Underpinning transport phenomena for the patterning of biomolecules.

Surface-based assays are increasingly being used in biology and medicine, which in turn demand increasing quantitation and reproducibility. This translates into more stringent requirements on the patterning of biological entities on surfaces (also referred to as biopatterning). This tutorial focuses on mass transport in the context of existing and emerging biopatterning technologies. We here develop a step-by-step analysis of how analyte transport affects surface kinetics, and of the advantages and limitations this entails in major categories of patterning methods, including evaporating sessile droplets, laminar flows in microfluidics or electrochemistry. Understanding these concepts is key to obtaining the desired pattern uniformity, coverage, analyte usage or processing time, and equally applicable to surface assays. A representative technological review accompanies each section, highlighting the technical progress enabled by transport control in e.g. microcontact printing, inkjet printing, dip-pen nanolithography and microfluidic probes. We believe this tutorial will serve researchers to better understand available patterning methods/principles, optimize conditions and to help design protocols/assays. By highlighting fundamental challenges and available approaches, we wish to trigger the development of new surface patterning methods and assays.

[1]  Robert J. Messinger,et al.  Making it stick: convection, reaction and diffusion in surface-based biosensors , 2008, Nature Biotechnology.

[2]  Manuel Théry,et al.  Anisotropy of cell adhesive microenvironment governs cell internal organization and orientation of polarity , 2006, Proceedings of the National Academy of Sciences.

[3]  Scott L Diamond,et al.  Printing chemical libraries on microarrays for fluid phase nanoliter reactions , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[4]  T. Fukuda,et al.  Three-dimensional hepatic lobule-like tissue constructs using cell-microcapsule technology. , 2017, Acta biomaterialia.

[5]  D. V. Nicolau,et al.  Protein microarray spots are modulated by patterning method, surface chemistry and processing conditions. , 2019, Biosensors & bioelectronics.

[6]  Sriram Natarajan,et al.  Continuous-flow microfluidic printing of proteins for array-based applications including surface plasmon resonance imaging. , 2008, Analytical biochemistry.

[7]  Ronald G. Larson,et al.  Transport and deposition patterns in drying sessile droplets , 2014 .

[8]  Alexandra M. Greiner,et al.  Interdigitated multicolored bioink micropatterns by multiplexed polymer pen lithography. , 2013, Small.

[9]  F. Frascella,et al.  A flow-through holed PDMS membrane as a reusable microarray spotter for biomedical assays. , 2015, Lab on a chip.

[10]  Liming Ying,et al.  Writing with DNA and protein using a nanopipet for controlled delivery. , 2002, Journal of the American Chemical Society.

[11]  A. Herr,et al.  Protein immobilization techniques for microfluidic assays. , 2013, Biomicrofluidics.

[12]  J. Greer,et al.  Quantification of ink diffusion in microcontact printing with self-assembled monolayers. , 2009, Langmuir : the ACS journal of surfaces and colloids.

[13]  J. Barnard,et al.  Characteristic size for onset of coffee-ring effect in evaporating lysozyme-water solution droplets. , 2012, The journal of physical chemistry. B.

[14]  Ralph G Nuzzo,et al.  Fabrication of patterned multicomponent protein gradients and gradient arrays using microfluidic depletion. , 2003, Analytical chemistry.

[15]  G. Rubloff,et al.  Spatial resolution in chitosan-based programmable biomolecular scaffolds , 2009 .

[16]  Thomas Gervais,et al.  Mass transport and surface reactions in microfluidic systems , 2006 .

[17]  Peter J. Yunker,et al.  Suppression of the coffee-ring effect by shape-dependent capillary interactions , 2011, Nature.

[18]  G. Zocchi,et al.  Local cooperativity mechanism in the DNA melting transition. , 2005, Physical review. E, Statistical, nonlinear, and soft matter physics.

[19]  G. Birarda,et al.  Protein Mixture Segregation at Coffee-Ring: Real-Time Imaging of Protein Ring Precipitation by FTIR Spectromicroscopy. , 2017, The journal of physical chemistry. B.

[20]  Andrew J. Senesi,et al.  Agarose-assisted dip-pen nanolithography of oligonucleotides and proteins. , 2009, ACS nano.

[21]  Chad A. Mirkin,et al.  Multiplexed protein arrays enabled by polymer pen lithography: addressing the inking challenge. , 2009, Angewandte Chemie.

[22]  Andreas C. Damianou,et al.  Pneumococcal galactose catabolism is controlled by multiple regulators acting on pyruvate formate lyase , 2017, Scientific Reports.

[23]  Yi Liu,et al.  Fusing Sensor Paradigms to Acquire Chemical Information: An Integrative Role for Smart Biopolymeric Hydrogels , 2016, Advanced healthcare materials.

[24]  C. Mirkin,et al.  Applications of dip-pen nanolithography. , 2007, Nature nanotechnology.

[25]  T. Fukuda,et al.  Hybrid 3D printing and electrodeposition approach for controllable 3D alginate hydrogel formation , 2017, Biofabrication.

[26]  J. Rogers,et al.  Nanoscale patterns of oligonucleotides formed by electrohydrodynamic jet printing with applications in biosensing and nanomaterials assembly. , 2008, Nano letters.

[27]  K. A. Brown,et al.  Material transport in dip-pen nanolithography , 2014 .

[28]  W. Pfleging,et al.  Direct writing of a conducting polymer pattern in aqueous solution by using an ultrashort laser pulse , 2017 .

[29]  M Paturzo,et al.  Dispensing nano-pico droplets and liquid patterning by pyroelectrodynamic shooting. , 2010, Nature nanotechnology.

[30]  Nagel,et al.  Contact line deposits in an evaporating drop , 2000, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[31]  L. Yeo,et al.  A Novel Acoustomicrofluidic Nebulization Technique Yielding New Crystallization Morphologies , 2018, Advanced materials.

[32]  A. Yodh,et al.  Surfactant-induced Marangoni eddies alter the coffee-rings of evaporating colloidal drops. , 2012, Langmuir : the ACS journal of surfaces and colloids.

[33]  Khellil Sefiane,et al.  Effect of TiO2 nanoparticles on contact line stick-slip behavior of volatile drops. , 2009, The journal of physical chemistry. B.

[34]  David P. Taylor,et al.  Convection-Enhanced Biopatterning with Recirculation of Hydrodynamically Confined Nanoliter Volumes of Reagents , 2016, Analytical chemistry.

[35]  Mingjun Zhang,et al.  Bio-Microarray Fabrication Techniques—A Review , 2006, Critical reviews in biotechnology.

[36]  A R Boccaccini,et al.  Electrophoretic deposition of biomaterials , 2010, Journal of The Royal Society Interface.

[37]  Gordon G Wallace,et al.  Liquid ink deposition from an atomic force microscope tip: deposition monitoring and control of feature size. , 2014, Langmuir : the ACS journal of surfaces and colloids.

[38]  J. Hoheisel,et al.  Personalised proteome analysis by means of protein microarrays made from individual patient samples , 2017, Scientific Reports.

[39]  B. Derby Inkjet Printing of Functional and Structural Materials: Fluid Property Requirements, Feature Stability, and Resolution , 2010 .

[40]  Ibrahim T. Ozbolat,et al.  A comprehensive review on droplet-based bioprinting: Past, present and future. , 2016, Biomaterials.

[41]  Ulrich S. Schubert,et al.  Inkjet printing of proteins , 2009 .

[42]  G. Payne,et al.  Electrodeposition of a biopolymeric hydrogel in track-etched micropores , 2013 .

[43]  H. Craighead,et al.  Single DNA molecule patterning for high-throughput epigenetic mapping. , 2011, Analytical chemistry.

[44]  A. Banerjee,et al.  Cardiac Restoration Stemming From the Placenta Tree: Insights From Fetal and Perinatal Cell Biology , 2018, Front. Physiol..

[45]  Kurt Hingerl,et al.  Diffusion of thiols during microcontact printing with rigid stamps , 2010 .

[46]  Alexandra M. Greiner,et al.  Micropatterning: Interdigitated Multicolored Bioink Micropatterns by Multiplexed Polymer Pen Lithography (Small 19/2013) , 2013 .

[47]  Yanlin Song,et al.  Rate-dependent interface capture beyond the coffee-ring effect , 2016, Scientific Reports.

[48]  F. Lanni,et al.  Diffusion of insulin-like growth factor-I and ribonuclease through fibrin gels. , 2007, Biophysical journal.

[49]  S. Saha,et al.  An Ink Transport Model for Prediction of Feature Size in Dip Pen Nanolithography , 2010 .

[50]  Daniel Attinger,et al.  Self-assembly of colloidal particles from evaporating droplets: role of DLVO interactions and proposition of a phase diagram. , 2010, Langmuir : the ACS journal of surfaces and colloids.

[51]  Jean-Louis Viovy,et al.  In-mold patterning and actionable axo-somatic compartmentalization for on-chip neuron culture. , 2016, Lab on a chip.

[52]  Hui Liu,et al.  Direct electrodeposition of carboxymethyl cellulose based on coordination deposition method , 2017, Cellulose.

[53]  Chih-Ming Ho,et al.  Photolithographic patterning of organosilane monolayer for generating large area two-dimensional B lymphocyte arrays. , 2008, Lab on a chip.

[54]  S. Fusco,et al.  Chitosan Electrodeposition for Microrobotic Drug Delivery , 2013, Advanced healthcare materials.

[55]  G M Whitesides,et al.  Patterning cells and their environments using multiple laminar fluid flows in capillary networks. , 1999, Proceedings of the National Academy of Sciences of the United States of America.