHIBIT B, AND, OR, NOR, Identity and Inverter gates. By combining the AND and XOR or the XOR and INHIBIT A gates, the half-adder and half-subtractor are constructed, respectively, opening the way to elementary computing by the use of enzymes.     

Probing of enzyme reactions by the biocatalyst-induced association or dissociation of redox labels linked to monolayer-functionalized electrodes

The activities of the enzymes tyrosinase and thrombin are probed by the association of the ferrocene boronic acid label to the enzyme-generated catechol ligand, and by the cleavage of the ligand-redox complex tethered to a peptide, respectively.     

An electrochemical/photochemical information processing system using a monolayer-functionalized electrode

An electroactive and photoisomerizable monolayer associated with a Au electrode acts as a Write-Read-Erase information processing system and as a flip-flop Set/Reset memory element.     

Probing biocatalytic transformations with CdSe-ZnS QDs

CdSe/ZnS QDs enable the optical probing of the biocatalytic oxidation of tyrosine derivatives and of the scission of peptides by thrombin. CdSe/ZnS QDs were modified with tyrosine methyl ester or with a tyrosine-containing peptide. The tyrosine units were reacted with tyrosinase/O2 to yield the respective l-DOPA and quinone derivatives. The luminescence of QDs modified by the enzyme-generated quinone units is quenched. The quinone-functionalized peptide associated with the QDs was cleaved by thrombin, a process that restored the luminescence of the QDs.     

DNA-based machines

Nucleic acids include substantial information in their base sequence and their hybridization-complexation motifs. Recent research efforts attempt to utilize this biomolecular information to develop DNA nanostructures exhibiting machine-like functions. DNA nano-assemblies revealing tweezers, motor, and walker activities exemplify a few such machines. The DNA-based machines provide new components that act as sensitive sensors, transporters, or drug delivery systems.