Nanomaterials. Programmable materials and the nature of the DNA bond.

For over half a century, the biological roles of nucleic acids as catalytic enzymes, intracellular regulatory molecules, and the carriers of genetic information have been studied extensively. More recently, the sequence-specific binding properties of DNA have been exploited to direct the assembly of materials at the nanoscale. This chapter draws an analogy between such building blocks and the familiar chemical concepts of “bonds” and “valency” and review two distinct but related strategies that have used this design principle in constructing new configurations of matter. Synthetic chemists regularly wield this degree of control over atoms by manipulating the formation of covalent bonds, and supramolecular chemists control the organization of larger molecular species through the manipulation of noncovalent interactions. The synthesis of nanomaterials and their assembly into larger well-defined architectures has conceptually similar goals.

Programmable Materials.

Nucleic acids are generally recognized as the carriers of genetic information, but they are undergoing a profound conceptual transformation toward programmable information materials. Here, we introduce and delineate the emerging field of nucleic acid information materials (NAIMs), defined as engineered systems that repurpose DNA and RNA, the quintessential molecules of life, from their biological genetic roles into programmable materials for information technology and biotechnology. This paradigm shift leverages their inherent molecular recognition, predictable self‐assembly, and vast information‐encoding capacity. We propose the development of molecular building blocks, the materials fabrication, the function design, and the system integration, as the evolution of NAIMs. We discuss how nucleic acids are used to create static nanostructures and then to construct dynamic intelligent systems, such as molecular robots, computational circuits, and next‐generation data storage media. We also explore the application of NAIMs in two distinct areas: (1) Biotechnology (BT), where they enable precision diagnostics, targeted drug delivery, and logic‐based computational diagnosis and (2) Information technology (IT), where they enable energy‐efficient molecular computation and ultra‐dense long‐term data storage; the combination of BT and IT serves as the cornerstone of the emerging field of bio‐semiconductors. Finally, we outline the main challenges for NAIMs regarding synthesis scalability, system integration, and in vivo stability, and offer a perspective on the future BT–IT convergence that NAIMs are rewiring.

Natural products that produced by animals, plants or microorganisms, especially polyketides (PKs), non-ribosomal peptides (NRPs) and their hybrids, exhibit an extremely wide range of biological activities, include antibacterial, antifungal, antitumor, antiviral and immunosuppressive activities, which underlie the critical roles of natural products in medical industry as various drugs. The biosynthetic pathways of PKs, NRPs and their hybrids share a templated multifunctional enzymology for skeleton assembly. Polyketide synthases (PKSs) usually catalyze C−C bond formation using short carboxylic acid as monomers, whereas non-ribosomal peptide synthetases (NRPSs) incorporate amino acids through C−N bond formation. Consistent with their catalytic cycles, both PKSs and NRPSs are often giant enzymes organized into modules, which each contains a common thiolation (T) domain for loading building blocks. A prototype of a PKS module consists of an acyltransferase (AT), a T domain and a β-ketoacyl synthase (KS) domain. A minimum NRPS module contains an adenylation (A) domain, a T domain and a condensation (C) domain. AT or A domain is responsible for recognition and activation of building blocks, while KS or C domain catalyzes the elongation of the growing skeleton. In general, modular PKSs or NRPSs appear to function as assembly lines, which program monomer polymerization/modification and chain tailoring/termination following a non-iteratively ″one domain, one function″ like co-linearity rule. Thus, the domain composition of each module and the number of modules can be used to predict the structure of skeleton. However, there are exceptions reported in recent years, as modules are now known to be both skipped and iterated during the normal biosynthetic processes. In addition, another origin for a lack of correlation between domain composition of the multienzyme complex and the final product structure has been identified recently. In this case, the missing building blocks are normally incorporated on the assembly lines, but they will be removed by the post-assembly modifications. These kind of building blocks which would not appear in the final products seem ″unnecessary″, but they are essential in the biosynthetic pathways exactly. In this review, we summarize these ″auxiliary″ building blocks, focus on the chemical mechanisms of the incorporation and removal of them and discuss their biological functions that have been reported since 2000. The related building blocks here include fatty acyls, amino acids, unnatural amino acids and fatty acyl-amino acids. Some of these ″auxiliary″ build blocks are involved in the biosynthesis of natural products with specific structures, such as 2,2′-bipyridine cores, tetrahydroisoquinoline alkaloids, β-lactam and macrocyclic lactam antibiotics. In this case, building blocks are incorporated by the PKSs, NRPSs or their hybrids assembly lines, but the chemical mechanisms are unusual. The biological functions of these kind of building blocks are considered to be strategies for protection of the reactive groups and mediation of molecular assembly and modifications. On the other hand, some of the ″auxiliary″ building blocks are present in biosynthesis of natural products which are structurally different from each other, however, the ″unnecessary″ building blocks are almost same and their chemical mechanisms of incorporation and removal are similar. These kind of building blocks are proposed to be very important for protection the chemical producers by prodrug generation. In summary, the molecules mentioned in this review could increase the knowledge regarding the ″auxiliary″ building blocks, add another layer of complexity to natural product biosynthesis, help to hypothesize biosynthetic pathways of other natural products with specific structures and assist the association of molecules and their gene clusters.

This Mini-Review Article outlines recent advances in the study of local electric field (LEF) governed enzyme catalysis and the application of the LEF principle in synthetic catalyst design. We start by discussing the electrostatics principles that drive enzyme catalysis, and its experimental verifications through vibrational Stark spectroscopy. Subsequently, we describe aspects of LEFs other than catalysis, i.e., induction of mechanistic crossovers, among others. Here, we focus on the early work done using computational tools, along with some recent contributions. Following an in-depth discussion of the role of LEFs in enzyme catalysis, we then highlight some recent works on designed local electric fields (D-LEF) and their applications in organic synthesis. Subsequently, we turn to D-LEFs in synthetic enzymes and supramolecular systems (cf. the work by the Head-Gordon group). We end by discussing some of the software packages that have been developed to analyze local electric fields computationally. Overall, the present Mini-Review Article paints an insightful picture of the current state of the art using LEF in enzyme catalysis and its application for further bioengineering and synthetic organic frameworks in a broad perspective.

Programmable smart materials that can respond locally to specific stimuli hold great potential for many applications, but controllable fabrication of these materials remains challenging. This work reports the development of novel programmable anisotropic materials with both magnetic and photothermal stimuli‐responsiveness, which are fabricated by anchoring thermosensitive poly(N‐isopropyl acrylamide) (PNIPAm) and magnetic Fe3O4 nanoparticles on the surface of MoS2 nanosheets. Further embedding PNIPAm‐MoS2/Fe3O4 into 3D‐printed hydrogel cubes results in stimuli‐responsive building blocks, and the magnetic field can precisely control their orientation and near‐infrared (NIR) light absorbing property. Particularly, the variation of the orientation of MoS2/Fe3O4 block results in obvious changes of their photothermal efficiency and optical property. By exploiting the anisotropy of MoS2/Fe3O4 and their NIR light responsiveness, thermally‐induced phase transitions in individual 3D printed hydrogel building block can be locally controlled for magnetic field‐assisted programming a quick response (QR) code. Alternatively, fluorescent QR code with high contrast and security level can be achieved by photothermal‐induced release of fluorescent dyes. These 3D printed magnetically programmed hydrogels hold great potential for application in information storage, intelligent materials, and precise therapy.

Active systems of self-rotating elements inherently exhibit chirality, making them of fundamental interest due to parity violation. Yet how rotational activity influences gelation and whether such chirality can persist into the arrested state remain unclear. Using large-scale hydrodynamic simulations, we investigate the gelation of adhesive spinners confined to quasi-2D monolayers at low Reynolds numbers. Unlike the coarsening dynamics of passive colloids, spinner gelation follows a different pathway, displaying structural chirality during the early stages of aggregation. However, this chirality dissipates upon dynamical arrest, resulting in a final gel structure that resembles a conventional colloidal gel. As a result, we find no sign of odd mechanical responses. Nonetheless, the elastic modulus and gelation time remain tunable through spinning activity, providing a potential avenue for the bottom-up design of programmable soft materials. Active systems of self-rotating elements are of fundamental interest due to their inherent chirality and parity violation. Here, the authors use large-scale hydrodynamic simulations to reveal that adhesive spinners confined to quasi-2D monolayers exhibit unique gelation pathways, with tunable elastic properties dependent on spinning activity, offering insights for designing programmable soft materials.

The making of a reconfigurable semiconductor with a soft ionic lattice

PurposeThe purpose of this paper is to explain a current implementation of a programmable and computational material, Logic Matter, and to describe potential applications for computational materials and self‐guided assembly.Design/methodology/approachFollowing an introduction, the paper describes the types of information currently found in architectural construction, then introduces Logic Matter, a building block embodying physical digital logic. Examples of structural optimization and construction scenarios are given, to demonstrate the benefits of programmable and computational physical materials for assembly.FindingsLogic Matter demonstrates a prototype with embedded digital logic and programmability, offering new applications for automated assembly, online material analysis and physical computing.Originality/valueThe paper describes the existing types of architectural construction information and proposes a novel application of programmable and computational material for automated assembly.

Bacterial cellulose (BC) has excellent material properties and can be produced sustainably through simple bacterial culture, but BC‐producing bacteria lack the extensive genetic toolkits of model organisms such as Escherichia coli (E. coli). Here, a simple approach is reported for producing highly programmable BC materials through incorporation of engineered E. coli. The acetic acid bacterium Gluconacetobacter hansenii is cocultured with engineered E. coli in droplets of glucose‐rich media to produce robust cellulose capsules, which are then colonized by the E. coli upon transfer to selective lysogeny broth media. It is shown that the encapsulated E. coli can produce engineered protein nanofibers within the cellulose matrix, yielding hybrid capsules capable of sequestering specific biomolecules from the environment and enzymatic catalysis. Furthermore, capsules are produced which can alter their own bulk physical properties through enzyme‐induced biomineralization. This novel system uses a simple fabrication process, based on the autonomous activity of two bacteria, to significantly expand the functionality of BC‐based living materials.

The experimental realization of DNA-based constructs that are sufficiently rigid so as to impart directionality to hybridization interactions marks a major milestone in the development of programmable materials assembly. The interest in nanoscale materials constructed by using DNA bonds has continued to grow steadily, but has seen a noteworthy explosion in relevance over the past several years. The premise of DNA origami is to fold a multithousand-base circular single-stranded DNA “scaffold,” obtained from a viral genome, by using short helper or “staple” oligonucleotides into a desired nanoscale shape. A conceptual leap in DNA origami was made in 2009 when these principles were extended from building 2D objects to those that fill 3D space. A fundamentally different approach to generating nanoscale DNA bonds is to use nanoparticles as templates for the immobilization and orientation of surface-bound oligonucleotides.

Pharmacological Characterization of Chemically Synthesized Monomeric phi29 pRNA Nanoparticles for Systemic Delivery

Thermosetting supramolecular polymerization of compartmentalized DNA fibers with stereo sequence and length control

In recent years, jointless soft robots have demonstrated various curvilinear motions unlike conventional robotic systems requiring complex mechanical joints and electrical design principles. The materials employed to construct soft robots are mainly programmable anisotropic polymeric materials to achieve contactless manipulation of miniaturized and lightweight soft robots through their anisotropic strain responsivity to external stimuli. Although reviews on soft actuators are extensive, those on untethered soft robots are scant. In this study, we focus on the recent progress in the manipulation of untethered soft robots upon receiving external stimuli such as magnetic fields, light, humidity, and organic solvents. For each external stimulus, we provide an overview of the working principles along with the characteristics of programmable anisotropic materials and polymeric composites used in soft robotic systems. In addition, potential applications for untethered soft robots are discussed based on the physicochemical properties of programmable anisotropic materials for the given external stimuli.

The term ‘Indic Knowledge Systems’(IKS) is associated with the entire gamut of Indic thought and education and spans a complete spectrum from Philosophy, Grammar, Linguistics, Political Science, and Performing Arts to Mathematics, Astronomy, Engineering, Agriculture and Medicine. While it is often treated as a vast body of knowledge with Indic origins, it is seldom recognised that these disparate subjects have a common set of building blocks and principles. In this chapter we look at some of the basic building blocks or ‘Elements’ of the Indic Knowledge Systems and the ‘Design Principles’ used to weave these elements into a tapestry of Knowledge Systems and a civilisation so rich, vibrant and sustainable. We start with an exploration of Joy or Happiness as the most fundamental human pursuit and show how this quest for happiness has been an underlying theme in IKS. After exploring the Indic conception of happiness and its varieties and gradations, we show how the quest for ānanda is co-terminus with the quest for jñāna or knowledge. We also dwell on the IKS attempts to balance the sensory-derived and inherent triggers of joy and how this optimisation problem has given rise to fundamental design principles of IKS - ‘Dharma’. We describe the varied definitions and application of Dharma as a design principle and also show how repeated application of the same at various levels of hierarchy - individual, society, country, global or cosmic levels gives rise to the institutionalised form of IKS or Indic civilisation as we see today.