A smart polymer for sequence-selective binding, pulldown, and release of DNA targets

Selective isolation of DNA is crucial for applications in biology, bionanotechnology, clinical diagnostics and forensics. We herein report a smart methanol-responsive polymer (MeRPy) that can be programmed to bind and separate single- as well as double-stranded DNA targets. Captured targets are quickly isolated and released back into solution by denaturation (sequence-agnostic) or toehold-mediated strand displacement (sequence-selective). The latter mode allows 99.8% efficient removal of unwanted sequences and 79% recovery of highly pure target sequences. We applied MeRPy for the depletion of insulin, glucagon, and transthyretin cDNA from clinical next-generation sequencing (NGS) libraries. This step improved the data quality for low-abundance transcripts in expression profiles of pancreatic tissues. Its low cost, scalability, high stability and ease of use make MeRPy suitable for diverse applications in research and clinical laboratories, including enhancement of NGS libraries, extraction of DNA from biological samples, preparative-scale DNA isolations, and sorting of DNA-labeled non-nucleic acid targets. © 2020, The Author(s)

Supramolecular Polymers in Aqueous Media

This review discusses one-dimensional supramolecular polymers that form in aqueous media. First, naturally occurring supramolecular polymers are described, in particular, amyloid fibrils, actin filaments, and microtubules. Their structural, thermodynamic, kinetic, and nanomechanical properties are highlighted, as well as their importance for the advancement of biologically inspired supramolecular polymer materials. Second, five classes of synthetic supramolecular polymers are described: systems based on (1) hydrogen-bond motifs, (2) large π-conjugated surfaces, (3) host–guest interactions, (4) peptides, and (5) DNA. We focus on recent studies that address key challenges in the field, providing mechanistic understanding, rational polymer design, important functionality, robustness, or unusual thermodynamic and kinetic properties

Separation, Immobilization, and Biocatalytic Utilization of Proteins by a Supramolecular Membrane

<div><p>Membrane separation of biomolecules and their application in biocatalysis is becoming increasingly important for biotechnology, demanding the development of new biocompatible materials with novel properties. In the present study, an entirely noncovalent water-based material is used as a membrane for size-selective separation, immobilization, and biocatalytic utilization of proteins. The membrane shows stable performance under physiological conditions, allowing filtration of protein mixtures with a 150 kDa molecular weight cutoff (∼8 nm hydrodynamic diameter cutoff). Due to the biocompatibility of the membrane, filtered proteins stay functionally active and retained proteins can be partially recovered. Upon filtration, large enzymes become immobilized within the membrane. They exhibit stable activity when subjected to a constant flux of substrates for prolonged periods of time, which can be used to carry out heterogeneous biocatalysis. The noncovalent membrane material can be easily disassembled, purified, reassembled, and reused, showing reproducible performance after recycling. The robustness, recyclability, versatility, and biocompatibility of the supramolecular membrane may open new avenues for manipulating biological systems.</p></div

Dispersing Perylene Diimide/SWCNT Hybrids: Structural Insights at the Molecular Level and Fabricating Advanced Materials

The unique properties of carbon nanotubes (CNT) are advantageous for emerging applications. Yet, the CNT insolubility hampers their potential. Approaches based on covalent and noncovalent methodologies have been tested to realize stable dispersions of CNTs. Noncovalent approaches are of particular interest as they preserve the CNT’s structures and properties. We report on hybrids, in which perylene diimide (PDI) amphiphiles are noncovalently immobilized onto single wall carbon nanotubes (SWCNT). The resulting hybrids were dispersed and exfoliated both in water and organic solvents in the presence of two different PDI derivatives, PP2b and PP3a. The dispersions were investigated using cryogenic transmission electron microscopy (cryo-TEM), providing unique structural insights into the exfoliation. A helical arrangement of PP2b assemblies on SWCNTs dominates in aqueous dispersions, while a single layer of PP2b and PP3a was found on SWCNTs in organic dispersions. The dispersions were probed by steady-state and time-resolved spectroscopies, revealing appreciable charge redistribution in the ground state, and an efficient electron transfer from SWCNTs to PDIs in the excited state. We also fabricated hybrid materials from the PP2b/SWCNT dispersions. A supramolecular membrane was prepared from aqueous dispersions and used for size-selective separation of gold nanoparticles. Hybrid buckypaper films were prepared from the organic dispersions. In the latter, high conductivity results from enhanced electronic communication and favorable morphology within the hybrid material. Our findings shed light onto SWCNT/dispersant molecular interactions, and introduce a versatile approach toward universal solution processing of SWCNT-based materials

Understanding the Effect of Fluorocarbons in Aqueous Supramolecular Polymerization: Ultrastrong Noncovalent Binding and Cooperativity

Achieving supramolecular polymerization based on strong yet reversible bonds represents a significant challenge. A solution may be offered by perfluoroalkyl groups, which have remarkable hydrophobicity. We tested the idea that a perfluorooctyl chain attached to a perylene diimide amphiphile can dramatically enhance the strength of supramolecular bonding in aqueous environments. Supramolecular structures and polymerization thermodynamics of this fluorinated compound (<b>1-F</b>) were studied in comparison to its non-fluorinated analogue (<b>1-H</b>). Depending on the amount of organic cosolvent, <b>1-F</b> undergoes cooperative or isodesmic aggregation. The switching between two polymerization mechanisms results from a change in polymer structure, as observed by cryogenic electron microscopy. <b>1-F</b> showed exceptionally strong noncovalent binding, with the largest directly measured association constant of 1.7 × 10⁹ M^–1 in 75:25 water/THF mixture (v/v). In pure water, the association constant of <b>1-F</b> is estimated to be at least in the order of 10¹⁵ M^–1 (based on extrapolation), 3 orders of magnitude larger than that of <b>1-H</b>. The difference in aggregation strength between <b>1-F</b> and <b>1-H</b> can be explained solely on the basis of the larger surface area of the fluorocarbon group, rather than a unique nature of fluorocarbon hydrophobicity. However, differences in aggregation mechanism and cooperativity exhibited by <b>1-F</b> appear to result from specific fluorocarbon conformational rigidity