{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/specific-nucleic-acid-detection-using-a","title":"Specific Nucleic Acid Detection Using a Nanoparticle Hybridization Assay","arxiv_id":"2409.03983","date":"2024-09-06","proceeding":null,"authors":["A. A. Aldakheel","C. B. Raub","H. T. Bui"],"abstract":"Simple methods to detect biomolecules including specific nucleic acid sequences have received renewed attention since the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) virus pandemic. Notably, biomolecule detection that uses some form of signal amplification will have some form of amplification-related error, which in the polymerase chain reaction involves mispriming and subsequent signal amplification in the no template control, ultimately providing a limit of detection. To demonstrate the feasibility of the detection of a DNA target sequence without molecular or chemical signal amplification that avoids amplification errors, a gold nanoparticle aggregation assay was developed and tested. Two primers bracketing a 94 base pair target sequence from SARS-CoV-2 were conjugated to 10 nm diameter gold nanoparticles by the salt aging method, with conjugation and primer-target hybridization confirmed by agarose gel electrophoresis and nanospectrophotometry. Upon mixing of both conjugated nanoparticles with target, a surface plasmon resonance shift of 6 nm was observed, and lower electrophoretic mobility of a band containing both DNA fluorescence and gold absorption signals. This did not occur in the presence of a control DNA molecule of the same size and composition as the target but with a randomly scrambled base position. Nanoparticle tracking at 30 frames per second using a sensitive darkfield microscope revealed a lower measured diffusion coefficient of scattering objects in the target mixture than in the control mixture or with bare gold nanoparticles.","url_abs":"https://arxiv.org/abs/2409.03983v1","url_pdf":"https://arxiv.org/pdf/2409.03983v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"specific-nucleic-acid-detection-using-a","repo_url":"https://github.com/Aldakheelarwa88/ABT_Diffusion_Videos","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null},{"paper_slug":"specific-nucleic-acid-detection-using-a","repo_url":"https://github.com/Aldakheelarwa88/AuNPs_Diffusion_Videos","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[],"methods":[{"method_slug":"attention","method_name":"Attention"},{"method_slug":"base","method_name":"BASE"},{"method_slug":"diffusion","method_name":"Diffusion"},{"method_slug":"softmax","method_name":"Softmax"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}