{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"institution":[{"name":"bioRxiv"}],"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T13:05:40Z","timestamp":1785416740112,"version":"3.56.0"},"posted":{"date-parts":[[2026,7,28]]},"group-title":"Bioengineering","reference-count":35,"publisher":"openRxiv","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"NIH\/NIAID","award":["5R61AI140465-03"],"award-info":[{"award-number":["5R61AI140465-03"]}]},{"name":"NIH\/NIAID","award":["R33AI140465"],"award-info":[{"award-number":["R33AI140465"]}]},{"name":"NIH\/NIAID","award":["R61AI140465"],"award-info":[{"award-number":["R61AI140465"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"accepted":{"date-parts":[[2026,7,28]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                <jats:p>CRISPR-based assays offer sensitive and specific nucleic acid detection for a broad range of diagnostic and surveillance applications. While standard solution-based assays are simple, they typically lack the ability to detect multiple targets individually without the need for more complex instrumentation and multi-step workflows. Surface-based strategies offer greater potential for multiplexing since the identity of a target can be associated with a location on a slide or a specific bead, as in the case of DNA arrays or Luminex bead assays. However, the design principles for optimizing surface-based CRISPR assays have yet to be developed. Here we present a multi-scale analytical framework integrating nanoscale enzyme kinetics, microscale diffusion constraints, and macroscale assay parameters that we use to develop a bead-based Cas13a assay where the bead becomes fluorescent when the target RNA for that bead is detected. The assay, which we call SurfCas, uses surface-bound guide RNAs and reporter RNAs to detect one or more soluble target RNAs in a one-pot assay. We show that SurfCas has a sensitivity approaching bulk reactions, and we demonstrate multiplexed detection of target RNAs in a complex biological matrix. The design principles we establish for surface-based CRISPR assays offer guidance on how to further improve SurfCas sensitivity and scale multiplexed detection of target RNAs in a single reaction.<\/jats:p>","DOI":"10.64898\/2026.07.27.739218","type":"posted-content","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T12:35:10Z","timestamp":1785242110000},"source":"Crossref","is-referenced-by-count":0,"title":["Bead-based RNA Detection with Cas13a: Multi-scale Design and Validation"],"prefix":"10.64898","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-5209-7578","authenticated-orcid":false,"given":"Abdul M.","family":"Bhuiya","sequence":"first","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5192-7947","authenticated-orcid":false,"given":"Siddhansh","family":"Agarwal","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States"},{"name":"Biohub, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3760-6482","authenticated-orcid":false,"given":"Carlos F.","family":"Ng","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melanie","family":"Ott","sequence":"additional","affiliation":[{"name":"Biohub, San Francisco, CA 94158, USA"},{"name":"Gladstone Infectious Disease Institute, Gladstone Institutes, San Francisco, CA 94158, USA"},{"name":"Department of Medicine, University of California, San Francisco, San Francisco, CA 94158, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7481-4056","authenticated-orcid":false,"given":"Sungmin","family":"Son","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States"},{"name":"Department of Bio and Brain Engineering, KAIST, Daejeon, Republic of Korea"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1890-5364","authenticated-orcid":false,"given":"Daniel A.","family":"Fletcher","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Berkeley, Berkeley, CA, United States"},{"name":"Biohub, San Francisco, CA 94158, USA"},{"name":"Division of Biological Systems and Engineering, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"54368","reference":[{"key":"2026073005550776000_2026.07.27.739218v1.1","doi-asserted-by":"crossref","unstructured":"van Dongen, J. 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