{"id":166868,"date":"2014-09-01T00:00:00","date_gmt":"2014-09-01T00:00:00","guid":{"rendered":"https:\/\/www.microsoft.com\/en-us\/research\/msr-research-item\/abstract-modelling-of-tethered-dna-circuits\/"},"modified":"2018-10-16T21:07:05","modified_gmt":"2018-10-17T04:07:05","slug":"abstract-modelling-of-tethered-dna-circuits","status":"publish","type":"msr-research-item","link":"https:\/\/www.microsoft.com\/en-us\/research\/publication\/abstract-modelling-of-tethered-dna-circuits\/","title":{"rendered":"Abstract modelling of tethered DNA circuits"},"content":{"rendered":"<div class=\"asset-content\">\n<p>Sequence-specific DNA interactions are a powerful means of programming nanoscale locomotion. These systems typically use a DNA track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a formal encoding. In this paper we present the first general encoding of tethered DNA species into a formal language, which allows the interactions between tethered species to be derived automatically using standard reaction rules. We apply this encoding to a previously published tethered DNA circuit architecture based on hairpin assembly reactions. This work enables automated analysis of large-scale tethered DNA circuits and, potentially, synthesis of optimized track layouts to implement specific logic functions.<\/p>\n<\/div>\n<p><!-- .asset-content --><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Sequence-specific DNA interactions are a powerful means of programming nanoscale locomotion. These systems typically use a DNA track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a [&hellip;]<\/p>\n","protected":false},"featured_media":0,"template":"","meta":{"msr-url-field":"","msr-podcast-episode":"","msrModifiedDate":"","msrModifiedDateEnabled":false,"ep_exclude_from_search":false,"_classifai_error":"","footnotes":""},"msr-content-type":[3],"msr-research-highlight":[],"research-area":[13546],"msr-publication-type":[193716],"msr-product-type":[],"msr-focus-area":[],"msr-platform":[],"msr-download-source":[],"msr-locale":[268875],"msr-post-option":[],"msr-field-of-study":[],"msr-conference":[],"msr-journal":[],"msr-impact-theme":[],"msr-pillar":[],"class_list":["post-166868","msr-research-item","type-msr-research-item","status-publish","hentry","msr-research-area-computational-sciences-mathematics","msr-locale-en_us"],"msr_publishername":"Springer","msr_edition":"International Conference on DNA Computing and Molecular Programming","msr_affiliation":"","msr_published_date":"2014-09-01","msr_host":"","msr_duration":"","msr_version":"","msr_speaker":"","msr_other_contributors":"","msr_booktitle":"","msr_pages_string":"132-147","msr_chapter":"","msr_isbn":"","msr_journal":"","msr_volume":"8727","msr_number":"","msr_editors":"","msr_series":"","msr_issue":"","msr_organization":"","msr_how_published":"","msr_notes":"","msr_highlight_text":"","msr_release_tracker_id":"","msr_original_fields_of_study":"","msr_download_urls":"","msr_external_url":"","msr_secondary_video_url":"","msr_longbiography":"","msr_microsoftintellectualproperty":1,"msr_main_download":"204679","msr_publicationurl":"","msr_doi":"10.1007\/978-3-319-11295-4_9","msr_publication_uploader":[{"type":"file","title":"Lakin&#8230;Phillips%20-%20DNA20.pdf","viewUrl":"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/02\/Lakin...Phillips20-20DNA20.pdf","id":204679,"label_id":0},{"type":"file","title":"Lakin&#8230;Phillips%20-%20DNA20%20-%20Supplement.pdf","viewUrl":"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/02\/Lakin...Phillips20-20DNA2020-20Supplement.pdf","id":204680,"label_id":0},{"type":"doi","title":"10.1007\/978-3-319-11295-4_9","viewUrl":false,"id":false,"label_id":0}],"msr_related_uploader":"","msr_attachments":[{"id":204680,"url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/02\/Lakin...Phillips20-20DNA2020-20Supplement.pdf"},{"id":204679,"url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-content\/uploads\/2016\/02\/Lakin...Phillips20-20DNA20.pdf"}],"msr-author-ordering":[{"type":"text","value":"Matthew R. Lakin","user_id":0,"rest_url":false},{"type":"text","value":"Rasmus Petersen","user_id":0,"rest_url":false},{"type":"text","value":"Kathryn E. Gray","user_id":0,"rest_url":false},{"type":"user_nicename","value":"aphillip","user_id":31075,"rest_url":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/microsoft-research\/v1\/researchers?person=aphillip"}],"msr_impact_theme":[],"msr_research_lab":[],"msr_event":[],"msr_group":[],"msr_project":[544545,170217],"publication":[],"video":[],"download":[],"msr_publication_type":"inproceedings","related_content":{"projects":[{"ID":544545,"post_title":"Station B","post_name":"stationb","post_type":"msr-project","post_date":"2019-03-11 15:56:07","post_modified":"2021-09-28 09:10:36","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/stationb\/","post_excerpt":"Our work on the Station B project has now been retired. We continue to actively explore the exciting intersection of computing and life sciences, with other projects located on\u00a0www.microsoft.com\/research. Building a platform for programming biology The ability to program biology could enable fundamental breakthroughs across a broad range of industries, including medicine, agriculture, food, construction, textiles, materials and chemicals. It could also help lay the foundation for a future bioeconomy based on sustainable technology. Despite&hellip;","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/544545"}]}},{"ID":170217,"post_title":"Programming DNA Circuits","post_name":"programming-dna-circuits","post_type":"msr-project","post_date":"2009-02-07 13:36:42","post_modified":"2020-03-06 10:49:40","post_status":"publish","permalink":"https:\/\/www.microsoft.com\/en-us\/research\/project\/programming-dna-circuits\/","post_excerpt":"Molecular devices made of nucleic acids show great potential for applications ranging from bio-sensing to intelligent nanomedicine. They allow computation to be performed at the molecular scale, while also interfacing directly with the molecular components of living systems. They form structures that are stable inside cells, and their interactions can be precisely controlled by modifying their nucleotide sequences. However, designing correct and robust nucleic acid devices is a major challenge, due to high system complexity&hellip;","_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-project\/170217"}]}}]},"_links":{"self":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166868","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item"}],"about":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/types\/msr-research-item"}],"version-history":[{"count":1,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166868\/revisions"}],"predecessor-version":[{"id":435015,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-item\/166868\/revisions\/435015"}],"wp:attachment":[{"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/media?parent=166868"}],"wp:term":[{"taxonomy":"msr-content-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-content-type?post=166868"},{"taxonomy":"msr-research-highlight","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-research-highlight?post=166868"},{"taxonomy":"msr-research-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/research-area?post=166868"},{"taxonomy":"msr-publication-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-publication-type?post=166868"},{"taxonomy":"msr-product-type","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-product-type?post=166868"},{"taxonomy":"msr-focus-area","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-focus-area?post=166868"},{"taxonomy":"msr-platform","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-platform?post=166868"},{"taxonomy":"msr-download-source","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-download-source?post=166868"},{"taxonomy":"msr-locale","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-locale?post=166868"},{"taxonomy":"msr-post-option","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-post-option?post=166868"},{"taxonomy":"msr-field-of-study","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-field-of-study?post=166868"},{"taxonomy":"msr-conference","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-conference?post=166868"},{"taxonomy":"msr-journal","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-journal?post=166868"},{"taxonomy":"msr-impact-theme","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-impact-theme?post=166868"},{"taxonomy":"msr-pillar","embeddable":true,"href":"https:\/\/www.microsoft.com\/en-us\/research\/wp-json\/wp\/v2\/msr-pillar?post=166868"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}