This Project Grant award from the National Institutes of Health's National Human Genome Research Institute provided $768,678 to Molecular Assemblies, Inc. to develop a fully enzymatic oligonucleotide synthesis cycle using engineered template-independent polymerases and a novel phosphate dNTP blocking group. The award supports the goals of the Human Genome Research program (CFDA 93.172) to accelerate genome research and its application to human health. Specifically, the awardee will engineer...
This Project Grant award from the National Human Genome Research Institute (CFDA 93.172 - Human Genome Research) provides $452,375 to The Trustees of Columbia University in the City of New York to develop a platform for rapid and efficient generation of multi-site sequence variants using template-guided gene synthesis. The project aims to advance this synthesis approach by optimizing predictive algorithms, experimental protocols, and robotic automation to produce kilobase-sized DNA constructs up...
This Project Grant award from the National Science Foundation (CFDA 47.084 - NSF Technology, Innovation, and Partnerships) provides $274,932 to Femtofluidics Incorporated to develop hardware that can rapidly and inexpensively synthesize DNA-encoded libraries (DELs) for accelerating drug discovery. The goal is to build a device that can perform combinatorial chemistry on nanoliter to picoliter volume droplets using an electronic substrate, without any moving or mechanical parts. This technology...
Triton Systems, Inc. received a $249,712 Project Grant award from the Department of Energy Office of Science on February 22, 2021 to develop a fast, scalable, automated, one-pot process for assembly of DNA oligonucleotides into large gene sequences. The work will be performed in Chelmsford, Massachusetts through February 21, 2022. The award is being made under the Office of Science Financial Assistance Program (CFDA #81.049), which supports basic research to deliver scientific discoveries and...
This Project Grant award from the National Science Foundation (NSF) Computer and Information Science and Engineering (CISE) program (CFDA 47.070) provides $500,000 to the Regents of the University of California at Riverside over a 3-year period from July 2025 to June 2028. The goal of the project is to develop new methods for improving de novo genome assembly, which is the computational process of reconstructing an organism's complete genomic sequence from fragmented DNA data. The research...
This Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training Program (CFDA 93.859) provides $394,857 to the University of Nebraska to develop a system to protect and concentrate large DNA molecules for genome analysis. The project aims to: Develop an inverted insert to protect DNA during cell lysis. Develop a roadblock to concentrate chromosomal DNA. The goal is to create a method to protect and concentrate large DNA molecules...
Micropure Genomics Inc. received a $274,199 Project Grant award from the National Science Foundation to advance methods for rapid, end-to-end sample preparation for sequencing applications. Under the NSF Technology, Innovation, and Partnerships program (CFDA 47.084), the company will develop an automated process relying on electro-hydrodynamic trapping to isolate genomic material like DNA or RNA from cells in a flow cartridge. The process aims to significantly reduce preparation time while...
This three-year, $930,252 Project Grant from the National Science Foundation's Division of Computing and Communication Foundations, under the Computer and Information Science and Engineering program, will support research exploring applications of digital microfluidic technology for DNA storage, computation, and synthetic biology. A team from the University of Minnesota will leverage an electronic platform developed by industrial partner Seagate to manipulate droplets and assemble DNA at...
This $350,000 Project Grant award from the National Institute of General Medical Sciences (NIGMS) Biomedical Research and Research Training program (CFDA 93.859) supports the development and demonstration of a novel, enzyme-based, single-molecule protein sequencing system by Electronic Biosciences, Inc. The innovative platform aims to leverage enzymatic processing and advanced bioinformatics to enable scalable, multiplexed protein sequencing with high accuracy and throughput. During this Phase I...
The National Human Genome Research Institute (NHGRI), under the Human Genome Research Federal Grant Program (CFDA 93.172), awarded a $384,418 Project Grant to Xgenomes Corp. on September 25, 2024 to develop a revolutionary DNA sequencing platform. The project aims to create a super-resolution single-molecule sequencing technology that can read short sequence "words" rather than individual nucleotides, enabling one or more orders of magnitude improvements in accuracy and cost over...
MULTIPLEXED IN VIVO DNA ASSEMBLY - PROJECT SUMMARY/ABSTRACT HIGH-THROUGHPUT AND LOW-COST SYNTHESIS OF LONG DNA FRAGMENTS COULD OPEN UP NEW FRONTIERS IN GENOMICS AND SYNTHETIC BIOLOGY BY FACILITATING THE PRODUCTION OF GENES, GENETIC PATHWAYS, VARIANT LIBRARIES, OR ENTIRE SYNTHETIC GENOMES. MICROARRAY PRINTING TECHNOLOGIES PROVIDE FOR HIGH-THROUGHPUT AND LOW-COST SYNTHESIS OF SHORT OLIGONUCLEOTIDES (CURRENTLY UP TO 300 BASES LONG), WHILE NEW TECHNOLOGIES, SUCH AS ENZYMATIC SYNTHESIS, HAVE THE POTENTIAL TO SYNTHESIZE LONGER SEQUENCES. LIBRARIES OF OPEN READING FRAMES OR REGULATORY ELEMENTS HAVE ALSO BEEN CONSTRUCTED. HOWEVER, ASSEMBLY OF THE ABOVE OR OTHER DNA ELEMENTS INTO LONGER FRAGMENTS REMAINS A CHALLENGE. WIDELY-USED IN VITRO DNA ASSEMBLY METHODS, SUCH AS GIBSON ASSEMBLY AND POLYMERASE CHAIN ASSEMBLY, REQUIRE CONSIDERABLE HANDS-ON TIME, ARE DIFFICULT TO MULTIPLEX AND SCALE, AND HAVE SIZE CONSTRAINTS ON THE LENGTH OF THE ASSEMBLED PRODUCT. IN ADDITION, ACCURATE LONG ASSEMBLIES FROM DE NOVO SYNTHESIZED DNA ARE DIFFICULT TO ACHIEVE WITHOUT A HIGH-THROUGHPUT ERROR CORRECTION STEP. TO OVERCOME THESE HURDLES, WE HAVE DEVELOPED A NOVEL, MULTIPLEXED METHOD TO PARSE, SEQUENCE VERIFY, AND STITCH TOGETHER DNA OF VARIOUS SIZES IN VIVO. USING THIS METHOD, COMPLEX POOLS OF ARRAY-SYNTHESIZED OLIGONUCLEOTIDES OR OTHER DNA ELEMENTS CAN BE TURNED INTO POSITIONALLY-ORDERED CELLULAR ARRAYS, WITH EACH POSITION CONTAINING A SEQUENCE-VERIFIED INPUT DNA. INPUT DNA IN THESE ARRAYS CAN THEN BE STITCHED TOGETHER RECURSIVELY BY BACTERIAL MATING. A KEY FEATURE OF OUR TECHNOLOGY IS EARLY ERROR DETECTION, WHEREBY INDIVIDUAL DNA INPUTS ARE SEQUENCE-VERIFIED PRIOR TO STITCHING. THAT IS, ERRORS THAT OCCUR DURING SHORT DNA SYNTHESIS ARE DETECTED AND REMOVED, RATHER THAN PROPAGATED INTO LONGER ASSEMBLIES. AT MAXIMAL THROUGHPUT, WE ESTIMATE THAT OUR TECHNOLOGY HAS THE POTENTIAL TO PRODUCE THOUSANDS OF DNA ASSEMBLIES IN PARALLEL AT A COST THAT IS AT LEAST AN ORDER OF MAGNITUDE CHEAPER THAN COMMERCIALLY AVAILABLE GENE SYNTHESIS TECHNOLOGIES. BECAUSE DNA STITCHING CAN OCCUR WITHIN BACTERIAL ARTIFICIAL CHROMOSOMES, IN VIVO DNA PARSING AND STITCHING CAN PERFORM MULTIPLEXED ASSEMBLY OF DNA CONSTRUCTS EXCEEDING 100KB, AT LEAST AN ORDER OF MAGNITUDE LONGER THAN CURRENT IN VITRO ASSEMBLY TECHNIQUES. IN VIVO ASSEMBLY USES A STEPWISE STITCHING PROCESS THAT CAN BE BRANCHED, ALLOWING THE CONSTRUCTION OF A WIDE VARIETY OF VARIANTS AT LOW INCREMENTAL COST. HERE, WE PROPOSE TO CONTINUE DEVELOPMENT OF THIS TECHNOLOGY I) BY BUILDING MANY GENES TO LEARN THE ERROR MODALITIES OF THE PROCESS, II) BY ASSEMBLING A ~100KB PRODUCT, AND III) BY DEVELOPING A MULTI-STEP ASSEMBLY PROCEDURE TO REDUCE ASSEMBLY TIME AND INCREASE PRODUCT ACCURACY. TOGETHER, THIS INTEGRATED SET OF AIMS WILL RESULT IN A NEW HIGH-THROUGHPUT DNA ASSEMBLY PLATFORM CAPABLE OF SYNTHESIZING LONG AND COMPLEX DNA CONSTRUCTS AND VARIANT LIBRARIES AT LOW COST.