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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.

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.

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.

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.

Tissue targeting and cargo packaging limitations are two of the most challenging barriers to in-vivo therapeutic delivery. Overcoming both of these issues, UC Berkeley researchers have developed engineered immune cells that produce enveloped delivery vehicles (EDVs) capable of encapsulating protein and/or RNA therapeutics that can be delivered to a target cell with a predetermined trigger. Triggers can either be the presence of a small molecule, or recognition of a specific antigen on the target cell. The researchers showed that delivery can be achieved in a co-cultured system using various strategies and that the system is compatible with multiple cargo proteins of interest including Cre recombinase and RNA-complexed Cas proteins. This technology opens possibilities for broader and safer in-vivo therapeutic delivery.

This technology introduces a novel class of synthetic genetic polymers, capable of enhancing protein target binding and mimicking antibodies, for therapeutic and diagnostic applications.

Achieving durable engraftment and spatial localization of engineered microbes in complex environments, such as the gut microbiome, has been a persistent challenge. Current methods to select and isolate engineered microbes in the lab rely on antibiotic-based selection systems, which are unsuitable for in vivo applications due to safety concerns, environmental risks, and regulatory hurdles. Moreover, these methods lack the precision needed for selective recovery and targeting within diverse microbial communities.  UC Berkeley researchers have developed an innovative framework that integrates plasmid-based systems and CRISPR-associated transposase systems (CASTs) to enable precise delivery of genetic cargoes encoding surface display systems. These systems, when expressed, allow engineered microbes to display modular binding domains capable of interacting with a range of targets, including but not limited to host associated mucus and magnetic particles. This modularity expands the toolkit for selective enrichment, spatial targeting, and functionalization of engineered microbes in diverse contexts. For example, modified microbes can be magnetized for recovery through magnetic separation or equipped with binding domains to interact with other substrates or biomolecules, unlocking targeted applications in microbiome engineering, therapeutic delivery, and biomanufacturing. This approach not only enables the enrichment and spatial targeting of engineered microbes within complex communities, such as those in the gut, but also provides a versatile method for isolating bacterial strains or directing microbes to specific niches without relying on antibiotics. By combining plasmid modularity with the precision and stability of CASTs, the platform establishes a robust and adaptable solution for microbiome modulation. 

Researchers from UC San Diego developed a new technology that facilitates pooling of nuclear expressed antisense RNAs (NEARs) to identify consequential RNA processing events such as alternative or constitutive RNA splicing or polyadenylation.This technology will identify a phenotype of interest and/or a group of RNA processing events (for example RNA splicing sites of interest or alternatively spliced exons), and transduce cells with a library of NEARs targeting these events. Applications include: Normal 0 false false false EN-US X-NONE X-NONE MicrosoftInternetExplorer4 /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0in 5.4pt 0in 5.4pt; mso-para-margin:0in; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman",serif;} Research tool. As screens to identify exons of phenotypic relevance in a high throughput manner.Therapeutic target identification. To identify therapeutic targets of cancer cell suppression, such as poison exons in cancer specific transcripts.Therapeutic discovery. As a therapeutic agent to identify therapeutic NEARs for splicing related disorders.  

Existing RNA-targeting tools for sequence-specific manipulation include anti-sense oligos (ASOs), designer PUF proteins and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas systems. However, there are significant limitations to each of the current tools. ASOs are usually not available for most RNA manipulations other than gene silencing. Designer proteins, such as PUF (Pumilio and FBF homology protein), possess low RNA recognition efficiency and it remains challenging to target RNA sequences >8-nucleotides (nt) in length. The bulky Cas protein (Cas13d: average 930 amino acids) leads to complication for transgene delivery and concerns of its immunogenicity due to its bacterial origin. Mutants of zinc finger(ZnF) proteins in ZRANB2 recognize a single-strand RNA containing a novel GGG motif with micromolar affinity, compared to the original motif GGU. These mutants serve as a foundation for RNA-binding ZnF designer protein engineering for in vivo RNA sequence-specific targeting.ZnFs are generally compact domains (~3kDa each) that have been successfully engineered for DNA recognition as modular arrays. A ZnF-based system has unique advantages, especially in a therapeutic context: (1) Broad application with the possibility to fuse with other effector domains; (2) High efficiency of RNA recognition (3 RNA bases recognized per 30-amino-acid ZnF) with a small size of protein. Only 4 ZnFs (~100 aa) is required for specific targeting in the transcriptome. (3) Humanized components without immunogenic concern.By engineering new sequence specificity of the ZRANB2 ZnF1, researchers from UC San Diego identified 13 mutants that altered their preferred RNA binding motif from GGU to GGG. They are N24R, N24H, N14D/N24R, N14D/N24H, N14R/N24R, N14R/N24H, N14H/N24R, N14H/N24H, N14Q/N24R, N14Q/N24H, N14E/N24R, N14S/N24R, N14E/N24H.

Hybridization capture approaches allow targeted high-throughput sequencing analysis at reduced costs compared to shotgun sequencing. Hybridization capture is particularly useful in analyses of genomic data from ancient, environmental, and forensic samples, where target content is low, DNA is fragmented and multiplex PCR or other targeted approaches often fail. Hybridization capture involves the use of "bait" nucleotides that capture genomic sequences that are of particular interest for the researcher. Current bait synthesis methods require large-scale oligonucleotide chemical synthesis and/or in vitro transcription. Both RNA and DNA bait generation requires synthesizing template oligonucleotides using phosphoramidite chemistry. Microarray-based synthesis generates oligonucleotides in femtomole scales with high chemical coupling error rates. Templates synthesized at small-scale require enzymatic amplification before use in hybridization capture.The solution proposed here involves a simple and highly efficient method to generate target probes using isothermal amplification. Target sequences are circularized and then amplified by rolling circle amplification. This method generates concatemers comprising thousands of copies of the target seqeuence. Restriction digestion of the amplified product then produces probes to use in target enrichment applications. 

Lipid Nanoparticles (LNPs) are a leading platform for nucleic acid delivery, widely used in therapeutics and vaccine development. However, the process of optimizing new LNP formulations has been significantly hindered by labor-intensive and costly screening methods, which require individual injections into animal models. Given the vast array of potential lipid compositions and formulation variables, these constraints severely impede the efficiency of research and development.To overcome these challenges, UC Berkeley researchers have developed a novel approach for identifying and characterizing functional nucleic acid delivery vehicles. This innovative method leverages circular RNA barcoding technology, enabling a more efficient screening process. Instead of relying on conventional cell sorting techniques, which restrict screening to specific organs and host species, this breakthrough allows direct detection of barcoded nucleic acids within circular RNAs in treated cells. By analyzing the barcodes detected, researchers can accurately determine which lipid compositions and formulations successfully delivered RNA molecules.  This technology represents a significant advancement in LNP research, offering a scalable, cost-effective solution that enhances the precision and scope of nucleic acid delivery screening.

A novel bioluminescent platform for in vivo tracking and visualization of RNA dynamics without the need for excitation light.

Professor Hideaki Tsutsui and colleagues from the University of California, Riverside have developed a portable handheld device for nucleic acid extraction. With its high-speed motor, knurled lysis chamber for rapid sample lysis, and quick nucleic acid extraction using paper disks, this device can yield ready-to-use extracts in just 12 minutes, significantly reducing the time required for sample preparation. This technology is advantageous over current methods as it can be expedited without the need for cumbersome specimen collection, packaging, and submission, shortening the turnaround time.  

Researchers at the University of California, Davis have developed a method and composition for modifying genetic sequences using Adenosine deaminases that act on RNA (ADARs).

This invention addresses the challenge of delivering macromolecules and other therapeutic cargo into the cell's cytoplasm by overcoming the endosomal membrane barrier. The innovation, developed by UC Berkeley researchers, involves improved versions of the ZF5.3 peptide. These improved peptide variants significantly enhance the efficiency of endosomal escape. This advancement provides a more effective and reliable method for intracellular delivery compared to existing alternatives, which often suffer from low efficiency or significant toxicity.

The invention is a self-selection DNA editing system for modifying microbial communities. It consists of a gene editing tool and a donor DNA with a bacteriocin unit. This unit is integrated into the target cell's genome, providing a survival advantage and ensuring that only the successfully modified cells proliferate. This allows for precise, targeted editing of microbial populations in various settings, including in vitro and in vivo environments.

This innovation addresses the limitations of producing proteins with non-natural monomers (NNMs), which have valuable applications in drug discovery and materials science. Researchers at UC Berkeley have developed novel PylRS-tRNAPyl pairs that enable the efficient incorporation of NNMs into proteins. This technology provides a significant advantage over existing methods by offering a broader range of NNM incorporation with high specificity and efficiency.Provided are compositions and methods for creating proteins that contain non-natural monomers (NNMs) using new PylRS-tRNAPyl pairs.  This technology works by introducing a subject PylRS, a tRNA, and an NNM into a host system, such as a bacterial cell, eukaryotic cell, or an in vitro translation system, allowing the tRNA to be acylated with the NNM by the PylRS.

      Raman spectroscopy, the inelastic scattering of light off molecular vibrations or solid- state phonons, is a critical method in chemical analytics, biological imaging, and materials or even art characterization. A common method for signal enhancement is surface enhanced Raman spectroscopy (SERS), where noble metal or dielectric nanostructures locally enhance the incoming and/or scattered field. SERS has found wide-spread applications in bio- analytics, fundamental science, viral and bacterial classification, and the study of tissue samples. Yet, obstacles towards more wide-spread adoption with wider scope are poor SERS substrate reproducibility and local hotspot fluctuations of metallic SERS substrates, and background emission from molecules, analytes, hot electrons, plasmons, or carriers in dielectrics that can significantly interfere with small signals of target analytes in SERS.       UC Berkeley researchers have developed an improved method for SERS that simultaneously minimizes spurious background emission, minimizes local heating even under high excitation powers, and maximizes the Raman signal enhancement of dielectric SERS substrates. Together these advantages render the method a powerful contender for sought after quantitative SERS and reliable analyte and single- molecule detection without fluctuations or other perturbations from SERS substrates. This enables commercially relevant usage, particularly in the biosciences and diagnostics, DNA/RNA sequencing, protein sequencing, determination of biomolecular binding constants, interconversion kinetics between biomolecular conformers, post-translational modifications, determination of molecular folding statuses, and classification of different proteoforms. It further has commercial potential in environmental monitoring, food safety, semiconductor inspection, polymer quality control and research, quality control in pharmaceuticals – including vesicles for drug delivery-, materials science, and physical science research.

Although viral delivery of CRISPR genome editors is the most widely used method for in vivo cell editing, viral vectors can be immunogenic, carry the risk of vector genome integration and can induce off-target DNA damage due to continuous genome editor expression. Lipid-nanoparticle (LNP):mRNA complexes are non-virally derived vehicles for in vivo delivery that have provided for genome editing in the liver. However, developing LNP:mRNA complexes that can edit non-liver tissues remains a challenge.  UCB researchers have created new LNP compositions and methods for delivery that have increased efficiency for delivering a molecular payload such as CRISPR-Cas effector proteins, guide RNAs, and/ nucleic acids encoding same.