Proceedings of the National Academy of Sciences<\/a>.<\/p>\nThe collaboration brought together the labs of RPI Professor Robert Linhardt, an internationally recognized leader in glycoscience and synthetic heparin research, and 溏心vlog免费B站 Professor Jason Dwyer, recipient of an Innovation Award from the Federation of Analytical Chemistry and Spectroscopy Societies for his advances in nanopore sensing and whose earlier research developed a simpler, faster way to analyze naturally sourced heparin for impurities. This collaboration focused on a class of molecules known as heparan sulfates.<\/p>\n
\u201cHeparan sulfates are a type of long-chain linked sugar molecules called polysaccharides that are as important to our biology as DNA,\u201d said Linhardt and Ke Xia, a research scientist at RPI and lead author of the paper, in an email. \u201cThis paper demonstrates it is possible to reduce the time required for sequencing heparan sulfate chains from years to minutes. This accomplishment will improve our understanding of polysaccharides and the glycome as much as the use of high-speed sequencers has improved the understanding of DNA and the genome.\u201d<\/p>\n
At RPI, Linhardt, in collaboration with the University of North Carolina, has developed a synthetic heparin offering greater production control than naturally sourced heparin.<\/p>\n
\u201cRPI is extraordinarily good at making and understanding this type of molecule, and we wanted to work with them for that reason,\u201d said Dwyer. \u201cWhat we\u2019re able to do is look at their samples with high throughput one molecule at a time, which is a tremendous advance over conventional studies that get a sort of average picture by looking at many, many molecules all at once. And when you look at something, a single molecule at a time, you can learn new and important things.\u201d<\/p>\n
Nanopore sensors \u2013 a nanofluidic hole, which is about one hundred thousandth times smaller than a human hair, located in an impermeable, silicon-based membrane \u2013 have been a promising tool in single-molecule research for more than 20 years. Using an ionic current, the sensor analyzes molecules as they pass through the pore. Dwyer\u2019s lab specializes in using special surface coatings to tailor the nanopore to work with the particularly challenging polysaccharides.<\/p>\n
While nanopores have been used in DNA sequencing for more than 15 years, analyzing molecules like polysaccharides (or glycans) is far more complex.<\/p>\n
\u201cThe human genome project sequenced DNA and that was a billion-dollar project. You had to figure out at each position which of four bases you had. It\u2019s basically a lottery with four numbers at each position of the DNA,\u201d Dwyer said. \u201cWith polysaccharide sequencing, you have 120 bases to choose from \u2013 and you have to get them right at every single position. So, the lottery odds are a lot worse. Basically, there\u2019s much more variety in these types of molecules \u2013 both chemical and structural.\u201d<\/p>\n
\u201cWe feel nanopores are well-suited to analyze polysaccharides, which can be even a more useful bio marker than DNA,\u201d added James Hagan, a third-year doctoral student who oversaw the experiment in Dwyer\u2019s lab. \u201cThese results build on earlier work in our laboratory that revealed key operating principles and showed us that nanopores had tremendous promise to characterize a wide range of unique polysaccharides.\u201d<\/p>\n
Rensselaer provided Dwyer\u2019s lab with four high-purity synthetic heparan sulfate samples, each with four different types of sugar units that could make different sequences. The combination of the solid-state nanopore, high-purity samples and machine learning allowed for a clear classification of the four molecules using only a minimal amount of sample.<\/p>\n
\u201cFast nanopore analysis \u2013 10 minutes for each analysis \u2013 gave clear differences between the signal generated by our four heparan sulfates providing us sequence information,\u201d said Linhardt and Xia. \u201cUsing machine learning we only required the results of 500 to 2,000 chains of each heparan sulfate to obtain a nearly 97% accurate prediction of the sequences. We have trained the machine to quickly read very long sequences comprised of four letters (sugar units). We are working to extend this technology to read more complex sequences made up of more sugar units in real time.\u201d<\/p>\n
\u201cThis is really further proof of the importance of nanopore sensors for polysaccharide sensing,\u201d Hagan said. \u201cTogether with the machine learning, the nanopore measurements were able to get down to the specific sequence of each of the molecules. With this combined approach we were able to differentiate each of the monosaccharides in the polysaccharide chain, which is really the most exciting outcome of this collaboration.\u201d<\/p>\n
The potential of this work goes beyond the quality assurance of synthetic heparin. The polysaccharides used in the paper, glycosaminoglycans, are present in all biological lifeforms and serve different and vital physiological roles.<\/p>\n
\u201cTo make our study more relevant today, COVID-19 has its surface decorated with glycans,\u201d Hagan said. \u201cBy building on this work, you could sequence those markers and pry yet more secrets from this virus, even to the point of better therapeutic interventions.\u201d<\/p>\n
This material is based upon work supported by the National Science Foundation under Grant No. CHE-1808344 to Prof. Dwyer, and the National Institute of Health under Grants No. CA231074, DK111958, and HL125371 to Prof. Linhardt.\u00a0Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the NSF or NIH.<\/em><\/p>\n","protected":false},"excerpt":{"rendered":"KINGSTON, R.I. \u2013 March 10, 2021 \u2013 Researchers from the 溏心vlog免费B站 and Rensselaer Polytechnic Institute have teamed up to perfect a fast, accurate test combining the use of a solid-state nanopore and machine learning to verify the identity and purity of synthetic heparan sulfate The work has implications for better characterizing viruses […]<\/p>\n","protected":false},"author":2,"featured_media":76045,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":"","_links_to":"","_links_to_target":""},"categories":[2],"tags":[12],"class_list":["post-76044","post","type-post","status-publish","format-standard","has-post-thumbnail","hentry","category-archives","tag-college-of-arts-and-sciences"],"acf":[],"_links":{"self":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts\/76044","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/comments?post=76044"}],"version-history":[{"count":0,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/posts\/76044\/revisions"}],"wp:featuredmedia":[{"embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/media\/76045"}],"wp:attachment":[{"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/media?parent=76044"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/categories?post=76044"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.uri.edu\/news\/wp-json\/wp\/v2\/tags?post=76044"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}