Corona Phase Molecular Recognition Research Articles

Corona Phase Molecular Recognition of Interleukin-6 Family Cytokines Using Nir Single Walled Carbon Nanotube

The Interleukin-6 (IL-6) family of cytokines regulate inflammation and play important roles in numerous biochemical pathways. Understanding the fundamental molecular recognition of these molecules with synthetic substrates is key to new biomedical technologies, including assays and sensors, therapeutics and purification methods. In this work, we use Corona Phase Molecular Recognition (CoPhMoRe) to engineer new carbon nanotubes corona phases and study nanotube binding to IL6. Library screening identifies two CoPhMoRe constructs based on carbon nanotube complexation with a p(AA68-rand-BA 16 -rand-CD 16 ) polymer (MK2) and a p(SS80-rand-BS 20 ) polymer (P14) corona phases respectively. Both exhibit KD of binding of 8.38 ng/mL and 16.7 μg/mL respectively, with MK2 construct having a response function consistent with two stage binding for IL-6. Comparative binding experiments show that both constructs appear to recognize the axially aligned alpha-helical structures present in the IL-6 and other IL-6 family cytokines. The findings from this study elucidate how nanoparticle interfaces can be designed to lock onto specific protein features, particularly alpha-helical structures, to enable molecular recognition and new types of sensing technologies.

Corona Phase Molecular Recognition of the Interleukin-6 (IL-6) Family of Cytokines Using nIR Fluorescent Single-Walled Carbon Nanotubes

The Interleukin-6 (IL-6) family of cytokines regulates inflammation and plays important roles in numerous biochemical pathways. Typically, cytokine levels are measured using enzyme-linked immunosorbent assay (ELISA) or western blot. However, these techniques usually require substantial processing time, cost, machinery, and specialist training. Understanding the fundamental molecular recognition mechanism of cytokines with synthetic substrates is key to developing new biomedical technologies such as assays, sensors, and therapeutics that overcome the above limitations. Herein, we use the corona phase molecular recognition (CoPhMoRe) approach to engineer new carbon nanotube constructs and study their binding to the inflammatory cytokines: IL-6, interleukin-11 (IL-11), ciliary neurotrophic factor (CNTF), and leukemia inhibitory factor (LIF). Library screening identified two polymer-based CoPhMoRe constructs consisting of single-walled carbon nanotubes complexed with p(AA68-rand-BA16-rand-CD16) polymer (MK2) or p(SS80-rand-BS20) polymer (P14) corona phases. The resulting dissociation constants (KD) were 8.38 ng/mL and 16.7 μg/mL, respectively, compared to that of the natural IL-6 receptor at ∼0.32 ng/mL. In addition, the MK2 constructs showed a nonmonotonic response function upon binding with IL-6. Comparative binding experiments suggest that both constructs appear to recognize the axially aligned α-helical structures present in the Interleukin-6 family. The findings from this study elucidate how nanoparticle interfaces, such as those produced by CoPhMoRe, can be designed to lock onto specific protein features. We find that the α-helical structure of the IL-6 family of cytokines can enable facile molecular recognition, opening the door to new types of label-free, low-cost sensing technologies.

Molecular Recognition and In Vivo Detection of Temozolomide and 5-Aminoimidazole-4-carboxamide for Glioblastoma Using Near-Infrared Fluorescent Carbon Nanotube Sensors

There is a pressing need for sensors and assays to monitor chemotherapeutic activity within the human body in real time to optimize drug dosimetry parameters such as timing, quantity, and frequency in an effort to maximize efficacy while minimizing deleterious cytotoxicity. Herein, we develop near-infrared fluorescent nanosensors based on single walled carbon nanotubes for the chemotherapeutic Temozolomide (TMZ) and its metabolite 5-aminoimidazole-4-carboxamide using Corona Phase Molecular Recognition as a synthetic molecular recognition technique. The resulting nanoparticle sensors are able to monitor drug activity in real-time even under in vivo conditions. Sensors can be engineered to be biocompatible by encapsulation in poly(ethylene glycol) diacrylate hydrogels. Selective detection of TMZ was demonstrated using U-87 MG human glioblastoma cells and SKH-1E mice with detection limits below 30 μM. As sensor implants, we show that such systems can provide spatiotemporal therapeutic information in vivo, as a valuable tool for pharmacokinetic evaluation. Sensor implants are also evaluated using intact porcine brain tissue implanted 2.1 cm below the cranium and monitored using a recently developed Wavelength-Induced Frequency Filtering technique. Additionally, we show that by taking the measurement of spatial and temporal analyte concentrations within each hydrogel implant, the direction of therapeutic flux can be resolved. In all, these types of sensors enable the real time detection of chemotherapeutic concentration, flux, directional transport, and metabolic activity, providing crucial information regarding therapeutic effectiveness.

Divalent Metal Cation Optical Sensing Using Single-Walled Carbon Nanotube Corona Phase Molecular Recognition.

Colloidal single-walled carbon nanotubes (SWCNTs) offer a promising platform for the nanoscale engineering of molecular recognition. Optical sensors have been recently designed through the modification of noncovalent corona phases (CPs) of SWCNTs through a phenomenon known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe constructs, DNA CPs are of great interest due to the breadth of the design space and our ability to control these molecules with sequence specificity at scale. Utilizing these constructs for metal ion sensing is a natural extension of this technology due to DNA's well-known coordination chemistry. Additionally, understanding metal ion interactions of these constructs allows for improved sensor design for use in complex aqueous environments. In this work, we study the interactions between a panel of 9 dilute divalent metal cations and 35 DNA CPs under the most controlled experimental conditions for SWCNT optical sensing to date. We found that best practices for the study of colloidal SWCNT analyte responses involve mitigating the effects of ionic strength, dilution kinetics, laser power, and analyte response kinetics. We also discover that SWCNT with DNA CPs generally offers two unique sensing states at pH 6 and 8. The combined set of sensors in this work allowed for the differentiation of Hg2+, Pb2+, Cr2+, and Mn2+. Finally, we implemented Hg2+ sensing in the context of portable detection within fish tissue extract, demonstrating nanomolar level detection.

(Invited) Real-Time Detection of Insulin Secreted By Pancreatic β-Cells Using Single-Walled Carbon Nanotube Sensors

Quantification of insulin is essential for diabetes research in general, and for the study of pancreatic β-cell function in particular. Fluorescent single-walled carbon nanotubes (SWCNTs) find many applications as optical nanosensors for biomolecules, proteins, and enzyme, with real-time feedback on target analyte binding1–4. Herein, fluorescent SWCNT are used for the recognition and real-time quantification of insulin5. Two approaches for rendering the SWCNT sensors for insulin are compared, using surface functionalization with either a natural insulin aptamer with known affinity to insulin, or a synthetic lipid-PEG, both of which show a modulation of the emitted fluorescence in response to insulin. Although the PEGylated-lipid has no prior affinity to insulin, its response to insulin is more stable and reproducible compared to the insulin aptamer-SWCNTs. The SWCNT sensors successfully detect and quantify insulin secreted by β-cells within the complex environment of the conditioned media, and the results are found to be in agreement with an enzyme-linked immunosorbent assay5. This novel analytical tool for real time quantification of insulin secreted by β-cells provides new opportunities for rapid assessment of β-cell function.(1) Bisker, G.; Dong, J.; Park, H. D.; Iverson, N. M.; Ahn, J.; Nelson, J. T.; Landry, M. P.; Kruss, S.; Strano, M. S. Protein-Targeted Corona Phase Molecular Recognition. Nat. Commun. 2016, 7, 1–14.(2) Bisker, G.; Bakh, N. A.; Lee, M. A.; Ahn, J.; Park, M.; O’Connell, E. B.; Iverson, N. M.; Strano, M. S. Insulin Detection Using a Corona Phase Molecular Recognition Site on Single-Walled Carbon Nanotubes. ACS Sensors 2018, 8 (2), 367–377.(3) Amir, D.; Hendler-Neumark, A.; Wulf, V.; Ehrlich, R.; Bisker, G. Oncometabolite Fingerprinting Using Fluorescent Single-Walled Carbon Nanotubes. Adv. Mater. Interfaces 2021.(4) Wulf, V.; Slor, G.; Rathee, P.; Amir, R. J.; Bisker, G. Dendron-Polymer Hybrids as Tailorable Coronae of Single-Walled Carbon Nanotube. ChemRxiv 2021. https://doi.org/10.26434/ChemRxiv.14452785.V1.(5) Ehrlich, R.; Hendler‐Neumark, A.; Wulf, V.; Amir, D.; Bisker, G. Optical Nanosensors for Real‐Time Feedback on Insulin Secretion by Β‐Cells. Small 2021, 17 (30), 2101660.

Nanosensor Detection of Synthetic Auxins In Planta using Corona Phase Molecular Recognition.

Synthetic auxins such as 1-naphthalene acetic acid (NAA) and 2,4-dichlorophenoxyacetic acid (2,4-D) have been extensively used in plant tissue cultures and as herbicides because they are chemically more stable and potent than most endogenous auxins. A tool for rapid in planta detection of these compounds will enhance our knowledge about hormone distribution and signaling and facilitate more efficient usage of synthetic auxins in agriculture. In this work, we show the development of real-time and nondestructive in planta NAA and 2,4-D nanosensors based on the concept of corona phase molecular recognition (CoPhMoRe), to replace the current state-of-the-art sensing methods that are destructive and laborious. By designing a library of cationic polymers wrapped around single-walled carbon nanotubes with general affinity for chemical moieties displayed on auxins and its derivatives, we developed selective sensors for these synthetic auxins, with a particularly large quenching response to NAA (46%) and a turn-on response to 2,4-D (51%). The NAA and 2,4-D nanosensors are demonstrated in planta across several plant species including spinach, Arabidopsis thaliana (A. thaliana), Brassica rapa subsp. chinensis (pak choi), and Oryza sativa (rice) grown in various media, including soil, hydroponic, and plant tissue culture media. After 5 h of 2,4-D supplementation to the hydroponic medium, 2,4-D is seen to accumulate in susceptible dicotyledon pak choi leaves, while no uptake is observed in tolerant monocotyledon rice leaves. As such, the 2,4-D nanosensor had demonstrated its capability for rapid testing of herbicide susceptibility and could help elucidate the mechanisms of 2,4-D transport and the basis for herbicide resistance in crops. The success of the CoPhMoRe technique for measuring these challenging plant hormones holds tremendous potential to advance the plant biology study.

(Invited) Tailored Functionalization of Single-Walled Carbon Nanotubes for Real-Time Monitoring of Hydrolytic Enzymes Activity

Single-walled carbon nanotubes (SWCNTs) have unique optical and physical properties, and they benefit from the ease of surface functionalization and biocompatibility. Semiconducting SWCNTs fluoresce in the near-infrared (nIR) part of the spectrum, which overlaps with the transparency window of biological samples. The SWCNTs fluorescence is sensitive to the environment, and depending on the surface functionalization, subtle changes in the proximity of the nanotube can result in significant spectral modulations. Hence, SWCNTs can be utilized as optical sensors enabling real-time detection with optical signal transduction1–3. Here, we demonstrate tailored functionalization of SWCNTs, which render the nanotubes substrate for hydrolytic enzymes. We show that the chemical composition and functional groups of the SWCNTs wrapping mediate the interaction between the nanotube and the enzymes. Our results open new avenues for monitoring enzymatic activity with fluorescent nanoparticles and hold great promise for biomedical research and applications.Reference(1) Hendler-Neumark, A.; Bisker, G. Fluorescent Single-Walled Carbon Nanotubes for Protein Detection. Sensors 2019, 19 (24), 5403.(2) Bisker, G.; Bakh, N. A.; Lee, M. A.; Ahn, J.; Park, M.; O’Connell, E. B.; Iverson, N. M.; Strano, M. S. Insulin Detection Using a Corona Phase Molecular Recognition Site on Single-Walled Carbon Nanotubes. ACS Sensors 2018, 8 (2), 367–377.(3) Bisker, G.; Dong, J.; Park, H. D.; Iverson, N. M.; Ahn, J.; Nelson, J. T.; Landry, M. P.; Kruss, S.; Strano, M. S. Protein-Targeted Corona Phase Molecular Recognition. Nat. Commun. 2016, 7, 1–14.

A synthetic mimic of phosphodiesterase type 5 based on corona phase molecular recognition of single-walled carbon nanotubes

Molecular recognition binding sites that specifically identify a target molecule are essential for life science research, clinical diagnoses, and therapeutic development. Corona phase molecular recognition is a technique introduced to generate synthetic recognition at the surface of a nanoparticle corona, but it remains an important question whether such entities can achieve the specificity of natural enzymes and receptors. In this work, we generate and screen a library of 24 amphiphilic polymers, preselected for molecular recognition and based on functional monomers including methacrylic acid, acrylic acid, and styrene, iterating upon a poly(methacrylic acid-co-styrene) motif. When complexed to a single-walled carbon nanotube, some of the resulting corona phases demonstrate binding specificity remarkably similar to that of phosphodiesterase type 5 (PDE5), an enzyme that catalyzes the hydrolysis of secondary messenger. The corona phase binds selectively to a PDE5 inhibitor, Vardenafil, as well as its molecular variant, but not to other potential off-target inhibitors. Our work herein examines the specificity and sensitivity of polymer "mutations" to the corona phase, as well as direct competitions with the native binding PDE5. Using structure perturbation, corona surface characterization, and molecular dynamics simulations, we show that the molecular recognition is associated with the unique three-dimensional configuration of the corona phase formed at the nanotube surface. This work conclusively shows that corona phase molecular recognition can mimic key aspects of biological recognition sites and drug targets, opening up possibilities for pharmaceutical and biological applications.

Implantable Nanosensors for Human Steroid Hormone Sensing In Vivo Using a Self-Templating Corona Phase Molecular Recognition.

Dynamic measurements of steroid hormones in vivo are critical, but steroid sensing is currently limited by the availability of specific molecular recognition elements due to the chemical similarity of these hormones. In this work, a new, self-templating synthetic approach is applied using corona phase molecular recognition (CoPhMoRe) targeting the steroid family of molecules to produce near infrared fluorescent, implantable sensors. A key limitation of CoPhMoRe has been its reliance on library generation for sensor screening. This problem is addressed with a self-templating strategy of polymer design, using the examples of progesterone and cortisol sensing based on a styrene and acrylic acid copolymer library augmented with an acrylated steroid. The pendant steroid attached to the corona backbone is shown to self-template the phase, providing a unique CoPhMoRE design strategy with high efficacy. The resulting sensors exhibit excellent stability and reversibility upon repeated analyte cycling. It is shown that molecular recognition using such constructs is viable even in vivo after sensor implantation into a murine model by employing a poly (ethylene glycol) diacrylate (PEGDA) hydrogel and porous cellulose interface to limit nonspecific absorption. The results demonstrate that CoPhMoRe templating is sufficiently robust to enable a new class of continuous, in vivo biosensors.

Immobilization and Function of nIR-Fluorescent Carbon Nanotube Sensors on Paper Substrates for Fluidic Manipulation.

Nanoparticle-based optical sensors are capable of highly sensitive and selective chemical interactions and can form the basis of molecular recognition for various classes of analytes. However, their incorporation into standardized in vitro assays has been limited by their incompatibility with packaging or form factors necessary for specific applications. Here, we have developed a technique for immobilizing nIR-fluorescent single-walled carbon nanotube (SWCNT) sensors on seven different types of paper substrates including nitrocellulose, nylon, poly(vinylidene fluoride), and cellulose. Sensors remain functional upon immobilization and exhibit nIR fluorescence in nonaqueous solvent systems. We then extend this system to the Corona Phase Molecular Recognition (CoPhMoRe) approach of synthetic molecular recognition by screening ssDNA-wrapped SWCNTs with different sequences against a panel of fat-soluble vitamins in canola oil, identifying a sensor which responds to β-carotene with a dissociation constant of 2.2 μM. Moreover, we pattern hydrophobic regions onto nitrocellulose using the wax printing method and form one-dimensional sensor barcodes for rapid multiplexing. Using a sensor array of select ssDNA wrappings, we are able to distinguish between Cu(II), Cd(II), Hg(II), and Pb(II) at a concentration of 100 μM. Finally, we demonstrate that immobilized sensors remain fluorescent and responsive for nearly 60 days when stability is addressed. This work represents a significant step toward the deployment of fluorescent nanoparticle sensors for point-of-use applications.

(Invited) Advances in NIR Fluorescent Swnt Sensors for Biomedical Applications

Our laboratory at MIT has been interested in how carbon nanosensors, such as those based on carbon nanotubes and graphene, can be applied to problems in precision medicine. Specifically, we are working on nIR fluorescent nanosensors based on single walled carbon nanotubes capable of implantation in-vivo for the continuous, real time, persistent monitoring of a wide range of important analytes in the human body. Precision medicine motivates the need for specific measurements and analysis of data on individuals within a complex human population. To address the challenge of adapting sensor platforms to different analytes of interest to stable, molecular recognition interfaces, we invented at MIT a technique called Corona Phase Molecular Recognition (CoPhMoRe) whereby synthetic, non-biological recognition sites are created from the three-dimensional structure of an adsorbed heteropolymer, selected from a combinatorial library once adsorbed to a nIR fluorescent single walled carbon nanotube. This platform is well suited for precision medicine due to the long term photostability of the CNT, and the label free nature of the detection, as well as lack of photobleaching. Our carbon nanotube sensors have been developed for a variety of important biomolecules such as, radical oxygen species, radical nitrogen species, carbohydrates such as glucose, and even proteins such as fibrinogen and insulin. The ability to implant a carbon nanotube sensor and measure the concentration of an analyte continuously and in real time will give physicians the data they need to assess the needs of individual patients.

Implanted Nanosensors in Marine Organisms for Physiological Biologging: Design, Feasibility, and Species Variability.

In recent decades, biologists have sought to tag animals with various sensors to study aspects of their behavior otherwise inaccessible from controlled laboratory experiments. Despite this, chemical information, both environmental and physiological, remains challenging to collect despite its tremendous potential to elucidate a wide range of animal behaviors. In this work, we explore the design, feasibility, and data collection constraints of implantable, near-infrared fluorescent nanosensors based on DNA-wrapped single-wall carbon nanotubes (SWNT) embedded within a biocompatible poly(ethylene glycol) diacrylate (PEGDA) hydrogel. These sensors are enabled by Corona Phase Molecular Recognition (CoPhMoRe) to provide selective chemical detection for marine organism biologging. Riboflavin, a key nutrient in oxidative phosphorylation, is utilized as a model analyte in in vitro and ex vivo tissue measurements. Nine species of bony fish, sharks, eels, and turtles were utilized on site at Oceanogràfic in Valencia, Spain to investigate sensor design parameters, including implantation depth, sensor imaging and detection limits, fluence, and stability, as well as acute and long-term biocompatibility. Hydrogels were implanted subcutaneously and imaged using a customized, field-portable Raspberry Pi camera system. Hydrogels could be detected up to depths of 7 mm in the skin and muscle tissue of deceased teleost fish ( Sparus aurata and Stenotomus chrysops) and a deceased catshark ( Galeus melastomus). The effects of tissue heterogeneity on hydrogel delivery and fluorescence visibility were explored, with darker tissues masking hydrogel fluorescence. Hydrogels were implanted into a living eastern river cooter ( Pseudemys concinna), a European eel ( Anguilla anguilla), and a second species of catshark ( Scyliorhinus stellaris). The animals displayed no observable changes in movement and feeding patterns. Imaging by high-resolution ultrasound indicated no changes in tissue structure in the eel and catshark. In the turtle, some tissue reaction was detected upon dissection and histopathology. Analysis of movement patterns in sarasa comet goldfish ( Carassius auratus) indicated that the hydrogel implants did not affect swimming patterns. Taken together, these results indicate that this implantable form factor is a promising technique for biologging using aquatic vertebrates with further development. Future work will tune the sensor detection range to the physiological range of riboflavin, develop strategies to normalize sensor signal to account for the optical heterogeneity of animal tissues, and design a flexible, wearable device incorporating optoelectronic components that will enable sensor measurements in moving animals. This work advances the application of nanosensors to organisms beyond the commonly used rodent and zebrafish models and is an important step toward the physiological biologging of aquatic organisms.

Insulin Detection Using a Corona Phase Molecular Recognition Site on Single-Walled Carbon Nanotubes.

Corona phase molecular recognition (CoPhMoRe) is a technique whereby an external, adsorbed phase around a colloidal nanoparticle is selected such that its molecular conformation or interaction recognizes a specific target analyte. In this work, we employ a high-throughput screening of a library of poly(ethylene glycol) (PEG)-conjugated lipids adsorbed onto near-infrared fluorescent single-walled carbon nanotubes to discover a corona phase selective for insulin. We find that a C16-PEG(2000 Da)-ceramide causes a 62% fluorescent intensity decrease of the (10,2) chirality nanotube in the presence of 20 μg/mL insulin. The insulin protein has no prior affinity toward the C16-PEG(2000 Da)-ceramide molecules in free solution, verified by isothermal titration calorimetry, and the interaction occurs only upon their adsorption onto the single-walled carbon nanotube scaffolds. Testing a panel of proteins originating from human blood as well as short 7 amino acid fragments of the insulin peptide rules out nonselective recognition mechanisms such as molecular weight, isoelectric point, and hydrophobicity-based detection. Interestingly, longer fragments of isolated α- and β-peptide chains of insulin are detected by the construct, albeit with lower affinity compared to that of the intact insulin protein, suggesting that the construct recognizes insulin in its native form and conformation. Finally, the insulin recognition and the quantification of its solution concentration were demonstrated both in buffer and in blood serum, showing that the CoPhMoRe construct works in this complex environment despite the presence of potential nonspecific adsorption. Our results further motivate the search for nonbiological synthetic recognition sites and open up a new path for continuous insulin monitoring in vivo with the hope of improving glycemic control in closed-loop artificial pancreas systems.

(Invited) Synthetic Protein Recognition Using Fluorescent Single-Walled Carbon Nanotubes

The ability to specifically and selectively recognize, detect, and monitor molecules of interest is essential for many biomedical applications, and is a crucial element in innumerable biological and chemical processes. Recently, a new concept for generating synthetic recognition sites was introduced, namely, Corona Phase Molecular Recognition (CoPhMoRe). In this approach, a heteropolymer is adsorbed onto the surface of an optically active nanoparticle, forming a structured 3-dimensional corona around it, such that it can selectively and specifically recognize a target molecule. The adsorbed polymer does not necessarily have any affinity towards the target analyte, but rather its pinned configuration when folded onto the particle scaffold forms a recognition site. This generic scheme has been demonstrated using fluorescent single walled carbon nanotubes (SWCNTs) as the underlying nanoparticles for optical signal transduction, monitoring spectral response of their fluorescence emission to reveal analyte adsorption onto the SWCNT corona. Initial demonstrations of SWCNT based CoPhMoRe include corona phases selective towards small molecules. In this talk, I will describe the first protein-targeted CoPhMoRe, where a phospholipid-PEG corona is shown to render the SWCNT a sensor for fibrinogen, the building block of blood clots. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications.

Nanoparticle-Templated Molecular Recognition Platforms for Detection of Biological Analytes.

Molecular recognition of biological analytes with optical nanosensors provides both spatial and temporal biochemical information. A recently developed sensing platform exploits near-infrared fluorescent single-wall carbon nanotubes combined with electrostatically pinned heteropolymers to yield a synthetic molecular recognition technique that is maximally transparent through biological matter. This molecular recognition technique is known as corona phase molecular recognition (CoPhMoRe). In CoPhMoRe, the specificity of a folded polymer toward an analyte does not arise from a pre-existing polymer-analyte chemical affinity. Rather, specificity is conferred through conformational changes undergone by a polymer that is pinned to the surface of a nanoparticle in the presence of an analyte and the subsequent modifications in fluorescence readout of the nanoparticles. The protocols in this article describe a novel single-molecule microscopy tool (near-infrared fluorescence and total internal reflection fluorescence [nIRF TIRF] hybrid microscope) to visualize the CoPhMoRe recognition process, enabling a better understanding of synthetic molecular recognition. We describe this requisite microscope for simultaneous single-molecule visualization of optical molecular recognition and signal transduction. We elaborate on the general procedures for synthesizing and identifying single-walled carbon nanotube-based sensors that employ CoPhMoRe via two biologically relevant examples of single-molecule recognition for the hormone estradiol and the neurotransmitter dopamine. © 2016 by John Wiley & Sons, Inc.

Protein-targeted corona phase molecular recognition

Corona phase molecular recognition (CoPhMoRe) uses a heteropolymer adsorbed onto and templated by a nanoparticle surface to recognize a specific target analyte. This method has not yet been extended to macromolecular analytes, including proteins. Herein we develop a variant of a CoPhMoRe screening procedure of single-walled carbon nanotubes (SWCNT) and use it against a panel of human blood proteins, revealing a specific corona phase that recognizes fibrinogen with high selectivity. In response to fibrinogen binding, SWCNT fluorescence decreases by >80% at saturation. Sequential binding of the three fibrinogen nodules is suggested by selective fluorescence quenching by isolated sub-domains and validated by the quenching kinetics. The fibrinogen recognition also occurs in serum environment, at the clinically relevant fibrinogen concentrations in the human blood. These results open new avenues for synthetic, non-biological antibody analogues that recognize biological macromolecules, and hold great promise for medical and clinical applications.

Chirality dependent corona phase molecular recognition of DNA-wrapped carbon nanotubes

Corona phase molecular recognition (CoPhMoRe) is a phenomenon whereby a polymer or surfactant corona phase wrapped around a nanoparticle selectively recognizes a particular molecule. The method can potentially generate non-biological, synthetic molecular recognition sites, analogous to antibodies, for a broad range of biomedical applications, including new types of sensors, laboratory and clinical assays, as well as inhibitors and targeted therapeutics. In this work, we utilize near infrared fluorescent single-walled carbon nanotubes (SWNTs) wrapped with specific single stranded DNA sequences to explore the (n,m) chirality dependence of CoPhMoRe. Specific DNA oligonucleotide sequences are known to recognize and interact uniquely with certain (n,m) SWNTs enabling their enrichment in ion exchange chromatography. We explore the CoPhMoRe effect using corona phases constructed from a library of 24 such sequences, screening against a biomolecule panel that includes common neurotransmitters, amino acids, saccharides and riboflavin. Example sequences include (ATT)4, (TAT)4 and (ATTT)3 which recognize (7,5), (6,5) and (8,4) SWNTs, respectively. We find that these recognition sequences indeed form CoPhMoRe phases that are distinct among SWNT chiralities, and appear to pack more densely as to exclude analyte adsorption on the chirality they recognize. These results have encouraging implications for the controlled design of CoPhMoRe phases for biomedical applications.

A Mathematical Formulation and Solution of the CoPhMoRe Inverse Problem for Helically Wrapping Polymer Corona Phases on Cylindrical Substrates

Corona phase molecular recognition (CoPhMoRe) is a new technique that generates a nanoparticle-coupled polymer phase, capable of recognizing a specific molecule with high affinity and selectivity. CoPhMoRe has been successfully demonstrated using polymer wrapped single walled carbon nanotubes, resulting in molecular recognition complexes, to date, for dopamine, estradiol, riboflavin, and l-thyroxine, utilizing combinatorial library screening. A rational alternative design to this empirical library screening is to solve the mathematical formulation that we introduce as the CoPhMoRe inverse problem. This inverse problem seeks a linear function representing the position of monomers or functional groups along a polymer backbone that results in a 3-dimensional structure capable of recognizing a specific molecule when mapped to a nanoparticle surface. The potential solution space for such an inverse problem is infinite in general, but for the specific constraint of a helically wrapping polymer, mapped to a cyli...

(Invited) Corona Phase Molecular Recognition (CoPhMoRe) to Enable New Nanosensor Interfaces

Our lab at MIT has been interested in how the 1D and 2D electronic structures of carbon nanotubes and graphene respectively can be utilized to advance new concepts in molecular detection. We introduce CoPhMoRe or corona phase molecular recognition1 as a method of discovering synthetic antibodies, or nanotube-templated recognition sites from a heteropolymer library. We show that certain synthetic heteropolymers, once constrained onto a single-walled carbon nanotube by chemical adsorption, also form a new corona phase that exhibits highly selective recognition for specific molecules. To prove the generality of this phenomenon, we report three examples of heteropolymers–nanotube recognition complexes for riboflavin, L-thyroxine and estradiol. The platform opens new opportunities to create synthetic recognition sites for molecular detection. We have also extended this molecular recognition technique to neurotransmitters, producing the first fluorescent sensor for dopamine. Another area of advancement in biosensor development is the use of near infrared fluorescent carbon nanotube sensors for in-vivo detection2. Here, we show that PEG-ligated d(AAAT)7 DNA wrapped SWNT are selective for nitric oxide, a vasodilator of blood vessels, and can be tail vein injected into mice and localized within the viable mouse liver. We use an SJL mouse model to study liver inflammation in vivo using the spatially and spectrally resolved nIR signature of the localized SWNT sensors. Zhang, JQ et. al. Molecular recognition using corona phase complexes made of synthetic polymers adsorbed on carbon nanotubes. Nature Nanotechnology, 8, 12, 2013, 959-968Iverson, NM, et. al. In vivo biosensing via tissue-localizable near-infrared-fluorescent single-walled carbon nanotubes. Nature Nanotechnology, 8, 11, 2013, 873-880

2D equation-of-state model for corona phase molecular recognition on single-walled carbon nanotube and graphene surfaces.

Corona phase molecular recognition (CoPhMoRe) has been recently introduced as a means of generating synthetic molecular recognition sites on nanoparticle surfaces. A synthetic heteropolymer is adsorbed and confined to the surface of a nanoparticle, forming a corona phase capable of highly selective molecular recognition due to the conformational imposition of the particle surface on the polymer. In this work, we develop a computationally predictive model for analytes adsorbing onto one type of polymer corona phase composed of hydrophobic anchors on hydrophilic loops around a single-walled carbon nanotube (SWCNT) surface using a 2D equation of state that takes into consideration the analyte-polymer, analyte-nanoparticle, and polymer-nanoparticle interactions using parameters determined independently from molecular simulation. The SWCNT curvature is found to contribute weakly to the overall interaction energy, exhibiting no correlation for three of the corona phases considered, and differences of less than 5% and 20% over a larger curvature range for two other corona phases, respectively. Overall, the resulting model for this anchor-loop CoPhMoRe is able to correctly predict 83% of an experimental 374 analyte-polymer library, generating experimental fluorescence responses within 20% error of the experimental values. The modeling framework presented here represents an important step forward in the design of suitable polymers to target specific analytes.