Automated methods for scalable, parallelized enzymatic biopolymer synthesis and modification using microfluidic devices

Banal, James; Berleant, Joseph Don; Shepherd, Tyson; Bathe, Mark

Title: Automated methods for scalable, parallelized enzymatic biopolymer synthesis and modification using microfluidic devices

Patent · Tue Dec 26 00:00:00 EST 2023

OSTI ID:2294023

Banal, James; Berleant, Joseph Don; Shepherd, Tyson; Bathe, Mark

Methods for the automated template-free synthesis of user-defined sequence controlled biopolymers using microfluidic devices are described. The methods facilitate simultaneous synthesis of up to thousands of uniquely addressed biopolymers from the controlled movement and combination of regents as fluid droplets using microfluidic and EWOD-based systems. In some forms, biopolymers including nucleic acids, peptides, carbohydrates, and lipids are synthesized from step-wise assembly of building blocks based on a user-defined sequence of droplet movements. In some forms, the methods synthesize uniquely addressed nucleic acids of up to 1,000 nucleotides in length. Methods for adding, removing and changing barcodes on biopolymers are also provided. Biopolymers synthesized according to the methods, and libraries and databases thereof are also described. Modified biopolymers, including chemically modified nucleotides and biopolymers conjugated to other molecules are described.

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Research Organization:: Massachusetts Inst. of Technology (MIT), Cambridge, MA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES); US Office of Naval Research (ONR); National Science Foundation (NSF)

DOE Contract Number:: SC0001088; CCF-1564025; N00014-16-121953; N00014-17-1-2609

Assignee:: Massachusetts Institute of Technology (Cambridge, MA)

Patent Number(s):: 11,851,651

Application Number:: 16/012,583

OSTI ID:: 2294023

Resource Relation:: Patent File Date: 06/19/2018

Country of Publication:: United States

Language:: English

References (59)

UNAFold Markham, Nicholas R.; Zuker, Michael Bioinformatics https://doi.org/10.1007/978-1-60327-429-6_1	book	January 2008
Applications of EWOD Systems for DNA Reaction and Analysis Lin, Tai-Hsuan; Yao, Da-Jeng Journal of Adhesion Science and Technology, Vol. 26, Issue 12-17 https://doi.org/10.1163/156856111X600578	journal	May 2012
All-electronic droplet generation on-chip with real-time feedback control for EWOD digital microfluidics Gong, Jian; Kim, Chang-Jin “CJ” Lab on a Chip, Vol. 8, Issue 6 https://doi.org/10.1039/b717417a	journal	January 2008
Nucleotide Analogs Siddiqi, Suhaib; Efcavitch, J. William; Mitchell, Judith https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/20110081647 US Patent Application 12/631074; 20110081647	patent-application	April 2011
Foldamers: A Manifesto Gellman, Samuel H. Accounts of Chemical Research, Vol. 31, Issue 4 https://doi.org/10.1021/ar960298r	journal	April 1998
Digital Microfluidics Choi, Kihwan; Ng, Alphonsus H. C.; Fobel, Ryan Annual Review of Analytical Chemistry, Vol. 5, Issue 1 https://doi.org/10.1146/annurev-anchem-062011-143028	journal	July 2012
Large-scale de novo DNA synthesis: technologies and applications Kosuri, Sriram; Church, George M. Nature Methods, Vol. 11, Issue 5 https://doi.org/10.1038/nmeth.2918	journal	April 2014
Array of oligonucleotides on a solid substrate Fodor, Stephen P. A.; Pirrung, Michael C.; Read, J. Leighton https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5445934 US Patent Document 5,445,934	patent	August 1995
Droplet extraction from a liquid column for on-chip microfluidics Yi, Uichong B.; De Guzman, Peter Patrick; Liu, Wayne P. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8304253 US Patent Document 8,304,253	patent	November 2012
Digital microfluidic platform for radiochemistry Van Dam, R. Michael; Kim, Chang-Jin; Chen, Supin https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9005544 US Patent Document 9,005,544	patent	April 2015
Localized droplet heating with surface electrodes in microfluidic chips Kim, Chang-Jin; Nelson, Wyatt C. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8459295 US Patent Document 8,459,295	patent	June 2013
Method and apparatus for real-time feedback control of electrical manipulation of droplets on chip Kim, Chang-Jin; Gong, Jian https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9266076 US Patent Document 9,266,076	patent	February 2016
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA Goldman, Nick; Bertone, Paul; Chen, Siyuan Nature, Vol. 494, Issue 7435 https://doi.org/10.1038/nature11875	journal	January 2013
Laser excited confocal microscope fluorescence scanner and method Mathies, Richard A.; Peck, Konan https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5091652 US Patent Document 5,091,652	patent	February 1992
AM-EWOD device and method of driving with variable voltage AC driving Hadwen, Benjamin James https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9169573 US Patent Document 9,169,573	patent	October 2015
Efficient tumor cell lysis mediated by a bispecific single chain antibody expressed in Escherichia coli. Gruber, M.; Schodin, B. A.; Wilson, E. R. The Journal of Immunology, Vol. 152, Issue 11, p. 5368-5374 https://doi.org/10.4049/jimmunol.152.11.5368	journal	June 1994
OligoArray 2.0: design of oligonucleotide probes for DNA microarrays using a thermodynamic approach Rouillard, J. -M. Nucleic Acids Research, Vol. 31, Issue 12 https://doi.org/10.1093/nar/gkg426	journal	June 2003
Template-free generation of RNA species that replicate with bacteriophage T7 RNA polymerase. Biebricher, C. K.; Luce, R. The EMBO Journal, Vol. 15, Issue 13, p. 3458-3465 https://doi.org/10.1002/j.1460-2075.1996.tb00712.x	journal	July 1996
"Diabodies": small bivalent and bispecific antibody fragments. Holliger, P.; Prospero, T.; Winter, G. Proceedings of the National Academy of Sciences, Vol. 90, Issue 14 https://doi.org/10.1073/pnas.90.14.6444	journal	July 1993
Electrowetting and electrowetting-on-dielectric for microscale liquid handling Lee, Junghoon; Moon, Hyejin; Fowler, Jesse Sensors and Actuators A: Physical, Vol. 95, Issue 2-3 https://doi.org/10.1016/S0924-4247(01)00734-8	journal	January 2002
Design of oligonucleotides for microarrays and perspectives for design of multi-transcriptome arrays Nielsen, H. B. Nucleic Acids Research, Vol. 31, Issue 13, p. 3491-3496 https://doi.org/10.1093/nar/gkg622	journal	July 2003
Real-time detection of DNA hybridization and melting on oligonucleotide arrays by using optical wave guides. Stimpson, D. I.; Hoijer, J. V.; Hsieh, W. T. Proceedings of the National Academy of Sciences, Vol. 92, Issue 14 https://doi.org/10.1073/pnas.92.14.6379	journal	July 1995
Combinatorial Synthesis of Peptidomimetics Using Digital Microfluidics Jebrail, Mais J.; Assem, Naila; Mudrik, Jared M. Journal of Flow Chemistry, Vol. 2, Issue 3 https://doi.org/10.1556/JFC-D-12-00012	journal	September 2012
Light-generated oligonucleotide arrays for rapid DNA sequence analysis. Pease, A. C.; Solas, D.; Sullivan, E. J. Proceedings of the National Academy of Sciences, Vol. 91, Issue 11 https://doi.org/10.1073/pnas.91.11.5022	journal	May 1994
Error-Prone Repair DNA Polymerases in Prokaryotes and Eukaryotes Goodman, Myron F. Annual Review of Biochemistry, Vol. 71, Issue 1 https://doi.org/10.1146/annurev.biochem.71.083101.124707	journal	June 2002
Direct fluorescence analysis of genetic polymorphisms by hybridization with oligonucleotide arrays on glass supports Guo, Zhen; Guilfoyle, Richard A.; Thiel, Andrew J. Nucleic Acids Research, Vol. 22, Issue 24 https://doi.org/10.1093/nar/22.24.5456	journal	January 1994
Selection of long oligonucleotides for gene expression microarrays using weighted rank-sum strategy Hu, Guangan; Llinás, Manuel; Li, Jingguang BMC Bioinformatics, Vol. 8, Issue 1 https://doi.org/10.1186/1471-2105-8-350	journal	September 2007
Design of 240,000 orthogonal 25mer DNA barcode probes Xu, Q.; Schlabach, M. R.; Hannon, G. J. Proceedings of the National Academy of Sciences, Vol. 106, Issue 7 https://doi.org/10.1073/pnas.0812506106	journal	January 2009
An Unnatural Biopolymer Cho, Charles Y.; Moran, Edmund J.; Cherry, Sara R. Science, Vol. 261, Issue 5126, p. 1303-1305 https://doi.org/10.1126/science.7689747	journal	September 1993
Chimeric human antibody molecules: mouse antigen-binding domains with human constant region domains. Morrison, S. L.; Johnson, M. J.; Herzenberg, L. A. Proceedings of the National Academy of Sciences, Vol. 81, Issue 21, p. 6851-6855 https://doi.org/10.1073/pnas.81.21.6851	journal	November 1984
Potent and nontoxic antisense oligonucleotides containing locked nucleic acids Wahlestedt, C.; Salmi, P.; Good, L. Proceedings of the National Academy of Sciences, Vol. 97, Issue 10 https://doi.org/10.1073/pnas.97.10.5633	journal	May 2000
Deoxynucleoside phosphoramidites—A new class of key intermediates for deoxypolynucleotide synthesis Beaucage, S. L.; Caruthers, M. H. Tetrahedron Letters, Vol. 22, Issue 20, p. 1859-1862 https://doi.org/10.1016/S0040-4039(01)90461-7	journal	January 1981
Nucleotide analogs Efcavitch, J. William; Siddiqi, Suhaib; Buzby, Philip https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8071755 US Patent Document 8,071,755	patent	December 2011
A Rewritable, Random-Access DNA-Based Storage System Tabatabaei Yazdi, S. M. Hossein; Yuan, Yongbo; Ma, Jian Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep14138	journal	September 2015
Electrode-voltage waveform for droplet-velocity and chip-lifetime improvements of digital microfluidic systems Chen, Tianlan; Dong, Cheng; Gao, Jie https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9808800 US Patent Document 9,808,800	patent	November 2017
Monolithically formed EWOD device and method of making the same Nelson, Wyatt C.; Kim, Chang-Jin https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8883014 US Patent Document 8,883,014	patent	November 2014
Bispecific antibody: a tool for diagnosis and treatment of disease Songsivilai, S.; Lachmann, P. J. Clinical & Experimental Immunology, Vol. 79, Issue 3 https://doi.org/10.1111/j.1365-2249.1990.tb08089.x	journal	March 1990
DNA analysis and diagnostics on oligonucleotide microchips. Yershov, G.; Barsky, V.; Belgovskiy, A. Proceedings of the National Academy of Sciences, Vol. 93, Issue 10 https://doi.org/10.1073/pnas.93.10.4913	journal	May 1996
Selection of oligonucleotide probes for protein coding sequences Wang, Xiaowei; Seed, Brian Bioinformatics, Vol. 19, Issue 7 https://doi.org/10.1093/bioinformatics/btg086	journal	May 2003
Expression profiling using microarrays fabricated by an ink-jet oligonucleotide synthesizer Hughes, Timothy R.; Mao, Mao; Jones, Allan R. Nature Biotechnology, Vol. 19, Issue 4 https://doi.org/10.1038/86730	journal	April 2001
Reversible DNA encapsulation in silica to produce ROS-resistant and heat-resistant synthetic DNA 'fossils' Paunescu, Daniela; Puddu, Michela; Soellner, Justus O. B. Nature Protocols, Vol. 8, Issue 12 https://doi.org/10.1038/nprot.2013.154	journal	November 2013
Recombinant immunoglobin preparations Cabilly, Shmuel; Heyneker, Herbert L.; Holmes, William E. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/4816567 US Patent Document 4,816,567	patent	March 1989
Next-Generation Digital Information Storage in DNA Church, G. M.; Gao, Y.; Kosuri, S. Science, Vol. 337, Issue 6102 https://doi.org/10.1126/science.1226355	journal	August 2012
Toward a DNA-Based Archival Storage System Bornholt, James; Lopez, Randolph; Carmean, Douglas M. IEEE Micro, Vol. 37, Issue 3, p. 98-104 https://doi.org/10.1109/MM.2017.70	journal	January 2017
Droplet manipulations on EWOD microelectrode array architecture Wang, Gary; Ho, Ching-Yen; Hwang, Wen Jang https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8834695 US Patent Document 8,834,695	patent	September 2014
Telomerase can act as a template- and RNA-independent terminal transferase Lue, Neal F.; Bosoy, Dimitry; Moriarty, Tara J. Proceedings of the National Academy of Sciences, Vol. 102, Issue 28 https://doi.org/10.1073/pnas.0502252102	journal	June 2005
Ab initiosynthesis by DNA polymerases Zyrina, Nadezhda V.; Antipova, Valeriya N.; Zheleznaya, Lyudmila A. FEMS Microbiology Letters, Vol. 351, Issue 1 https://doi.org/10.1111/1574-6968.12326	journal	November 2013
Nucleic acid memory Zhirnov, Victor; Zadegan, Reza M.; Sandhu, Gurtej S. Nature Materials, Vol. 15, Issue 4 https://doi.org/10.1038/nmat4594	journal	March 2016
Random access in large-scale DNA data storage Organick, Lee; Ang, Siena Dumas; Chen, Yuan-Jyue Nature Biotechnology, Vol. 36, Issue 3 https://doi.org/10.1038/nbt.4079	journal	February 2018
Decoding neural transcriptomes and epigenomes via high-throughput sequencing Shin, Jaehoon; Ming, Guo-li; Song, Hongjun Nature Neuroscience, Vol. 17, Issue 11, p. 1463-1475 https://doi.org/10.1038/nn.3814	journal	October 2014
Antibodies with altered effector functions Winter, Gregory Paul; Duncan, Alexander Robert; Burton, Dennis R. https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/5624821 US Patent Document 5,624,821	patent	April 1997
Sequencing by hybridization: Towards an automated sequencing of one million M13 clones arrayed on membranes Drmanac, Radoje; Drmanac, Snezana; Labat, Ivan Electrophoresis, Vol. 13, Issue 1 https://doi.org/10.1002/elps.11501301115	journal	January 1992
Terminal deoxynucleotidyl transferase: The story of a misguided DNA polymerase Motea, Edward A.; Berdis, Anthony J. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics, Vol. 1804, Issue 5 https://doi.org/10.1016/j.bbapap.2009.06.030	journal	May 2010
Methods and apparatus for synthesizing nucleic acids Efcavitch, J. William; Siddiqi, Suhaib https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/8808989 US Patent Document 8,808,989	patent	August 2014
Design of antisense oligonucleotides stabilized by locked nucleic acids Kurreck, J. Nucleic Acids Research, Vol. 30, Issue 9 https://doi.org/10.1093/nar/30.9.1911	journal	May 2002
Photo-cleavable nucleotides for primer free enzyme mediated DNA synthesis Mathews, Anu Stella; Yang, Haikang; Montemagno, Carlo Organic & Biomolecular Chemistry, Vol. 14, Issue 35 https://doi.org/10.1039/C6OB01371F	journal	January 2016
EWOD device with calibrated serial dilution function Hadwen, Benjamin James; Brown, Christopher; Deacon, Julie Karen https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/9539573 US Patent Document 9,539,573	patent	January 2017
Locked nucleic acid (LNA): fine-tuning the recognition of DNA and RNA Braasch, Dwaine A.; Corey, David R. Chemistry & Biology, Vol. 8, Issue 1, p. 1-7 https://doi.org/10.1016/S1074-5521(00)00058-2	journal	January 2001
Polypeptide variants Idusogie, Esohe Ekinaduese; Presta, Leonard G.; Mulkerrin, Michael George https://doi.org/https://image-ppubs.uspto.gov/dirsearch-public/print/downloadPdf/6194551 US Patent Document 6,194,551	patent	February 2001

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