Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules

Budassi, Julia; Cho, NaHyun; Del Valle, Anthony; Sokolov, Jonathan; Rainer, ed., Alberto

doi:10.1371/journal.pone.0250054

Title: Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules

Journal Article · 06 September 2023 · PLoS ONE

DOI: https://doi.org/10.1371/journal.pone.0250054 · OSTI ID:1998819

Budassi, Julia; Cho, NaHyun;

;

; Rainer, ed., Alberto

We describe a method for fragmenting, in-situ, surface-adsorbed and immobilized DNAs on polymethylmethacrylate(PMMA)-coated silicon substrates using microfluidic delivery of the cutting enzyme DNase I. Soft lithography is used to produce silicone elastomer (Sylgard 184) gratings which form microfluidic channels for delivery of the enzyme. Bovine serum albumin (BSA) is used to reduce DNase I adsorption to the walls of the microchannels and enable diffusion of the cutting enzyme to a distance of 10mm. Due to the DNAs being immobilized, the fragment order is maintained on the surface. Possible methods of preserving the order for application to sequencing are discussed.

View Journal Article

Cite

Export

Save

Sponsoring Organization:: USDOE

Grant/Contract Number:: SC0012704

OSTI ID:: 1998819

Journal Information:: PLoS ONE, Journal Name: PLoS ONE Journal Issue: 9 Vol. 18; ISSN 1932-6203

Publisher:: Public Library of Science (PLoS)Copyright Statement

Country of Publication:: United States

Language:: English

References (70)

Soft Lithography Xia, Younan; Whitesides, George M. Angewandte Chemie International Edition, Vol. 37, Issue 5, p. 550-575 https://doi.org/10.1002/(SICI)1521-3773(19980316)37:5<550::AID-ANIE550>3.0.CO;2-G	journal	March 1998
Minimizing the surface effect of PDMS–glass microchip on polymerase chain reaction by dynamic polymer passivation Xia, Yong-Mei; Hua, Zhi-Shan; Srivannavit, Onnop Journal of Chemical Technology & Biotechnology, Vol. 82, Issue 1 https://doi.org/10.1002/jctb.1631	journal	January 2006
Protein Denaturation in Foam Clarkson, J. R.; Cui, Z. F.; Darton, R. C. Journal of Colloid and Interface Science, Vol. 215, Issue 2 https://doi.org/10.1006/jcis.1999.6256	journal	July 1999
Surface Modification of Sylgard-184 Poly(dimethyl siloxane) Networks by Ultraviolet and Ultraviolet/Ozone Treatment Efimenko, Kirill; Wallace, William E.; Genzer, Jan Journal of Colloid and Interface Science, Vol. 254, Issue 2, p. 306-315 https://doi.org/10.1006/jcis.2002.8594	journal	October 2002
PDMS microfluidics developed for polymer based photonic biosensors Fürjes, P.; Holczer, E. G.; Tóth, E. Microsystem Technologies, Vol. 21, Issue 3 https://doi.org/10.1007/s00542-014-2130-y	journal	April 2014
Surface molecular property modifications for poly(dimethylsiloxane) (PDMS) based microfluidic devices Wong, Ieong; Ho, Chih-Ming Microfluidics and Nanofluidics, Vol. 7, Issue 3 https://doi.org/10.1007/s10404-009-0443-4	journal	April 2009
Inhibition of on-chip PCR using PDMS–glass hybrid microfluidic chips Crabtree, H. John; Lauzon, Jana; Morrissey, Yuen C. Microfluidics and Nanofluidics, Vol. 13, Issue 3 https://doi.org/10.1007/s10404-012-0968-9	journal	March 2012
Anti-fouling Coatings of Poly(dimethylsiloxane) Devices for Biological and Biomedical Applications Zhang, Hongbin; Chiao, Mu Journal of Medical and Biological Engineering, Vol. 35, Issue 2 https://doi.org/10.1007/s40846-015-0029-4	journal	April 2015
pH-dependent specific binding and combing of DNA Allemand, J. F.; Bensimon, D.; Jullien, L. Biophysical Journal, Vol. 73, Issue 4 https://doi.org/10.1016/S0006-3495(97)78236-5	journal	October 1997
PCR microfluidic devices for DNA amplification Zhang, Chunsun; Xu, Jinliang; Ma, Wenli Biotechnology Advances, Vol. 24, Issue 3 https://doi.org/10.1016/j.biotechadv.2005.10.002	journal	May 2006
Long walk to genomics: History and current approaches to genome sequencing and assembly Giani, Alice Maria; Gallo, Guido Roberto; Gianfranceschi, Luca Computational and Structural Biotechnology Journal, Vol. 18 https://doi.org/10.1016/j.csbj.2019.11.002	journal	January 2020
Dissection, acquisition and amplification of targeted position of electrostatically stretched DNA Kurosawa, Osamu; Washizu, Masao Journal of Electrostatics, Vol. 65, Issue 7 https://doi.org/10.1016/j.elstat.2005.03.094	journal	June 2007
Fabrication of microporous PMMA using ionic liquids: An improved route to classical ScCO2 foaming process Trigo-López, Miriam; Vallejos, S.; Reglero Ruiz, José A. Polymer, Vol. 183 https://doi.org/10.1016/j.polymer.2019.121867	journal	November 2019
A microfluidic chip based on surfactant-doped polydimethylsiloxane (PDMS) in a sandwich configuration for low-cost and robust digital PCR Fu, Yayun; Zhou, Hongbo; Jia, Chunping Sensors and Actuators B: Chemical, Vol. 245 https://doi.org/10.1016/j.snb.2017.01.161	journal	June 2017
A Method for Filling Complex Polymeric Microfluidic Devices and Arrays Monahan, Jennifer; Gewirth, Andrew A.; Nuzzo, Ralph G. Analytical Chemistry, Vol. 73, Issue 13 https://doi.org/10.1021/ac001426z	journal	May 2001
Surface Modification of Poly(dimethylsiloxane) Microfluidic Devices by Ultraviolet Polymer Grafting Hu, Shuwen; Ren, Xueqin; Bachman, Mark Analytical Chemistry, Vol. 74, Issue 16 https://doi.org/10.1021/ac025700w	journal	August 2002
Convenient Method for Modifying Poly(dimethylsiloxane) To Be Airtight and Resistive against Absorption of Small Molecules Ren, Kangning; Zhao, Yihua; Su, Jing Analytical Chemistry, Vol. 82, Issue 14 https://doi.org/10.1021/ac100830t	journal	June 2010
Digital Polymerase Chain Reaction in an Array of Femtoliter Polydimethylsiloxane Microreactors Men, Yongfan; Fu, Yusi; Chen, Zitian Analytical Chemistry, Vol. 84, Issue 10 https://doi.org/10.1021/ac300761n	journal	April 2012
Rapid Prototyping of Microfluidic Systems in Poly(dimethylsiloxane) Duffy, David C.; McDonald, J. Cooper; Schueller, Olivier J. A. Analytical Chemistry, Vol. 70, Issue 23, p. 4974-4984 https://doi.org/10.1021/ac980656z	journal	October 1998
Tagmentation on Microbeads: Restore Long-Range DNA Sequence Information Using Next Generation Sequencing with Library Prepared by Surface-Immobilized Transposomes Chen, He; Yao, Jiacheng; Fu, Yusi ACS Applied Materials & Interfaces, Vol. 10, Issue 14 https://doi.org/10.1021/acsami.8b01560	journal	March 2018
Materials for Microfluidic Chip Fabrication Ren, Kangning; Zhou, Jianhua; Wu, Hongkai Accounts of Chemical Research, Vol. 46, Issue 11 https://doi.org/10.1021/ar300314s	journal	June 2013
Selective Deposition of Proteins and Cells in Arrays of Microwells Ostuni, Emanuele; Chen, Christopher S.; Ingber, Donald E. Langmuir, Vol. 17, Issue 9 https://doi.org/10.1021/la001372o	journal	May 2001
Solution Assembled and Microcontact Printed Monolayers of Dodecanethiol on Gold: A Multivariate Exploration of Chemistry and Contamination Graham, Daniel J.; Price, David D.; Ratner, Buddy D. Langmuir, Vol. 18, Issue 5 https://doi.org/10.1021/la010059z	journal	February 2002
Reversible Binding of DNA on NiCl₂-Treated Mica by Varying the Ionic Strength Piétrement, Olivier; Pastré, David; Fusil, Stéphane Langmuir, Vol. 19, Issue 7 https://doi.org/10.1021/la026942u	journal	February 2003
Poly(dimethylsiloxane) Contamination in Microcontact Printing and Its Influence on Patterning Oligonucleotides Thibault, Christophe; Séverac, Childérick; Mingotaud, Anne-Françoise Langmuir, Vol. 23, Issue 21 https://doi.org/10.1021/la701841j	journal	September 2007
Patterned Protein Layers on Solid Substrates by Thin Stamp Microcontact Printing James, C. D.; Davis, R. C.; Kam, L. Langmuir, Vol. 14, Issue 4, p. 741-744 https://doi.org/10.1021/la9710482	journal	February 1998
Printing Patterns of Proteins Bernard, Andre; Delamarche, Emmanuel; Schmid, Heinz Langmuir, Vol. 14, Issue 9, p. 2225-2229 https://doi.org/10.1021/la980037l	journal	April 1998
Monolayers on disordered substrates: self-assembly of alkyltrichlorosilanes on surface-modified polyethylene and poly(dimethylsiloxane) Ferguson, Gregory S.; Chaudhury, Manoj K.; Biebuyck, Hans A. Macromolecules, Vol. 26, Issue 22 https://doi.org/10.1021/ma00074a007	journal	October 1993
Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells Peters, Brock A.; Kermani, Bahram G.; Sparks, Andrew B. Nature, Vol. 487, Issue 7406 https://doi.org/10.1038/nature11236	journal	July 2012
Haplotype-resolved genome sequencing of a Gujarati Indian individual Kitzman, Jacob O.; MacKenzie, Alexandra P.; Adey, Andrew Nature Biotechnology, Vol. 29, Issue 1 https://doi.org/10.1038/nbt.1740	journal	January 2011
Three decades of nanopore sequencing Deamer, David; Akeson, Mark; Branton, Daniel Nature Biotechnology, Vol. 34, Issue 5 https://doi.org/10.1038/nbt.3423	journal	May 2016
Haplotyping germline and cancer genomes with high-throughput linked-read sequencing Zheng, Grace X. Y.; Lau, Billy T.; Schnall-Levin, Michael Nature Biotechnology, Vol. 34, Issue 3 https://doi.org/10.1038/nbt.3432	journal	February 2016
Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing Amini, Sasan; Pushkarev, Dmitry; Christiansen, Lena Nature Genetics, Vol. 46, Issue 12 https://doi.org/10.1038/ng.3119	journal	October 2014
Coming of age: ten years of next-generation sequencing technologies Goodwin, Sara; McPherson, John D.; McCombie, W. Richard Nature Reviews Genetics, Vol. 17, Issue 6 https://doi.org/10.1038/nrg.2016.49	journal	May 2016
Tandem repeats mediating genetic plasticity in health and disease Hannan, Anthony J. Nature Reviews Genetics, Vol. 19, Issue 5 https://doi.org/10.1038/nrg.2017.115	journal	February 2018
Simple Surface Modification of Poly(dimethylsiloxane) via Surface Segregating Smart Polymers for Biomicrofluidics Gökaltun, Aslıhan; Kang, Young Bok; Yarmush, Martin L. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-43625-5	journal	May 2019
A micropatterned substrate for on-surface enzymatic labelling of linearized long DNA molecules Varapula, Dharma; LaBouff, Eric; Raseley, Kaitlin Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-51507-z	journal	October 2019
Non-random DNA fragmentation in next-generation sequencing Poptsova, Maria S.; Il'icheva, Irina A.; Nechipurenko, Dmitry Yu. Scientific Reports, Vol. 4, Issue 1 https://doi.org/10.1038/srep04532	journal	March 2014
Molecular Combing of Single DNA Molecules on the 10 Megabase Scale Kaykov, Atanas; Taillefumier, Thibaud; Bensimon, Aaron Scientific Reports, Vol. 6, Issue 1 https://doi.org/10.1038/srep19636	journal	January 2016
Exploring both sequence detection and restriction endonuclease cleavage kinetics by recognition site via single-molecule microfluidic trapping Xu, Weilin; Muller, Susan J. Lab Chip, Vol. 11, Issue 3 https://doi.org/10.1039/C0LC00176G	journal	January 2011
Conventional and emerging strategies for the fabrication and functionalization of PDMS-based microfluidic devices Shakeri, Amid; Khan, Shadman; Didar, Tohid F. Lab on a Chip, Vol. 21, Issue 16 https://doi.org/10.1039/D1LC00288K	journal	January 2021
Grafting epoxy-modified hydrophilic polymers onto poly(dimethylsiloxane) microfluidic chip to resist nonspecific protein adsorption Wu, Dapeng; Zhao, Baoxia; Dai, Zhongpeng Lab on a Chip, Vol. 6, Issue 7 https://doi.org/10.1039/b600765a	journal	January 2006
PDMS absorption of small molecules and consequences in microfluidic applications Toepke, Michael W.; Beebe, David J. Lab on a Chip, Vol. 6, Issue 12 https://doi.org/10.1039/b612140c	journal	January 2006
Surface modification of PDMS by gradient-induced migration of embedded Pluronic Wu, Zhigang; Hjort, Klas Lab on a Chip, Vol. 9, Issue 11 https://doi.org/10.1039/b901651a	journal	January 2009
Neutravidin coated surfaces for single DNA molecule analysis Kim, Yoori; Jo, Kyubong Chemical Communications, Vol. 47, Issue 22 https://doi.org/10.1039/c0cc05396a	journal	January 2011
Oxygen plasma treatment for reducing hydrophobicity of a sealed polydimethylsiloxane microchannel Tan, Say Hwa; Nguyen, Nam-Trung; Chua, Yong Chin Biomicrofluidics, Vol. 4, Issue 3 https://doi.org/10.1063/1.3466882	journal	September 2010
Observation by fluorescence microscopy of transcription on single combed DNA Gueroui, Z.; Place, C.; Freyssingeas, E. Proceedings of the National Academy of Sciences, Vol. 99, Issue 9 https://doi.org/10.1073/pnas.092561399	journal	April 2002
Capturing native long-range contiguity by in situ library construction and optical sequencing Schwartz, Jerrod J.; Lee, Choli; Hiatt, Joseph B. Proceedings of the National Academy of Sciences, Vol. 109, Issue 46 https://doi.org/10.1073/pnas.1202680109	journal	October 2012
Post Curing as an Effective Means of Ensuring the Long-term Reliability of PDMS Thin Films for Dielectric Elastomer Applications Zakaria, Shamsul; Madsen, Frederikke Bahrt; Skov, Anne Ladegaard Polymer-Plastics Technology and Engineering, Vol. 56, Issue 1 https://doi.org/10.1080/03602559.2016.1211689	journal	September 2016
PH- and salt-dependent molecular combing of DNA: experiments and phenomenological model Benke, Annegret; Mertig, Michael; Pompe, Wolfgang Nanotechnology, Vol. 22, Issue 3 https://doi.org/10.1088/0957-4484/22/3/035304	journal	December 2010
A New Method for Straightening DNA Molecules for Optical Restriction Mapping Yokota, H.; Johnson, F.; Lu, H. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.1064	journal	March 1997
Stretching DNA with a Receding Meniscus: Experiments and Models Bensimon, D.; Simon, A. J.; Croquette, V. Physical Review Letters, Vol. 74, Issue 23 https://doi.org/10.1103/PhysRevLett.74.4754	journal	June 1995
Molecular surgery of DNA based on electrostatic micromanipulation Yamamoto, T.; Kurosawa, O.; Kabata, H. IEEE Transactions on Industry Applications, Vol. 36, Issue 4 https://doi.org/10.1109/28.855954	journal	January 2000
Real-Time DNA Sequencing from Single Polymerase Molecules Eid, John; Fehr, Adrian; Gray, Jeremy Science, Vol. 323, Issue 5910, p. 133-138 https://doi.org/10.1126/science.1162986	journal	January 2009
Dynamic Molecular Combing: Stretching the Whole Human Genome for High-Resolution Studies Michalet, Xavier; Ekong, Rosemary; Fougerousse, Françoise Science, Vol. 277, Issue 5331 https://doi.org/10.1126/science.277.5331.1518	journal	September 1997
Alignment and sensitive detection of DNA by a moving interface Bensimon, A.; Simon, A.; Chiffaudel, A. Science, Vol. 265, Issue 5181 https://doi.org/10.1126/science.7522347	journal	September 1994
Ordered restriction maps of Saccharomyces cerevisiae chromosomes constructed by optical mapping Schwartz, D.; Li, X.; Hernandez, L. Science, Vol. 262, Issue 5130 https://doi.org/10.1126/science.8211116	journal	October 1993
Long-read sequence assembly of the gorilla genome Gordon, D.; Huddleston, J.; Chaisson, M. J. P. Science, Vol. 352, Issue 6281 https://doi.org/10.1126/science.aae0344	journal	March 2016
Study of the Effect of Material of Microfluid Chip on the Polymerase Chain Reaction Tupik, A. N.; Rudnitskaya, G. E.; Lukashenko, T. A. Technical Physics, Vol. 65, Issue 9 https://doi.org/10.1134/S1063784220090261	journal	September 2020
Recent advances in nonbiofouling PDMS surface modification strategies applicable to microfluidic technology Gokaltun, Aslihan; Yarmush, Martin L.; Asatekin, Ayse TECHNOLOGY, Vol. 05, Issue 01 https://doi.org/10.1142/S2339547817300013	journal	March 2017
Soft Lithography in Biology and Biochemistry Whitesides, George M.; Ostuni, Emanuele; Takayama, Shuichi Annual Review of Biomedical Engineering, Vol. 3, Issue 1 https://doi.org/10.1146/annurev.bioeng.3.1.335	journal	August 2001
Next-Generation DNA Sequencing Methods Mardis, Elaine R. Annual Review of Genomics and Human Genetics, Vol. 9, Issue 1 https://doi.org/10.1146/annurev.genom.9.081307.164359	journal	September 2008
Comparison of Conventional Surface Cleaning Methods for Si Molecular Beam Epitaxy Okumura, H.; Akane, T.; Tsubo, Y. Journal of The Electrochemical Society, Vol. 144, Issue 11 https://doi.org/10.1149/1.1838088	journal	November 1997
Next-generation sequencing library construction on a surface Feng, Kuan; Costa, Justin; Edwards, Jeremy S. BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-4797-4	journal	May 2018
Bead-linked transposomes enable a normalization-free workflow for NGS library preparation Bruinsma, Stephen; Burgess, Joshua; Schlingman, Daniel BMC Genomics, Vol. 19, Issue 1 https://doi.org/10.1186/s12864-018-5096-9	journal	October 2018
Opportunities and challenges in long-read sequencing data analysis Amarasinghe, Shanika L.; Su, Shian; Dong, Xueyi Genome Biology, Vol. 21, Issue 1 https://doi.org/10.1186/s13059-020-1935-5	journal	February 2020
Compounds from Silicones Alter Enzyme Activity in Curing Barnacle Glue and Model Enzymes Rittschof, Daniel; Orihuela, Beatriz; Harder, Tilmann PLoS ONE, Vol. 6, Issue 2 https://doi.org/10.1371/journal.pone.0016487	journal	February 2011
Systematic Comparison of Three Methods for Fragmentation of Long-Range PCR Products for Next Generation Sequencing Knierim, Ellen; Lucke, Barbara; Schwarz, Jana Marie PLoS ONE, Vol. 6, Issue 11 https://doi.org/10.1371/journal.pone.0028240	journal	November 2011
DNA bridges: A novel platform for single-molecule sequencing and other DNA-protein interaction applications Righini, Maurizio; Costa, Justin; Zhou, Wei PLOS ONE, Vol. 16, Issue 11 https://doi.org/10.1371/journal.pone.0260428	journal	November 2021
Long-Read Sequencing Emerging in Medical Genetics Mantere, Tuomo; Kersten, Simone; Hoischen, Alexander Frontiers in Genetics, Vol. 10 https://doi.org/10.3389/fgene.2019.00426	journal	May 2019

Similar Records

Sylgard® Cure Inhibition Characterization

Technical Report · 2012 · OSTI ID:1053123

Ortiz-Acosta, Denisse; Densmore, Crystal

Layer‐by‐Layer Engineered All‐Liquid Microfluidic Chips for Enzyme Immobilization

Journal Article · 2021 · Advanced Materials · OSTI ID:1837313

Liu, Tan; Yin, Yixuan; Yang, Yang; +2 more

Quantitation of exposure to benzo(a)pyrene with monoclonal antibodies

Journal Article · 1985 · Environ. Health Perspect.; (United States) · OSTI ID:5446683

Santella, R M; Hsieh, L L; Lin, C D; +2 more

Title: Microfluidic delivery of cutting enzymes for fragmentation of surface-adsorbed DNA molecules

Citation Formats

References (70)

Similar Records

Related Subjects