Scientists from the RNA Institute at the University of Albany (UAlbany) have developed new methods for designing and assembling DNA nanostructures that enhance their potential for use in various applications from medicine to materials science to data storage. Specifically, they can assemble these structures without the extreme heat and controlled cooling that is typically required.

They also showed that they could assemble these structures in several unconventional buffers including substances like nickel. Full details of the work are published in a new Science Advances paper titled, “Counter ions influence the isothermal self-assembly of DNA nanostructures.”

While DNA is most commonly recognized for its role in storing genetic information, it also works well for constructing nanoscale objects. Scientists can create precise structures as small as a few nanometers by programming DNA base pairs and engineering them into shapes with intricate architectures. These structures can be used to accurately place things like biomolecules, cells, and nanoparticles in the context of drug delivery and other use cases.

To create these structures, scientists usually have to heat and cool DNA strands in special buffer solutions that typically contain magnesium ions. This need for precise temperature control limits its use for practical applications in biomedicine for example. Also, DNA nanostructures assembled in magnesium can be unstable in biological environments.

The UAlbany team’s approach offers a way to assemble DNA nanostructures at moderate temperatures using metal ions other than magnesium. “We typically assemble DNA nanostructures by mixing the component DNA strands in a buffer solution, heating the solution to high temperatures, then cooling it down to lower temperatures,” explained Arun Richard Chandrasekaran, PhD, senior author on the study and a senior research scientist at the RNA Institute. With our approach, “DNA nanostructures can be assembled isothermally, that is, at constant moderate temperatures around 68°F or 98.6°F.”

Since their method does not require thermal cyclers or other heating equipment, “it simplifies the process of nanostructure synthesis and opens up the possibility of assembling these structures at constant temperatures,” he said.

Chandrasekaran and his colleagues have previously demonstrated the feasibility of using ions other than magnesium for nanostructure assembly including calcium, barium, sodium, potassium, and lithium at high temperatures. In the current study, they demonstrated that nickel and strontium could also be used with the important distinction that these ions work at moderate temperatures.

Being able to assemble DNA nanostructures at moderate temperatures will make it easier to construct DNA nanodevices for drug delivery and diagnostics using temperature-sensitive proteins like enzymes and antibodies. “Importantly, this work brings us closer to imagining how these nanostructures could actually be made and used in the human body for things like targeted drug delivery or precision diagnostics,” Chandrasekaran said. “While we still have a long way to go before this is possible, demonstrating DNA nanostructure assembly at body temperature is a promising step.”

Pancreatic cancer is one of the deadliest cancers worldwide, with a five-year survival rate of 13%. The poor prognosis is due in part both to late detection and the cancer’s capacity to adapt and resist therapy. Laboratory studies by researchers at the University of Verona, the University of Glasgow, and the Botton-Champalimaud Pancreatic Cancer Centre, have now implicated extrachromosomal DNA (ecDNA) carrying the MYC oncogene as a hidden driver of this adaptability.

“Pancreatic cancer is often called a silent killer because it’s hard to detect until it’s too late,” said Peter Bailey, PhD, director of translational research at the Botton-Champalimaud Pancreatic Cancer Centre. “We know that part of its lethality arises from the ability of tumor cells to ‘shape shift’ under stress. Our study shows that ecDNA forms a big part of that story.” Bailey is co-corresponding author of the team’s published paper in Nature, titled “MYC ecDNA promotes intratumor heterogeneity and plasticity in PDAC.” In their paper the researchers’ stated, “Collectively, our work establishes MYC ecDNAs as a key driver of genomic plasticity in PDAC, where they promote rapid and flexible adaptation by amplifying oncogenes, creating heterogeneity, and enabling reversible phenotypic changes.”

Intratumor heterogeneity and phenotypic plasticity drive tumor progression and therapy resistance, the team wrote. However, “… the genetic mechanisms underlying phenotypic heterogeneity are still poorly understood.” For their newly reported study, the investigators sequenced a large panel of patient-derived organoids (PDOs), finding that some pancreatic cancer cells gain a major survival edge by carrying copies of critical cancer genes—such as MYC—on circular pieces of DNA that exist outside of the chromosomes that house most of our genetic material.

These ecDNA genetic rings are free in the cell nucleus, enabling tumor cells to swiftly ramp up gene expression, change their shape, and survive in otherwise hostile environments. The researchers discovered ecDNA to be surprisingly common in pancreatic tumors, particularly for oncogenes like MYC, which drives cancer growth and metabolism. “… we provide a detailed analysis of ecDNAs in PDAC,” they noted. “We have demonstrated that ecDNAs are a major source of high-level amplifications in key PDAC oncogenes and a major contributor to MYC heterogeneity in PDAC.”

Elena Fiorini, PhD, co-first author and senior postdoc, explained, “We saw far more variability in MYC copy number when MYC was on ecDNA. Some cells carried dozens—or even hundreds—of extra MYC copies, giving them a large growth advantage under certain conditions.” The authors further noted, “PDOs and tissues harboring MYC on ecDNA displayed significant heterogeneity of MYC copy number and expression, compared with tumors having MYC on chromosomal DNA.”

Such flexibility underscores the profound intratumor heterogeneity characteristic of pancreatic cancer, where myriad sub-populations coexist and respond differently to treatment. Targeting one subset often fails against another, fueling resistance. “… Overall, we found a heterogeneous landscape of genomic amplifications in PDOs and that ecDNA tumors display features of more biologically aggressive disease,” the team pointed out.

Added Daniel Schreyer, co-first author and a former University of Glasgow PhD student, “It’s effectively a ‘bet-hedging’ strategy. You get pockets of cells that carry very high MYC levels, which is beneficial under certain conditions, and others with fewer copies, which might do better in another environment—all within the same tumor.”

A key advantage of this study is that the organoids—mini-3D replicas of pancreatic tumors grown in the lab—were derived directly from patients with early-stage disease. These organoids preserve much of the genetic make-up of the original tumor, making them excellent testbeds for studying cancer. Unlike methods that artificially introduce ecDNA, these lab models reflect genuine ecDNA variants found in real tumors.

“This approach offers real-world insight into how dynamic and disordered a tumor can be,” said Fiorini. “We see firsthand that even when two patients both have MYC on ecDNA, the structure of that circular DNA can differ substantially—leading to big variations in MYC expression.”

To see how ecDNA drives adaptation, the researchers grew patient-derived organoids and removed vital growth signals—such as WNT factors—and then observed how these organoids responded to the stress. “We found that organoids bearing MYC on extrachromosomal DNA could shift their dependency on WNT,” explained Antonia Malinova, PhD, co-first author and a former PhD student at the University of Verona. “Essentially, cells with high levels of ecDNA became more self-sufficient, no longer needing those external signals to survive.”

The authors stated, “Our analysis revealed that MYC amplification on ecDNA provides a deterministic mechanism for rapid environmental adaptation. A WNT-depleted culture environment drove the rapid selection of cells carrying from dozens to hundreds of ecDNA molecules that could proliferate independently of stromal signals.”

The study also revealed a clear link between high MYC levels and changes in tumor cell shape and behavior. When MYC ecDNA levels soared, cells morphed into more aggressive, solid structures—losing their more organized, gland-like architecture. “Here, we show that extrachromosomal DNA (ecDNA) is a major source of high-level focal amplification in key oncogenes and a major contributor of MYC heterogeneity in pancreatic ductal adenocarcinoma (PDAC),” the investigators stated.

“What’s remarkable,” said co-corresponding author Vincenzo Corbo, PhD, from the University of Verona, “is how rapidly these ecDNA-based copies can appear or disappear depending on the environment. If the cancer is under pressure—say, lacking key growth factors—cells with ecDNA can crank up MYC expression to survive. But if that pressure lifts, they can lose some of these extra DNA circles to avoid the downsides of carrying too many copies.”

Indeed, expressing MYC at high levels can trigger DNA damage, forcing cancer cells to carefully balance the costs and benefits of ecDNA retention. “That was unexpected,” said Corbo. “It challenges the assumption that more MYC is always better for a cancer cell—there’s a real fitness cost to maintaining such high levels.”

Although extrachromosomal DNA only appears in about 15% of patient samples in the reported study, that subset might be particularly aggressive or prone to therapy resistance. As a result, detecting or disrupting ecDNA could open new therapeutic windows. “We might imagine a strategy that exploits the vulnerabilities introduced by ecDNA,” noted Corbo. “Perhaps pushing cancer cells to dial MYC up to a point where they can’t handle the DNA damage, or blocking the molecular circuits that maintain these DNA rings so cells lose them altogether.”

However, the authors caution that such ideas remain early-stage. “ecDNA is a double-edged sword—helpful for quick adaptation but costly to maintain,” Corbo pointed out. “The challenge is to tip that balance in favor of the patient.”

The new work broadens our understanding of genomic plasticity—challenging the notion that the genome is always “fixed.” “We knew the tumor’s surroundings could drive changes, but not that WNT signaling could so directly rewrite DNA,” Bailey commented. “We assumed we’d see mostly epigenetic shifts, so seeing this level of genomic re-engineering was definitely a surprise.”

And with pancreatic cancer cases projected to rise in the coming years, insights into ecDNA’s role could guide future strategies to intercept or exploit this genetic feature—potentially making tumors more vulnerable to treatment.

Recently, scientists have been able to explore gene circuitry in individual cells using methods that suppress particular genes and measure the impact on the expression of other genes. These methods, however, fail to capture spatial information such as the effects from, or on, neighboring cells, which can provide important clues to a cell or gene’s role in health and disease.

Now, a technology developed in the Spatial Technology Platform at the Broad Institute of MIT and Harvard builds on these methods with cutting-edge spatial advances. Their method, known as Perturb-FISH, combines imaging-based spatial transcriptomic measurements with large-scale detection of CRISPR guide RNAs.

The researchers demonstrated Perturb-seq’s ability to uncover new cellular and functional insights, including the effects of autism-related genes on cellular activity and the interactions between human tumor and immune cells in an animal model. Further refinements to Perturb-FISH could make it even more widely accessible and enable a range of new biological investigations. The technology and demonstrations of its utility are published in Cell.

“With Perturb-FISH, we’ve developed a powerful new way to examine the roles of genes and genetic circuits in tissue development, homeostasis, and dysfunction,” said co-senior author Sami Farhi, director of the Spatial Technology Platform at the Broad Institute.

“Our team is dedicated to devising spatial tools for the benefit of the scientific community, and we hope this new method is just the first of many more that we’ll build and share.” Farhi led the work along with co-senior author Brian Cleary, a former Broad Fellow and Merkin Institute Fellow who is now an assistant professor at Boston University.

Gone FISH-ing

Previously, researchers had combined single-cell RNA sequencing with CRISPR screening to examine gene networks within cells using tools such as Perturb-seq, but the cells’ spatial context wasn’t captured. Another method known as optical pooled screening measures the effects of gene-editing perturbations on cell fitness or other phenotypes, but doesn’t capture gene transcriptional states.

Scientists in the Spatial Technology Platform aimed to develop a comprehensive method that could measure at once which genes are altered in a cell, which genetic perturbation caused the changes, and the location of those affected cells in relation to other cells.

Key developments that made Perturb-FISH possible were computational methods developed by Cleary and a new way of amplifying the signal from single molecules (either CRISPR guide RNAs or gene transcripts) so they can be detected over background levels of fluorescence.

Traditional amplification methods don’t work with molecules as small as guide RNAs, so first author and former postdoctoral researcher Loϊc Binan devised an innovative strategy to generate many local copies of each guide RNA at its original site. By combining that with a fluorescence-based spatial transcriptomic method called MERFISH, Perturb-FISH can reveal both the identity of each perturbation and the cell’s transcriptome in their spatial context.

Researchers at Kumamoto University have successfully executed a practical trial of a new genome-editing technique that allows for the partial inhibition of essential gene function without causing lethality. This innovative approach, which leverages CRISPR-Cas9 technology, opens new doors for genetic research and agricultural advancements by enabling the study and modification of genes that were previously difficult to analyze.

Genes that are crucial for survival often pose a challenge for researchers, as completely disabling them can be fatal to the organism. Traditional gene knockout methods, including CRISPR-Cas9, typically result in complete loss of function, making it difficult to investigate these vital genetic components.

To address this limitation, the research team led by Associate Professor Takashi Ishida, Faculty of Advanced Science and Technology, Kumamoto University, conceived a method to introduce hypomorphic mutations, which reduce—but do not entirely eliminate—gene function.

Using the model plant Arabidopsis thaliana, the team successfully applied their method to the HPY2 gene, which is essential for cell division and plant growth. While complete loss of this gene results in seedling lethality, the newly engineered hypomorphic mutants exhibited delayed growth but remained viable, paving the way for researchers to analyze gene function in greater detail in future studies.

Applications for agriculture and beyond

This breakthrough, published in the Journal of Plant Research, has significant implications beyond basic genetic research. By fine-tuning gene activity instead of completely disabling genes, this technique could be used to enhance desirable traits in crops without causing harmful side effects. For example, modifying genes responsible for stress resistance in plants could lead to crops that are more resilient to climate change while maintaining their growth and yield.

“This method provides a powerful tool for studying genes that were previously inaccessible due to their essential nature,” said Associate Professor Ishida. “It also opens up new possibilities for precision breeding in agriculture, where controlled gene modification is key to improving traits without unintended consequences.”