Controlled DNA Patterning by Chemical Lift-Off Lithography: Matrix Matters

Guiding Metal Organic Framework Morphology via Monolayer Artificial Defect-Induced Preferential Facet Selection

Guiding metal organic framework (MOF) morphology, especially without the need for chemical additives, still remains a challenge. For the first time, we report a unique surface guiding approach in controlling the crystal morphology formation of zeolitic imidazole framework-8 (ZIF-8) and HKUST-1 MOFs on disrupted alkanethiol self-assembled monolayer (SAM)-covered Au substrates. Selective molecule removal is applied to generate diverse SAM matrices rich in artificial molecular defects in a monolayer to direct the dynamic crystal growth process. When a 11-mercaptoundecanol alkanethiol monolayer is ruptured, the hydroxyl tail groups of surface residue molecules act as nucleating sites by coordination with precursor metal ions. Meanwhile, the exposed alkane chain backbones stabilize a particular facet of MOF nuclei in the dynamic growth by slowing down their crystal growth rates along a specific direction. The competitive formation between the [110] and [100] planes of ZIF-8 ultimately regulates the crystal shapes from rhombic dodecahedron, truncated rhombic dodecahedron, and truncated cube to cube. Similarly, changeable morphologies of HKUST-1 crystals are also achieved from cube and tetrakaidekahedron to octahedron, originating from the competitive selection between the [100] and [111] planes. In addition to the artificial matrix preferred orientation of initial nucleation, parameters such as temperature also play a crucial role in the resulting crystal morphology. Standing on the additive-free MOF crystal morphology growth control, porous architectures prepared in this approach can act as templates for ligand-free metal (Au, Ag, and Cu) nanocluster synthesis. The nanocluster-embedded MOF structures represent distinct crystal morphology-dependent optical properties, and interestingly, their fluorescence emission can be highly enhanced by facet-induced nanocluster packing alignments. These findings not only provide a unique thought on MOF crystal morphology guidance but also pave a new route for the accompanied property investigation and further application.

Gap-directed chemical lift-off lithographic nanoarchitectonics for arbitrary sub-micrometer patterning

We introduce a unique soft lithographic operation that exploits stamp roof collapse-induced gaps to selectively remove an alkanethiol self-assembled monolayer (SAM) on Au to generate surface patterns that are orders of magnitude smaller than structures on the original elastomer stamp. The smallest achieved feature dimension is 5 nm using a micrometer-scale structured stamp in a chemical lift-off lithography (CLL) process. Molecular patterns retained in the gaps between stamp features and their circumscribed or inscribed circles follow mathematical predictions, and their sizes can be tuned by altering the stamp structure dimensions, including height, pitch, and shape. These generated surface molecular patterns can function as biorecognition arrays or be transferred to the underneath Au layer for metallic structure creation. By combining CLL process with this gap phenomenon, soft material properties that are previously thought as demerits can be used to achieve sub-10 nm features in a straightforward sketch.

Toward a Quantitative Relationship between Nanoscale Spatial Organization and Hybridization Kinetics of Surface Immobilized Hairpin DNA Probes

Hybridization of DNA probes immobilized on a solid support is a key process for DNA biosensors and microarrays. Although the surface environment is known to influence the kinetics of DNA hybridization, so far it has not been possible to quantitatively predict how hybridization kinetics is influenced by the complex interactions of the surface environment. Using spatial statistical analysis of probes and hybridized target molecules on a few electrochemical DNA (E-DNA) sensors, functioning through hybridization-induced conformational change of redox-tagged hairpin probes, we developed a phenomenological model that describes how the hybridization rates for single probe molecules are determined by the local environment. The predicted single-molecule rate constants, upon incorporation into numerical simulation, reproduced the overall kinetics of E-DNA sensor surfaces at different probe densities and different degrees of probe clustering. Our study showed that the nanoscale spatial organization is a major factor behind the counterintuitive trends in hybridization kinetics. It also highlights the importance of models that can account for heterogeneity in surface hybridization. The molecular level understanding of hybridization at surfaces and accurate prediction of hybridization kinetics may lead to new opportunities in development of more sensitive and reproducible DNA biosensors and microarrays.

Narrower Nanoribbon Biosensors Fabricated by Chemical Lift-off Lithography Show Higher Sensitivity

Wafer-scale nanoribbon field-effect transistor (FET) biosensors fabricated by straightforward top-down processes are demonstrated as sensing platforms with high sensitivity to a broad range of biological targets. Nanoribbons with 350 nm widths (700 nm pitch) were patterned by chemical lift-off lithography using high-throughput, low-cost commercial digital versatile disks (DVDs) as masters. Lift-off lithography was also used to pattern ribbons with 2 μm or 20 μm widths (4 or 40 μm pitches, respectively) using masters fabricated by photolithography. For all widths, highly aligned, quasi-one-dimensional (1D) ribbon arrays were produced over centimeter length scales by sputtering to deposit 20 nm thin-film In₂O₃ as the semiconductor. Compared to 20 μm wide microribbons, FET sensors with 350 nm wide nanoribbons showed higher sensitivity to pH over a broad range (pH 5 to 10). Nanoribbon FETs functionalized with a serotonin-specific aptamer demonstrated larger responses to equimolar serotonin in high ionic strength buffer than those of microribbon FETs. Field-effect transistors with 350 nm wide nanoribbons functionalized with single-stranded DNA showed greater sensitivity to detecting complementary DNA hybridization vs 20 μm microribbon FETs. In all, we illustrate facile fabrication and use of large-area, uniform In₂O₃ nanoribbon FETs for ion, small-molecule, and oligonucleotide detection where higher surface-to-volume ratios translate to better detection sensitivities.

Photothermal Intracellular Delivery Using Gold Nanodisk Arrays

Local heating using pulsed laser-induced photothermal effects on plasmonic nanostructured substrates can be used for intracellular delivery applications. However, the fabrication of plasmonic nanostructured interfaces is hampered by complex nanomanufacturing schemes. Here, we demonstrate the fabrication of large-area plasmonic gold (Au) nanodisk arrays that enable photothermal intracellular delivery of biomolecular cargo at high efficiency. The Au nanodisks (350 nm in diameter) were fabricated using chemical lift-off lithography (CLL). Nanosecond laser pulses were used to excite the plasmonic nanostructures, thereby generating transient pores at the outer membranes of targeted cells that enable the delivery of biomolecules via diffusion. Delivery efficiencies of >98% were achieved using the cell impermeable dye calcein (0.6 kDa) as a model payload, while maintaining cell viabilities at >98%. The highly efficient intracellular delivery approach demonstrated in this work will facilitate translational studies targeting molecular screening and drug testing that bridge laboratory and clinical investigations.

Recent progress in creating complex and multiplexed surface-grafted macromolecular architectures

Surface-grafted macromolecules, including polymers, DNA, peptides, etc., are versatile modifications to tailor the interfacial functions in a wide range of fields. In this review, we aim to provide an overview of the most recent progress in engineering surface-grafted chains for the creation of complex and multiplexed surface architectures over micro- to macro-scopic areas. A brief introduction to surface grafting is given first. Then the fabrication of complex surface architectures is summarized with a focus on controlled chain conformations, grafting densities and three-dimensional structures. Furthermore, recent advances are highlighted for the generation of multiplexed arrays with designed chemical composition in both horizontal and vertical dimensions. The applications of such complicated macromolecular architectures are then briefly discussed. Finally, some perspective outlooks for future studies and challenges are suggested. We hope that this review will be helpful to those just entering this field and those in the field requiring quick access to useful reference information about the progress in the properties, processing, performance, and applications of functional surface-grafted architectures.

Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors

We detect short oligonucleotides and distinguish between sequences that differ by a single base, using label-free, electronic field-effect transistors (FETs). Our sensing platform utilizes ultrathin-film indium oxide FETs chemically functionalized with single-stranded DNA (ssDNA). The ssDNA-functionalized semiconducting channels in FETs detect fully complementary DNA sequences and differentiate these sequences from those having different types and locations of single base-pair mismatches. Changes in charge associated with surface-bound ssDNA vs double-stranded DNA (dsDNA) alter FET channel conductance to enable detection due to differences in DNA duplex stability. We illustrate the capability of ssDNA-FETs to detect complementary RNA sequences and to distinguish from RNA sequences with single nucleotide variations. The development and implementation of electronic biosensors that rapidly and sensitively detect and differentiate oligonucleotides present new opportunities in the fields of disease diagnostics and precision medicine.

Structure and Function Analysis of DNA Monolayers Created from Self-Assembling DNA-Dendron Conjugates

Short sequences of DNA immobilized on gold surfaces can be used to capture an array of target molecules because of their high level of specificity. Depending on the nature of the target molecules, the proper density and distribution of the immobilized DNA molecules are fundamental to the quality of the sensor. With the aim to control the packing density and minimize the heterogeneity of the surfaces, DNA-dendron conjugate molecules were synthesized in solution and used to make self-assembled monolayers of single-stranded DNA surfaces on gold. The headgroups used were polyamido amine dendrons (cleaved cystamine core dendrimers) of generations two through five. The structural composition of these self-assembled monolayers was characterized using grazing angle Fourier-transform infrared and X-ray photoelectron spectroscopies. Surface plasmon resonance was used to measure surface densities of the probe monolayers and each monolayer's ability to capture fully complementary DNA strands from solution. The surface density of the probe monolayers was found to decrease with increasing dendron generation number, while the hybridization efficiency increased with increasing dendron generation number.

Scalable Fabrication of Quasi-One-Dimensional Gold Nanoribbons for Plasmonic Sensing

Plasmonic nanostructures have a wide range of applications, including chemical and biological sensing. However, the development of techniques to fabricate submicrometer-sized plasmonic structures over large scales remains challenging. We demonstrate a high-throughput, cost-effective approach to fabricate Au nanoribbons via chemical lift-off lithography (CLL). Commercial HD-DVDs were used as large-area templates for CLL. Transparent glass slides were coated with Au/Ti films and functionalized with self-assembled alkanethiolate monolayers. Monolayers were patterned with lines via CLL. The lifted-off, exposed regions of underlying Au were selectively etched into large-area grating-like patterns (200 nm line width; 400 nm pitch; 60 nm height). After removal of the remaining monolayers, a thin In2O3 layer was deposited and the resulting gratings were used as plasmonic sensors. Distinct features in the extinction spectra varied in their responses to refractive index changes in the solution environment with a maximum bulk sensitivity of ∼510 nm/refractive index unit. Sensitivity to local refractive index changes in the near-field was also achieved, as evidenced by real-time tracking of lipid vesicle or protein adsorption. These findings show how CLL provides a simple and economical means to pattern large-area plasmonic nanostructures for applications in optoelectronics and sensing.

Differential Charging in Photoemission from Mercurated DNA Monolayers on Ferromagnetic Films

Spin-dependent and enantioselective electron-molecule scattering occurs in photoelectron transmission through chiral molecular films. This spin selectivity leads to electron spin filtering by molecular helices, with increasing magnitude concomitant with increasing numbers of helical turns. Using ultraviolet photoelectron spectroscopy, we measured spin-selective surface charging accompanying photoemission from ferromagnetic substrates functionalized with monolayers of mercurated DNA hairpins that constitute only one helical turn. Mercury ions bind specifically at thymine-thymine mismatches within self-hybridized single-stranded DNA, enabling precise control over the number and position of Hg²⁺ along the helical axis. Differential charging of the organic layers, manifested as substrate-magnetization-dependent photoionization energies, was observed for DNA hairpins containing Hg²⁺; no differences were measured for hairpin monolayers in the absence of Hg²⁺. Inversion of the DNA helical secondary structure at increased metal loading led to complementary inversion in spin selectivity. We attribute these results to increased scattering probabilities from relativistic enhancement of spin-orbit interactions in mercurated DNA.

Chemical Lift-Off Lithography of Metal and Semiconductor Surfaces

Chemical lift-off lithography (CLL) is a subtractive soft-lithographic technique that uses polydimethylsiloxane (PDMS) stamps to pattern self-assembled monolayers of functional molecules for applications ranging from biomolecule patterning to transistor fabrication. A hallmark of CLL is preferential cleavage of Au-Au bonds, as opposed to bonds connecting the molecular layer to the substrate, i.e., Au-S bonds. Herein, we show that CLL can be used more broadly as a technique to pattern a variety of substrates composed of coinage metals (Pt, Pd, Ag, Cu), transition and reactive metals (Ni, Ti, Al), and a semiconductor (Ge) using straightforward alkanethiolate self-assembly chemistry. We demonstrate high-fidelity patterning in terms of precise features over large areas on all surfaces investigated. We use patterned monolayers as chemical resists for wet etching to generate metal microstructures. Substrate atoms, along with alkanethiolates, were removed as a result of lift-off, as previously observed for Au. We demonstrate the formation of PDMS-stamp-supported bimetallic monolayers by performing CLL on two different metal surfaces using the same PDMS stamp. By expanding the scope of the surfaces compatible with CLL, we advance and generalize CLL as a method to pattern a wide range of substrates, as well as to produce supported metal monolayers, both with broad applications in surface and materials science.

Spin Selectivity in Photoinduced Charge-Transfer Mediated by Chiral Molecules

Optical control and readout of electron spin and spin currents in thin films and nanostructures have remained attractive yet challenging goals for emerging technologies designed for applications in information processing and storage. Recent advances in room-temperature spin polarization using nanometric chiral molecular assemblies suggest that chemically modified surfaces or interfaces can be used for optical spin conversion by exploiting photoinduced charge separation and injection from well-coupled organic chromophores or quantum dots. Using light to drive photoexcited charge-transfer processes mediated by molecules with central or helical chirality enables indirect measurements of spin polarization attributed to the chiral-induced spin selectivity effect and of the efficiency of spin-dependent electron transfer relative to competitive relaxation pathways. Herein, we highlight recent approaches used to detect and to analyze spin selectivity in photoinduced charge transfer including spin-transfer torque for local magnetization, nanoscale charge separation and polarization, and soft ferromagnetic substrate magnetization- and chirality-dependent photoluminescence. Building on these methods through systematic investigation of molecular and environmental parameters that influence spin filtering should elucidate means to manipulate electron spins and photoexcited states for room-temperature optoelectronic and photospintronic applications.

Micropatterned Viral Membrane Clusters for Antiviral Drug Evaluation

The function of biological nanoparticles, such as membrane-enveloped viral particles, is often enhanced when the particles form higher-order supramolecular assemblies. While there is intense interest in developing biomimetic platforms that recapitulate these collective properties, existing platforms are limited to mimicking individual virus particles. Here, we present a micropatterning strategy to print linker molecules selectively onto bioinert surfaces, thereby enabling controlled tethering of biomimetic viral particle clusters across defined geometric patterns. By controlling the linker concentration, it is possible to tune the density of tethered particles within clusters while enhancing the signal intensity of encapsulated fluorescent markers. Time-resolved tracking of pore formation and membrane lysis revealed that an antiviral peptide can disturb clusters of the membrane-enclosed particles akin to the targeting of individual viral particles. This platform is broadly useful for evaluating the performance of membrane-active antiviral drug candidates, whereas the micropatterning strategy can be applied to a wide range of biological nanoparticles and other macromolecular entities.

Finely Tunable Surface Wettability by Two-Dimensional Molecular Manipulation

Local molecular environment governs material interface properties, especially the substrate's exposing behavior and overall functionality expression. Although current techniques can provide efficient surface property modification, challenges in molecule spatial distribution and composition controls limited the generation of homogeneous and finely tunable molecular environment. In this study, Au-thiolate rupturing operation in chemical lift-off lithography (CLL) is used to manipulate the substrate interface molecular environment. The creation of randomly distributed artificial self-assembled monolayer defects generates vacancies for substrate property modification through back-insertion of molecules with opposite functionalities. Surface wettability adjustment is utilized as an example, where well-controllable molecule distribution provides finely tunable substrate affinity toward liquids with different physical properties. The distinct property difference between two surface regions assists microdroplet formation when liquids flow through, not only water solution but also low-surface-tension organic liquids. These microdroplet arrays become a template to guide material assembly in its formation process and act as pH-sensitive platforms for high-throughput detection. Furthermore, the tunability of the molecular pattern in this approach helps minimize the coffee-ring effect and the sweet-spot issue in matrix-assisted laser desorption/ionization mass spectrometry. Two-dimensional molecular manipulation in the CLL operation, therefore, holds the capability toward controlling homogeneous material surface property and toward exhibiting behavior adjustments.

Single Molecule Profiling of Molecular Recognition at a Model Electrochemical Biosensor

The spatial arrangement of target and probe molecules on the biosensor is a key aspect of the biointerface structure that ultimately determines the properties of interfacial molecular recognition and the performance of the biosensor. However, the spatial patterns of single molecules on practical biosensors have been unknown, making it difficult to rationally engineer biosensors. Here, we have used high-resolution atomic force microscopy to map closely spaced individual probes as well as discrete hybridization events on a functioning electrochemical DNA sensor surface. We also applied spatial statistical methods to characterize the spatial patterns at the single molecule level. We observed the emergence of heterogeneous spatiotemporal patterns of surface hybridization of hairpin probes. The clustering of target capture suggests that hybridization may be enhanced by proximity of probes and targets that are about 10 nm away. The unexpected enhancement was rationalized by the complex interplay between the nanoscale spatial organization of probe molecules, the conformational changes of the probe molecules, and target binding. Such molecular level knowledge may allow one to tailor the spatial patterns of the biosensor surfaces to improve the sensitivity and reproducibility.

Large-Area, Ultrathin Metal-Oxide Semiconductor Nanoribbon Arrays Fabricated by Chemical Lift-Off Lithography

Nanoribbon- and nanowire-based field-effect transistors (FETs) have attracted significant attention due to their high surface-to-volume ratios, which make them effective as chemical and biological sensors. However, the conventional nanofabrication of these devices is challenging and costly, posing a major barrier to widespread use. We report a high-throughput approach for producing arrays of ultrathin (∼3 nm) In2O3 nanoribbon FETs at the wafer scale. Uniform films of semiconducting In2O3 were prepared on Si/SiO2 surfaces via a sol-gel process prior to depositing Au/Ti metal layers. Commercially available high-definition digital versatile discs were employed as low-cost, large-area templates to prepare polymeric stamps for chemical lift-off lithography, which selectively removed molecules from self-assembled monolayers functionalizing the outermost Au surfaces. Nanoscale chemical patterns, consisting of one-dimensional lines (200 nm wide and 400 nm pitch) extending over centimeter length scales, were etched into the metal layers using the remaining monolayer regions as resists. Subsequent etch processes transferred the patterns into the underlying In2O3 films before the removal of the protective organic and metal coatings, revealing large-area nanoribbon arrays. We employed nanoribbons in semiconducting FET channels, achieving current on-to-off ratios over 107 and carrier mobilities up to 13.7 cm2 V-1 s-1. Nanofabricated structures, such as In2O3 nanoribbons and others, will be useful in nanoelectronics and biosensors. The technique demonstrated here will enable these applications and expand low-cost, large-area patterning strategies to enable a variety of materials and design geometries in nanoelectronics.

Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates

Aptamers are chemically synthesized oligonucleotides or peptides with molecular recognition capabilities. We investigated recognition of substrate-tethered small-molecule targets, using neurotransmitters as examples, and fluorescently labeled DNA aptamers. Substrate regions patterned via microfluidic channels with dopamine or   l-tryptophan were selectively recognized by previously identified dopamine or l-tryptophan aptamers, respectively. The on-substrate dissociation constant determined for the dopamine aptamer was comparable to, though, slightly greater than the previously determined solution dissociation constant. Using prefunctionalized neurotransmitter-conjugated oligo(ethylene glycol) alkanethiols and microfluidics patterning, we produced multiplexed substrates to capture and to sort aptamers. Substrates patterned with l-3,4-dihydroxyphenylalanine, l- threo-dihydroxyphenylserine, and l-5-hydroxytryptophan enabled comparison of the selectivity of the dopamine aptamer for different targets via simultaneous determination of in situ binding constants. Thus, beyond our previous demonstrations of recognition by protein binding partners (i.e., antibodies and G-protein-coupled receptors), strategically optimized small-molecule-functionalized substrates show selective recognition of nucleic acid binding partners. These substrates are useful for side-by-side target comparisons and future identification and characterization of novel aptamers targeting neurotransmitters or other important small molecules.

Small-Molecule Patterning via Prefunctionalized Alkanethiols

Interactions between small molecules and biomolecules are important physiologically and for biosensing, diagnostic, and therapeutic applications. To investigate these interactions, small molecules can be tethered to substrates through standard coupling chemistries. While convenient, these approaches co-opt one or more of the few small-molecule functional groups needed for biorecognition. Moreover, for multiplexing, individual probes require different surface functionalization chemistries, conditions, and/or protection/deprotection strategies. Thus, when placing multiple small-molecules on surfaces, orthogonal chemistries are needed that preserve all functional groups and are sequentially compatible. Here, we approach high-fidelity small-molecule patterning by coupling small-molecule neurotransmitter precursors, as examples, to monodisperse asymmetric oligo(ethylene glycol)alkanethiols during synthesis and prior to self-assembly on Au substrates. We use chemical lift-off lithography to singly and doubly pattern substrates. Selective antibody recognition of pre-functionalized thiols was comparable to or better than recognition of small molecules functionalized to alkanethiols after surface assembly. These findings demonstrate that synthesis and patterning approaches that circumvent sequential surface conjugation chemistries enable biomolecule recognition and afford gateways to multiplexed small-molecule functionalized substrates.

Precision-Guided Nanospears for Targeted and High-Throughput Intracellular Gene Delivery

An efficient nonviral platform for high-throughput and subcellular precision targeted intracellular delivery of nucleic acids in cell culture based on magnetic nanospears is reported. These magnetic nanospears are made of Au/Ni/Si (∼5 μm in length with tip diameters <50 nm) and fabricated by nanosphere lithography and metal deposition. A magnet is used to direct the mechanical motion of a single nanospear, enabling precise control of position and three-dimensional rotation. These nanospears were further functionalized with enhanced green fluorescent protein (eGFP)-expression plasmids via a layer-by-layer approach before release from the underlying silicon substrate. Plasmid functionalized nanospears are guided magnetically to approach target adherent U87 glioblastoma cells, penetrating the cell membrane to enable intracellular delivery of the plasmid cargo. After 24 h, the target cell expresses green fluorescence indicating successful transfection. This nanospear-mediated transfection is readily scalable for the simultaneous manipulation of multiple cells using a rotating magnet. Cell viability >90% and transfection rates >80% were achieved, which exceed conventional nonviral intracellular methods. This approach is compatible with good manufacturing practices, circumventing barriers to the translation and clinical deployment of emerging cellular therapies.

Self-standing aptamers by an artificial defect-rich matrix

The classical alkanethiol post-passivation can prevent nonspecific binding of nucleotide bases onto supporting substrates and help aptamers transition from a "lying down" to a "standing up" orientation. However, the surface probes display lower binding affinity towards targets than those in bulk solutions due to unsatisfied hybridization spaces on the alkanethiol passivated substrate. To overcome this challenge, an artificial defect-rich matrix possessing an aptamer "self-standing" property created by chemical lift-off lithography (CLL) is demonstrated. This approach provided artificial defects on a hydroxyl-terminated alkanethiol self-assembled monolayer (SAM), which allowed the insertion of thiolated aptamers. The diluted surface molecular environment assisted aptamers not only to "self-stand" on the surface, but also to separate from each other, providing a suitable surface aptamer density and sufficient space for capturing targets. With this approach, the binding affinity of the aptamer towards a target was comparable to solution-type probes, showing higher recognition efficiency than that in conventional methods.

Large Area Nanoparticle Alignment by Chemical Lift-Off Lithography

Nanoparticle alignment on the substrate attracts considerable attention due to its wide application in different fields, such as mechanical control, small size electronics, bio/chemical sensing, molecular manipulation, and energy harvesting. However, precise nanoparticle positioning and deposition control with high fidelity are still challenging. Herein, a straightforward strategy for high quality nanoparticle-alignment by chemical lift-off lithography (CLL) is demonstrated. This technique creates high resolution self-assembled monolayer (SAM) chemical patterns on gold substrates, enabling nanoparticle-selective deposition and precise alignment. The fabricated nanoparticle arrangement geometries and dimensions are well-controllable in a large area. With proper nanoparticle surface functionality control and adequate substrate molecular manipulation, well-defined nanoparticle arrays with single-particle-wide alignment resolution are achieved.

Wafer-scale bioactive substrate patterning by chemical lift-off lithography

The creation of bioactive substrates requires an appropriate interface molecular environment control and adequate biological species recognition with minimum nonspecific attachment. Herein, a straightforward approach utilizing chemical lift-off lithography to create a diluted self-assembled monolayer matrix for anchoring diverse biological probes is introduced. The strategy encompasses convenient operation, well-tunable pattern feature and size, large-area fabrication, high resolution and fidelity control, and the ability to functionalize versatile bioarrays. With the interface-contact-induced reaction, a preformed alkanethiol self-assembled monolayer on a Au surface is ruptured and a unique defect-rich diluted matrix is created. This post lift-off region is found to be suitable for insertion of a variety of biological probes, which allows for the creation of different types of bioactive substrates. Depending on the modifications to the experimental conditions, the processes of direct probe insertion, molecular structure change-required recognition, and bulky biological species binding are all accomplished with minimum nonspecific adhesion. Furthermore, multiplexed arrays via the integration of microfluidics are also achieved, which enables diverse applications of as-prepared substrates. By embracing the properties of well-tunable pattern feature dimension and geometry, great local molecular environment control, and wafer-scale fabrication characteristics, this chemical lift-off process has advanced conventional bioactive substrate fabrication into a more convenient route.

Surface functional DNA density control by programmable molecular defects

Spatially programmable molecular-level defects via straightforward chemical lift-off manipulation leads to the direct regulation of complex surface DNA densities.

Molecular conformations of DNA targets captured by model nanoarrays

An open question in single molecule nanoarrays is how the chemical and morphological heterogeneities of the solid support affect the properties of biomacromolecules. We generated arrays that allowed individually-resolvable DNA molecules to interact with tailored surface heterogeneities and revealed how molecular conformations are impacted by surface interactions.

Self-Collapse Lithography

We report a facile, high-throughput soft lithography process that utilizes nanoscale channels formed naturally at the edges of microscale relief features on soft, elastomeric stamps. Upon contact with self-assembled monolayer (SAM) functionalized substrates, the roof of the stamp collapses, resulting in the selective removal of SAM molecules via a chemical lift-off process. With this technique, which we call self-collapse lithography (SCL), sub-30 nm patterns were achieved readily using masters with microscale features prepared by conventional photolithography. The feature sizes of the chemical patterns can be varied continuously from ∼2 μm to below 30 nm by decreasing stamp relief heights from 1 μm to 50 nm. Likewise, for fixed relief heights, reducing the stamp Young's modulus from ∼2.0 to ∼0.8 MPa resulted in shrinking the features of resulting patterns from ∼400 to ∼100 nm. The self-collapse mechanism was studied using finite element simulation methods to model the competition between adhesion and restoring stresses during patterning. These results correlate well with the experimental data and reveal the relationship between the line widths, channel heights, and Young's moduli of the stamps. In addition, SCL was applied to pattern two-dimensional arrays of circles and squares. These chemical patterns served as resists during etching processes to transfer patterns to the underlying materials (e.g., gold nanostructures). This work provides new insights into the natural propensity of elastomeric stamps to self-collapse and demonstrates a means of exploiting this behavior to achieve patterning via nanoscale chemical lift-off lithography.

Analyzing Spin Selectivity in DNA-Mediated Charge Transfer via Fluorescence Microscopy

Understanding spin-selective interactions between electrons and chiral molecules is critical to elucidating the significance of electron spin in biological processes and to assessing the potential of chiral assemblies for organic spintronics applications. Here, we use fluorescence microscopy to visualize the effects of spin-dependent charge transport in self-assembled monolayers of double-stranded DNA on ferromagnetic substrates. Patterned DNA arrays provide background regions for every measurement to enable quantification of substrate magnetization-dependent fluorescence due to the chiral-induced spin selectivity effect. Fluorescence quenching of photoexcited dye molecules bound within DNA duplexes is dependent upon the rate of charge separation/recombination upon photoexcitation and the efficiency of DNA-mediated charge transfer to the surface. The latter process is modulated using an external magnetic field to switch the magnetization orientation of the underlying ferromagnetic substrates. We discuss our results in the context of the current literature on the chiral-induced spin selectivity effect across various systems.

Polymer-Pen Chemical Lift-Off Lithography

We designed and fabricated large arrays of polymer pens having sub-20 nm tips to perform chemical lift-off lithography (CLL). As such, we developed a hybrid patterning strategy called polymer-pen chemical lift-off lithography (PPCLL). We demonstrated PPCLL patterning using pyramidal and v-shaped polymer-pen arrays. Associated simulations revealed a nanometer-scale quadratic relationship between contact line widths of the polymer pens and two other variables: polymer-pen base line widths and vertical compression distances. We devised a stamp support system consisting of interspersed arrays of flat-tipped polymer pens that are taller than all other sharp-tipped polymer pens. These supports partially or fully offset stamp weights thereby also serving as a leveling system. We investigated a series of v-shaped polymer pens with known height differences to control relative vertical positions of each polymer pen precisely at the sub-20 nm scale mimicking a high-precision scanning stage. In doing so, we obtained linear-array patterns of alkanethiols with sub-50 nm to sub-500 nm line widths and minimum sub-20 nm line width tunable increments. The CLL pattern line widths were in agreement with those predicted by simulations. Our results suggest that through informed design of a stamp support system and tuning of polymer-pen base widths, throughput can be increased by eliminating the need for a scanning stage system in PPCLL without sacrificing precision. To demonstrate functional microarrays patterned by PPCLL, we inserted probe DNA into PPCLL patterns and observed hybridization by complementary target sequences.

Patterning of supported gold monolayers via chemical lift-off lithography

The supported monolayer of Au that accompanies alkanethiolate molecules removed by polymer stamps during chemical lift-off lithography is a scarcely studied hybrid material. We show that these Au-alkanethiolate layers on poly(dimethylsiloxane) (PDMS) are transparent, functional, hybrid interfaces that can be patterned over nanometer, micrometer, and millimeter length scales. Unlike other ultrathin Au films and nanoparticles, lifted-off Au-alkanethiolate thin films lack a measurable optical signature. We therefore devised fabrication, characterization, and simulation strategies by which to interrogate the nanoscale structure, chemical functionality, stoichiometry, and spectral signature of the supported Au-thiolate layers. The patterning of these layers laterally encodes their functionality, as demonstrated by a fluorescence-based approach that relies on dye-labeled complementary DNA hybridization. Supported thin Au films can be patterned via features on PDMS stamps (controlled contact), using patterned Au substrates prior to lift-off (e.g., selective wet etching), or by patterning alkanethiols on Au substrates to be reactive in selected regions but not others (controlled reactivity). In all cases, the regions containing Au-alkanethiolate layers have a sub-nanometer apparent height, which was found to be consistent with molecular dynamics simulations that predicted the removal of no more than 1.5 Au atoms per thiol, thus presenting a monolayer-like structure.

Molecular dynamics simulations of nanoscale engravings on an alkanethiol monolayer

Thermal stability of nanoscale engravings on alkanethiol monolayer.

Double-Sided Opportunities Using Chemical Lift-Off Lithography

We discuss the origins, motivation, invention, development, applications, and future of chemical lift-off lithography, in which a specified pattern of a self-assembled monolayer is removed, i.e., lifted off, using a reactive, patterned stamp that is brought into contact with the monolayer. For Au substrates, this process produces a supported, patterned monolayer of Au on the stamp in addition to the negative pattern in the original molecular monolayer. Both the patterned molecular monolayer on the original substrate and the patterned supported metal monolayer on the stamp are useful as materials and for further applications in sensing and other areas. Chemical lift-off lithography effectively lowers the barriers to and costs of high-resolution, large-area nanopatterning. On the patterned monolayer side, features in the single-nanometer range can be produced across large (square millimeter or larger) areas. Patterns smaller than the original stamp feature sizes can be produced by controlling the degree of contact between the stamp and the lifted-off monolayer. We note that this process is different than conventional lift-off processes in lithography in that chemical lift-off lithography removes material, whereas conventional lift-off is a positive-tone patterning method. Chemical lift-off lithography is in some ways similar to microtransfer printing. Chemical lift-off lithography has critical advantages in the preparation of biocapture surfaces because the molecules left behind are exploited to space and to orient functional(ized) molecules. On the supported metal monolayer side, a new two-dimensional material has been produced. The useful important chemical properties of Au (vis-à-vis functionalization with thiols) are retained, but the electronic and optical properties of bulk Au or even Au nanoparticles are not. These metal monolayers do not quench excitation and may be useful in optical measurements, particularly in combination with selective binding due to attached molecular recognition elements. In contrast to materials such as graphene that have bonding confined to two dimensions, these metal monolayers can be straightforwardly patterned-by patterning the stamp, the initial monolayer, or the initial substrate. Well-developed thiol-Au and related chemistries can be used on the supported monolayers. As there is little quenching and photoabsorption, spectroscopic imaging methods can be used on these functionalized materials. We anticipate that the properties of the metal monolayers can be tuned by varying the chemical, physical, and electronic connections made by and to the supporting molecular layers. That is, the amount of charge in the layer can be determined by controlling the density of S-Au (or other) connections and the molecular backbone and functionality, which determine the strength with which the chemical contact withdraws charge from the metal. This process should work for other coinage-metal substrates and additional systems where the binding of the outermost layers to the substrate is weaker than the molecule-substrate attachment.