Cut and Paste for Cancer Treatment: A DNA Nanodevice that Cuts Out an RNA Marker Sequence to Activate a Therapeutic Function

Abstract

DNA nanotechnology uses oligonucleotide strands to assemble molecular structures capable of performing useful operations. Here, we assembled a multifunctional prototype DNA nanodevice, DOCTR, that recognizes a single nucleotide mutation in a cancer marker RNA. The nanodevice then cuts out a signature sequence and uses it as an activator for a “therapeutic” function, namely, the cleavage of another RNA sequence. The proposed design is a prototype for a gene therapy DNA machine that cleaves a housekeeping gene only in the presence of a cancer‐causing point mutation and suppresses cancer cells exclusively with minimal side effects to normal cells.

Manufacturing Reusable NAND Logic Gates and Their Initial Circuits for DNA Nanoprocessors

“…The output of the NAND gates can be detected either by an RNA‐cleaving Dz activity (Figure 2) or by a molecular beacon probe (Figure S4), which provides versatility in application. For example, the RNA‐cleaving function can be tailored for suppressing mRNA in gene therapy applications, [32, 33] while the MB probe can be used for monitoring the gate's outputs in a re‐usable format [21] . Indeed, the designed NAND gates could be re‐used at least five times in an RNase H‐containing buffer with the reset time of 5–7 min, which is limited by the catalytic activity of RNase H. The NAND gates could be stabilized by a covalent crosslink and isolated in a simple and robust procedure, which preserved the accurate digital response.…”

The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field

“…, quantum dots) that is synchronized with the activation of therapeutic responses inside diseased cells . The Kolpashchikov lab at the University of Central Florida uses strand displacement for the design of multistrand DNA nanodevices programmed to recognize single nucleotide variations, including in cancer marker RNAs . In addition, Marc Van Der Hofstadt at Laboratoire Jean Perrin, Sorbonne Université, has utilized DNA switches in a programmable extracellular medium that are active at 37 °C and can thus function in the presence of living cells .…”

“…49 The Kolpashchikov lab at the University of Central Florida uses strand displacement for the design of multistrand DNA nanodevices programmed to recognize single nucleotide variations, 50 including in cancer marker RNAs. 51 In addition, Marc Van Der Hofstadt at Laboratoire Jean Perrin, Sorbonne Universite, has utilized DNA switches in a programmable extracellular medium that are active at 37 °C and can thus function in the presence of living cells. 52 Nucleic acids' programmable organization, which was demonstrated by Oleg Gang's group at Columbia University and Brookhaven National Laboratory, has produced precise nucleic acid architectures 53 in the form of DNA nanochambers for organized arrays.…”

Rapid and Specific Imaging of Extracellular Signaling Molecule Adenosine Triphosphate with a Self-Phosphorylating DNAzyme

“…DNA can be chemically synthesized as a single-stranded polymer, which can form diverse structural arrangements to perform functions such as catalysis under confined conditions. − The first catalytically active DNA (referred to as deoxyribozyme or DNAzyme) was obtained by an in vitro selection technique in 1994 and cleaves RNA . To date, many other RNA-cleaving DNAzymes (RCDz) have been identified. − These RCDz generally require specific cofactors for catalysis, making them of great appeal for biosensing applications in clinical diagnostics, drug discovery, environmental monitoring, and nanodevices. − Since the first report of an RCDz sensor for intracellular metal imaging by Lu and co-workers, significant interest has been sparked in the use of RCDz as sensors and imaging agents for diverse targets in living cells and in vivo. − Although many achievements have been made with RCDz-based sensors for cell-based imaging, the temporal resolution (i.e., the speed at which a signal readout can be obtained) of these RCDz sensors is generally on the order of minutes and hours, − limiting their ability to accurately measure signaling molecules that take place within the second or subsecond time scale during cellular processes and rapidly evolving behaviors. Thus, it is highly desirable to derive fast-responsive DNAzyme sensors with high temporal resolution or rapid response kinetics…”