University of California

Markus De Raad

Trent Russell Northen

John Christopher Anderson

David Sukovich

Benjamin P Bowen

Noel Seunghyun Ha

Oliver Ruebel

Curt R Fischer

Onur Erbilgin

Cyrus Modavi

Disclosed herein are systems and methods for associating metabolites with genes. In some embodiments, after potential metabolites are identified based on spectroscopy data of the content of an organism, possible reactions capable of producing the potential metabolites are determined. The possible reactions are compared to gene sequences in a database, and an association score for the likelihood that a gene sequence is related to the potential metabolites is calculated.

Metabolite, annotation, and gene integration system and method

Disclosed herein include systems, devices, and methods for droplet deposition for mass spectrometry. In some embodiments, a microfluidic device comprising wells is reversibly sealed to a mass spectrometry surface and used to deposit contents of droplets (e.g., enzymes and substrates), or products thereof, onto the mass spectrometry surface. The contents of droplets can be analyzed by laser desorption/ionization to, for example, identify a substrate of an enzyme or an enzyme capable of catalyzing a substrate to a product.

Picoliter droplet sample processing and deposition for mass spectrometry

Disclosed herein are methods, systems and compositions for determining substrate specificity of an enzyme. The disclosed methods, systems and compositions can be used for identifying enzymes capable of modifying substrates of interest and/or quantifying enzymatic activity.

Methods for determining gene functions

Traditional enzyme characterization methods are low-throughput, and therefore limit engineering efforts in synthetic biology and biotechnology. Here we propose a DNA-linked enzyme-coupled assay (DLEnCA) to monitor enzyme reactions in a high-throughput manner. Throughput is improved by removing the need for protein purification and by limiting the need for liquid chromatography mass spectrometry (LCMS) product detection by linking enzymatic function to DNA modification. DLEnCA is generalizable for many enzymatic reactions, and here we adapt it for glucosyltransferases, methyltransferases, and oxidoreductases. The assay utilizes cell free transcription/translation systems to produce enzymes of interest, while UDP-Glucose and T4-&#x3b2;-glucosyltransferase are used to modify DNA, which is detected post-reaction using qPCR or similar means of DNA analysis. For monitoring methyltransferases, consumption of SAM is observed by coupling to EcoRI methyltransferase. For monitoring oxidoreductases, consumption of NADH is observed by coupling to Taq orDNA ligase. OleD and two glucosyltransferases fromwere used to verify the assay's generality toward glucosyltransferases. Two methyltransferases from human andwere used to verify the assay's generality towards methyltransferases. We show DLEnCA's utility by mapping out the substrate specificity for these enzymes and observing the multiple steps of a biosynthetic pathway.

Growing community of inventors

Berkeley, CA, United States of America

Markus De Raad