Chemical Amplification Process Research Articles

Abstract 19: Proteome-wide biomarker discovery using digital MosaicNeedles

Abstract Changes in transcript levels detected by transcriptome profiling have been widely used as a surrogate for proteomics. However, recent studies have shown accumulating evidence that phenotypes of diseases that show correlations with protein levels cannot be explained by transcript levels. Hence a proteome-wide biomarker search will provide valuable information for cancer research that is not achievable from a strictly genomic approach. NanoMosaic is a digital immunoassay technology that uses a sub-100 nm nanoneedle sensor to detect single molecules. Over a billion nanoneedles are fabricated on a silicon substrate, thus named MosaicNeedlesTM, and formatted into 96, 384 or 1536 isolated well configurations at standard microplate dimensions. Each nanoneedle is a label-free biosensor, that is functionalized with capture antibodies. Each individual nanoneedle shifts its scattering spectrum when an antigen binds to it. The spectrum shift is further enhanced using a chemical amplification process. At low concentrations, the binding events of molecules to the MosaicNeedlesTM follow a Poisson distribution which insure that the number of molecules can be quantitated by counting the number of nanoneedles that display a spectrum change. Imaging automation is achieved by TessieTM instrument that reads the entire MosaicNeedlesTM and analyzes the color spectrum of individual nanoneedles. High multiplexing level up to 50 analytes can be achieved by parallelizing the detection in a microarray format within each well. NanoMosaic uses a hypothesis-free approach to construct its protein biomarker discovery panel, also known as proteome-wide association study (PWAS) panel. Individual protein analytes included in the PWAS panel are evenly spaced across the exome. Therefore, a sub-group of the entire human proteome or secretome can be interrogated in a hypothesis-free way before the entire proteome or a reflexive protein sub-group is interrogated. This approach addresses the limitations of the availability of the affinity reagents (antibodies, nanobodies, aptamers and etc.) that would be needed to simultaneously interrogate the whole proteome. Once valuable targets of interest are identified by running the PWAS-panel against a cohort of samples, mechanism studies can then be done using pathway specific panels whose design can be informed by previous PWAS results. In conclusion, NanoMosaic provides a solution to conduct a proteome-wide search for disease relevant biomarkers using its hypothesis-free PWAS-panels. The use of MosaicNeedlesTM provides higher sensitivity, wider dynamic range, lower cost and higher throughput than is currently possible by mass spectrometry or traditional immunoassay methods. Citation Format: Qimin Quan, Joshua Ritchey, Joe Wilkinson, John Geanacopoulos, Alaina Kaiser, John Boyce. Proteome-wide biomarker discovery using digital MosaicNeedles [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 19.

High‐Gain Chemically Gated Organic Electrochemical Transistor

AbstractOrganic electrochemical transistors (OECTs) have exhibited promising performance as transducers and amplifiers of low potentials due to their exceptional transconductance, enabled by the volumetric charging of organic mixed ionic/electronic conductors (OMIECs) employed as the channel material. OECT performance in aqueous electrolytes as well as the OMIECs’ redox activity has spurred a myriad of studies employing OECTs as chemical transducers. However, the OECT's large (potentiometrically derived) transconductance is not fully leveraged in common approaches that directly conduct chemical reactions amperometrically within the OECT electrolyte with direct charge transfer between the analyte and the OMIEC, which results in sub‐unity transduction of gate to drain current. Hence, amperometric OECTs do not truly display current gains in the traditional sense, falling short of the expected transistor performance. This study demonstrates an alternative device architecture that separates chemical transduction and amplification processes on two different electrochemical cells. This approach fully utilizes the OECT's large transconductance to achieve current gains of 103 and current modulations of four orders of magnitude. This transduction mechanism represents a general approach enabling high‐gain chemical OECT transducers.

An enzyme-responsive system programmed for the double release of bioactive molecules through an intracellular chemical amplification process

The rise of chemical biology has led to the development of sophisticated molecular devices designed to explore and manipulate biological processes. Within this framework, we developed the first chemical system programmed for the selective internalization and subsequent enzyme-catalyzed double release of bioactive compounds inside a targeted population of cells. This system is composed of five distinct units including a targeting ligand, an enzymatic trigger, a self-immolative linker and two active compounds articulated around a chemical amplifier. Designed as such, this molecular assembly is capable in an autonomous manner to recognize a selected population of cells, penetrate into the intracellular medium through endocytosis and transform a single enzymatic activation step into the release of two active units. Demonstrating that an enzyme-catalyzed amplification process can occur spontaneously under the conditions prevailing within the cells could be an important step toward the development of innovative molecular systems for a diverse range of applications spanning drug delivery, biological sensors and diagnostics.

Two-Photon Acid Generation Systems Based on Dibenzylidene Ketone Dyes Intermolecular Sensitization

A couple of two-photon absorption dyes containing triphenylamine groups as the electron donor were synthesized. They were combined with commonly used photoacid generator N-(trifluoromethanesulfonyloxy)-1,8-naphthalimide (NIOTf) to build two-photon acid generation systems (2PAGs). The photochemical and photophysical properties of these dyes as well as their photosensitizing mechanism were investigated. Both of the two dyes have a greatly enhanced two-photon absorption cross-section over 1000 GM. The photoacid quantum yields of 2PAGs were measured in acetonitrile solution by one-photon process. Fluorescence quenching experiments were carried out and confirmed the electron transfer mechanism in resin films. Also, the acid-catalyzed chemical amplification processes in resin films were studied with a Ti/sapphire regenerative amplifier by attenuated total reflectance Fourier transform infrared spectroscopy, and both 2PAGs exhibited superior efficiencies via two-photon absorption in comparison with isopropylthio...

A route to enantiopure RNA precursors from nearly racemic starting materials

The single-handedness of biological molecules is critical for molecular recognition and replication processes and would seem to be a prerequisite for the origin of life. A drawback of recently reported synthetic routes to RNA is the requirement for enantioenriched reactants, which fails to address the puzzle of how the single chirality of biological molecules arose. Here, we report the synthesis of highly enantioenriched RNA precursor molecules from racemic starting materials, with the molecular asymmetry derived solely from a small initial imbalance of the amino-acid enantiomers present in the reaction mixture. Acting as spectators to the main reaction chemistry, the amino acids orchestrate a sequence of physical and chemical amplification processes. The emergence of molecules of single chirality from complex, multi-component mixtures supports the robustness of this synthesis process under potential prebiotic conditions and provides a plausible explanation for the single-handedness of biological molecules before the emergence of self-replicating informational polymers.

Polymeric photoacid generators for direct photochemical modification of surface

AbstractTo achieve easy spin coating and enhanced efficiency in the photolithographic process for the direct photochemical modification of surface, we incorporated photoacid generator (PAG) into polymer backbone. Bis‐(4‐hydroxy‐phenyl)‐(4‐methoxy‐3,5‐dimethyl‐phenyl)‐sulfonium chloride was synthesized as a monomer, and was polymerized with sebacoyl chloride and terephthaloyl chloride. The resulting polymeric PAG in chloride salt form was converted to the p‐toluenesulfonate and 1‐naphthol‐5‐sulfonate forms with ion‐exchange reactions. By the photolithographic process with the polymeric PAG, the protecting groups of the linker molecules self‐assembled onto a glass plate were micropatterned to produce an amine pattern for the microarray of oligonucleotides. The acids generated from the polymeric PAG effectively deprotect the acid‐labile protecting groups of the linker molecules through a chemical amplification process in the exposed region. After the treatment of the patterned amino groups with a fluorescent dye, the pattern profiles were observed with a fluorescence scanner. The fluorescence image reveals a well‐defined pattern at a micro level, which clearly indicates that the polymeric PAGs have a great potential in photochemical surface modification for the microarray of oligonucleotides. Copyright © 2007 John Wiley & Sons, Ltd.

Molecular Glass Resists for High-Resolution Patterning

This paper describes a series of photoresists constructed from glass-forming, low-molecular-weight organic compounds, also known as molecular glasses. Compared with traditional polymeric resists, molecular glass resists are composed of smaller and more-uniform molecular building blocks. In this work, both positive-tone and negative-tone molecular glass photoresists with a range of core structures were designed and synthesized for study in advanced lithography. These molecular glass resists have asymmetric, rigid cores, which is important for producing glassy materials with glass transition temperatures substantially above room temperature. For positive-tone molecular glass photoresists, amorphous films could be obtained by partial protection of the core structure. Images were produced using photoacid-generator-catalyzed deprotection chemistry. Amorphous negative-tone resists were obtained by mixing molecular glass core structures with another minor resist component such as a photo cross-linker. It was shown by SEC that the molecular weight of the exposed and cross-linked negative-tone resist was less than 2000 g/mol, thus indicating that the solubility change is largely due to a molecular-weight increase. Both types of materials exhibited high sensitivity and resolution. Several resist characteristics were studied to assess their potential as high-resolution resists. These molecular glasses showed high fluorocarbon etch resistance that is comparable to that of poly(hydroxystyrene). Lower line edge roughness was obtained for the negative-tone molecular glass compared to a negative-tone polymeric e-beam resist. The resulting materials exhibited high sensitivity and resolution close to the tool limit under 248 nm exposures when using a chemical amplification process. A well-resolved pattern as small as 50 nm was obtained for the negative-tone molecular glass by e-beam exposure, indicating the excellent potential of using low molecular molar mass molecular glasses to form high-resolution structures.

Highly Sensitive Biomolecular Fluorescence Detection Using Nanoscale ZnO Platforms

Fluorescence detection is currently one of the most widely used methods in the areas of basic biological research, biotechnology, cellular imaging, medical testing, and drug discovery. Using model protein and nucleic acid systems, we demonstrate that engineered nanoscale zinc oxide structures can significantly enhance the detection capability of biomolecular fluorescence. Without any chemical or biological amplification processes, nanoscale zinc oxide platforms enabled increased fluorescence detection of these biomolecules when compared to other commonly used substrates such as glass, quartz, polymer, and silicon. The use of zinc oxide nanorods as fluorescence enhancing substrates in our biomolecular detection permitted sub-picomolar and attomolar detection sensitivity of proteins and DNA, respectively, when using a conventional fluorescence microscope. This ultrasensitive detection was due to the presence of ZnO nanomaterials which contributed greatly to the increased signal-to-noise ratio of biomolecular fluorescence. We also demonstrate the easy integration potential of zinc oxide nanorods into periodically patterned nanoplatforms which, in turn, will promote the assembly and fabrication of these materials into multiplexed, high-throughput, optical sensor arrays. These zinc oxide nanoplatforms will be extremely beneficial in accomplishing highly sensitive and specific detection of biological samples involving nucleic acids, proteins and cells, particularly under detection environments involving extremely small sample volumes of ultratrace-level concentrations.

Micropatterning of self-assembled monolayers on silicon amplified with photochemically generated atomic oxygen

Vacuum ultraviolet (VUV) light of 172 nm in wavelength radiated from an excimer lamp has been applied to the photochemical micropatterning of an organic monolayer which was prepared from 1-hexadecanol and was covalently attached to a Si(1 1 1) surface with a Si O R form. Based on water contact angle measurements and X-ray photoelectron spectroscopy, it was shown that, with the VUV-irradiation in the presence of atmospheric oxygen, the hexadecyloxy monolayer was gradually decomposed and etched, followed by oxidation of the underlying Si substrate surface. Since, the VUV light simultaneously excites atmospheric oxygen molecules as well as the monolayer itself, atomic oxygen species are generated just on the monolayer surface. These photochemically generated oxygen atoms accelerate degradation and etching of the monolayer. By locally promoting this chemical amplification process with oxygen, namely, irradiating the monolayer surface thorough a photomask, the monolayer could be micropatterned. In addition, the patterned monolayer was successfully employed as a microtemplate for fabrication of microdimples on the Si substrate through chemical etching or that of organic microstructures through selective adsorption of organosilane molecules.

A single component photoimaging system with styrene copolymers having t-BOC-protected quinizarin dye precursors and photoacid generating groups in a single polymer chain

A styrene monomer tBQSt, having a tert-butyloxycarbonyloxy (t-BOC)-protected quinizarin dye precursor as a pendent, has been copolymerized with N-(tosyloxy)maleimide (TsOMI) to obtain a dual functional polymer P(tBQSt/TsOMI). The polymer P(tBQSt/TsOMI), as a single component photoimaging system without using an external photoacid generator (PAG), was applied for fluorescent photopatterning by dry process based on the chemical amplification (CA) process. The TsOMI units in the polymer chains were responsible for photochemical generation of p-toluenesulfonic acid by UV exposure and the acid generated in the solution cast polymer film induced the catalytic deprotection of acid labile t-BOC groups of the quinizarin dye precursors. Accordingly, the quinizarin moieties were regenerated in the polymer chains by the CA process, thereby recovering the original color and fluorescence of the quinizarin dye. Fluorescent patterns were readily delineated on the thin polymer films by imagewise UV exposure even without a wet development process.

The first synthesis of a transition metal-catalyzed homopolymer having pendentt-boc-protected quinizarin for patterned fluorescence images

A homopolymer having pendentt-Boc-protected quinizarin moieties has been prepared for patterned fluorescence images. The homopolymer P{t-BQN (2-norbornenylmethyl di-tert-butoxycarbonylquinizarin)}5 was prepared by palladium-catalyzed addition polymerization. Thet-Boc-protecting groups of the polymer were efficiently removed during chemical amplification process and revealed original properties of quinizarin, allowing patterned fluorescence images in the polymer film.

An efficient photoresist development simulator based on cellular automata with experimental verification

An efficient and practical photoresist development simulator based on cellular automata is presented. Image reversal and chemical amplification processes are also simulated using this simulator. To verify the simulator, a series of experiments have been designed and performed using the Shipley SNR-248 negative resist, a stepper, and a deep ultraviolet source at 248 nm. Experiments were performed for periodic and isolated lines with pitches 300, 400, 500, and 1000 nm, for exposure energy doses of 11, 13, 17, and 23 mJ/cm/sup 2/, and with developer temperatures of 0, 20, and 80/spl deg/C. In all cases, the simulator results were found to be in very good agreement with the corresponding experimental results. The simulator has also successfully reproduced the incomplete opening effect observed in the case of close-spaced parallel lines.

Photoacid‐generating sulfonyloxymaleimide polymers and their application to photoimaging

AbstractSynthesis and properties of photoacid generating polymers based on four sulfonyloxymaleimides (RsOMI), N‐(tosyloxy)maleimide (TsOMI), N‐(methanesulfonyloxy)maleimide (MsOMI), N‐(trifluoromethanesulfonyloxy)maleimide (TfOMI), and N‐(10‐camphorsulfonyloxy)maleimide (CsOMI) are described. The RsOMI polymers photochemically produce corresponding sulfonic acids (RsOH), TsOH, MsOH, TfOH and 10‐camphorsulfonic acid (CSA) which can catalyze deprotection of the acid‐labile t‐BOC groups in the same polymer chains via a chemical amplification process. The photoacid generating polymers with concurrent acid‐labile groups offer great potential for applications in functional transformation and photoimaging.

Simulation of the negative chemical amplification deep-ultraviolet process in integrated circuit fabrication

Chemically amplified resists are able to produce nearly vertical line-edge profiles from low-contrast images, because acid generated upon exposure catalyses a crosslinking reaction during the subsequent post-exposure bake. A three-dimensional model for the chemical amplification process and resist etching has been developed in the framework of this research work. Based on this model, an algorithm for the simulation of the chemical amplification process and resist etching process has been implemented. The final resist profiles produced by this algorithm are in very good qualitative agreement with experimental data, and the dependence of the final resist profile on the post-exposure bake time and the number of crosslinking sites has been successfully reproduced.

Synthesis and Chemically Amplified Photo-Cross-Linking Reaction of a Polyimide Containing an Epoxy Group

A new polyimide, PI(6FDA/ep-AHHFP), containing an epoxy group was synthesized by the reaction of epichlorohydrin with PI(6FDA/AHHFP), which was prepared from 4,4‘-(1,1,1,3,3,3-hexafluoro-2-propylidene)diphthalic anhydride (6FDA) and 2,2-bis(3-amino-4-hydroxyphenyl)hexafluoropropane (AHHFP) in the presence of benzyl(trimethyl)ammonium chloride at 110−120 °C. This polyimide having an epoxy group is highly soluble in most common solvents. Photochemical reactivity of PI(6FDA/ep-AHHFP) was examined in the presence of diphenyliodonium hexafluoroarsenate as an acid generator. The conversion and the curing rate were determined by the absorbance change in the IR band at 905 cm-1 for the epoxy group. The activation energy for cross-linking reaction of PI(6FDA/ep-AHHFP) was found to be ∼6 kJ/mol. The reaction radius of an acid in PI(6FDA/ep-AHHFP) containing diphenyliodonium hexafluoroarsenate as a photoacid generator was determined to be about 19−30 A in the chemical amplification process when heated for 5−40 min a...

Patterning Characteristics of a Chemically-Amplified Negative Resist in Synchrotron Radiation Lithography

To explore the applicability of synchrotron radiation X-ray lithography for fabricating sub-quartermicron devices, we investigate the patterning characteristics of the chemically-amplified negative resist SAL601-ER7. Since these characteristics depend strongly on the conditions of the chemical amplification process, the effects of post-exposure baking and developing conditions on sensitivity and resolution are examined. The resolution-limiting factors are investigated, revealing that pattern collapse during the development process and fog caused by Fresnel diffraction, photo-electron scattering, and acid diffusion in the resist determine the resolution and the maximum aspect ratio of the lines and spaces pattern. Using the model of a swaying beam supported at one end, it is shown that pattern collapse depends on the resist pattern's flexural stiffness. Patterning stability, which depends on the delay time between exposure and baking, is also discussed.