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The aim of this work is to artificially reproduce scalable cellular-like compartments on a chip, thus realizing specialized small volume systems to study the behaviour of interacting biomolecules by few binding events. In particular, we show an unprecedented solution-based protein-binding assay based on arrays of oil-confined water droplets containing protein targets, labelled ligands and other compounds.

Printing biology is our way to define a novel field employing material printing techniques generally used in plastic electronics to solve important issues of biology by miniaturized and high-throughput platforms. In this field, we already showed the possibility to use Dip Pen Lithography to fabricate single-cell biochips [1]. Also,we employed non-contact patterning methods such as inkjet printing methods to fabricate microarrays for drug screening at solid-liquid interfaces [2] or in picoliter-scale liquid droplets [3] so enabling high-throughput screening of chemical libraries onto disease-based targets. In this regard, printing methods would greatly reduce times and costs of standard drug screening campaigns which are commonly based on complex liquid handling robotics and are time and reagent consuming (micro-, nanoliter scale). In this work, we show a low-cost, general and miniaturized printing biology approach for drug screening, by combining Inkjet Printing and Dip Pen Lithography to develop the biochip. We show the possibility to precisely deliver femtoliter scale droplets of protein targets by Dip Pen Lithography by finely tuning the deposition parameters and ink formulation. Protein solutions are spiked with glycerol at 30 % v/v and are deposited at defined values of humidity (50 % -70 % R.H.). This permits to obtain microscale droplet arrays where picoliter volumes of drug candidates solutions are readily deposited by inkjet printing. In this way, it is possible to produce different drug targets concentration directly on-chip. Fluorescence confocal microscopy is here used to quantify drug-ligand interaction by means of standard intensity based imaging and fluctuation techniques that permit mapping concentration and important biophysical parameters including diffusion coefficients of fluorolabeled (or intrinsically fluorescent) ligands at nanomolar concentration. Outputs obtained on different systems by means of such a miniaturized approach are compared with the ones obtained on standard microliters volumes samples, confirming the ability of our biochip printing methodology to discriminate ligand-target interactions in different compounds. MiUR and the PRIN2012 program are acknowledged for fudings.

Our studies in the field of printing nanobiology in aqueous solution are proposed to highlight the role of water in the processes of interaction between biomolecules in drug- screening devices fabricated by bioprinting technologies and to emphasize the influence of water evaporation on the diffusion of molecules in droplets of picoliter-scale.

The first step for prevention and treatment of diseases is the accurate diagnosis. However, proper diagnostic technologies are not available in developing countries due to the lack of reliable electrical power, refrigeration and trained personnel. For this reason, there is an urgent need of low cost, rapid assays not requiring any external support. By coupling such technologies to communication infrastructures, healthcare in areas without access to medical personnel would be possible. “Paper” like substrates are ideal for fabricating such devices since they are cheap, easy to degradate after use and compatible with most of existing printing technologies [1]. We had previously shown the possibility to efficiently deposit oligonucleotides by Dip Pen Lithography(DPL) onto glass surfaces [2]. In this work, we deposited oligonucleotides on nylon substrate for the fabrication of biochips usable for detecting the activity of human topoisomerase I. Subsequently, the chip will be modified to detect the Malariacausing Plasmodium parasites through the detection of Plasmodium topoisomerase I activity [3]. We optimized oligonucleotides printing on nylon substrate, obtaining efficient deposition at 10 - 1 uM oligonucleotide concentrations, 70% relative humidity and 30% glycerol v/v. We obtained circular spots with diameter in the range of 30 - 50 microns, with the dimension being a function of dwell time (1s – 20 s). DPL operation needs ultra tiny amounts of DNA (as low as 0.5 uL, 10 - 1 uM concentration) for printing thousands of spots in a single run so reducing material consumption in comparison with standard bioprinting techniques [4]. In a first set of experiments, the printed oligonucleotides was hybridized with a fluorescence-labelled complementary probe to detect and quantify DNA after DPL deposition. In subsequent experiment, the spotted oligonucleotides generate a topoisomerase substrate, which upon reaction with the enzyme will be coupled to a fluorescently labelled oligonucleotide to allow detection of a signal. In conclusion, the combination of DPL and topoisomerase detection onto nylon substrates would be a suitable solution for point-of-care diagnostic chips fabrication.

The multiplexed, high-throughput fabrication of microarrays is of vital importance for many applications in life sciences, including drug screening, medical diagnostics and cell biology. In single cell investigations, features smaller than 10 μm are needed for functional manipulation of sub-cellular structures. Several top-down methodologies like electron beam lithography and microcontact printing can be employed for indirect surface patterning at this scale, however those approaches often require clean rooms and multiplexing of several different biomolecules on the same surface is limited [1]. To overcome these obstacles, we combined Dip-pen nanolithography (DPN) and DNA-directed immobilization (DDI) of proteins to fabricate cell-compatible functionalized glass surfaces [2]. We optimized ink formulation for ssDNA printing and the produced arrays were then functionalized with epidermal growth factor (EGF) taking advantage of covalent ssDNA-streptavidin conjugates as adaptor molecules. The surface-immobilized EGF was used for recruiting EGFR in the plasma membrane of MCF7 cells. Via this bottom-up structuring approach, we were able to analyse multiple protein-protein interactions simultaneously in individual living cells [3]. To improve the efficiency of multiplexed surface patterning, we developed a prototype of a robust custom plotter based on 2D polymer-pen lithography (2D-PPL) [4]. This device enables rapid fabrication of microarrays at ambient conditions in a multiplexed direct-writing mode. The printing process was carried out by polymeric pyramidal pens onto which multiple (up to 36) ssDNA solutions can be loaded through a microfluidic inkwell device. Subsequent to optimization of ink viscosity and surface tension by glycerol and tween-20, DNA arrays were plotted and used for DDI of EGF-bearing ssDNA-streptavidin conjugates. The resulting microarrays covered areas of about 0.5 cm2, and were capable of recruiting and activating EGF receptors in sub-cellular regions within human MCF7 cells [4]. References [1] G. Arrabito, B. Pignataro. 2012. Solution Processed Micro- and Nano- Bioarrays for Multiplexed Biosensing. Anal. Chem. 84:5450–5462. [2] G. Arrabito et al. 2013. Biochips for Cell Biology by Combined Dip-Pen Nanolithography and DNA-Directed Protein Immobilization. Small. 9:4243-4249. [3] S. Gandor et al. 2013. A Protein-Interaction Array Inside a Living Cell. Angew. Chem. Int. Ed. Engl. 52:4790–4794. [4] G. Arrabito, et al. 2014. Low-cost Plotter Device for Sub-Cellular Scale Microarray Fabrication. Small. DOI: 10.1002/smll.201303390.

In this thesis work, solution dispensing techniques have been employed for the realization of complex biological arrays. Inkjet printing techniques were employed for the generation of drug screening platforms. This approach was initially proved with a model enzyme system like Glucose Oxidase substrate covalently linked to a functionalized silicon oxide support. On this support an enzymatic substrate (D-glucose)/inhibitor (D-glucal) couple was accurately dispensed. A simple optical detection method was used to prove the screening capability of the microarray with the possibility to assay with high reproducibility at the single spot level. Afterwards, this methodology has been extended to CYP450 enzymes like CYP3A4, one of the main targets for the phase I drug metabolism via a droplet microreactors arrays containing CYP3A4 enzyme mixed with model inhibitors (erythromycin) and enzymatic chemiluminescent substrates (Luciferin-Isopropylacetate). The enzymatic activity was detected by using easy and low cost optical measurements of spot brightness. As a second main objective, high-throughput and multiplexed Dip Pen Nanopatterning methodologies in liquid format were combined with Proteic Ligand DNA-Directed Immobilization for the creation of complex protein biochips on modified glass surfaces displaying spots of cell-specific ligands with lateral dimensions minor than one single cell. In a first application the epidermal growth factor (EFG) protein arrays were realized to display specific single cell adhesion activity. As a second application, immobilized proteic ligands were used to recruit designed cellular receptors which presented intracellular protein domain whose interaction with a cytosolic binding partner was monitored and perturbated.

Drug screening is the complex process of retrieving chemical compounds able to modulate the activity of biological targets which are of interest for certain diseases. Conventional miniaturized drug screening technologies are based on robotic dispensers coupled with microwell arrays. However these devices require time and reagent consuming (micro-, nanoliter scale) instrumental tools, liquid handling robotics and complex detectors. Here we show a low-cost and efficient drug screening methodology based on inkjet printing for delivering molecular systems in picoliter volumes coupled with easily-implemented detection tools for probing target-drug interaction. We firstly show up a screening platform for a model enzyme/substrate couple and we extend this approach to systems of clear interest for medicinal chemistry. The approach was initially proved with a model enzyme system like Glucose Oxidase substrate covalently linked to a functionalized silicon oxide support. On this support an enzymatic substrate (D-glucose)/inhibitor (D-glucal) couple was accurately dispensed. A simple colorimetric detection method based on the production of a red quinoneimine dye in a reaction catalyzed by Horseradish Peroxidase proved the screening capability of the microarray at the single spot level. Occurrence of competitive inhibition was verified at the solid-liquid interface with a similar behavior occurring for such system in a solution phase. Afterwards, this methodology has been extended to CYP450 enzymes like CYP3A4, one of the main targets for the phase I drug metabolism via a droplet microreactors arrays containing CYP3A4 enzyme mixed with model inhibitors (i.e. ketoconazole and erythromycin) and enzymatic chemiluminescent substrates (Luciferin- Isopropylacetate). Enzymatic activity in picoliter liquid spots was detected by using a low cost optical method. Accordingly, bioluminescence given by D-luciferin upon reaction with oxygen in a reaction catalyzed by Luciferase enzyme leads to a production of photons that increase spot brightness which can be quantified by Charge-coupled device camera.

In this work, we show a low-cost, speed, microarray-based drug screening platform that employs inkjet printing drug dispensing on an enzymatic-rich surface. Mixtures of a model substrate (Dglucose)/ inhibitor (D-glucal) couple have been inkjet printed on a target enzymatic monolayer (glucose oxidase) linked to a functionalized silicon oxide solid surface [1]. It has been possible to fabricate microarrays with quality factors as high as those of conventional pin printing spotting. By a simple horseradish-based colorimetric enzymatic assay, the detection of biological activity at the single spot has been proved. The figure shows a scheme of the platform: molecular inks of the enzymatic substrate or a substrate/inhibitor mixture are dispensed on the enzymatic-rich surface with detection at the single spots. Optical intensity measurements showed a competitive inhibition mechanism at the solid-liquid interface, along with overcompeting effects at lower inhibitor concentrations [2]. This methodology is extended to CYP450 enzymes like CYP3A4, one of the main targets for the phase I drug metabolism. In this respect, sol-gel enzymatic encapsulation strategies inside a polymer matrix prepared by MTMOS (methyltrimethoxysilane) precursors [3] or alginate are envisioned. The evaluation of the biological activity is realized via a fluorescent-based assay. In conclusion, we show how inkjet printing methodologies may investigate interesting physicochemical activities of functional biomolecules at a solid surfaces including their interaction and reaction behavior. Moreover, if coupled with a simple and generalized detection method they may satisfy speed, low-cost, miniaturized and high-throughput screening needs by dispensing entire chemical libraries on solid supported biological targets.