[ { "id": "https://authors.library.caltech.edu/records/tbn7q-sa464", "eprint_id": 120382, "eprint_status": "archive", "datestamp": "2023-08-20 08:45:45", "lastmod": "2023-12-13 17:12:21", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Fornace-Mark-E", "name": { "family": "Fornace", "given": "Mark E." }, "orcid": "0000-0002-5829-5839" }, { "id": "Huang-Jining", "name": { "family": "Huang", "given": "Jining" }, "orcid": "0000-0002-3798-4790" }, { "id": "Newman-Cody-T", "name": { "family": "Newman", "given": "Cody T." } }, { "id": "Porubsky-Nicholas-J", "name": { "family": "Porubsky", "given": "Nicholas J." }, "orcid": "0000-0001-6330-2645" }, { "id": "Pierce-Marshall-B", "name": { "family": "Pierce", "given": "Marshall B." } }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" } ] }, "title": "NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems", "ispublished": "unpub", "full_text_status": "public", "note": "The content is available under CC BY NC ND 4.0 License. \n\nWe thank all the NUPACK users that have helped out as alpha and beta testers over the years, as well as the many\nNUPACK users that have emailed support@nupack.org to request features or report bugs. This work was supported by the National Science Foundation (Software Elements NSF-OAC-1835414, INSPIRE NSF-CHE-1643606, Molecular Programming Project NSF-CCF-1317694, XSEDE NSF-ACI-1548562), by the National Institutes of Health (National Research Service Award T32 GM007616), by a Schmidt Academy Scholarship, by the Caltech cloud credits program from Amazon Web Services, and by the Programmable Molecular Technology Center (PMTC) within the Beckman Institute at Caltech. \n\nThe authors declare the following competing financial interest(s): a patent.\n\n
Submitted - nupack-analysis-and-design-of-nucleic-acid-structures-devices-and-systems.pdf
", "abstract": "NUPACK is a growing software suite for the analysis and design of nucleic acid structures, devices, and systems serving the needs of researchers in the fields of nucleic acid nanotechnology, molecular programming, synthetic biology, and across the life sciences. NUPACK algorithms are unique in treating complex and test tube ensembles containing arbitrary numbers of interacting strand species, providing crucial tools for capturing concentration effects essential to analyzing and designing the intermolecular interactions that are a hallmark of these fields. The all-new NUPACK web app (nupack.org) has been re-architected for the cloud, leveraging a cluster that scales dynamically in response to user demand to enable rapid job submission and result inspection even at times of peak user demand. The web app exploits the all-new NUPACK 4 scientific code base as its backend, offering enhanced physical models (coaxial and dangle stacking subensembles), dramatic speedups (20-120x for test tube analysis), and increased scalability for large complexes. NUPACK 4 algorithms can also be run locally using the all-new NUPACK Python module.", "date": "2023-03-29", "date_type": "published", "id_number": "CaltechAUTHORS:20230324-864239000.6", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230324-864239000.6", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "NSF", "grant_number": "OAC-1835414" }, { "agency": "NSF", "grant_number": "CHE-1643606" }, { "agency": "NSF", "grant_number": "CCF-1317694" }, { "agency": "NSF", "grant_number": "ACI-1548562" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "T32 GM007616" }, { "agency": "Schmidt Academy of Software Engineering" }, { "agency": "Amazon Web Services" }, { "agency": "Caltech Beckman Institute" } ] }, "local_group": { "items": [ { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.26434/chemrxiv-2022-xv98l", "primary_object": { "basename": "nupack-analysis-and-design-of-nucleic-acid-structures-devices-and-systems.pdf", "url": "https://authors.library.caltech.edu/records/tbn7q-sa464/files/nupack-analysis-and-design-of-nucleic-acid-structures-devices-and-systems.pdf" }, "resource_type": "monograph", "pub_year": "2023", "author_list": "Fornace, Mark E.; Huang, Jining; et el." }, { "id": "https://authors.library.caltech.edu/records/1cnh8-6rf45", "eprint_id": 120328, "eprint_status": "archive", "datestamp": "2023-10-09 22:04:36", "lastmod": "2023-12-22 23:42:26", "type": "monograph", "metadata_visibility": "show", "creators": { "items": [ { "id": "Schulte-Samuel-J", "name": { "family": "Schulte", "given": "Samuel J." }, "orcid": "0000-0001-9982-6504" }, { "id": "Huang-Jining", "name": { "family": "Huang", "given": "Jining" }, "orcid": "0000-0002-3798-4790" }, { "id": "Pierce-N-A", "name": { "family": "Pierce", "given": "Niles A." }, "orcid": "0000-0003-2367-4406" } ] }, "title": "HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing", "ispublished": "unpub", "full_text_status": "public", "note": "The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. \n\nWe thank M. Schwarzkopf and K. S. Lee for performing preliminary studies. We thank M. E. Bronner for reading a draft of the manuscript. We thank M. Schwarzkopf, K. S. Lee, L. M. Hochrein, G. Shin, B. J. Wold, and R. F. Ismagilov for helpful discussions. We thank G. Shin of the Molecular Technologies resource within the Beckman Institute at Caltech for providing HCR reagents. This work was funded by the Shurl and Kay Curci Foundation, by the Richard N. Merkin Institute for Translational Research at Caltech, by the National Aeronautics and Space Administration (Translational Research Institute for Space Health; NNX16AO69A), and by the National Institutes of Health (NIBIB R01EB006192 and NIGMS training grant GM008042 to S.J.S.).\n\nCompeting Interest Statement. Patents, pending patent applications, and the startup company Molecular Instruments.\n\nSubmitted - 20220918-508442v1full.pdf
Supplemental Material - media1.pdf
Supplemental Material - media2.mp4
Supplemental Material - media3.mp4
", "abstract": "The lateral flow assay format enables rapid, instrument-free, at-home testing for SARS-CoV-2. Due to the absence of signal amplification, this simplicity comes at a cost in sensitivity. Here, we enhance sensitivity by developing an amplified lateral flow assay that incorporates isothermal, enzyme-free signal amplification based on the mechanism of hybridization chain reaction (HCR). The simplicity of the user experience is maintained using a disposable 3-channel lateral flow device to automatically deliver reagents to the test region in three successive stages without user interaction. To perform a test, the user loads the sample, closes the device, and reads the result by eye after 60 minutes. Detecting gamma-irradiated SARS-CoV-2 virions in a mixture of saliva and extraction buffer, the current amplified HCR lateral flow assay achieves a limit of detection of 200 copies/\u03bcL using available antibodies to target the SARS-CoV-2 nucleocapsid protein. By comparison, five commercial unamplified lateral flow assays that use proprietary antibodies exhibit limits of detection of 500 copies/\u03bcL, 1000 copies/\u03bcL, 2000 copies/\u03bcL, 2000 copies/\u03bcL, and 20,000 copies/\u03bcL. By swapping out antibody probes to target different pathogens, amplified HCR lateral flow assays offer a platform for simple, rapid, and sensitive at-home testing for infectious disease. As an alternative to viral protein detection, we further introduce an HCR lateral flow assay for viral RNA detection.", "date": "2023-03-28", "date_type": "published", "id_number": "CaltechAUTHORS:20230322-367067000.13", "official_url": "https://resolver.caltech.edu/CaltechAUTHORS:20230322-367067000.13", "rights": "No commercial reproduction, distribution, display or performance rights in this work are provided.", "funders": { "items": [ { "agency": "Shurl and Kay Curci Foundation" }, { "agency": "Caltech Merkin Institute for Translational Research" }, { "agency": "NASA", "grant_number": "NNX16AO69A" }, { "agency": "NIH", "grant_number": "R01EB006192" }, { "agency": "NIH Predoctoral Fellowship", "grant_number": "GM008042" } ] }, "local_group": { "items": [ { "id": "COVID-19" }, { "id": "Richard-Merkin-Institute" }, { "id": "Division-of-Biology-and-Biological-Engineering" } ] }, "doi": "10.1101/2022.09.18.508442", "primary_object": { "basename": "media3.mp4", "url": "https://authors.library.caltech.edu/records/1cnh8-6rf45/files/media3.mp4" }, "related_objects": [ { "basename": "20220918-508442v1full.pdf", "url": "https://authors.library.caltech.edu/records/1cnh8-6rf45/files/20220918-508442v1full.pdf" }, { "basename": "media1.pdf", "url": "https://authors.library.caltech.edu/records/1cnh8-6rf45/files/media1.pdf" }, { "basename": "media2.mp4", "url": "https://authors.library.caltech.edu/records/1cnh8-6rf45/files/media2.mp4" } ], "resource_type": "monograph", "pub_year": "2023", "author_list": "Schulte, Samuel J.; Huang, Jining; et el." } ]