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D&D‑seq Uses Base Editing to Map DNA–Protein Interactions in Single Cells
A new molecular recording strategy is giving researchers a way to capture DNA–protein interactions in single cells, including the weak and transient contacts that shape gene regulation but often slip past existing assays. The method, called D&D‑seq (docking and deamination followed by sequencing), layers a base‑editing enzyme onto an antibody‑binding nanobody, turning fleeting interactions into durable sequence marks.
The paper is titled “Single-cell mapping of regulatory DNA-protein interactions,” and was published recently in Cell.
“D&D-seq couples an antibody-binding nanobody to a cytosine base editor, a combination that enables detection of weak or transient factor binding through targeted cytosine-to-uracil [C→U] editing at protein-bound genomic sites,” the authors wrote. Those edits become a molecular breadcrumb trail, revealing where regulatory proteins have interacted with the genome.
This approach directly addresses a long‑standing gap in the field. Traditional methods for mapping transcription factor binding, such as ChIP‑seq or CUT&RUN, “cannot be easily incorporated into high-throughput single-cell workflows, limiting applications to bulk analysis or to single-cell profiling of only the strongest interacting chromatin factors. Single-cell profiling of TF binding in primary samples has been mainly restricted to inferential approaches based on expression levels of downstream TF target genes or through motif analysis of assay for transposase-accessible chromatin using sequencing (ATAC-seq) peaks, but identification of specific TF-binding sites requires more direct methods,” according to the authors.
The team demonstrated that D&D‑seq can map binding sites for transcription factors and other regulatory proteins, like chromatin remodeling proteins, across multiple cell types and conditions. One application involved profiling CTCF binding in primary T cells carrying an IDH2 mutation commonly found in leukemia. Because D&D‑seq operates at single‑cell resolution, it exposes heterogeneity in regulatory wiring that is often masked in population‑level assays.
Crucially, the method is platform‑agnostic. The authors showed that D&D‑seq can be integrated into standard single‑cell multiomics workflows, including ATAC‑seq, scATAC‑seq, and whole‑genome sequencing. That compatibility allows researchers to pair DNA–protein interaction maps with chromatin accessibility, gene expression, and genomic variation—all within the same cell.
As transcription factors and other regulatory proteins increasingly emerge as therapeutic targets, tools that reveal how these factors behave in patient‑derived cells will be essential. D&D‑seq offers a way to monitor how mutations, drugs, or engineered perturbations reshape regulatory landscapes at single‑cell resolution.
“We’re entering an era of medicine in which transcription factors and other gene-activity regulators will increasingly be therapeutic targets,” said Dan Landau, MD, PhD, the Bibliowicz Family professor of medicine and a member of the Sandra and Edward Meyer Cancer Center and the Englander Institute for Precision Medicine at Weill Cornell, who is also an oncologist at NewYork-Presbyterian/Weill Cornell Medical Center. “This kind of technology should have an important role in developing and evaluating such therapies.”
Although the method is still evolving, its conceptual elegance and technical flexibility have already sparked broad interest. By turning DNA into a recording surface for protein activity, D&D‑seq opens a new window into the “regulome”—one that captures the subtle, transient interactions that drive cellular identity and disease.
The post D&D‑seq Uses Base Editing to Map DNA–Protein Interactions in Single Cells appeared first on GEN – Genetic Engineering and Biotechnology News.
You know when you are at the eye doctor getting an updated prescription, and suddenly the world snaps into sharper focus? Physicists at the University of California (UC), Berkeley, have now done something similar for electron microscopy. By introducing phase contrast into a cryo‑electron microscope, they have delivered dramatically sharper images of some of biology’s smallest and most elusive proteins.
The advance comes from a new laser phase plate (LPP), described in the paper “Laser phase plate improves structure determination of small proteins by cryo‑EM,” which was published recently in Science. Led by physicist Holger Mueller, PhD, of UC Berkeley and Lawrence Berkeley National Laboratory, the team demonstrated that a laser‑driven phase plate can overcome one of cryo‑EM’s most persistent limitations: poor contrast for small proteins.
Cryo‑EM has transformed structural biology over the past decade, earning a Nobel Prize in 2017 for enabling high‑resolution structures without crystallization. But despite its impact, the technique still struggles with proteins below ~70 kilodaltons—a size range that includes about 90% of the human proteome. “Because of signal-to-noise limitations, the majority of human and animal proteins are too small to be analyzed by these methods [cryo-EM and cryoelectron tomography]. The increase in signal-to-noise ratio provided by this laser phase plate is expected to overcome these important limitations.”
The new LPP begins to address that problem. The LPP uses an intense, continuous‑wave laser to shift the phase of the electron beam itself. This produces true phase contrast without dimming or destabilizing the beam. Mueller described the laser focus as “75 kilowatts focused to a few microns… That’s more powerful than what you use for welding. It has more power than a military laser. It builds up the brightest continuous laser focus ever.”
Installed in a custom Thermo Fisher Titan Krios, the LPP immediately improved the clarity and resolvability of small proteins, including hemoglobin, which sits at the lower limit of what today’s cryo‑EM instruments can handle. As the authors wrote in the abstract: “Here, we show that the laser phase plate (LPP)… enhances the resolution in single-particle reconstruction of small proteins by improving specimen-motion correction, recovery of information from the early frames, as well as particle visualization, 3D classification, and alignment.”
These improvements were achieved using standard defocus ranges and reconstruction workflows. “For the most challenging cases—small particles, bad specimens—the laser produces a very considerable advantage,” Mueller said.
The impact extends beyond single‑particle analysis. Cryo‑electron tomography (cryo‑ET), which assembles multiple angular views of a molecule or protein into a three-dimensional image, stands to benefit even more. “With cryo-ET, we’re looking at small, very complicated cellular material that’s incredibly crowded inside the cell,” said Bridget Carragher, PhD, founding technical director of imaging at Biohub. “It’s like a forest of trees, and you’re trying to find one leaf on one tree in there. Cryo-ET needs a dramatic step forward in contrast, so we can start to see what’s going on inside the cell. That’s what the laser phase plate promises to give us.”
Biohub is developing a dual‑laser version of the system, designed to reduce component wear and minimize aberrations. Meanwhile, Mueller’s team is pushing toward imaging proteins as small as 17 kilodaltons, a threshold that would open access to vast regions of the human proteome previously invisible to cryo‑EM.
“This technology is a step function change for biology,” said Stephani Otte, PhD, Biohub’s vice president of imaging science. “What was once invisible will become visible—and that changes everything about how we understand disease.”
“The bottom line is, if you have a large protein and a really good sample—a fresh one or one frozen without bubbles, for example—you may not need the phase plate to get a single, high-quality image. But for a small protein and a bad sample, laser-on is best,” Mueller said. “This could fill an enormous gap in our knowledge of protein structures that can’t be crystallized or are too small for today’s cryo-EM. And it will be revolutionary for cryo-ET.”
The post Laser‑Driven Phase Contrast Enhances Cryo‑EM Resolution of Small Proteins appeared first on GEN – Genetic Engineering and Biotechnology News.
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STAT+: Updated: Tracking RFK Jr.’s promises to remake health in America
Updated June 11, 2026
WASHINGTON — A pledge to “Make America Healthy Again” earned Robert F. Kennedy Jr. his job atop U.S. health agencies a year and some change ago. He’s now had the opportunity to turn his words into action, with mixed results.
“All one needs” to prove the health secretary’s attentiveness is to “review my unprecedented list of accomplishments on a wide range of issues, all of which I drove,” Kennedy posted on X on Wednesday in response to a journalist.
Updated June 11, 2026
WASHINGTON — A pledge to “Make America Healthy Again” earned Robert F. Kennedy Jr. his job atop U.S. health agencies a year and some change ago. He’s now had the opportunity to turn his words into action, with mixed results.
“All one needs” to prove the health secretary’s attentiveness is to “review my unprecedented list of accomplishments on a wide range of issues, all of which I drove,” Kennedy posted on X on Wednesday in response to a journalist.
Can any of the new obesity medications in development stand out from the pack? Which company just broke records with its IPO? And will the Food and Drug Administration allow greater access to experimental peptides?
We discuss all that and more on this week’s episode of “The Readout LOUD,” STAT’s biotech podcast.
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