Optically Controlled Signal Amplification for DNA Computation

Abstract

The hybridization chain reaction (HCR) and fuel-catalyst cycles have been applied to address the problem of signal amplification in DNA-based computation circuits. While they function efficiently, these signal amplifiers cannot be switched ON or OFF quickly and noninvasively. To overcome these limitations, a light-activated initiator strand for the HCR, which enabled fast optical OFF → ON switching, was developed. Similarly, when a light-activated version of the catalyst strand or the inhibitor strand of a fuel-catalyst cycle was applied, the cycle could be optically switched from OFF → ON or ON → OFF, respectively. To move the capabilities of these devices beyond solution-based operations, the components were embedded in agarose gels. Irradiation with customizable light patterns and at different time points demonstrated both spatial and temporal control. The addition of a translator gate enabled a spatially activated signal to travel along a predefined path, akin to a chemical wire. Overall, the addition of small light-cleavable photocaging groups to DNA signal amplification circuits enabled conditional control as well as fast photocontrol of signal amplification.

Optochemical Control of Biological Processes in Cells and Animals

“…[183] Similarly, light-controlled amplification circuits relying on toehold-mediated strand-displacement reactions have also been developed. [184] Optical control of DNA computation devices provides many opportunities for spatiotemporal detection of oligonucleotides involved in the development of diseases and other biological processes.…”

DNA Computing: NOT Logic Gates See the Light

“…While we have employed a single caging group type, the use of orthogonal caging groups has been reported for wavelength-selective oligonucleotide activation. − The development of new caging groups should allow the use of two or more caged NOT gates within the same circuit activated using different wavelengths of light at different time points. , DNA circuitry has been employed for a diverse set of functions including the programming of templated synthesis, nucleic acid transcription factors, CRISPR-Cas activity, miRNA imaging, ion sensing nanomachines, and RNA sensing DNA origami . Moreover, DNA logic gates have been employed in increasingly complex systems including within cellular environments. ,− By leveraging photochemical control, DNA strand displacement reactions triggered in a temporally and spatially controlled manner have been used in the interrogation of endogenous RNA, ,, signal amplification through HCR, , and activation of cellular signaling pathways through the assembly of cell surface receptors . As shown here, the temporal control introduced by photochemical manipulation of DNA circuitry can be used to precisely trigger strand displacement cascades thereby allowing the design and implementation of new DNA logic gates.…”

“…Photochemical methods of controlling biomolecule function offer the ability to regulate synthetic DNA and endogenous biological circuits spatially and temporally in a noninvasive manner. − Light-activated nucleic acid molecules that have been developed by us and others utilize photocaging groups that block Watson–Crick binding, thereby inhibiting base pairing and nucleic acid hybridization. Light-induced cleavage of caging groups from nucleobases has been used to externally trigger the function of antisense agents, splice switching oligonucleotides, triplex-forming oligonucleotides, antagomirs, siRNAs, , gRNAs, − hybridization chain reaction initiators, PCR primers, and DNA logic gates for in vitro and in cellulo applications. − Photochemical control of DNA hybridization is a precise tool that adds an additional layer of regulation to DNA computation circuits insulated from the rest of the circuit mechanisms.…”

Photochemical NOT Gate for DNA Computing

“…A nucleic acid light-control methodology that has been developed by us, 20 and others, 21 is the introduction of photocaging groups onto the Watson-Crick face of nucleobases thereby blocking base pairing and nucleic acid hybridization. Using this approach, light-induced cleavage of the caging groups has been used to externally trigger the function of antisense agents, 22 splice switching oligonucleotides, 23 triplexforming oligonucleotides, 24 antagomirs, 25 siRNAs, 26 gRNAs, 27 hybridization chain reaction initiators, 28 PCR primers, 29 and DNA logic gates for in vitro and in cellulo applications. 30,31 Photochemical control of DNA hybridization is a precise tool that adds an additional layer of regulation to DNA computation circuits that is insulated from the rest of the circuit mechanisms.…”