Molecular electronics sensors on a scalable semiconductor chip: A platform for single-molecule measurement of binding kinetics and enzyme activity.

For nearly 50 years, the vision of using single molecules in circuits has been seen as providing the ultimate miniaturization of electronic chips. An advanced example of such a molecular electronics chip is presented here, with the important distinction that the molecular circuit elements play the role of general-purpose single-molecule sensors. The device consists of a semiconductor chip with a scalable array architecture. Each array element contains a synthetic molecular wire assembled to span nanoelectrodes in a current monitoring circuit. A central conjugation site is used to attach a single probe molecule that defines the target of the sensor. The chip digitizes the resulting picoamp-scale current-versus-time readout from each sensor element of the array at a rate of 1,000 frames per second. This provides detailed electrical signatures of the single-molecule interactions between the probe and targets present in a solution-phase test sample. This platform is used to measure the interaction kinetics of single molecules, without the use of labels, in a massively parallel fashion. To demonstrate broad applicability, examples are shown for probe molecule binding, including DNA oligos, aptamers, antibodies, and antigens, and the activity of enzymes relevant to diagnostics and sequencing, including a CRISPR/Cas enzyme binding a target DNA, and a DNA polymerase enzyme incorporating nucleotides as it copies a DNA template. All of these applications are accomplished with high sensitivity and resolution, on a manufacturable, scalable, all-electronic semiconductor chip device, thereby bringing the power of modern chips to these diverse areas of biosensing.

Peptide Brush Polymers and Nanoparticles with Enzyme-Regulated Structure and Charge for Inducing or Evading Macrophage Cell Uptake.

Cellular uptake by macrophages and ensuing clearance by the mononuclear phagocyte system stands as a significant biological barrier for nanoparticle therapeutics. While there is a growing body of work investigating the design principles essential for imparting nanomaterials with long-circulating characteristics and macrophage evasion, there is still a widespread need for examining stimuli-responsive systems, particularly well-characterized soft materials, which differ in their physiochemical properties prior to and after an applied stimulus. In this work, we describe the synthesis and formulation of polymeric nanoparticles (NPs) and soluble homopolymers (Ps) encoded with multiple copies of a peptide substrate for proteases. We examined the macrophage cell uptake of these materials, which vary in their peptide charge and conjugation (via the N- or C-terminus). Following treatment with a model protease, thermolysin, the NPs and Ps undergo changes in their morphology and charge. After proteolysis, zwitterionic NPs showed significant cellular uptake, with the C-terminus NP displaying higher internalization than its N-terminus analogue. Enzyme-cleaved homopolymers generally avoided assembly and uptake, though at higher concentrations, enzyme-cleaved N-terminus homopolymers assembled into discrete cylindrical structures, whereas C-terminus homopolymers remained dispersed. Overall, these studies highlight that maintaining control over NP and polymer design parameters can lead to well-defined biological responses.

ROMPISA: Ring-Opening Metathesis Polymerization-Induced Self-Assembly.

Herein we report a polymerization-induced self-assembly (PISA) process with ring-opening metathesis polymerization (ROMP). We utilize a peptide-based norbornenyl monomer as a hydrophobic unit to provide a range of nanostructures at room temperature yet at high solids concentrations of 20 wt % in combination with an oligoethylene glycol based norbornenyl monomer. Evaluation of the polymerizations under mild conditions highlight that good control is maintained along with high monomer conversion of greater than 99%, indicating that the living polymerization is unaffected during the PISA process. The demonstration broadens the scope of the PISA process to a new living polymerization methodology toward the development of easily accessible and highly functionalized nanostructures in situ.

Biosynthetic Polymers as Functional Materials.

The synthesis of functional polymers encoded with biomolecules has been an extensive area of research for decades. As such, a diverse toolbox of polymerization techniques and bioconjugation methods has been developed. The greatest impact of this work has been in biomedicine and biotechnology, where fully synthetic and naturally derived biomolecules are used cooperatively. Despite significant improvements in biocompatible and functionally diverse polymers, our success in the field is constrained by recognized limitations in polymer architecture control, structural dynamics, and biostabilization. This Perspective discusses the current status of functional biosynthetic polymers and highlights innovative strategies reported within the past five years that have made great strides in overcoming the aforementioned barriers.

Liquid Crystal Interfaces Programmed with Enzyme-Responsive Polymers and Surfactants.

Synthesis of biologically active peptide-polymer amphiphiles (PPAs), and characterization of assemblies formed by PPAs at the interfaces of liquid crystal (LC) microdroplets, is shown to permit the use of PPAs in strategies that can trigger ordering transitions in LC microdroplets in response to targeted biomolecular events.

Poly(oligonucleotide).

Here we report the preparation of poly(oligonucleotide) brush polymers and amphiphilic brush copolymers from nucleic acid monomers via graft-through polymerization. We describe the polymerization of PNA-norbornyl monomers to yield poly-PNA (poly(peptide nucleic acid)) via ring-opening metathesis polymerization (ROMP) with the initiator, (IMesH2)(C5H5N)2(Cl)2RuCHPh.1 In addition, we present the preparation of poly-PNA nanoparticles from amphiphilic block copolymers and describe their hybridization to a complementary single-stranded DNA (ssDNA) oligonucleotide.

Polymerization of Protecting-Group-Free Peptides via ROMP.

A study was conducted to survey the tolerance of ring-opening metathesis polymerization (ROMP) with respect to amino acid (a.a) identity of pentapeptide-modified norbornene-based monomers. A library of norbornyl-pentapeptides were prepared with the general structure, norbornyl-GX2PLX5, where residue 'X' was changed at each of the two positions (2 or 5) alternately to consist of the natural amino acids F, A, V, R, S, K, N, T, M, Q, H, W, C, Y, E, Q, and D. Each peptide monomer, free of protecting groups, was mixed in turn under a standard set of polymerization conditions with the ROMP initiator (IMesH2)C5H5N)2(Cl)2Ru=CHPh. Two sets of polymerization reactions were performed, one with Monomer:Initiator (M:I) ratio of 20:1, and another with M:I of 200:1. For the nucleophilic amino acids cysteine and lysine, polymerization reactions were quantitatively compared to those of their protected analogues. Furthermore, we describe polymerization of macromonomers containing up to 30 a.a. to test for tolerance of ROMP to peptide molecular weight. These reactions were studied via SEC-MALS and NMR. Finally, with knowledge of sequence scope in hand, we prepared a set of enzyme-substrate containing brush polymers and studied them with respect to their bioactivity.

Polymerization of a peptide-based enzyme substrate.

Polymers of norbornenyl-modified peptide-based enzyme substrates have been prepared via ring-opening metathesis polymerization (ROMP). Peptides displayed on water-soluble homopolymers retain the ability to be enzymatically processed by a disease-associated enzyme. In contrast, when the peptides are densely arrayed on a nanoparticle derived from a self-assembled amphiphilic block-copolymer, they function with reduced activity as enzymatic substrates.