Scientists are looking for ways to make these programmable nanodevices operate stably inside living cells. If successful, they will revolutionize the way we interact with and control living beings at the molecular level, with DNA strand displacement circuits gradually approaching becoming cellular machines.
The journal Intelligent Computing recently published an article titled "From Test Tube to Cell: The Regression of DNA Computational Circuits?" From the Test Tube to the Cell: A Homecoming for DNA Computing?), outlining significant advances in introducing DNA computing circuits into living cells. The authors describe how dynamic nanodevices powered by DNA strand displacement reactions can quickly be computed, sensed, and controlled in real time within biological systems – opening the door to a new generation of "molecular robots" that interact directly with the cellular environment.
At the heart of this technology is the DNA strand displacement circuit, which is a key component of dynamic DNA nanotechnology. These circuits employ a foothold-mediated strand displacement technique: an incoming DNA strand binds to a short, exposed region called a foothold, and then replaces the existing DNA strand through branching migration.
Basic systems such as seesaw gates and hybridization chain reactions enable complex logic operations and signal amplification, while co-gates require multiple inputs to produce outputs, enabling complex control. These individual elements can be combined into a larger network that simulates a formal chemical reaction pathway. DNA strand replacement technology can also be attached to structural nanodevices such as DNA origami and DNA assembly, enabling controlled shape changes and expanding their biological applications.
On the left, preassembled DNA circuits in vitro are delivered to living cells. On the right, the RNA anterior portal autonomously transcribes from a chromosome or plasmid and then converts into a functional RNA circuit. Either way, functional circuits sense the transcriptional and metabolic state of the cell and perform signal integration and other calculations that ultimately activate a variety of biological processes such as post-transcriptional gene regulation. Image credit: Hyeyun Jung et al.
According to the authors, "DNA strand replacement reactions can be triggered by biological components such as nucleic acids, small molecules, proteins, and ions. "Nucleic acids, such as DNA and RNA, can be applied to transcriptome analysis and live-cell monitoring using complementary substrate designs as direct inputs. Input detection can be achieved with aptamers, which are single-stranded nucleic acid sequences that bind to a target or ligand with high affinity and specificity.
To connect aptamers to DNA strand displacement modules, various methods such as structure switching aptamers, association footings, hidden footings, remote footings, transient footings, chemical ligation, metal footing, and DNases have been developed to ensure precise signal transduction from biological targets to downstream circuits.
At present, DNA strand replacement is mainly used in vitro, and its application in vivo faces many challenges, such as rapid degradation of DNA-degrading enzymes. To enhance stability, the researchers explored end-guard structure modifications such as hairpin structures and protein binding sites, as well as chemical modifications such as 2'-O-methylation.
Since most cells are inherently rejective of DNA, delivery of these nanodevices into cells requires specialized techniques such as transfection methods and transformation protocols. Once in the cell, cellular factors such as salt concentration, molecular crowding, and heterogeneous environment can all affect the chain replacement reaction. To overcome the limitations of direct delivery, researchers are also developing transcribable RNA nanodevices encoded into plasmids or chromosomes, allowing cells to express these circuits.
DNA strand replacement has been applied to innovations in computational models. By combining the computational principle with DNA strand substitution, the structured algorithms of traditional computation can be combined with stochastic biochemical processes and chemical reactions in biological systems to achieve biocompatible computational models. In the future, DNA strand replacement technology may enable autonomous DNA nanomachines to precisely control biological processes, thereby advancing healthcare and life science research.
編譯自/ScitechDaily