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.

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.

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

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

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).

      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. 

Optimizing the editing efficiency of CRISPR-mediated enzymes is still needed.  This is especially true in therapeutic use cases, when it would be ideal to attain high rates of editing via a low, transient dose of the enzyme in the ribonucleoprotein (RNP) format used for multiple ex vivo clinical trials. Because many CRISPR enzymes are of bacterial origin, fusion to NLS motifs can greatly enhance editing efficiency. However, CRISPR protein yields can decrease – sometimes dramatically – if the construct bears toomany NLSs. UC Berkeley researchers have developed CRISPR proteins with enhanced editing efficiencies by introducing multiple nuclear localization signal (NLS) fused at rationally selected sites within the backbone of CRISPR-Cas9. These Cas9 variants showed they can improve editing efficiency in T cells compared to constructs with terminally-fused NLS sequences and can be produced with high purity and yield.  

Before recombinant antibody expression plasmids can be designed, sequncing of the antibody light and heavy chain variable regions is necessary. Several other methods of sequencing antibody variable regions are available. Some involve high throughput RNA sequencing. These techniques are unavailable to many labs; they require the preparation of RNA-seq libraries, and computational analysis. As a result, the cost of performing such techniques is substantial and with sequencing cores being oversubscribed, turnaround can be as long as weeks to months. Other methods involve PCR and Sanger sequencing. However PCR amplification of variable regions results from difficulties in generating universal primers that can amplify any given variable region - particularly given the inherent low sequence identity in the 5' leader sequence of antibody light chains and heavy chains upstream of the variable regions. Sometimes degenerate primers can be used, but amplification success rate is only 80-90% due to non-specific priming and/or failure to prime at all. In addition, there is a significant risk that the variable regions of the parental myeloma line can amplify using the degenerate primers. 5' RACE (rapid amplification of 5' cDNA ends) can also be used, but mRNA degradation, cDNA purification and poly-A addition between reverse transcription and PCR, makes the technique long and difficult to perform. Non degenerate primers can be used, but each variable region requires multiple amplification attempts with different primer sets as well as sequence validation using mass spectrometry. And with both of these methods, primer derived mutations can be introduced. Mass spectrometry can be used to determine antibody variable regions, but these can result in ambiguous sequences because of isobaric residues such as isoleucine and leucine. But this method is time consuming, requires huge amounts of purified monoclonal antibody, is expensive and is inaccessible to most researchers. This technology involves a template switch reverse transcription of hybridoma RNA with at least three chain specific RT primers - one for the kappa chain, one for the lambda chain, and at least one for the heavy chain (for efficiency, this can be limited to IgG in a first pass). These are amplified in three separate PCR reactions and sequenced using Sanger sequencing.

TnpB protein has generated interest as a potential compact genome-editing tool, due to the short amino acid sequence (408 AAs for ISDra2 TnpB), which overlaps with the wRNA sequence in their genomes of origin. There is a need for compositions and methods that provide more efficient TnpB systems. UC Berkeley researchers have created variant TnpB proteins and variant wRNAs that increase cleavage activity and/or DNA binding activity (e.g., revealed as endonuclease activity such as on-target endonuclease activity). These variant TnpB proteins include an amino acid sequence having one or more amino acid substitutions relative to a corresponding wild type TnpB protein. Also provided are variant TnpB wRNAs that can form a complex with a TnpB protein and a second nucleotide sequence that can hybridize to a target sequence of a target nucleic acid, thereby guiding the complex to the target sequence.

Brief description not available

Various ubiquitin plasmids from Michael Rape lab, including but not limited to: pCS2-no his-ubiquitin wtpCS2-no his-ubiquitin all RpET30a-ubiquitin (no tag)pET30a-ubiquitin K0 (no tag) 

When model organisms are exposed to chemicals, resulting mutagenesis can provide insights on the chemical’s genotoxicity, which is an indicator of the chemical’s potential to cause cancer or birth defects. In fact, direct mutagenesis assays in bacteria are one of the three assays required by regulatory agencies for demonstrating the safety of potential clinical compounds. Mutagenesis assays are also used to study various DNA processes, such as replication, repair, damage tolerization, and homeostasis.

Researchers at the University of California, Davis have identified a short peptide which rapidly promotes protein degradation in cancerous enzymes and induces cell differentiation to kill lymphomas.

Researchers at the University of California, Davis have developed a virally derived homolog to increase the inflammatory response desirable in cancer immunotherapy.

Researchers at the University of California, Davis have developed a viral peptide therapeutic that targets MYC-based cancerous tumors.

Researchers at the University of California, Davis (“UC Davis”) have developed fusion proteins effective in inhibiting the replication of diverse groups of viruses that can be useful in controlling vector-borne virus transmission as well as reducing vector populations.

Presently, antiviral strategies are mostly focused on targeting viral proteins. However, the high mutation rates of RNA viruses, such as SARS-CoV-2, make the development of effective antiviral drugs very challenging. Disrupting viral-host interactions such as by targeting pro-viral, non-essential human genes will more likely prove effective against new variants or future coronavirus outbreaks.