DNA Balance for Native Characterization of Chemically Modified DNA

Native Characterization of Noncanonical Nucleic Acid Thermodynamics via Programmable Dynamic DNA Chemistry

Folding thermodynamics, quantitatively described using parameters such as ΔGfold°, ΔHfold°, and ΔSfold°, is essential for characterizing the stability and functionality of noncanonical nucleic acid structures but remains difficult to measure at the molecular level. Leveraging the programmability of dynamic deoxyribonucleic acid (DNA) chemistry, we introduce a DNA-based molecular tool capable of performing a free energy shift assay (FESA) that directly characterizes the thermodynamics of noncanonical DNA structures in their native environments. FESA operates by the rational design of a reference DNA probe that is energetically equivalent to a target noncanonical nucleic acid structure in a series of toehold-exchange reactions, yet is structurally incapable of folding. As a result, a free energy shift (ΔΔGrxn°) is observed when plotting the reaction yield against the free energy of each toehold-exchange. We mathematically demonstrated that ΔGfold°, ΔHfold°, and ΔSfold° of the analyte can be calculated based on ΔΔGrxn°. After validating FESA using six DNA hairpins by comparing the measured ΔGfold°, ΔHfold°, and ΔSfold° values against predictions made by NUPACK software, we adapted FESA to characterize noncanonical nucleic acid structures, encompassing DNA triplexes, G-quadruplexes, and aptamers. This adaptation enabled the successful characterization of the folding thermodynamics for these complex structures under various experimental conditions. The successful development of FESA marks a paradigm shift and a technical advancement in characterizing the thermodynamics of noncanonical DNA structures through molecular tools. It also opens new avenues for probing fundamental chemical and biophysical questions through the lens of molecular engineering and dynamic DNA chemistry.

DNA nanostructures for exploring cell-cell communication

The process of coordinating between the same or multiple types of cells to jointly execute various instructions in a controlled and carefully regulated environment is a very appealing field. In order to provide clearer insight into the role of cell-cell interactions and the cellular communication of this process in their local communities, several interdisciplinary approaches have been employed to enhance the core understanding of this phenomenon. DNA nanostructures have emerged in recent years as one of the most promising tools in exploring cell-cell communication and interactions due to their programmability and addressability. Herein, this review is dedicated to offering a new perspective on using DNA nanostructures to explore the progress of cell-cell communication. After briefly outlining the anchoring strategy of DNA nanostructures on cell membranes and the subsequent dynamic regulation of DNA nanostructures, this paper highlights the significant contribution of DNA nanostructures in monitoring cell-cell communication and regulating its interactions. Finally, we provide a quick overview of the current challenges and potential directions for the application of DNA nanostructures in cellular communication and interactions.

Versatile DNA Balances via Adjacent Base Stacking for Homogeneous Assay of Energy Parameters, Small Molecules, And Ribonuclease

Homogeneous assays often obviate any separation and washing steps, thus minimizing the risks of contamination and false positive. DNA toehold exchange is a homogeneous, reversible process whose thermodynamic properties can be finely tuned for various assay applications. However, the developed probes often rely on direct interactions of analytes with DNA strands involved in toehold exchange, limiting the versatility of probe design. Here, the coaxial adjacent stacking between one auxiliary strand and another invading strand offers a favorable ΔG to shift one DNA balance, while the auxiliary strand is independent of the DNA balance itself. Therefore, such a DNA balance allowed fine tuning of the equilibrium via adjustment of the auxiliary strand alone. The energy contribution of base stacking can be quantified in a homogeneous solution based on the difference in the equilibrium constant. Besides, the proof of concept for DNA balance allows effective assay of a small molecule or ribonuclease in a homogeneous solution. This novel DNA balance via adjacent base stacking provides an interesting alternative to homogeneously assay various analytes.

DNA framework-engineered chimeras platform enables selectively targeted protein degradation

A challenge in developing proteolysis targeting chimeras (PROTACs) is the establishment of a universal platform applicable in multiple scenarios for precise degradation of proteins of interest (POIs). Inspired by the addressability, programmability, and rigidity of DNA frameworks, we develop covalent DNA framework-based PROTACs (DbTACs), which can be synthesized in high-throughput via facile bioorthogonal chemistry and self-assembly. DNA tetrahedra are employed as templates and the spatial position of each atom is defined. Thus, by precisely locating ligands of POI and E3 ligase on the templates, ligand spacings can be controllably manipulated from 8 Å to 57 Å. We show that DbTACs with the optimal linker length between ligands achieve higher degradation rates and enhanced binding affinity. Bispecific DbTACs (bis-DbTACs) with trivalent ligand assembly enable multi-target depletion while maintaining highly selective degradation of protein subtypes. When employing various types of warheads (small molecules, antibodies, and DNA motifs), DbTACs exhibit robust efficacy in degrading diverse targets, including protein kinases and transcription factors located in different cellular compartments. Overall, utilizing modular DNA frameworks to conjugate substrates offers a universal platform that not only provides insight into general degrader design principles but also presents a promising strategy for guiding drug discovery.

Facile Synthesis of Light-Switchable Polymers with Diazocine Units in the Main Chain

Unlike azobenzene, the photoisomerization behavior of its ethylene-bridged derivative, diazocine, has hardly been explored in synthetic polymers. In this communication, linear photoresponsive poly(thioether)s containing diazocine moieties in the polymer backbone with different spacer lengths are reported. They were synthesized in thiol-ene polyadditions between a diazocine diacrylate and 1,6-hexanedithiol. The diazocine units could be reversibly photoswitched between the (Z)- and (E)-configurations with light at 405 nm and 525 nm, respectively. Based on the chemical structure of the diazocine diacrylates, the resulting polymer chains differed in their thermal relaxation kinetics and molecular weights (7.4 vs. 43 kDa) but maintained a clearly visible photoswitchability in the solid state. Gel permeation chromatography (GPC) measurements indicated a hydrodynamic size expansion of the individual polymer coils as a result of the Z→E pincer-like diazocine switching motion on a molecular scale. Our work establishes diazocine as an elongating actuator that can be used in macromolecular systems and smart materials.

Controllable DNA hybridization by host-guest complexation-mediated ligand invasion

Dynamic regulation of nucleic acid hybridization is fundamental for switchable nanostructures and controllable functionalities of nucleic acids in both material developments and biological regulations. In this work, we report a ligand-invasion pathway to regulate DNA hybridization based on host-guest interactions. We propose a concept of recognition handle as the ligand binding site to disrupt Watson-Crick base pairs and induce the direct dissociation of DNA duplex structures. Taking cucurbit[7]uril as the invading ligand and its guest molecules that are integrated into the nucleobase as recognition handles, we successfully achieve orthogonal and reversible manipulation of DNA duplex dissociation and recovery. Moreover, we further apply this approach of ligand-controlled nucleic acid hybridization for functional regulations of both the RNA-cleaving DNAzyme in test tubes and the antisense oligonucleotide in living cells. This ligand-invasion strategy establishes a general pathway toward dynamic control of nucleic acid structures and functionalities by supramolecular interactions.

Recent advances in constructing high-order DNA structures

Molecular self-assembly is widely used in the fields of biosensors, molecular devices, efficient catalytic materials, and medical biomaterials. As the carrier of genetic information, DNA is a kind of biomacromolecule composed of deoxyribonucleotide units. DNA nanotechnology extends DNA of its original properties as a molecule that stores and transmits genetic information from its biological environment. By taking advantage of its unique base pairing and inherent biocompatibility to produce structurally-defined supramolecular structures. With the continuously development of DNA technology, the assembly method of DNA nanostructures is not only limited on the basis of DNA hybridization but also other biochemical interactions. In this review, we summarize the latest methods used to construct high-order DNA nanostructures. The problems of DNA nanostructures are discussed and the future directions in this field are provided.