Programmable DNA Interstrand Crosslinking by Alkene-Alkyne [2 + 2] Photocycloaddition

DNA Aptamers with Chemically Locked Ends for Virus Infection Inhibition

Nucleic acid aptamers, known as chemical antibodies, demonstrate remarkable affinity and specificity for targets. Therefore, aptamers are proposed as an alternative to an antibody in extensive applications. However, nucleic acid aptamers exhibit poor tolerance to degradation by nucleases, which severely hampers their biological applications. Herein, we developed a biological regulation pattern for aptamers by utilizing small-molecule-mediated terminal manipulation, which could prevent the interaction of DNA aptamers with exonucleases and help aptamers persist in the desired conformation with high stability. Diagonal T-T bases were designed in the ends of aptamers and could be chemically cross-linked with trioxsalen via photocatalyzed cycloaddition. Aptamers with different patterns of terminal T-T cross-linking sites were synthesized. Experimental investigation and molecular dynamics simulations combinedly revealed that the cross-linking efficiency of ends depended on multiple factors: (i) the number of T-T cross-linking sites in the terminal sequences, (ii) the spatial conformation of aptamers, and (iii) the competitive binding ability of the T-T sites with trioxsalen compared to other base sites. The aptamers with locked ends exhibited superior exonuclease resistance, especially with both 3'- and 5'-cross-linked ends, thus demonstrating a great target binding capability. Notably, in the application exploration, the terminal locked aptamers, which bound to receptor-binding domains on SARS-CoV-2, showed superior performance in virus infection inhibition. This work puts forward a paradigm to develop a biological regulation pattern for aptamers based on chemical terminal manipulation of DNA, potentially promoting the clinical applications of nucleic acid drugs.

Multifunctional DNA nanomaterials: a new frontier in rheumatoid arthritis diagnosis and treatment

Rheumatoid arthritis (RA) remains a challenging autoimmune disease due to its complex and heterogeneous pathophysiology, which complicates therapeutic and diagnostic efforts. Advances in DNA nanotechnology have introduced DNA nanomaterials as promising tools to overcome these barriers. This review focuses on three primary categories of DNA nanomaterials applied in RA: DNA nanostructures, DNA aptamers, and DNA-modified nanoparticles. DNA nanostructures, such as tetrahedral framework nucleic acids (tFNAs) and DNA origami, demonstrate anti-inflammatory properties and facilitate precise, controlled drug delivery. DNA aptamers, functioning as molecular recognition ligands, surpass traditional antibodies with their high specificity, low immunogenicity, and thermal stability, offering significant potential in biomarker detection and therapeutic interventions. While DNA-modified nanoparticles, which integrate DNA with materials like gold or lipids, have shown significant progress in bioimaging and drug delivery in other fields, their application in RA remains limited and warrants further exploration. Furthermore, advancements in stimulus-responsive systems are being explored to enable controlled drug release, which could significantly improve the specificity and efficiency of DNA nanomaterials in therapeutic applications. Despite their immense potential, challenges such as stability under physiological conditions, safety concerns, and clinical regulatory complexities persist. Overcoming these limitations is essential. This review highlights how DNA nanomaterials, beyond serving as delivery platforms, are poised to redefine RA treatment and diagnosis, opening the door to more personalized and effective approaches.

XPD stalled on cross-linked DNA provides insight into damage verification

The superfamily 2 helicase XPD is a central component of the general transcription factor II H (TFIIH), which is essential for transcription and nucleotide excision DNA repair (NER). Within these two processes, the helicase function of XPD is vital for NER but not for transcription initiation, where XPD acts only as a scaffold for other factors. Using cryo-EM, we deciphered one of the most enigmatic steps in XPD helicase action: the active separation of double-stranded DNA (dsDNA) and its stalling upon approaching a DNA interstrand cross-link, a highly toxic form of DNA damage. The structure shows how dsDNA is separated and reveals a highly unusual involvement of the Arch domain in active dsDNA separation. Combined with mutagenesis and biochemical analyses, we identified distinct functional regions important for helicase activity. Surprisingly, those areas also affect core TFIIH translocase activity, revealing a yet unencountered function of XPD within the TFIIH scaffold. In summary, our data provide a universal basis for NER bubble formation, XPD damage verification and XPG incision.

Visible-Light-Mediated [2+2] Photocycloadditions of Alkynes

Visible-light-mediated [2+2] photocycloaddition reaction can be considered an ideal solution due to its green and sustainable properties, and is one of the most efficient methods to synthesize four-membered ring motifs. Although research on the [2+2] photocycloaddition of alkynes is challenging because of the diminished reactivity of alkynes, and the more significant ring strain of the products, remarkable achievements have been made in this field. In this article, we highlight the recent advances in visible-light-mediated [2+2] photocycloaddition reactions of alkynes, with focus on the reaction mechanism and the late-stage synthetic applications. Advances in obtaining cyclobutenes, azetines, and oxetene active intermediates continue to be breakthroughs in this fascinating field of research.

Synthesis and properties of 6-alkynyl-5-aryluracils

The development of a new and straightforward chemoselective method for the synthesis of uracil-based structures by combining Suzuki-Miyaura and Sonogashira-Hagihara cross-coupling is reported. The methodology was applied to synthesize a series of novel compounds. The tolerance of the combination of different functional groups was tested. The influence of different functional groups on the physical properties was studied by ultraviolet-visible (UV-vis) and fluorescence spectroscopy, providing new insights into the potential applications of uracil-based structures.

BN-Phenanthrene- and BN-Pyrene-Based Fluorescent Uridine Analogues

Two unprecedented fluorescent nucleosides that feature BN-doped polycyclic aromatic hydrocarbons are presented. One of them, having a BN-modified phenanthrene moiety incorporated, shows blue fluorescence but suffers from poor stability under aqueous conditions. The other nucleoside comprises an internally BN-doped pyrene as the chromophore. It shows green fluorescence in various solvents and is stable under aqueous and alkaline conditions.

Biomass RNA for the Controlled Synthesis of Degradable Networks by Radical Polymerization

Nucleic acids extracted from biomass have emerged as sustainable and environmentally friendly building blocks for the fabrication of multifunctional materials. Until recently, the fabrication of biomass nucleic acid-based structures has been facilitated through simple crosslinking of biomass nucleic acids, which limits the possibility of material properties engineering. This study presents an approach to convert biomass RNA into an acrylic crosslinker through acyl imidazole chemistry. The number of acrylic moieties on RNA was engineered by varying the acylation conditions. The resulting RNA crosslinker can undergo radical copolymerization with various acrylic monomers, thereby offering a versatile route for creating materials with tunable properties (e.g., stiffness and hydrophobic characteristics). Further, reversible-deactivation radical polymerization methods, such as atom transfer radical polymerization (ATRP) and reversible addition-fragmentation chain transfer (RAFT), were also explored as additional approaches to engineer the hydrogel properties. The study also demonstrated the metallization of the biomass RNA-based material, thereby offering potential applications in enhancing electrical conductivity. Overall, this research expands the opportunities in biomass-based biomaterial fabrication, which allows tailored properties for diverse applications.

A tolane-modified 5-ethynyluridine as a universal and fluorogenic photochemical DNA crosslinker

We report the fluorescent nucleoside ToldU and its application as a photoresponsive crosslinker in three different DNA architectures with enhanced fluorescence emission of the crosslinked products. The fluorogenic ToldU crosslinking reaction enables the assembly of DNA polymers in a hybridization chain reaction for the concentration-dependent detection of a specific DNA sequence.