Sequencing by Avidity Enables High Accuracy With Low Reagent Consumption

Autor: Sinan Arslan, Matthew Kellinger, Semyon Kruglyak, Jake LeVieux, Adeline Mah, Haosen Wang, Junhua Zhao, Chunhong Zhou, John Bailey, Matthew Byrne, Chiting Chang, Steve Chen, Claudia Dennler, Samantha Dennler, Vivian Dien, Derek Fuller, Francisco Garcia, Minghao Guo, Ryan Kelley, Omid Khandan, Michael Klein, Michael Kim, Bill Lin, Yu Liu, Tyler Lopez, Peter Mains, Andrew Price, Hermes Taylor, Ramreddy Tippana, Austin Tomaney, Richard Zhang, Minna Abtahi, Mark Ambroso, Rosi Bajari, Ava Bellizi, Chris Benitez, Daniel Berard, Lorenzo Berti, Kelly Blease, Angela Blum, Andrew Boddicker, Leo Bondar, Chris Bui, Kevin Cappa, Joshua Chan, Victor Chang, Katia Charov, Xiyi Chen, Rodger Constandse, Weston Damron, Mariam Dawood, Nicole Debruno, John Dmalanta, Laure Edoli, Keerthi Elango, Nikka Faustino, Chao Feng, Matthew Ferrari, Kieth Frankie, Adam Fries, Anne Galloway, Vlad Gavrila, Gregory Gemmen, James Ghadiali, Logan Goddard, Adriana Roginski, Garren Hendricks, Jendrick Hentschel, Doris Hseih, Yu-Hsein Hwang-fu, Scott Im, Chaoyi Jin, Daniel Kincade, Bryan Lajooie, Shawn Levy, Yu Li, Vincent Liang, William Light, Jonathan Lipsher, Tsungli Liu, Guixia Long, Rui Ma, Jack Mailloux, Kyle Mandla, Anyssa Martinez, Max Mass, Michael Meron, Celyne Moh, Rachel Moore, Juan Moreno, Jordan Neysmith, Cassandra Niman, Jesus Nunez, Micah Ojeda, Jenna Owens, Sara Espinosa Ortiz, Geoffrey Piland, Dan Proctor, Josua Purba, Michael Ray, Daisong Rong, Virginia Saade, Sanchari Saha, Luqmanal Sirajudeen, Gudrun Stengel, Ryan Stinson, Michael Stone, Keoni Sundseth, Eileen Thai, Connor Thompson, Gustav Santo Tomas, Christy Trejo, Greg Trieger, Diane Truong, Ben Tse, Benjamin Voiles, Henry Vuong, Jennifer Wong, Chiung-Ting Wu, Hua Yu, Ming Yu, Cindy Zhang, Da Zhao, Frank Zheng, Molly He, Michael Previte

We present a novel sequencing chemistry implemented as part of the AVITI system. Relying on the proximal DNA binding sites created through DNA amplification on a solid support, avidity sequencing uses multivalent nucleotide ligands on dye-labeled cor

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::f97fa97146160e939ade0e785052a2c6
https://doi.org/10.21203/rs.3.rs-1965701/v1

Free Energy of a Polymer in Slit-like Confinement from the Odijk Regime to the Bulk

Autor: Gary W. Slater, Andrew C. Guthrie, Albert Kamanzi, David Sean, Daniel Berard, Jason S. Leith, Sabrina Leslie, Hendrick W. de Haan, Christopher M. J. McFaul

Publikováno v: Macromolecules. 49:9266-9271

We directly measure the free energy of confinement for semiflexible polymers from the nanoscale to bulk regimes in slit-like confinement. We use convex lens-induced confinement (CLiC) microscopy of DNA to directly count molecules at equilibrium in a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::1abac14f4f3afe79d3e7ae43355eba5b
https://doi.org/10.1021/acs.macromol.6b01805

Continuous Confinement Fluidics: Getting Lots of Molecules into Small Spaces with High Fidelity

Autor: Walter Reisner, Robert Sladek, Sabrina Leslie, François Michaud, Sara Mahshid, Mohammed Jalal Ahamed, Daniel Berard

Publikováno v: Macromolecules. 49:2853-2859

Confining DNA molecules with high throughput and structural integrity is an important challenge in nanochannel-based genomic mapping technology. Here we demonstrate dynamic confinement and linearization of DNA polymers within an embedded nanogroove a

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::08000e46fe5086d9e1b2b931697c0288
https://doi.org/10.1021/acs.macromol.5b02617

Visualizing structure-mediated interactions in supercoiled DNA molecules

Autor: Fedor Kouzine, Catherine Leroux, Alexander Hofkirchner, Craig J. Benham, Cynthia Shaheen, Zhi Ming Xu, Laura N Saunders, Sabrina Leslie, Daniel Berard, David Levens, Shane Scott, Jill Laurin, Barbara Gravel

Publikováno v: Nucleic Acids Research

We directly visualize the topology-mediated interactions between an unwinding site on a supercoiled DNA plasmid and a specific probe molecule designed to bind to this site, as a function of DNA supercoiling and temperature. The visualization relies o

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::69957da973849bea3bc80b13c65108e1
https://pubmed.ncbi.nlm.nih.gov/29684182

Rotation-induced macromolecular spooling of DNA

Autor: Tyler N. Shendruk, Sabrina Leslie, Gary W. Slater, Julian Wolf, David Sean, Justin Dragoman, Sophie Battat, Daniel Berard

Publikováno v: Physical Review X, Vol 7, Iss 3, p 031005 (2017)
Shendruk, T N, Sean, D, Berard, D J, Wolf, J, Dragoman, J, Battat, S, Slater, G W & Leslie, S R 2017, ' Rotation-Induced Macromolecular Spooling of DNA ', Physical Review X, vol. 7, no. 3, 031005 . https://doi.org/10.1103/PhysRevX.7.031005

Genetic information is stored in a linear sequence of base-pairs; however, thermal fluctuations and complex DNA conformations such as folds and loops make it challenging to order genomic material for in vitro analysis. In this work, we discover that

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2b9250cb00ffe728a76fe37ccf1a5a27
http://arxiv.org/abs/1706.01861