DNA self-assembly: from chirality to evolution

Macroscopic handedness inversion of terbium coordination polymers achieved by doping homochiral ligand analogues

Inspired by natural biological systems, chiral or handedness inversion by altering external and internal conditions to influence intermolecular interactions is an attractive topic for regulating chiral self-assembled materials. For coordination polymers, the regulation of their helical handedness remains little reported compared to polymers and supramolecules. In this work, we choose the chiral ligands R-pempH2 (pempH2 = (1-phenylethylamino)methylphosphonic acid) and R-XpempH2 (X = F, Cl, Br) as the second ligand, which can introduce C-H⋯π and C-H⋯X interactions, doped into the reaction system of the Tb(R-cyampH)3·3H2O (cyampH2 = (1-cyclohexylethylamino)methylphosphonic acid) coordination polymer, which itself can form a right-handed superhelix by van der Waals forces, and a series of superhelices R-1H-x, R-2F-x, R-3Cl-x, and R-4Br-x with different doping ratios x were obtained, whose handedness is related to the second ligand and its doping ratio, indicating the decisive role of interchain interactions of different strengths in the helical handedness. This study could provide a new pathway for the design and self-assembly of chiral materials with controllable handedness and help the further understanding of the mechanism of self-assembly of coordination polymers forming macroscopic helical systems.

Application of intelligent responsive DNA self-assembling nanomaterials in drug delivery

Smart nanomaterials are nano-scaled materials that respond in a controllable and reversible way to external physical or chemical stimuli. DNA self-assembly is an effective way to construct smart nanomaterials with precise structure, diverse functions and wide applications. Among them, static structures such as DNA polyhedron, DNA nanocages and DNA hydrogels, as well as dynamic reactions such as catalytic hairpin reaction, hybridization chain reaction and rolling circle amplification, can serve as the basis for building smart nanomaterials. Due to the advantages of DNA, such as good biocompatibility, simple synthesis, rational design, and good stability, these materials have attracted increasing attention in the fields of pharmaceuticals and biology. Based on their specific response design, DNA self-assembled smart nanomaterials can deliver a variety of drugs, including small molecules, nucleic acids, proteins and other drugs; and they play important roles in enhancing cellular uptake, resisting enzymatic degradation, controlling drug release, and so on. This review focuses on different assembly methods of DNA self-assembled smart nanomaterials, therapeutic strategies based on various intelligent responses, and their applications in drug delivery. Finally, the opportunities and challenges of smart nanomaterials based on DNA self-assembly are summarized.

Biomimetic Self-Assembled Chiral Inorganic Nanomaterials: A New Strategy for Solving Medical Problems

The rapid expansion of the study of chiral inorganic structures has led to the extension of the functional boundaries of inorganic materials. Nature-inspired self-assembled chiral inorganic structures exhibit diverse morphologies due to their high assembly efficiency and controlled assembly process, and they exhibit superior inherent properties such as mechanical properties, chiral optical activity, and chiral fluorescence. Although chiral self-assembled inorganic structures are becoming more mature in chiral catalysis and chiral optical regulation, biomedical research is still in its infancy. In this paper, various forms of chiral self-assembled inorganic structures are summarized, which provides a structural starting point for various applications of chiral self-assembly inorganic structures in biomedical fields. Based on the few existing research statuses and mechanism discussions on the chiral self-assembled materials-mediated regulation of cell behavior, molecular probes, and tumor therapy, this paper provides guidance for future chiral self-assembled structures to solve the same or similar medical problems. In the field of chiral photonics, chiral self-assembled structures exhibit a chirality-induced selection effect, while selectivity is exhibited by chiral isomers in the medical field. It is worth considering whether there is some correspondence or juxtaposition between these phenomena. Future chiral self-assembled structures in medicine will focus on the precise treatment of tumors, induction of soft and hard tissue regeneration, explanation of the biochemical mechanisms and processes of its medical effects, and improvement of related theories.

Label-Free Detection of DNA Supramolecular Structure Formation by Surface-Enhanced Raman Spectroscopy

The precise self-assembly of DNA molecules can be used to create nanoprecision supramolecular materials. However, the lack of methods to characterize such supramolecular materials limits their development. Surface-enhanced Raman spectroscopy (SERS) is widely used to detect the secondary structure of simple DNA molecules, but its application in the revealing of complex DNA supramolecular information remains challenging. Herein, we proposed a modified SERS-based platform able to provide structural information on DNA supramolecular materials. The silver nanoparticle-enhanced substrate uses acetonitrile as an internal standard and modifier, and calcium ions are used as an aggregating agent to induce the formation of stable "hotspots" of silver nanoparticles, where the base planes in DNA supramolecules are perpendicular to the surface of the substrate, obtaining enhanced Raman signals of base ring in both single-stranded DNA and DNA supramolecules for the first time. The structure of DNA supramolecules was efficiently characterized using this technique, showing the great application potential of this technique in the structural analysis of nucleic acids and their ligands.

Phosphorus Compounds of Natural Origin: Prebiotic, Stereochemistry, Application

Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.

Topoisomerase IIβ targets DNA crossovers formed between distant homologous sites to induce chromatin opening

Type II DNA topoisomerases (topo II) flip the spatial positions of two DNA duplexes, called G- and T- segments, by a cleavage-passage-resealing mechanism. In living cells, these DNA segments can be derived from distant sites on the same chromosome. Due to lack of proper methodology, however, no direct evidence has been described so far. The beta isoform of topo II (topo IIβ) is essential for transcriptional regulation of genes expressed in the final stage of neuronal differentiation. Here we devise a genome-wide mapping technique (eTIP-seq) for topo IIβ target sites that can measure the genomic distance between G- and T-segments. It revealed that the enzyme operates in two distinctive modes, termed proximal strand passage (PSP) and distal strand passage (DSP). PSP sites are concentrated around transcription start sites, whereas DSP sites are heavily clustered in small number of hotspots. While PSP represent the conventional topo II targets that remove local torsional stresses, DSP sites have not been described previously. Most remarkably, DSP is driven by the pairing between homologous sequences or repeats located in a large distance. A model-building approach suggested that topo IIβ acts on crossovers to unknot the intertwined DSP sites, leading to chromatin decondensation.

The influence of Ni2+ and other ions on the trigonal structure of DNA

We present a new structure of a DNA dodecamer obtained in the presence of Ni²⁺ ions. The DNA forms Ni-guanine cross-links between neighboring molecules. Our results show that an adequate dosage of Ni²⁺ may help to form well-defined DNA nanostructures. We also compare our structure with other dodecamers which present unique features and also crystallize in trigonal unit cells, strongly influenced by the counterions associated with DNA. In all cases, the DNA duplexes form parallel pseudo-helical columns in the crystal, similar to DNA-protamine and native DNA fibers.

Loop-closure kinetics reveal a stable, right-handed DNA intermediate in Cre recombination

In Cre site-specific recombination, the synaptic intermediate is a recombinase homotetramer containing a pair of loxP DNA target sites. The enzyme system's strand-exchange mechanism proceeds via a Holliday-junction (HJ) intermediate; however, the geometry of DNA segments in the synapse has remained highly controversial. In particular, all crystallographic structures are consistent with an achiral, planar Holliday-junction (HJ) structure, whereas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-handed chiral junction. We use the kinetics of loop closure involving closely spaced (131-151 bp) loxP sites to investigate the in-aqueo ensemble of conformations for the longest-lived looped DNA intermediate. Fitting the experimental site-spacing dependence of the loop-closure probability, J, to a statistical-mechanical theory of DNA looping provides evidence for substantial out-of-plane HJ distortion, which unequivocally stands in contrast to the square-planar intermediate geometry from Cre-loxP crystal structures and those of other int-superfamily recombinases. J measurements for an HJ-isomerization-deficient Cre mutant suggest that the apparent geometry of the wild-type complex is consistent with temporal averaging of right-handed and achiral structures. Our approach connects the static pictures provided by crystal structures and the natural dynamics of macromolecules in solution, thus advancing a more comprehensive dynamic analysis of large nucleoprotein structures and their mechanisms.

Effect of static magnetic field on DNA synthesis: The interplay between DNA chirality and magnetic field left-right asymmetry

Interactions between magnetic fields (MFs) and living cells may stimulate a large variety of cellular responses to a MF, while the underlying intracellular mechanisms still remain a great puzzle. On a fundamental level, the MF - cell interaction is affected by the two broken symmetries: (a) left-right (LR) asymmetry of the MF and (b) chirality of DNA molecules carrying electric charges and subjected to the Lorentz force when moving in a MF. Here we report on the chirality-driven effect of static magnetic fields (SMFs) on DNA synthesis. This newly discovered effect reveals how the interplay between two fundamental features of symmetry in living and inanimate nature-DNA chirality and the inherent features of MFs to distinguish the left and right-manifests itself in different DNA synthesis rates in the upward and downward SMFs, consequently resulting in unequal cell proliferation for the two directions of the field. The interplay between DNA chirality and MF LR asymmetry will provide fundamental knowledge for many MF-induced biological phenotypes.

The Rich World of p53 DNA Binding Targets: The Role of DNA Structure

The tumor suppressor functions of p53 and its roles in regulating the cell cycle, apoptosis, senescence, and metabolism are accomplished mainly by its interactions with DNA. p53 works as a transcription factor for a significant number of genes. Most p53 target genes contain so-called p53 response elements in their promoters, consisting of 20 bp long canonical consensus sequences. Compared to other transcription factors, which usually bind to one concrete and clearly defined DNA target, the p53 consensus sequence is not strict, but contains two repeats of a 5′RRRCWWGYYY3′ sequence; therefore it varies remarkably among target genes. Moreover, p53 binds also to DNA fragments that at least partially and often completely lack this consensus sequence. p53 also binds with high affinity to a variety of non-B DNA structures including Holliday junctions, cruciform structures, quadruplex DNA, triplex DNA, DNA loops, bulged DNA, and hemicatenane DNA. In this review, we summarize information of the interactions of p53 with various DNA targets and discuss the functional consequences of the rich world of p53 DNA binding targets for its complex regulatory functions.

Supramolecular super-helix formation via self-assembly of naphthalene diimide functionalised with bile acid derivatives

The design of chiral chromophores that lead to self-assembly of higher order helical structures is a powerful tool to understand the hierarchical helical structures of molecules of nature. In this work, we present a self-assembled helical super-structure produced via facial stacking of a bile acid bolaamphiphile derivative with a naphthalene diimide core (NDI-DCA), driven by solvophobic effects in THF–H₂O solvent mixtures. The chirality of the helical microstructure is directed by the multiple chiral centres in the precursor molecule. The chirality of the hierarchical assemblies was observed using circular dichroism (CD), Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) measurements. We propose that the NDI-DCA super-structures are formed via similar interactions and mechanisms to those observed in biological molecules such as proteins and DNA.

Central-to-Helical-to-Axial-to-Central Transfer of Chirality with a Photoresponsive Catalyst

Recent advances in molecular design have displayed striking examples of dynamic chirality transfer between various elements of chirality, e.g., from central to either helical or axial chirality and vice versa. While considerable progress in atroposelective synthesis has been made, it is intriguing to design chiral molecular switches able to provide selective and dynamic control of axial chirality with an external stimulus to modulate stereochemical functions. Here, we report the synthesis and characterization of a photoresponsive bis(2-phenol)-substituted molecular switch 1. The unique design exhibits a dynamic hybrid central-helical-axial transfer of chirality. The change of preferential axial chirality in the biaryl motif is coupled to the reversible switching of helicity of the overcrowded alkene core, dictated by the fixed stereogenic center. The potential for dynamic control of axial chirality was demonstrated by using ( R)-1 as switchable catalyst to direct the stereochemical outcome of the catalytic enantioselective addition of diethylzinc to aromatic aldehydes, with successful reversal of enantioselectivity for several substrates.

A metastable structure for the compact 30-nm chromatin fibre

The structure of compact 30‐nm chromatin fibres is still debated. We present here a novel unified model that reconciles all experimental observations into a single framework. We propose that compact fibres are formed by the interdigitation of the two nucleosome stacks in a 2‐start crossed‐linker structure to form a single stack. This process requires that the dyad orientation of successive nucleosomes relative to the helical axis alternates. The model predicts that, as observed experimentally, the fibre‐packing density should increase in a stepwise manner with increasing linker length. This model structure can also incorporate linker DNA of varying lengths.

Excess counterion condensation on polyelectrolyte kinks and branch points and the interaction of skewed charged lines

We have developed explicit formulas for the excess number of counterions condensed on kinked and intersecting charged lines caused by the more intense electric field in the neighborhood of the kink or intersection. As expected, the number of additionally bound counterions is greater for more pronounced kinks, and also increases with the number of lines that intersect at a common point. We have also analyzed the electrostatic interaction potential as a function of distance between two charged lines in skewed orientation. Our finding in this case is that in a range of close distances the lines must cross a free energy barrier in order to separate.