Researchers at the University of California, Davis have developed a targeted gene editing system that reactivates the silenced CDKL5 gene by precise epigenetic modulation to treat CDKL5 deficiency disorder (CDD).

A breakthrough in synthetic biology: an evolved DNA polymerase that synthesizes natural and modified RNA, paving the way for advancements in epigenetics, vaccine development, and drug discovery.

Researchers at the University of California, Davis have developed advanced epigenetic methods and systems that detect and assess developmental risks in embryos caused by maternal stress prior to conception.

RNA-guided systems mediate diverse functions ranging from mobile genetic element propagation to adaptive immunity. These systems comprise proteins that use guide RNAs bearing sequence complementarity to nucleic acid substrates, facilitating programmable recognition of different substrates by the same protein or enzyme. In RNA-guided systems known to date, one or two continuous segments in the guideRNA determines target specificity and can be altered to direct the system to a new target, including genomic DNA in eukaryotic cells. However, there are constraints to such systems, e.g., protein size and the need for a protospacer adjacent motif (PAM) in target DNA. However, there is a need for nucleic acid guided systems that overcome constraints of known systems, such as protein size or protospacer adjacent motif.UC Berkeley researchers have developed a programmable RNA-guided nucleic acid targeting platform termed the Viral Interference Programmable Repeat (VIPR) system. The system employs a repeat-based guide RNA architecture and an associated targeting protein to direct sequence-specific recognition of nucleic acid substrates. Target specificity is programmable through modification of selected guide regions, enabling adaptable targeting of DNA or RNA substrates across different biological contexts, including cellular and viral genetic material.

A highly precise and efficient gene-editing tool designed to correct single-nucleotide DNA mutations responsible for genetic diseases.

RNA-guided DNA targeting systems have fundamentally changed the landscape of genomic research and therapeutic development, yet the large size of traditional CRISPR tools creates a "delivery bottleneck" for therapeutic vectors. While the TIGR-Tas protein family offers a compact alternative for streamlined delivery, naturally occurring TasR proteins often lack the cleavage efficiency required for complex biological environments. UC Berkeley researchers have overcome this by engineering high-performance variants of ParTasR. This system is approximately one-quarter the size of Cas9. The engineered proteins demonstrate significantly higher on-target cleavage activity than wild-type sequences, offering a potent and hyper-compact alternative for the next generation of in vivo genome editing. 

Brief description not available

Brief description not available

RNA editing enables safe, reversible, and dose-tunable genetic correction without the permanent genomic risks or cargo limits of traditional DNA editing. However, conventional RNA editing tools often lack the ability to perform precise, large-scale modifications or site specific cut and paste operations on transcripts, which limits their therapeutic and research utility. UC Berkeley researchers have developed a programmable RNA editing platform that utilizes Type III CRISPR-Cas complexes integrated with a ligase to generate chimeric RNA molecules. This method enables robust RNA trans splicing, allowing for the replacement of defective exons, the insertion of large genetic sequences into transcripts, and the creation of novel fusion proteins. This approach provides a transient and potentially safer method for correcting genetic errors at the transcript level while offering greater flexibility for large scale RNA engineering. 

Together with Researchers at the University of Texas at Austin, researchers at the University of California, Davis have developed a method for synthesizing long polynucleotides using scaffolded cooperative binding and enzymatic ligation to improve yield, modification compatibility, and assembly accuracy.

A novel method for detecting, diagnosing, monitoring, and treating gastrointestinal cancers by analyzing DNA methylation levels in patient samples.

Brief description not available

Brief description not available

When a delivered plasmid lacks exclusion genes during bacterial conjugation is a phenomenon known as lethal zygosis. The effect of this lethal zygosis is a severe bottleneck for genetic engineering. UC researchers have developed materials and methods that improve bacterial conjugation.  This replication incompetent vectors that include a nucleic acid sequence that can encode an exclusion polypeptide in a donor bacterial cell can protect a recipient bacterial cell from lethal zygosis.

Nucleic acids such as DNA and RNA find many different applications in research. They can act as research reagents, diagnostic agents, therapeutic agents, and more. Nucleic acids are made by enzymes, which are macromolecules that catalyze reactions. Since nucleic acids are so frequently used in research, there is continued interest in finding new and improved ways to synthesize them. Researchers at UC Santa Cruz have developed ways to continuously synthesize nucleic acids without the use of enzymes.

Researchers at the University of California, Davis have developed novel antisense oligonucleotide (ASO) therapies that enhance ADNP protein expression to address haploinsufficiency in ADNP syndrome.

Crop engineering is often limited by a poor understanding of plant regulatory architecture and the extreme rarity of natural activating mutations. To address this, UC Berkeley researchers developed a high-throughput pipeline using protoplast-based Massively Parallel Reporter Assays (MPRA) to screen thousands of cis-regulatory mutations simultaneously. This platform identifies specific "cis-genic" modifications - such as precise deletions and substitutions that tune gene expression to enhance complex traits like photosynthetic efficiency. By focusing on modifications that do not involve foreign DNA, this technology enables the rapid development of improved crop varieties that are currently unregulated by U.S statues for genetically modified organisms.

This technology represents a groundbreaking approach to treating Primary Open Angle Glaucoma by directly targeting the trabecular meshwork pathology with lipid nanoparticle-mediated delivery of gene editing tools or anti-sense oligos.

Manual interpretation of real-time quantitative PCR (RT-qPCR) data is prone to human error, noise, and variability, leading to potential misdiagnosis or test redundancies. UC Berkeley researchers have developed a novel deep learning framework that significantly improves diagnostic accuracy by fusing Long Short-Term Memory (LSTM) networks with Vision Transformers (ViT). This hybrid architecture captures both sequential fluorescence patterns and structural amplification dynamics from raw time-series data and image-based renderings. By leveraging a uniquely curated dataset of over 24,000 verified samples, the system accurately discriminates between true-positive and true-negative samples, predicts viral dilutions, and forecasts patient re-test outcomes, providing an objective tool for early triage and increased laboratory throughput.

CRISPR-derived nucleases offer unprecedented precision and ease of use for targeting specific genomic sites. However, the efficient delivery of gene editing tools into plant cells remains a significant hurdle. Current methods rely on a laborious and time-consuming tissue culture pipeline and can induce undesirable changes to the genome and epigenome. To circumvent these limitations, one alternative is to use plant viral vectors for the delivery of compact gene editors and their guide RNA (gRNA). UC Berkeley and UC Davis inventors found that the use of tobacco rattle virus (TRV) vectors to deliver reRNA and variant TnpB proteins to plants results in surprisingly high efficiencies of genome editing not only in the infiltrated cells, but also systemically (e.g., seeds and non-infiltrated leaves). Delivery via TRV caused systemic viral spread into the shoot apical and floral meristematic regions, leading to unexpectedly high efficiencies of genome editing in non-infiltrated cells (i.e., spread of genome editing), for example, surprisingly high efficiencies of genome editing in non-infiltrated systemic leaves as well as in the germline (e.g., seeds).

A novel RT assay for detecting chemical adducts on RNA, utilizing fluorescence quenching to indicate the presence of modifications.

A novel device leveraging centrifugal microfluidics to accelerate bacterial growth and rapidly determine antibiotic susceptibility.

Parkinson’s disease and related synucleinopathies currently lack disease-modifying cures, as existing treatments only manage symptoms associated with alpha-synuclein (aSyn) aggregation. To address this, UC Berkeley researchers have developed a suite of non-viral, CRISPR-mediated strategies designed for the permanent downregulation of the endogenous SNCA gene and the LRRK2 risk allele. By utilizing precise base editing of regulatory regions, genomic excision of non-coding sequences, and splicing modulation, this platform provides a durable, single-administration alternative to transient RNA-targeting therapies. The invention further enables allele-selective knockout of the LRRK2 G2019S mutation, employing a specialized CRISPR-Cas9 variant to discriminate between mutant and wild-type genes, thereby offering a highly specific and permanent therapeutic intervention for neurodegenerative disorders.

Achieving precise and tunable control over endogenous gene expression in eukaryotic cells remains a significant challenge, particularly for therapeutic applications or detailed biological studies where fine-tuning is required rather than complete on/off switching. This innovation, developed by UC Berkeley researchers, addresses this by providing a novel, programmable method for transcriptional tuning. The innovation is a two-domain fusion protein comprising the transcriptional repression domain (TRD) of the methyl-CpG-binding domain (MBD) protein MeCP2 linked to a dead Cas9 (dCas9) domain. When combined with a single guide RNA (sgRNA) that targets a specific endogenous gene, this fusion protein partially inhibits, or "tunes," the expression of that gene. Unlike traditional methods like RNAi or full CRISPR interference (CRISPRi), which often aim for complete knockdown, this system offers a highly specific and titratable way to dial down gene expression, providing a distinct advantage in studies requiring subtle modulation of gene dosage or for developing dose-dependent therapeutic strategies.

An engineered polymerase enabling the synthesis of threose nucleic acid (TNA) for advanced therapeutic applications.